GBB Publications (via University Database)
2025
Basile,
L., Poli, C., Santema, L. L., Lesenciuc, R. C.,
Fraaije, M. W., & Binda, C. (2025). Altering
substrate specificity of a thermostable bacterial monoamine oxidase
by structure-based mutagenesis. Archives of
Biochemistry and Biophysics, 764, Article
110276. https://doi.org/10.1016/j.abb.2024.110276
Guerriere,
T. B., Vancheri, A., Ricotti, I., Serapian, S. A., Eggerichs, D.,
Tischler, D., Colombo, G., Mascotti, M. L., Fraaije, M.
W., & Mattevi, A. (2025). Dehydrogenase versus
oxidase function: The interplay between substrate binding and
flavin microenvironment. ACS
Catalysis, 15(2), 1046-1060. https://doi.org/10.1021/acscatal.4c05944
Kaya,
S. G., Hovan, A., & Fraaije, M. W. (2025).
Engineering of LOV-domains for their use as protein
tags. Archives of Biochemistry and
Biophysics, 763, Article 110228. https://doi.org/10.1016/j.abb.2024.110228
Fan,
X., & Fraaije, M. W. (2025). Flavin
transferase ApbE: From discovery to applications.
The Journal of Biological Chemistry, Article
108453. Advance online publication. https://doi.org/10.1016/j.jbc.2025.108453
Yancheva,
Y. D., Kaya, S. G., Belyy,
A., Fraaije, M. W., & Tych, K.
M. (2025). Impact of Ligand-Induced Oligomer
Dissociation on Enzyme Diffusion, Directly Observed at the
Single-Molecule Level. Nano Letters,
25(6), 2373–2380. Article 4c05792. https://doi.org/10.1021/acs.nanolett.4c05792
Damada,
P., Rozeboom, H., & Fraaije,
M. (2025). Recombinant production and
characterization of six ene-reductases from Pencillium
steckii. ChemBioChem, Article
e202401007. Advance online publication. https://doi.org/10.1002/cbic.202401007
Tjallinks,
G., Angeleri, N., Nguyen, Q.-T., Mannucci, B., Arentshorst,
M., Visser, J., Ram, A. F. J., Fraaije, M. W., &
Mattevi, A. (2025). Structural and Mechanistic
Characterization of the Flavin-Dependent Monooxygenase and Oxidase
Involved in Sorbicillinoid Biosynthesis. ACS
chemical biology, Article 4c00783. Advance online
publication. https://doi.org/10.1021/acschembio.4c00783
Presutti,
C., Vreeker, E., Sasidharan, S.,
Ferdinando, Z., Stuart, M.,
Juhaniewicz-Dębińska, J., Maglia, G.,
Roos, W. H., & Poolman, B. (2025).
Balancing Permeability and Stability: A Study of Hybrid
Membranes for Synthetic Cells Using Lipids and PBd-b-PEO Block
Copolymers. Biomacromolecules, Article
4c01651. Advance online publication. https://doi.org/10.1021/acs.biomac.4c01651
Vreeker,
E., Grünewald, F., van der Heide, N.
J., Bonini, A., Marrink, S.
J., Tych, K. K., & Maglia, G.
(2025). Nanopore-Functionalized Hybrid Lipid-Block Copolymer
Membranes Allow Efficient Single-Molecule Sampling and Stable
Sensing of Human Serum. Advanced
materials, 37(15), Article e2418462. https://doi.org/10.1002/adma.202418462
Lu,
C., Bonini, A., Viel, J. H.,
& Maglia, G. (2025). Toward single-molecule
protein sequencing using nanopores. Nature
Biotechnology, 43(3), 312-322. https://doi.org/10.1038/s41587-025-02587-y
Karapanagioti,
F., Obermaier, S., Slotboom, D.
J., & Poolman, B. (2025). The
Saccharomyces cerevisiae amino acid transporter Lyp1 has a broad
substrate spectrum. FEBS Letters.
Advance online publication. https://doi.org/10.1002/1873-3468.70044
Kosir,
T., Das, H., Pedersen, M. P., Richard, A.-K.,
Anteghini, M., Martins Dos Santos, V., Oeljeklaus, S., van
der Klei, I. J., & Warscheid, B. (2025).
Integrative Omics reveals changes in the cellular landscape
of peroxisome-deficient pex3 yeast cells.
Microbial Cell, 12(1), 9-33. https://doi.org/10.15698/mic2025.02.842
Ul
Haq, F., Vilachã, J. F., Op de Beeck, K., Van
Camp, G., Marrink, S.-J., & Vandeweyer, G. (2025).
Exploring the conformational space of ROS1 kinase domain and
the impact of allosteric mutations. Journal of
Biomolecular Structure & Dynamics, 1-16. Advance
online publication. https://doi.org/10.1080/07391102.2024.2448677
Bieker,
S., Timme, M., Woge, N., Hassan, D. G., Brown, C.
M., Marrink, S. J., Melo, M. N., &
Holthuis, J. C. M. (2025). Hexokinase-I directly binds to a
charged membrane-buried glutamate of mitochondrial VDAC1 and
VDAC2. Communications biology,
8(1), Article 212. https://doi.org/10.1038/s42003-025-07551-9
Wang,
L., Brasnett, C., Borges-Araújo, L.,
Souza, P. C. T., & Marrink, S. J. (2025).
Martini3-IDP: Improved Martini 3 force field for disordered
proteins. Nature Communications,
16(1), Article 2874. https://doi.org/10.1038/s41467-025-58199-2
Brasnett,
C., & Marrink, S. J. (2025).
MartiniGlass: a Tool for Enabling Visualization of
Coarse-Grained Martini Topologies. Journal of
chemical information and modeling, Article 4c02277.
Advance online publication. https://doi.org/10.1021/acs.jcim.4c02277
Ye,
R., Xu, C., Ding, Z. J., Zheng, S. J., Marrink, S.
J., Zhang, D., & Zhou, R. (2025).
Mutagenesis-based optimal design of plant peptide
phytosulfokine for enhanced biological activity.
Computational and Structural Biotechnology
Journal, 27, 1296-1304. https://doi.org/10.1016/j.csbj.2025.03.029
Brandner,
A. F., Smith, I. P. S., Marrink, S. J., Souza, P. C.
T., & Khalid, S. (2025). Systematic Approach to
Parametrization of Disaccharides for the Martini 3 Coarse-Grained
Force Field. Journal of chemical information and
modeling, 65(3), 1537-1548. https://doi.org/10.1021/acs.jcim.4c01874
et
al., Amaro, R. E., Åqvist, J., Bahar, I., Battistini, F.,
Bellaiche, A., Beltran, D., Biggin, P. C., & Marrink, S.
J. (2025). The need to implement FAIR principles in
biomolecular simulations. Nature
Methods, 22(4), 641-645. https://doi.org/10.1038/s41592-025-02635-0
Davoudi,
S., Vainikka, P. A., Marrink, S. J., & Ghysels, A.
(2025). Validation of a Coarse-Grained Martini 3 Model for
Molecular Oxygen. Journal of Chemical Theory and
Computation, 21(1), 428-439. Article 4c01348.
https://doi.org/10.1021/acs.jctc.4c01348
Hermann,
A., Hiller, E., Hubel, P., Biermann, L., Benatto Perino, E.
H., Kuipers, O. P., Hausmann, R., & Lilge, L.
(2025). Genetic Code Expansion for Controlled Surfactin
Production in a High Cell-Density Bacillus subtilis Strain.
Microorganisms, 13(2), Article 353.
https://doi.org/10.3390/microorganisms13020353
Wang,
C., Wambui, J., Fernandez-Cantos, M. V., Jurt,
S., Broos, J., Stephan, R., & Kuipers, O.
P. (2025). Heterologous Expression and
Characterization of Estercin A, a Class II Lanthipeptide Derived
from Clostridium estertheticum CF016, with Antimicrobial Activity
against Clinically Relevant Pathogens. Journal of
Natural Products, Article 4c00814. Advance online
publication. https://doi.org/10.1021/acs.jnatprod.4c00814
Arias-Orozco,
P., Cebrián, R., de Jong, A., &
Kuipers, O. P. (2025). Synechococsins: Lanthipeptides
acting as defensive signals to disarm offensive competitors?
Microbiological Research, 291,
Article 127965. https://doi.org/10.1016/j.micres.2024.127965
Wagenaar,
G. T. M., & Moll, G. N. (2025). Advances in
the therapeutic potentials of ligands of the apelin receptor
APJ. European Journal of Pharmacology,
Article 177302. https://doi.org/10.1016/j.ejphar.2025.177302
Guo,
Y., Navarro-Muñoz, J., Rodenbach, C., Dwars, E.,
Dieleman, C., van den Hout, B., Sanders, B., Zhou, M., Arogunjo,
A., Cox, R. J., Driessen, A. J. M., & Collemare,
J. (2025). Identification of a Biosynthetic Gene Cluster for
the Production of the Blue-Green Pigment Xylindein by the Fungus
Chlorociboria aeruginascens. Journal of Natural
Products, Article 4c00350. Advance online publication.
https://doi.org/10.1021/acs.jnatprod.4c00350
Smith,
E. N., van Aalst, M., Weber, A. P. M., Ebenhöh,
O., & Heinemann, M. (2025). Alternatives to
photorespiration: A system-level analysis reveals mechanisms of
enhanced plant productivity. Science
Advances, 11(13), Article eadt9287. https://doi.org/10.1126/sciadv.adt9287
Satanowski,
A., Marchal, D. G., Perret, A., Petit, J.-L., Bouzon, M.,
Döring, V., Dubois, I., He, H., Smith, E. N.,
Pellouin, V., Petri, H. M., Rainaldi, V., Nattermann, M., Burgener,
S., Paczia, N., Zarzycki, J., Heinemann, M., Bar-Even,
A., & Erb, T. J. (2025). Design and implementation of
aerobic and ambient CO2-reduction as an entry-point for enhanced
carbon fixation. Nature
Communications, 16(1), Article 3134. https://doi.org/10.1038/s41467-025-57549-4
Li,
X., de Assis Souza, R., & Heinemann, M.
(2025). The rate of glucose metabolism sets the cell
morphology across yeast strains and species.
Current Biology, 35(4), 788-798. https://doi.org/10.1016/j.cub.2024.12.039
Jiang,
R., Casilli, F., Thunnissen, A.-M. W.
H., & Roelfes, G. (2025). An
artificial copper-Michaelase featuring a genetically encoded
bipyridine ligand for asymmetric additions to nitroalkenes.
Angewandte Chemie (International ed. in
English), Article e202423182. Advance online
publication. https://doi.org/10.1002/anie.202423182
Zhou,
H., Kunzendorf, A., Xu, G.,
Frietema, H. O. T., Thunnissen, A.-M. W. H.,
& Poelarends, G. J. (2025). Engineering
2-Deoxy-D-ribose-5-phosphate Aldolase for anti- and syn-Selective
Epoxidations of α,β-Unsaturated Aldehydes.
Angewandte Chemie (International ed. in
English), Article e202503054. Advance online
publication. https://doi.org/10.1002/anie.202503054
Leveson-Gower,
R. B., Tiessler-Sala, L., Rozeboom, H.
J., Thunnissen, A. M. W. H., Maréchal, J.
D., & Roelfes, G. (2025). Evolutionary
Specialization of a Promiscuous Designer Enzyme.
ACS Catalysis, 15(3), 1544-1552. https://doi.org/10.1021/acscatal.4c06409
2024
Pećanac,
O., Martin, C., Savino, S., Rozeboom, H. J.,
Fraaije, M., & Lončar, N. (2025). Biochemical
and Structural Characterisation of a Bacterial
Lactoperoxidase. ChemBioChem,
26(2), Article e202400713. https://doi.org/10.1002/cbic.202400713
Guerriere,
T. B., Fraaije, M. W., & Mattevi, A. (2025).
Biochemical and structural insights into pinoresinol
hydroxylase from Pseudomonas sp. Archives of
Biochemistry and Biophysics, 764, Article
110247. https://doi.org/10.1016/j.abb.2024.110247
Carraretto,
D., Alonso-Cotchico, L., Martin, C., Trajković, M., van Beek,
H. L., Mattevi, A., Fraaije, M. W., Lucas, M. F.,
& Lončar, N. (2025). Broadening the Catalytic Scope
of the Peroxygenase Activity of a Bacterial Tyrosine
Hydroxylase. ChemCatChem,
17(4), Article e202401819. https://doi.org/10.1002/cctc.202401819
de
Gonzalo, G., Coto-Cid, J. M., Lončar, N., & Fraaije,
M. W. (2024). Asymmetric Sulfoxidations Catalyzed by
Bacterial Flavin-Containing Monooxygenases.
Molecules, 29(15), Article 3474. https://doi.org/10.3390/molecules29153474
Ashley,
B., Demingo, C., Rozeboom, H., Bianciardi,
N., Dunleavy, T., Haaksma, J. J., Guo,
Y., & Fraaije, M. W. (2024).
Biocatalytic Cleavage of para-Acetoxy Benzyl Ethers:
Application to Protecting Group Chemistry. ACS
Catalysis, 15(1), 105-113. https://doi.org/10.1021/acscatal.4c04257
Guo,
Y., Ashley, B., Marić,
I., Saifuddin, M., Dunleavy, T.,
Onet, A., & Fraaije, M. W. (2024).
Biocatalytic Oxidative Amination of para-Substituted
Phenols. ChemCatChem, 16(17),
Article e202400277. https://doi.org/10.1002/cctc.202400277
Russo,
S., Rozeboom, H. J., Wijma, H.
J., Poelarends, G. J., & Fraaije, M.
W. (2024). Biochemical, kinetic, and structural
characterization of a Bacillus tequilensis nitroreductase.
The FEBS Journal, 291(17), 3889 -
3903. Article 17210. https://doi.org/10.1111/febs.17210
Tjallinks,
G., Mattevi, A., & Fraaije, M. W. (2024).
Biosynthetic Strategies of Berberine Bridge Enzyme-like
Flavoprotein Oxidases toward Structural Diversification in Natural
Product Biosynthesis. Biochemistry,
63(17), 2089-2110. https://doi.org/10.1021/acs.biochem.4c00320
Santema,
L. L., Rotilio, L., Xiang, R., Tjallinks, G.,
Guallar, V., Mattevi, A., & Fraaije, M. W. (2024).
Discovery and biochemical characterization of thermostable
glycerol oxidases. Applied Microbiology and
Biotechnology, 108(1), 1-14. Article 61. https://doi.org/10.1007/s00253-023-12883-9
Purwani,
N. N., Rozeboom, H. J., Willers, V.
P., Wijma, H. J., & Fraaije, M.
W. (2024). Discovery of a new class of bacterial
heme-containing CC cleaving oxygenases. New
Biotechnology, 83, 82-90. https://doi.org/10.1016/j.nbt.2024.07.002
Lee,
M., & Fraaije, M. W. (2024).
Equipping Saccharomyces cerevisiae with an Additional Redox
Cofactor Allows F 420-Dependent Bioconversions in Yeast.
ACS Synthetic Biology, 13(3),
921–929. https://doi.org/10.1021/acssynbio.3c00718
Yang,
G., Pećanac, O., Wijma, H.
J., Rozeboom, H. J., de Gonzalo, G.,
Fraaije, M. W., & Mascotti, M. L. (2024).
Evolution of the catalytic mechanism at the dawn of the
Baeyer-Villiger monooxygenases. Cell
reports, 43(5), Article 114130. https://doi.org/10.1016/j.celrep.2024.114130
Barone,
M., Pizzorni, L., Fraaije, M. W., Mascotti, M. L.,
& Mattevi, A. (2024). Evolution, Structure, and
Drug-Metabolising Activity of Mammalian Prenylcysteine
Oxidases. The Journal of Biological
Chemistry, 300(11), Article 107810. https://doi.org/10.1016/j.jbc.2024.107810
Russo,
S., Luján, A. P., Fraaije, M.
W., & Poelarends, G. J. (Accepted/In
press). Flavin-Dependent Nitroreductases: Privileged Enzymes
for Chemical and Photochemical Synthesis.
ChemCatChem, Article e202401304. https://doi.org/10.1002/cctc.202401304
Santema,
L. L., Rozeboom, H. J., Borger, V. P.,
Kaya, S. G., & Fraaije, M. W. (2024).
Identification of a robust bacterial pyranose oxidase which
displays an unusual pH dependence. The Journal of
Biological Chemistry, 300(11), Article 107885.
https://doi.org/10.1016/j.jbc.2024.107885
Damada,
P. H., & Fraaije, M. W. (2024).
Identification of Five Robust Novel Ene-Reductases from
Thermophilic Fungi. Catalysts,
14(11), Article 764. https://doi.org/10.3390/catal14110764
Chunkrua,
P., Leschonski, K. P., Gran-Scheuch, A. A., Vreeke, G.
J. C., Vincken, J.-P., Fraaije, M. W., van Berkel, W.
J. H., de Bruijn, W. J. C., & Kabel, M. A. (2024).
Prenylation of aromatic amino acids and plant phenolics by an
aromatic prenyltransferase from Rasamsonia emersonii.
Applied Microbiology and Biotechnology,
108(1), Article 421. https://doi.org/10.1007/s00253-024-13254-8
Boverio,
A., Jamil, N., Mannucci, B., Mascotti, M.
L., Fraaije, M. W., & Mattevi, A. (2024).
Structure, mechanism, and evolution of the last step in
vitamin C biosynthesis. Nature
Communications, 15(1), Article 4158. https://doi.org/10.1038/s41467-024-48410-1
Russo,
S., Prats Luján, A., Fraaije,
M., & Poelarends, G. J. (2024).
Synthesis of Pharmaceutically Relevant Arylamines Enabled by
a Nitroreductase from Bacillus tequilensis.
ChemBioChem, 25(10), Article
e202300846. https://doi.org/10.1002/cbic.202300846
Fraaije,
M. W., & Tong, Y. (2024). Variant flavoproteins comprising covalently tethered
flavin cofactor, and means and methods related thereto.
(Patent No. WO2024136655).
Capra,
N., Lelièvre, C., Touré, O., Fossey-Jouenne, A.,
Vergne-Vaxelaire, C., Janssen, D., Thunnissen,
A.-M. W. H., & Zaparucha, A. (2024). Adapting an
acyl CoA ligase from Metallosphaera sedula for lactam
formation by structure-guided protein engineering.
Frontiers in Catalysis, 4, Article
1360129. https://doi.org/10.3389/fctls.2024.1360129
Gran-Scheuch,
A., Wijma, H. J., Capra, N.,
van Beek, H. L., Trajkovic, M., Baldenius, K.,
Breuer, M., Thunnissen, A.-M. W. H., &
Janssen, D. B. (2024). Bioinformatics and
Computationally Supported Redesign of Aspartase for β-Alanine
Synthesis by Acrylic Acid Hydroamination. ACS
Catalysis, 15(2), 928-938. Article 4c05525. https://doi.org/10.1021/acscatal.4c05525
Toplak,
A., Cabri, W., Nuijens, T., Ricci, A., & Janssen, D.
B. (2024). Method for the preparation
of lactulose. (Patent No. WO2024208687).
Cabri,
W., Halmschlag, B. S., Toplak, A., Janssen, D.
B., Teixeira de Oliveira, E. F., Nuijens,
T., & Wijma, H. J. (2024). Thermostable subtilisin variants and their
use. (Patent No. WO2024133313).
van
Haastert, P. J. M., Keizer-Gunnink, I.,
& Kortholt, A. (2024). Analysis of cGMP Signaling
in Dictyostelium. In A. R. Kimmel (Ed.), Dictyostelium
discoideum: Methods and Protocols (pp. 177-194). (Methods in
molecular biology (Clifton, N.J.); Vol. 2814). Humana Press. https://doi.org/10.1007/978-1-0716-3894-1_13
van
Haastert, P. J. M., Keizer-Gunnink, I.,
& Kortholt, A. (2024). GRminusRD: A Sensitive
Assay to Detect Activation Processes at the Plasma Membrane in
Living Cells. In A. R. Kimmel (Ed.), Dictyostelium
discoideum: Methods and protocols (pp. 133-147). (Methods in
molecular biology (Clifton, N.J.); Vol. 2814). Humana Press. https://doi.org/10.1007/978-1-0716-3894-1_10
van
Haastert, P. J. M. (2024). Pseudopod Tracking and
Statistics During Cell Movement in Buffer and Chemotaxis. In
C. Beta, & C. Martinez-Torres (Eds.), Cell Motility and
Chemotaxis: Methods and Protocols (Vol. 2828, pp. 185-204).
(Methods in molecular biology; Vol. 2828). Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4023-4_14
Gilsbach,
B. K., Ho, F. Y., Riebenbauer, B., Zhang,
X., Guaitoli, G., Kortholt, A., &
Gloeckner, C. J. (2024). Intramolecular feedback regulation
of the LRRK2 Roc G domain by a LRRK2 kinase-dependent
mechanism. eLife, 12, Article
RP91083. https://doi.org/10.7554/eLife.91083
Iannotta,
L., Fasiczka, R., Favetta, G., Zhao, Y., Giusto, E., Dall'Ara, E.,
Wei, J., Ho, F. Y., Ciriani, C., Cogo, S., Tessari,
I., Iaccarino, C., Liberelle, M., Bubacco, L., Taymans, J.-M.,
Manzoni, C., Kortholt, A., Civiero, L., Hilfiker, S.,
... Greggio, E. (2024). PAK6 rescues pathogenic
LRRK2-mediated ciliogenesis and centrosomal cohesion defects in a
mutation-specific manner. Cell death &
disease, 15(10), Article 752. https://doi.org/10.1038/s41419-024-07124-4
Ahuja,
G., Arauz, Y. L. A., van Heuvelen, M. J.
G., Kortholt, A., Oroszi,
T., & van der Zee, E. A. (2024). The
effects of whole-body vibration therapy on immune and brain
functioning: current insights in the underlying cellular and
molecular mechanisms. Frontiers in
Neurology, 15, Article 1422152. https://doi.org/10.3389/fneur.2024.1422152
Galenkamp,
N. S., Zernia, S., Van Oppen, Y.
B., van den Noort, M., Argeitis, A.
M., & Maglia, G. (2024). Allostery
can convert binding free energies into concerted domain motions in
enzymes. Nature Communications,
15(1), Article 10109. https://doi.org/10.1038/s41467-024-54421-9
Sauciuc,
A., Whittaker, J., Tadema,
M., Tych, K., Guskov, A.,
& Maglia, G. (2024). Blobs form during the
single-file transport of proteins across nanopores.
Proceedings of the National Academy of
Sciences, 121(38), Article e2405018121. https://doi.org/10.1073/pnas.2405018121
Sauciuc,
A., & Maglia, G. (2024). Controlled
Translocation of Proteins through a Biological Nanopore for
Single-Protein Fingerprint Identification. Nano
Letters, 24, 14118–14124. Article
4c04510. https://doi.org/10.1021/acs.nanolett.4c04510
Baldelli,
M., Muccio, G. D., Sauciuc, A., Rocca, B. M. D.,
Viola, F., Balme, S., Bonini, A., Maglia,
G., & Chinappi, M. (2024). Controlling
Electroosmosis in Nanopores Without Altering the Nanopore Sensing
Region. Advanced materials,
36(33), Article 2401761. https://doi.org/10.1002/adma.202401761
Maglia,
G., Yelleswarapu, M., Wloka, C., &
Straathof, S. (2024). Large conical
nanopores and uses thereof in analyte sensing. (Patent No.
WO2024205413).
Maglia,
G., Zhang, X., & Kjems, J. (2024). Nanobody-functionalized biological nanopores and
means and methods related thereto. (Patent No.
WO2024117910).
Maglia,
G., Zhang, S., & Heron, A. (2024). Nanopore-based analysis of proteins. (Patent
No. WO2024091124).
Maglia,
G., & Sauciuc, A. (2024). Nanopore systems and methods for single-molecule
polymer profiling. (Patent No. WO2024091123).
Sauciuc,
A., Whittaker, J., Tadema,
M., Tych, K., Guskov, A.,
& Maglia, G. (2024). Unravelled proteins form
blobs during translocation across nanopores. (bioRxiv).
https://doi.org/10.1101/2024.01.23.576815
Volarić,
J., van der Heide, N. J., Mutter, N.
L., Samplonius, D. F., Helfrich,
W., Maglia, G., Szymanski,
W., & Feringa, B. L. (2024). Visible
Light Control over the Cytolytic Activity of a Toxic Pore-Forming
Protein. ACS chemical biology,
19(2), 451–461. Article 3c00640. https://doi.org/10.1021/acschembio.3c00640
Heinen,
L., van den Noort, M., King, M. S., Kunji, E.
R. S., & Poolman, B. (2025). Synthetic
syntrophy for adenine nucleotide cross-feeding between
metabolically active nanoreactors. Nature
Nanotechnology, 20, 112-120. https://doi.org/10.1038/s41565-024-01811-1
Foster,
A. J., van den Noort, M., & Poolman,
B. (2024). Bacterial cell volume regulation and the
importance of cyclic di-AMP. Microbiology and
Molecular Biology Reviews, 88(2), Article
e0018123. https://doi.org/10.1128/mmbr.00181-23
Patiño-Ruiz,
M. F., Anshari, Z. R., Gaastra,
B., Slotboom, D. J., & Poolman,
B. (2024). Chemiosmotic nutrient transport in
synthetic cells powered by electrogenic antiport coupled to
decarboxylation. Nature
Communications, 15(1), Article 7976. https://doi.org/10.1038/s41467-024-52085-z
Coenradij,
J., Bailoni, E., & Poolman, B.
(2024). Construction of Out-of-Equilibrium Metabolic Networks
in Nano- and Micrometer-Sized Vesicles. Journal of
visualized experiments : JoVE, (206), Article 66627. https://doi.org/10.3791/66627
Linnik,
D., Maslov, I., Punter, C.
M., & Poolman, B. (2024). Dynamic
structure of E. coli cytoplasm: supramolecular complexes and cell
aging impact spatial distribution and mobility of proteins.
Communications biology, 7(1),
Article 508. https://doi.org/10.1038/s42003-024-06216-3
Szomek,
M., Akkerman, V., Lauritsen, L., Walther, H.-L., Juhl, A. D.,
Thaysen, K., Egebjerg, J. M., Covey, D. F., Lehmann, M., Wessig,
P., Foster, A. J., Poolman, B., Werner,
S., Schneider, G., Müller, P., & Wüstner, D. (2024).
Ergosterol promotes aggregation of natamycin in the yeast
plasma membrane. Biochimica et Biophysica Acta -
Biomembranes, 1866(7), Article 184350. https://doi.org/10.1016/j.bbamem.2024.184350
Nemchinova,
M., Schuurman-Wolters, G. K., Whittaker,
J. J., Arkhipova, V., Marrink, S. J.,
Poolman, B., & Guskov, A. (2024).
Exploring the Ligand Binding and Conformational Dynamics of
the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ.
The Journal of Physical Chemistry B,
128(32), 7822-7832. https://doi.org/10.1021/acs.jpcb.4c02662
Karapanagioti,
F., Atlason, Ú. Á., Slotboom,
D. J., Poolman, B., & Obermaier,
S. (2024). Fitness landscape of substrate-adaptive
mutations in evolved amino acid-polyamine-organocation
transporters. eLife, 13,
Article RP93971. https://doi.org/10.7554/eLife.93971
Monterroso,
B., Margolin, W., Boersma, A. J., Rivas, G., Poolman,
B., & Zorrilla, S. (2024). Macromolecular
Crowding, Phase Separation, and Homeostasis in the Orchestration of
Bacterial Cellular Functions. Chemical
reviews, 124(4), 1899–1949. Article
3c00622. https://doi.org/10.1021/acs.chemrev.3c00622
Foster,
A. J., Li, H., Drougkas, P.,
Schuurman-Wolters, G. K., ten Kate, J., Paulino,
C., & Poolman, B. (2024).
Membrane-embedded CdaA is required for efficient synthesis of
second messenger cyclic di-AMP. Communications
biology, 7(1), Article 1710. https://doi.org/10.1038/s42003-024-07420-x
van
der Sleen, L., Stevens, J. A., Marrink,
S. J., Poolman, B., & Tych, K.
(2024). Probing the stability and interdomain interactions in
the ABC transporter OpuA using single-molecule optical
tweezers. Cell reports,
43(4), Article 114110. https://doi.org/10.1016/j.celrep.2024.114110
Bailoni,
E., Patiño-Ruiz, M. F., Stan, A. R.,
Schuurman-Wolters, G. K., Exterkate, M., Driessen, A.
J. M., & Poolman, B. (2024).
Synthetic Vesicles for Sustainable Energy Recycling and
Delivery of Building Blocks for Lipid Biosynthesis.
ACS Synthetic Biology, 13(5),
1549–1561. https://doi.org/10.1021/acssynbio.4c00073
Iyer,
A., Frallicciardi, J., le Paige, U. B. A.,
Narasimhan, S., Luo, Y., Alvarez Sieiro, P., Syga, L.,
van den Brekel, F., Minh Tran, B., Tjioe, R.,
Schuurman-Wolters, G., C A Stuart, M., Baldus,
M., van Ingen, H., & Poolman, B. (2024). The
structure and function of the bacterial osmotically inducible
protein Y. Journal of Molecular
Biology, 436(16), Article 168668. https://doi.org/10.1016/j.jmb.2024.168668
van
den Noort, M., Drougkas, P., Paulino,
C., & Poolman, B. (2024). The
substrate-binding domains of the osmoregulatory ABC importer OpuA
transiently interact. eLife,
12, Article 90996. https://doi.org/10.7554/eLife.90996
The
Atomwise AIMS Program, Wallach, I., Bernard, D., Nguyen, K., Ho,
G., Morrison, A., Stecula, A., Rosnik, A., Garaeva, A.
A., Borowska, A., & Slotboom, D.
J. (2024). AI is a viable alternative to high
throughput screening: a 318-target study.
Scientific Reports, 14(1), Article
7526. https://doi.org/10.1038/s41598-024-54655-z
Diamanti,
E., Souza, P. C. T., Setyawati, I.,
Bousis, S., Monjas, L., Swier, L. J. Y. M.,
Shams, A., Tsarenko, A., Stanek, W. K., Jäger,
M., Marrink, S. J., Slotboom, D.
J., & Hirsch, A. K. H. (2024). Author
Correction: Identification of inhibitors targeting the
energy-coupling factor (ECF) transporters.
Communications biology, 7, Article
70. https://doi.org/10.1038/s42003-024-05770-0
Nijland,
M., Lefebvre, S. N., Thangaratnarajah,
C., & Slotboom, D. J. (2024).
Bidirectional ATP-driven transport of cobalamin by the
mycobacterial ABC transporter BacA. Nature
Communications, 15(1), Article 2626. https://doi.org/10.1038/s41467-024-46917-1
Martínez
Felices, J. M., Barreto, Y. B.,
Thangaratnarajah, C., Whittaker, J. J.,
Alencar, A. M., Guskov, A., & Slotboom, D.
J. (2024). Cobalamin decyanation by the membrane
transporter BtuM. Structure,
32. https://doi.org/10.1016/j.str.2024.04.014
Shams,
A., Bousis, S., Diamanti, E., Elgaher, W. A. M.,
Zeimetz, L., Haupenthal, J., Slotboom, D. J.,
& Hirsch, A. K. H. (2024). Expression and
characterization of pantothenate energy-coupling factor
transporters as an anti-infective drug target.
Protein Science, 33(11), Article
e5195. https://doi.org/10.1002/pro.5195
Exapicheidou,
I. A., Shams, A., Ibrahim, H., Tsarenko, A.,
Backenköhler, M., Hamed, M. M., Diamanti, E., Volkamer,
A., Slotboom, D. J., & Hirsch, A. K.
H. (2024). Hit optimization by dynamic combinatorial
chemistry on Streptococcus pneumoniae energy-coupling factor
transporter ECF-PanT. Chemical communications
(Cambridge, England), 60, 870–873. https://doi.org/10.1039/d3cc04738e
Borowska,
A. M., Chiariello, M. G., Garaeva, A.
A., Rheinberger, J., Marrink, S.
J., Paulino, C., & Slotboom, D.
J. (2024). Structural basis of the obligatory exchange
mode of human neutral amino acid transporter ASCT2.
Nature Communications, 15(1),
Article 6570. https://doi.org/10.1038/s41467-024-50888-8
Partipilo,
M., & Jan Slotboom, D. (2024). The
S-component fold: a link between bacterial transporters and
receptors. Communications biology,
7(1), Article 610. https://doi.org/10.1038/s42003-024-06295-2
Dong,
J., Bai, Y., Wang, Q., Chen, Q., Li, X., Wang, Y., Ji, H., Meng,
X., Pijning, T., Svensson, B., Dijkhuizen,
L., Abou Hachem, M., & Jin, Z. (2024). Insights
into the Structure–Function Relationship of GH70 GtfB
α-Glucanotransferases from the Crystal Structure and Molecular
Dynamic Simulation of a Newly Characterized Limosilactobacillus
reuteri N1 GtfB Enzyme. Journal of Agricultural
and Food Chemistry, 72(10), 5391-5402. Article
acs.jafc.4c00104. https://doi.org/10.1021/acs.jafc.4c00104
Ten
Kate, G. A., Sanders, P., Dijkhuizen, L., & van
Leeuwen, S. S. (2024). Kinetics and products of Thermotoga
maritima β-glucosidase with lactose and cellobiose.
Applied Microbiology and Biotechnology,
108(1), Article 349. https://doi.org/10.1007/s00253-024-13183-6
Li,
Z., Waghmare, P. R., Dijkhuizen, L., Meng, X., &
Liu, W. (2024). Research advances on the consolidated
bioprocessing of lignocellulosic biomass.
Engineering Microbiology, 4(2),
Article 100139. https://doi.org/10.1016/j.engmic.2024.100139
Dong,
J., Abou Hachem, M., Wang, Y., Li, X., Zhang, B., Pijning,
T., Svensson, B., Dijkhuizen, L., Jin, Z.,
& Bai, Y. (2024). Tailor-Made α-Glucans by
Engineering the Processivity of α-Glucanotransferases via
Tunnel-Cleft Active Center Interconversions.
Journal of Agricultural and Food Chemistry,
72(19), 11041–11050. https://doi.org/10.1021/acs.jafc.4c01842
Pijning,
T., & Dijkhuizen, L. (2024).
Unprecedented Diversity of the Glycoside Hydrolase Family 70:
A Comprehensive Analysis of Sequence, Structure, and
Function. Journal of Agricultural and Food
Chemistry, 72(30), 16911-16929. Article
4c04807. https://doi.org/10.1021/acs.jafc.4c04807
Garcia-Morena,
D., Fernandez-Cantos, M. V., Escalera, S. L.,
Lok, J., Iannone, V., Cancellieri, P., Maathuis, W., Panagiotou,
G., Aranzamendi, C., Aidy, S. E.,
Kolehmainen, M., El-Nezami, H., Wellejus, A., & Kuipers,
O. P. (2024). In Vitro Influence of Specific
Bacteroidales Strains on Gut and Liver Health Related to Metabolic
Dysfunction-Associated Fatty Liver Disease.
Probiotics and Antimicrobial Proteins.
Advance online publication. https://doi.org/10.1007/s12602-024-10219-1
Zerbes,
R. M., Colina-Tenorio, L., Bohnert, M., von der Malsburg, K.,
Peikert, C. D., Mehnert, C. S., Perschil, I., Klar, R. F. U.,
de Boer, R., Kram, A., van der Klei,
I., Oeljeklaus, S., Warscheid, B., Rampelt, H., & van
der Laan, M. (2025). Coordination of cytochrome bc1 complex
assembly at MICOS. Embo Reports,
26, 353-384. https://doi.org/10.1038/s44319-024-00336-x
Chen,
H., de Boer, R., Krikken, A.
M., Wu, F., & van der Klei, I.
(2024). Hansenula polymorpha cells lacking the ER-localized
peroxins Pex23 or Pex29 show defects in mitochondrial function and
morphology. Open Biology,
13(5), Article bio060271. https://doi.org/10.1242/bio.060271
Jansen,
R. L. M., de Boer, R., de Lange, E. M.
F., Koster, J., Vlijm, R., Waterham, H.
R., & van der Klei, I. J. (2024).
Overexpression of PEX14 results in mistargeting to
mitochondria, accompanied by organelle fragmentation and clustering
in human embryonic kidney cells. Biochimica et
Biophysica Acta - Molecular Cell Research,
1871(6), Article 119754. https://doi.org/10.1016/j.bbamcr.2024.119754
de
Lange, E. M. F., Mol, F. N., van der
Klei, I. J., & Vlijm, R. (2024). STED
super-resolution microscopy unveils the dynamics of Atg30 on yeast
Pex3-labeled peroxisomes. Iscience,
27(8), Article 110481. https://doi.org/10.1016/j.isci.2024.110481
Pedersen,
M. P., Wolters, J. C., de Boer,
R., Krikken, A. M., & van der Klei,
I. J. (2024). The Hansenula polymorpha mitochondrial
carrier family protein Mir1 is dually localized at peroxisomes and
mitochondria. Biochimica et Biophysica Acta -
Molecular Cell Research, 1871(5), Article
119742. https://doi.org/10.1016/j.bbamcr.2024.119742
Pereira,
G. P., Alessandri, R., Domínguez, M., Araya-Osorio, R.,
Grünewald, L., Borges-Araújo, L., Wu, S.,
Marrink, S. J., Souza, P. C. T., & Mera-Adasme, R.
(2024). Bartender: Martini 3 Bonded Terms via Quantum
Mechanics-Based Molecular Dynamics. Journal of
Chemical Theory and Computation, 20(13),
5763–5773. https://doi.org/10.1021/acs.jctc.4c00275
Ozturk,
T. N., König, M., Carpenter, T. S., Pedersen, K.
B., Wassenaar, T. A., Ingólfsson, H. I.,
& Marrink, S. J. (2024). Building complex
membranes with Martini 3. Methods in
Enzymology, 701, 237-285. https://doi.org/10.1016/bs.mie.2024.03.010
Brasnett,
C., Kiani, A., Sami, S.,
Otto, S., & Marrink, S. J. (2024).
Capturing chemical reactions inside biomolecular condensates
with reactive Martini simulations. Communications
chemistry, 7(1), Article 151. https://doi.org/10.1038/s42004-024-01234-y
Chiariello,
M. G., Zarmiento-Garcia, R., &
Marrink, S. J. (2024). Martini 3 Coarse-Grained Model
for the Cofactors Involved in Photosynthesis.
International Journal of Molecular Sciences,
25(14), Article 7947. https://doi.org/10.3390/ijms25147947
Brown,
C. M., & Marrink, S. J. (2024).
Modeling membranes in situ. Current Opinion
in Structural Biology, 87, Article 102837. https://doi.org/10.1016/j.sbi.2024.102837
Cofas-Vargas,
L. F., Olivos-Ramirez, G. E., Chwastyk, M., Moreira, R. A., Baker,
J. L., Marrink, S. J., & Poma, A. B. (2024).
Nanomechanical footprint of SARS-CoV-2 variants in complex
with a potent nanobody by molecular simulations.
Nanoscale, 2024(40), 18824-18834. https://doi.org/10.1039/d4nr02074j
Pedersen,
K. B., Borges-Araújo, L., Stange, A. D., Souza, P. C.
T., Marrink, S. J., & Schiøtt, B. (2024).
OLIVES: A Go̅-like Model for Stabilizing Protein
Structure via Hydrogen Bonding Native Contacts in the Martini 3
Coarse-Grained Force Field. Journal of Chemical
Theory and Computation, 20(18), 8049-8070. https://doi.org/10.1021/acs.jctc.4c00553
Vilachã,
J. F., Wassenaar, T. A., & Marrink,
S. J. (2024). Structural Aspects of the ROS1 Kinase
Domain and Oncogenic Mutations.
Crystals, 14(2), Article 106. https://doi.org/10.3390/cryst14020106
Cornet,
J., Coulonges, N., Pezeshkian, W., Penissat-Mahaut, M.,
Desgrez-Dautet, H., Marrink, S. J., Destainville, N.,
Chavent, M., & Manghi, M. (2024). There and back again:
bridging meso- and nano-scales to understand lipid vesicle
patterning. Soft Matter,
2024(20), Article d4sm00089g. https://doi.org/10.1039/d4sm00089g
Park,
P., Matsubara, D. K., Barzotto, D. R., Lima, F. S., Chaimovich,
H., Marrink, S. J., & Cuccovia, I. M. (2024).
Vesicle protrusion induced by antimicrobial peptides suggests
common carpet mechanism for short antimicrobial peptides.
Scientific Reports, 14(1), Article
9701. https://doi.org/10.1038/s41598-024-60601-w
Guo,
L., Stoffels, K., Broos, J., &
Kuipers, O. P. (2024). Altering Specificity and
Enhancing Stability of the Antimicrobial Peptides Nisin and
Rombocin through Dehydrated Amino Acid Residue Engineering.
Peptides, 174, Article 171152. https://doi.org/10.1016/j.peptides.2024.171152
Guo,
L., Kuipers, O. P., & Broos,
J. (2024). An Engineered Nisin Analogue with a
Hydrophobic Moiety Attached at Position 17 Selectively Inhibits
Enterococcus faecium Strains. ACS chemical
biology, 19(9), 2023-2031. Article 4c00337. https://doi.org/10.1021/acschembio.4c00337
Yi,
Y., Liang, L., de Jong, A., &
Kuipers, O. P. (2024). A systematic comparison of
natural product potential, with an emphasis on RiPPs, by mining of
bacteria of three large ecosystems.
GENOMICS, 116(4), Article 110880. https://doi.org/10.1016/j.ygeno.2024.110880
Lilge,
L., & Kuipers, O. P. (2024). A
two-step regulatory circuit involving Spo0A-AbrB activates
mersacidin biosynthesis in Bacillus subtilis.
International journal of antimicrobial
agents, 63(5), Article 107155. https://doi.org/10.1016/j.ijantimicag.2024.107155
Xu,
Y., Reuvekamp, R., & Kuipers, O. P. (2024).
Biosynthesis of Antimicrobial Ornithine-Containing Lacticin
481 Analogues by Use of a Combinatorial Biosynthetic Pathway in
Escherichia coli. ACS Synthetic
Biology, 13(12), 4209-4217. https://doi.org/10.1021/acssynbio.4c00650
Xia,
Y., Wei, X., Gao, P., Wang, C., de Jong, A.,
Chen, J. H. K., Rodríguez-Sánchez, M. J.,
Rodríguez-Nogales, A., Diez-Echave, P., Gálvez, J.,
García, F., Wu, W., Kao, R. Y. T., Li, H., Cebrián,
R., Kuipers, O. P., & Sun, H. (2024).
Bismuth-based drugs sensitize Pseudomonas aeruginosa to
multiple antibiotics by disrupting iron homeostasis.
Nature Microbiology, 9(10),
2600-2613. https://doi.org/10.1038/s41564-024-01807-6
Bustamante,
M., Koopman, F., Martens, J., Brons, J.
K., DelaFuente, J., Hackl, T., Kuipers,
O. P., van Doorn, G. S., & de Vos, M.
G. J. (2024). Community context influences the
conjugation efficiency of Escherichia coli.
FEMS Microbes, 5, Article xtae023.
https://doi.org/10.1093/femsmc/xtae023
Fu,
Y., Pateri, E., & Kuipers, O. P. (2024).
Discovery, Biosynthesis, and Characterization of Rodencin, a
Two-Component Lanthipeptide, Harboring d-Amino Acids Introduced by
the Unusual Dehydrogenase RodJA.
Journal of Natural Products, 87(10),
2344-2354. https://doi.org/10.1021/acs.jnatprod.4c00170
Liu,
F., van Heel, A. J., & Kuipers, O.
P. (2024). Engineering circular bacteriocins:
structural and functional effects of α-helix exchanges and
disulfide introductions in circularin A. Frontiers
in Microbiology, 15, Article 1337647. https://doi.org/10.3389/fmicb.2024.1337647
Guo,
L., Stoffels, K., Broos, J., &
Kuipers, O. P. (2024). Engineering hybrid lantibiotics
yields the highly stable and bacteriocidal peptide cerocin
V. Microbiological Research,
282, Article 127640. https://doi.org/10.1016/j.micres.2024.127640
Ariza,
J. J., García-López, J. D., Aguinaga-Casañas, M. A.,
Baños, A., García, F., Kuipers, O. P., &
Cebrián, R. (2024). Enhancing food preservation and
safety: Synergistic effects of Allium-derived organosulfur
compounds and outer membrane permeabilization peptide L-11.
Food control, 165, Article 110691.
https://doi.org/10.1016/j.foodcont.2024.110691
Guo,
L., Kuipers, O. P., & Broos,
J. (2024). Facile Halogenation of Antimicrobial
Peptides As Demonstrated by Producing Bromotryptophan-Labeled Nisin
Variants with Enhanced Antimicrobial Activity.
Journal of Natural Products, 87(6),
1548-1555. https://doi.org/10.1021/acs.jnatprod.4c00118
Fernandez-Cantos,
M. V., Babu, A. F., Hanhineva, K., & Kuipers, O.
P. (2024). Identification of metabolites produced by
six gut commensal Bacteroidales strains using non-targeted LC-MS/MS
metabolite profiling. Microbiological
Research, 283, Article 127700. https://doi.org/10.1016/j.micres.2024.127700
Guo,
L., Wambui, J., Wang, C., Broos,
J., Stephan, R., & Kuipers, O. P. (2024).
Rombocin, a Short Stable Natural Nisin Variant, Displays
Selective Antimicrobial Activity against Listeria monocytogenes and
Employs a Dual Mode of Action to Kill Target Bacterial
Strains. ACS Synthetic Biology,
13(1), 370–383. Article 3c00612. https://doi.org/10.1021/acssynbio.3c00612
Vargiu,
M., Xu, Y., Kuipers, O.,
& Roelfes, G. (2024). Selective Aza-Michael
Addition to Dehydrated Amino Acids in Natural Antimicrobial
Peptides. ChemBioChem, 25(7),
Article e202400043. https://doi.org/10.1002/cbic.202400043
van
Eldijk, T. J. B., Sheridan, E. A., Martin, G.,
Weissing, F. J., Kuipers, O. P., &
Van Doorn, G. S. (2024). Temperature dependence of the
mutation rate towards antibiotic resistance.
JAC-Antimicrobial Resistance, 6(3),
Article dlae085. https://doi.org/10.1093/jacamr/dlae085
Arias-Orozco,
P., Zhou, L., Yi, Y.,
Cebrián, R., & Kuipers, O. P. (2024).
Uncovering the diversity and distribution of biosynthetic
gene clusters of prochlorosins and other putative RiPPs in marine
Synechococcus strains. Microbiology
Spectrum, 12(1), 1-19. https://doi.org/10.1128/spectrum.03611-23
Moll,
G. N. (2024). Agonists of galanin subtype 2 receptor
may prevent pancreatic cancer and agonists of angiotensin II type 2
receptor may prevent colorectal cancer. European
Journal of Pharmacology, 978, Article 176772.
https://doi.org/10.1016/j.ejphar.2024.176772
Cowan,
D. A., Albers, S. V., Antranikian, G., Atomi, H., Averhoff, B.,
Basen, M., Driessen, A. J. M., Jebbar, M., Kelman, Z.,
Kerou, M., Littlechild, J., Müller, V., Schönheit, P.,
Siebers, B., & Vorgias, K. (2024). Extremophiles in a
changing world. Extremophiles,
28(2), Article 26. https://doi.org/10.1007/s00792-024-01341-7
Zhang,
X., Nijland, J. G., & Driessen, A. J.
M. (2024). Maltose accumulation induced cell death in
Saccharomyces cerevisiae. Fems Yeast
Research, 24, Article foae012. https://doi.org/10.1093/femsyr/foae012
Hoekzema,
M., Jiang, J., & Driessen, A. J.
M. (2024). Optimizing Archaeal Lipid Biosynthesis in
Escherichia coli. ACS Synthetic
Biology, 13(8), 2470-2479. https://doi.org/10.1021/acssynbio.4c00235
Schoenmakers,
L. L. J., den Uijl, M. J., Postma, J. L., van
den Akker, T. A. P., Huck, W. T. S., & Driessen,
A. J. M. (2024). SecYEG-mediated translocation in a
model synthetic cell. Synthetic biology (Oxford,
England), 9(1), Article ysae007. https://doi.org/10.1093/synbio/ysae007
Rao,
A., & Driessen, A. J. M. (2024).
Unraveling the multiplicity of geranylgeranyl reductases in
Archaea: Potential roles in saturation of terpenoids.
Extremophiles, 28(1), Article 14. https://doi.org/10.1007/s00792-023-01330-2
Cavalca,
L., Atlason, Ú. Á., Trofin, A.,
Ribeiro, C. M., Pavan, F. R., Deuss, P. J.,
& Scheffers, D.-J. (2024). Selectivity and
Activity of Benzene-1,2,4-triol and its Dimers as Antimicrobial
Compounds Against Xanthomonas citri subsp. citri.
ChemPlusChem, 89(6), Article
e202300616. https://doi.org/10.1002/cplu.202300616
van
Groesen, E., Mons, E., Kotsogianni, I., Arts, M., Tehrani, K. H. M.
E., Wade, N., Lysenko, V., Stel, F. M., Zwerus, J. T., De
Benedetti, S., Bakker, A., Chakraborty, P., van der
Stelt, M., Scheffers, D.-J., Gooskens, J., Smits, W.
K., Holden, K., Gilmour, P. S., Willemse, J., ... Martin, N. I.
(2024). Semisynthetic guanidino lipoglycopeptides with potent
in vitro and in vivo antibacterial activity.
Science Translational Medicine,
16(759), Article eabo4736. https://doi.org/10.1126/scitranslmed.abo4736
Losa,
J., & Heinemann, M. (2024).
Contribution of different macromolecules to the diffusion of
a 40 nm particle in Escherichia coli. Biophysical
Journal, 123(10), 1211-1221. https://doi.org/10.1016/j.bpj.2024.03.040
Terpstra,
H. M., Gómez-Sánchez, R.,
Veldsink, A. C., Otto, T. A., Veenhoff,
L. M., & Heinemann, M. (2024).
PunctaFinder: An algorithm for automated spot detection in
fluorescence microscopy images. Molecular Biology
of the Cell, 35(12), Article 35:mr9. https://doi.org/10.1091/mbc.E24-06-0254
Freese,
T., Elzinga, N., Heinemann,
M., Lerch, M. M., & Feringa, B.
L. (2024). The relevance of sustainable laboratory
practices. RSC Sustainability,
2(5), 1300-1336. Article d4su00056k. https://doi.org/10.1039/D4SU00056K
Liu,
Y., Liu, C., Tang, S., Xiao, H., Wu, X., Peng, Y., Wang, X., Que,
L., Di, Z., Zhou, D., & Heinemann, M. (2024).
The "weaken-fill-repair" model for cell budding: Linking cell
wall biosynthesis with mechanics.
Iscience, 27(10), Article 110981. https://doi.org/10.1016/j.isci.2024.110981
Veen,
M. J., Aalbers, F. S., Rozeboom, H.
J., Thunnissen, A.-M. W. H., Sauer, D.
F., & Roelfes, G. (2025). Artificial Gold
Enzymes Using a Genetically Encoded Thiophenol-Based
Noble-Metal-Binding Ligand. Angewandte Chemie
(International ed. in English), 64(12),
Article e202421912. https://doi.org/10.1002/anie.202421912
Longwitz,
L., Leveson-Gower, R. B., Rozeboom, H.
J., Thunnissen, A.-M. W. H., &
Roelfes, G. (2024). Boron catalysis in a designer
enzyme. Nature, 629,
824–829. https://doi.org/10.1038/s41586-024-07391-3
Longwitz,
L., Kamer, M. D., Brouwer, B.,
Thunnissen, A. M. W. H., & Roelfes, G.
(2024). Boron Designer Enzyme with a Hybrid Catalytic
Dyad. ACS Catalysis, 14(24),
18469-18476. https://doi.org/10.1021/acscatal.4c06052
2023
Ravenstijn,
M., Jansen, R. C., du Bois, G., Yzer, S., &
Klaver, C. C. W. (2024). Empowering patients with high
myopia: The significance of education. Acta
ophthalmologica, 102(3), 357-363. https://doi.org/10.1111/aos.15779
Ravenstijn,
M., du Bois, G., Jansen, R. C., Liu, C., Luyten, G. P.
M., van Leeuwen, R., Dickman, M. M., Reus, N. J., Yzer, S., &
Klaver, C. C. W. (2023). A view from the clinic -
Perspectives from Dutch patients and professionals on high myopia
care. Ophthalmic & physiological optics : the
journal of the British College of Ophthalmic Opticians
(Optometrists), 43(3), 327-336. https://doi.org/10.1111/opo.13091
Santema,
L. L., Basile, L., Binda, C., & Fraaije, M.
W. (2024). Discovery and structural characterization
of a thermostable bacterial monoamine oxidase. The
FEBS Journal, 291(5), 849-864. https://doi.org/10.1111/febs.16973
Rotilio,
L., Boverio, A., Nguyen, Q.-T., Mannucci, B.,
Fraaije, M., & Mattevi, A. (2023). A biosynthetic
aspartate N-hydroxylase performs successive oxidations by holding
intermediates at a site away from the catalytic center.
The Journal of Biological Chemistry,
299(7), Article 104904. https://doi.org/10.1016/j.jbc.2023.104904
Arentshorst,
M., Kooloth Valappil, P., Mózsik, L.,
Regensburg-Tuïnk, T. J. G., Seekles, S., Tjallinks,
G., Fraaije, M., Visser, J., & Ram, A. F.
J. (2023). A CRISPR/Cas9-based multicopy integration system
for protein production in Aspergillus niger. The
FEBS Journal, 5127-5140. Article 16891. https://doi.org/10.1111/febs.16891
Marić,
I., Guo, Y., Fürst, M. J. L.
J., Van Aelst, K., Van den Bosch, S., De Simone, M.,
Martins, L. O., Sels, B. F., & Fraaije, M. W.
(2023). A One-Pot, Whole-Cell Biocatalysis Approach for
Vanillin Production using Lignin Oil. Advanced
Synthesis and Catalysis, 365(22), 3987-3995.
https://doi.org/10.1002/adsc.202300868
Boverio,
A., van Beek, H. L., Savino, S.,
Ranoux, A., Huijgen, W. J. J., Raaijmakers, H. W. C.,
Fraaije, M. W., & Lončar, N. (2023).
Biochemical and Structural Characterization of a Uronic Acid
Oxidase from Citrus sinensis.
ChemCatChem, 15(21), Article
e202300847. https://doi.org/10.1002/cctc.202300847
Tong,
Y., Rozeboom, H. J., Loonstra, M.
R., Wijma, H. J., & Fraaije, M.
W. (2023). Characterization of two bacterial
multi-flavinylated proteins harboring multiple covalent flavin
cofactors. BBA Advances, 4,
Article 100097. https://doi.org/10.1016/j.bbadva.2023.100097
Tjallinks,
G., Boverio, A., Jager, A. W., Kaya, S.
G., Mattevi, A., & Fraaije, M. W. (2023).
Efficient Oxidation of 5-Hydroxymethylfurfural Using a
Flavoprotein Oxidase from the Honeybee Apis mellifera.
ChemBioChem, 24(24), Article
e202300588. https://doi.org/10.1002/cbic.202300588
Bailleul,
G., Yang, G., Nicoll, C. R., Mattevi, A.,
Fraaije, M. W., & Mascotti, M. L. (2023).
Evolution of enzyme functionality in the flavin-containing
monooxygenases. Nature Communications,
14(1), Article 1042. https://doi.org/10.1038/s41467-023-36756-x
Tong,
Y., Kaya, S. G., Russo, S.,
Rozeboom, H. J., Wijma, H. J., &
Fraaije, M. W. (2023). Fixing Flavins: Hijacking a
Flavin Transferase for Equipping Flavoproteins with a Covalent
Flavin Cofactor. Journal of the American Chemical
Society, 145(49), 27140–27148. https://doi.org/10.1021/jacs.3c12009
Yang,
G., Wijma, H. J., Rozeboom, H.
J., Mascotti, M. L., & Fraaije, M.
W. (2023). Identification and characterization of
archaeal and bacterial F420-dependent thioredoxin
reductases. The FEBS Journal,
290(19), 4777-4791. https://doi.org/10.1111/febs.16896
Nicoll,
C. R., Massari, M., Fraaije, M. W., Mascotti, M.
L., & Mattevi, A. (2023). Impact of ancestral
sequence reconstruction on mechanistic and structural
enzymology. Current Opinion in Structural
Biology, 82, Article 102669. https://doi.org/10.1016/j.sbi.2023.102669
Guo,
Y., Alvigini, L., Saifuddin, M., Ashley,
B., Trajkovic, M., Alonso-Cotchico, L.,
Mattevi, A., & Fraaije, M. W. (2023).
One-pot biocatalytic synthesis of rac-syringaresinol from a
lignin-derived phenol. ACS Catalysis,
13(22), 14639-14649. https://doi.org/10.1021/acscatal.3c04399
Tjallinks,
G., Boverio, A., Maric, I.,
Rozeboom, H., Arentshorst, M., Visser, J., Ram, A. F. J.,
Mattevi, A., & Fraaije, M. W. (2023).
Structure elucidation and characterization of patulin
synthase, insights into the formation of a fungal mycotoxin.
The FEBS Journal, 290(21),
5114-5126. Article 16804. https://doi.org/10.1111/febs.16804
Eggerichs,
D., Weindorf, N., Mascotti, M. L., Welzel, N.,
Fraaije, M. W., & Tischler, D. (2023). Vanillyl
alcohol oxidase from Diplodia corticola: Residues Ala420 and Glu466
allow for efficient catalysis of syringyl derivatives.
The Journal of Biological Chemistry,
299(7), Article 104898. https://doi.org/10.1016/j.jbc.2023.104898
Delgado-Arciniega,
E., Wijma, H. J., Hummel, C., &
Janssen, D. B. (2023). Computationally Supported
Inversion of Ketoreductase Stereoselectivity.
ChemBioChem, 24(9), Article
e202300032. https://doi.org/10.1002/cbic.202300032
Jóźwik,
I. K., Bombino, E., Abdulmughni, A., Hartz, P.,
Rozeboom, H. J., Wijma, H. J., Kappl, R.,
Janssen, D. B., Bernhardt, R., & Thunnissen, A.-M.
W. H. (2023). Regio- and stereoselective steroid
hydroxylation by CYP109A2 from Bacillus megaterium explored by
X-ray crystallography and computational modeling.
The FEBS Journal, 290(20),
5016-5035. https://doi.org/10.1111/febs.16906
Oun,
A., Hoeksema, E., Soliman, A., Brouwer,
F., García-Reyes, F., Pots,
H., Trombetta-Lima, M., Kortholt,
A., & Dolga, A. M. (2023).
Characterization of Lipopolysaccharide Effects on LRRK2
Signaling in RAW Macrophages. International
Journal of Molecular Sciences, 24(2), Article
1644. https://doi.org/10.3390/ijms24021644
Pathak,
P., Alexander, K. K., Helton, L. G., Kentros, M., LeClair,
T. J., Zhang, X., Ho, F. Y., Moore, T.
T., Hall, S., Guaitoli, G., Gloeckner, C. J., Kortholt,
A., Rideout, H., & Kennedy, E. J. (2023). Doubly
Constrained C-terminal of Roc (COR) Domain-Derived Peptides Inhibit
Leucine-Rich Repeat Kinase 2 (LRRK2) Dimerization.
ACS chemical neuroscience, 14(11),
1971-1980. Article 00259. https://doi.org/10.1021/acschemneuro.3c00259
Zhang,
X., & Kortholt, A. (2023). LRRK2
Structure-Based Activation Mechanism and Pathogenesis.
Biomolecules, 13(4), Article 612. https://doi.org/10.3390/biom13040612
Iannotta,
L., Emanuele, M., Favetta, G., Tombesi, G., Vandewynckel, L., Lara
Ordóñez, A. J., Saliou, J.-M., Drouyer, M., Sibran, W.,
Civiero, L., Nichols, R. J., Athanasopoulos, P.
S., Kortholt, A., Chartier-Harlin, M.-C.,
Greggio, E., & Taymans, J.-M. (2023). PAK6-mediated
phosphorylation of PPP2R2C regulates LRRK2-PP2A complex
formation. Frontiers in Molecular
Neuroscience, 16, Article 1269387. https://doi.org/10.3389/fnmol.2023.1269387
Sabogal-Guáqueta,
A. M., Marmolejo-Garza, A.,
Trombetta-Lima, M., Oun, A., Hunneman,
J., Chen, T., Koistinaho, J., Lehtonen, S.,
Kortholt, A., Wolters, J. C., Bakker, B.
M., Eggen, B. J. L., Boddeke,
E., & Dolga, A. (2023).
Species-specific metabolic reprogramming in human and mouse
microglia during inflammatory pathway induction.
Nature Communications, 14(1),
Article 6454. https://doi.org/10.1038/s41467-023-42096-7
Bonini,
A., Sauciuc, A., & Maglia, G.
(2024). Engineered nanopores for exopeptidase protein
sequencing. Nature Methods,
21, 16-17. https://doi.org/10.1038/s41592-023-02136-y
Sauciuc,
A., Morozzo Della Rocca, B., Tadema, M. J.,
Chinappi, M., & Maglia, G. (2024).
Translocation of linearized full-length proteins through an
engineered nanopore under opposing electrophoretic force.
Nature Biotechnology, 42, 1275-1281.
https://doi.org/10.1038/s41587-023-01954-x
Lucas,
F. L. R., Finol-Urdaneta, R. K., Van Thillo, T., McArthur, J.
R., van der Heide, N. J., Maglia, G.,
Dedecker, P., Strauss, O., & Wloka, C. (2023). Evidence
of Cytolysin A nanopore incorporation in mammalian cells assessed
by a graphical user interface.
Nanoscale, 15(23),
16914–16923. https://doi.org/10.1039/d3nr01977b
Paulo,
G., Sun, K., Di Muccio, G., Gubbiotti, A., Morozzo della Rocca, B.,
Geng, J., Maglia, G., Chinappi, M., & Giacomello,
A. (2023). Hydrophobically gated memristive nanopores for
neuromorphic applications. Nature
Communications, 14(1), Article 8390. https://doi.org/10.1038/s41467-023-44019-y
Straathof,
S., Di Muccio, G., Yelleswarapu, M., Alzate Banguero,
M., Wloka, C., van der Heide, N. J.,
Chinappi, M., & Maglia, G. (2023). Protein
Sizing with 15 nm Conical Biological Nanopore YaxAB.
Acs Nano, 17(14), 13685–13699.
https://doi.org/10.1021/acsnano.3c02847
Abraham
Versloot, R. C., Arias-Orozco, P.,
Tadema, M. J., Rudolfus Lucas, F. L.,
Zhao, X., Marrink, S. J., Kuipers, O.
P., & Maglia, G. (2023). Seeing the
Invisibles: Detection of Peptide Enantiomers, Diastereomers, and
Isobaric Ring Formation in Lanthipeptides Using Nanopores.
Journal of the American Chemical Society,
145(33), 18355-18365. Article 4076. https://doi.org/10.1021/jacs.3c04076
Zhang,
X., Galenkamp, N. S., van der Heide, N.
J., Moreno, J., Maglia, G., & Kjems, J.
(2023). Specific Detection of Proteins by a
Nanobody-Functionalized Nanopore Sensor. Acs
Nano, 17(10), 9167-9177. Article 12733. https://doi.org/10.1021/acsnano.2c12733
Minh
Tran, B., Michiel Punter, C., Linnik,
D., Iyer, A., & Poolman, B.
(2024). Single-protein diffusion in the periplasm of
Escherichia coli. Journal of Molecular
Biology, 436(4), Article 168420. https://doi.org/10.1016/j.jmb.2023.168420
Bailoni,
E., Partipilo, M., Coenradij,
J., Grundel, D. A. J., Slotboom, D.
J., & Poolman, B. (2023). Minimal
Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane
Perspective. ACS Synthetic Biology,
12. https://doi.org/10.1021/acssynbio.3c00062
Poolman,
B. (2023). Physicochemical homeostasis in
bacteria. FEMS Microbiology Reviews,
47(4), Article fuad033. https://doi.org/10.1093/femsre/fuad033
Mantovanelli,
L., Linnik, D. S., Punter,
M., Kojakhmetov, H. J., Śmigiel, W.
M., & Poolman, B. (2023). Simulation-based
Reconstructed Diffusion unveils the effect of aging on protein
diffusion in Escherichia coli. PLoS Computational
Biology, 19(9), Article e1011093. https://doi.org/10.1371/journal.pcbi.1011093
Tran,
B. M., Linnik, D. S., Punter, C.
M., Śmigiel, W. M., Mantovanelli,
L., Iyer, A., O’Byrne, C., Abee, T.,
Johansson, J., & Poolman, B. (2023).
Super-resolving microscopy reveals the localizations and
movement dynamics of stressosome proteins in Listeria
monocytogenes. Communications biology,
6(1), Article 51. https://doi.org/10.1038/s42003-023-04423-y
Partipilo,
M., Claassens, N. J., & Slotboom, D. J.
(2023). A Hitchhiker’s Guide to Supplying Enzymatic
Reducing Power into Synthetic Cells. ACS Synthetic
Biology, 12, 947-962. Article 3c00070. https://doi.org/10.1021/acssynbio.3c00070
Partipilo,
M., Whittaker, J. J., Pontillo,
N., Coenradij, J., Herrmann,
A., Guskov, A., & Slotboom, D.
J. (2023). Biochemical and structural insight into the
chemical resistance and cofactor specificity of the formate
dehydrogenase from Starkeya novella. The FEBS
Journal, 290(17), 4238-4255. https://doi.org/10.1111/febs.16871
Thangaratnarajah,
C., Nijland, M., Borges-Araújo, L.,
Jeucken, A., Rheinberger, J., Marrink, S.
J., Souza, P. C. T., Paulino,
C., & Slotboom, D. J. (2023).
Expulsion mechanism of the substrate-translocating subunit in
ECF transporters. Nature
Communications, 14(1), Article 4484. https://doi.org/10.1038/s41467-023-40266-1
Diamanti,
E., Souza, P. C. T., Setyawati, I., Bousis, S.,
Gómez, L. M., Swier, L. J. Y. M., Shams, A., Tsarenko,
A., Stanek, W. K., Jäger, M., Marrink, S.
J., Slotboom, D. J., & Hirsch, A. K. H.
(2023). Identification of inhibitors targeting the
energy-coupling factor (ECF) transporters.
Communications biology, 6(1),
Article 1182. https://doi.org/10.1038/s42003-023-05555-x
Colucci,
E., Anshari, Z., Patiño-Ruiz,
M., Nemchinova, M., Whittaker,
J., Slotboom, D., & Guskov, A.
(2023). Mutation in glutamate transporter homologue GltTk
provides insights into pathologic mechanism of episodic ataxia
6. Nature Communications, 14,
Article 1799. https://doi.org/10.1038/s41467-023-37503-y
van
der Zouwen, A. J., Jeucken, A., van der Pol,
E., Boerema, G., Slotboom, D. J., & Witte,
M. D. (2023). The linkage-type and the exchange
molecule affect the protein-labeling efficiency of iminoboronate
probes. Organic & Biomolecular
Chemistry, 21, 9173-9181. https://doi.org/10.1039/d3ob01269g
Li,
X., Wang, Y., Wu, J., Jin, Z., Dijkhuizen, L.,
Svensson, B., & Bai, Y. (2024). Designing starch
derivatives with desired structures and functional properties via
rearrangements of glycosidic linkages by starch-active
transglycosylases. Critical Reviews in Food
Science and Nutrition, 64(23), 8265-8278. https://doi.org/10.1080/10408398.2023.2198604
Fang,
Y., Dong, M., van Leeuwen, S. S., Dijkhuizen,
L., Meng, X., & Liu, W. (2023). Biochemical
characterization of glycoside hydrolase family 31
α-glucosidases from Myceliophthora thermophila for
α-glucooligosaccharide synthesis.
International Journal of Biological
Macromolecules, 252, Article 126452. https://doi.org/10.1016/j.ijbiomac.2023.126452
van
der Toorn, M. V., Chatziioannou, A. C., Pellis, L.,
Haandrikman, A., van der Zee, L., & Dijkhuizen, L.
(2023). Biological Relevance of Goat Milk Oligosaccharides to
Infant Health. Journal of Agricultural and Food
Chemistry, 71(38), 13935–13949. https://doi.org/10.1021/acs.jafc.3c02194
Scheurink,
T. A. W., Borkent, J., Gangadin, S.
S., El Aidy, S., Mandl, R., & Sommer,
I. E. C. (2023). Association between gut permeability,
brain volume, and cognition in healthy participants and patients
with schizophrenia spectrum disorder. Brain and
Behavior, 13(6), Article e3011. https://doi.org/10.1002/brb3.3011
Jansma,
J., Thome, N. U., Schwalbe, M., Chatziioannou,
A. C., Elsayed, S. S., van Wezel, G. P., van den Abbeele, P., van
Hemert, S., & El Aidy, S. (2023). Dynamic
effects of probiotic formula ecologic®825 on human small
intestinal ileostoma microbiota: A network theory approach.
Gut Microbes, 15(1), Article
2232506. https://doi.org/10.1080/19490976.2023.2232506
Mahdy,
M. S., Azmy, A. F., Dishisha, T., Mohamed, W. R., Ahmed, K. A.,
Hassan, A., Aidy, S. E., & El-Gendy, A. O. (2023).
Irinotecan-gut microbiota interactions and the capability of
probiotics to mitigate Irinotecan-associated toxicity.
BMC Microbiology, 23(1), Article 53.
https://doi.org/10.1186/s12866-023-02791-3
Jansma,
J., Chatziioannou, A. C., Castricum, K., van Hemert,
S., & El Aidy, S. (2023). Metabolic network
construction reveals probiotic-specific alterations in the
metabolic activity of a synthetic small intestinal
community. Msystems, 8(5),
Article 00332-23. https://doi.org/10.1128/msystems.00332-23
Waclawiková,
B., Cesar Telles de Souza, P., Schwalbe,
M., Neochoritis, C. G., Hoornenborg, W.,
Nelemans, S. A., Marrink, S. J., & El Aidy,
S. (2023). Potential binding modes of the gut
bacterial metabolite, 5-hydroxyindole, to the intestinal L-type
calcium channels and its impact on the microbiota in rats.
Gut Microbes, 15(1), Article
2154544. https://doi.org/10.1080/19490976.2022.2154544
de
Boer, R., & van der Klei, I. J. (2023).
Correlative Light- and Electron Microscopy in Peroxisome
Research. In M. Schrader (Ed.), Peroxisomes: Methods and
protocols (2nd ed., pp. 93-104). (Methods in molecular biology
(Clifton, N.J.); Vol. 2643). Humana Press. https://doi.org/10.1007/978-1-0716-3048-8_7
Wu,
F., de Boer, R., & van der Klei, I.
J. (2023). Gluing yeast peroxisomes - composition and
function of membrane contact sites. Journal of
Cell Science, 136(11), Article 259440. https://doi.org/10.1242/jcs.259440
Jansen,
R. L. M., van den Noort, M., Krikken, A.
M., Bibi, C., Böhm, A., Schuldiner, M., Zalckvar,
E., & van der Klei, I. J. (2023). Novel
targeting assay uncovers targeting information within peroxisomal
ABC transporter Pxa1. Biochimica et Biophysica
Acta - Molecular Cell Research, 1870(5),
Article 119471. https://doi.org/10.1016/j.bbamcr.2023.119471
van
Tilburg, M. P. A., Marrink, S. J.,
König, M., & Grünewald, F.
(2024). Shocker─A Molecular Dynamics Protocol and Tool
for Accelerating and Analyzing the Effects of Osmotic
Shocks. Journal of Chemical Theory and
Computation, 20, Article 3c00961. https://doi.org/10.1021/acs.jctc.3c00961
Empereur-Mot,
C., Pedersen, K. B., Capelli, R., Crippa, M., Caruso, C., Perrone,
M., Souza, P. C. T., Marrink, S. J., & Pavan, G.
M. (2023). Automatic Optimization of Lipid Models in the
Martini Force Field Using SwarmCG. Journal of
chemical information and modeling, 63(12),
3827–3838. https://doi.org/10.1021/acs.jcim.3c00530
Ramírez-Palacios,
C., & Marrink, S. J. (2023).
Computational prediction of ω-transaminase selectivity
by deep learning analysis of molecular dynamics
trajectories. QRB Discovery,
4, Article e1. https://doi.org/10.1017/qrd.2022.22
Stępień,
P., Świątek, S., Robles, M. Y. Y., Markiewicz-Mizera, J.,
Balakrishnan, D., Inaba-Inoue, S., De Vries, A. H.,
Beis, K., Marrink, S. J., & Heddle, J. G. (2023).
CRAFTing Delivery of Membrane Proteins into Protocells using
Nanodiscs. ACS Applied Materials &
Interfaces, 15, 56689–56701. https://doi.org/10.1021/acsami.3c11894
Gilbert,
B. R., Thornburg, Z. R., Brier, T. A., Stevens, J.
A., Grünewald, F., Stone, J. E.,
Marrink, S. J., & Luthey-Schulten, Z. (2023).
Dynamics of chromosome organization in a minimal bacterial
cell. Frontiers in Cell and Developmental
Biology, 11, Article 1214962. https://doi.org/10.3389/fcell.2023.1214962
Hilpert,
C., Beranger, L., Souza, P. C. T., Vainikka, P.
A., Nieto, V., Marrink, S. J., Monticelli, L.,
& Launay, G. (2023). Facilitating CG Simulations with
MAD: The MArtini Database Server. Journal of
chemical information and modeling, 63(3),
702–710. Article 9. https://doi.org/10.1021/acs.jcim.2c01375
Melcrová,
A., Maity, S., Melcr, J., de
Kok, N. A. W., Gabler, M., van der Eyden, J., Stensen, W.,
Svendsen, J. S. M., Driessen, A. J. M., Marrink,
S. J., & Roos, W. H. (2023). Lateral
membrane organization as target of an antimicrobial peptidomimetic
compound. Nature Communications,
14(1), Article 4038. https://doi.org/10.1038/s41467-023-39726-5
Borges-Araújo,
L., Borges-Araújo, A. C., Ozturk, T. N., Ramirez-Echemendia,
D. P., Fábián, B., Carpenter, T. S., Thallmair, S.,
Barnoud, J., Ingólfsson, H. I., Hummer, G., Tieleman, D.
P., Marrink, S. J., Souza, P. C. T., & Melo, M. N.
(2023). Martini 3 Coarse-Grained Force Field for
Cholesterol. Journal of Chemical Theory and
Computation, 19(20), 7387–7404. https://doi.org/10.1021/acs.jctc.3c00547
Vainikka,
P., & Marrink, S. J. (2023). Martini
3 Coarse-Grained Model for Second-Generation Unidirectional
Molecular Motors and Switches. Journal of Chemical
Theory and Computation, 19, 596-604. Article
00796. https://doi.org/10.1021/acs.jctc.2c00796
Tharmasothirajan,
A., Melcr, J., Linney, J., Gensch, T., Krumbach, K.,
Ernst, K. M., Brasnett, C., Poggi, P., Pitt, A. R.,
Goddard, A. D., Chatgilialoglu, A., Marrink, S. J.,
& Marienhagen, J. (2023). Membrane manipulation by free
fatty acids improves microbial plant polyphenol synthesis.
Nature Communications, 14(1),
Article 5619. https://doi.org/10.1038/s41467-023-40947-x
Pezeshkian,
W., Grünewald, F., Narykov, O., Lu, S.,
Arkhipova, V., Solodovnikov, A., Wassenaar, T.
A., Marrink, S. J., & Korkin, D. (2023).
Molecular architecture and dynamics of SARS-CoV-2 envelope by
integrative modeling. Structure,
31(4), 492-503. Article 202302006. https://doi.org/10.1016/j.str.2023.02.006
Ren,
M., Zhao, L., Ma, Z., An, H., Marrink, S. J., &
Sun, F. (2023). Molecular Basis of PIP2-dependent
Conformational Switching of Phosphorylated CD44 in binding
FERM. Biophysical Journal, 2675-2685.
https://doi.org/10.1016/j.bpj.2023.05.021
Stevens,
J. A., Grünewald, F., van Tilburg,
P. A. M., König, M., Gilbert, B. R.,
Brier, T. A., Thornburg, Z. R., Luthey-Schulten, Z., &
Marrink, S. J. (2023). Molecular dynamics simulation
of an entire cell. Frontiers in
Chemistry, 11, Article 1106495. https://doi.org/10.3389/fchem.2023.1106495
Blanco-González,
A., Marrink, S. J., Piñeiro, Á., &
García-Fandiño, R. (2023). Molecular insights into
the effects of focused ultrasound mechanotherapy on lipid bilayers:
Unlocking the keys to design effective treatments.
Journal of Colloid and Interface Science,
650(Pt B), 1201-1210. Article 07077. https://doi.org/10.1016/j.jcis.2023.07.077
Ingólfsson,
H. I., Rizuan, A., Liu, X., Mohanty, P., Souza, P. C. T.,
Marrink, S. J., Bowers, M. T., Mittal, J., & Berry, J.
(2023). Multiscale simulations reveal TDP-43 molecular level
interactions driving condensation. Biophysical
Journal, 122(22), 4370-4381. https://doi.org/10.1016/j.bpj.2023.10.016
Chiariello,
M. G., Grünewald, F.,
Zarmiento-Garcia, R., & Marrink, S. J.
(2023). pH-Dependent Conformational Switch Impacts Stability
of the PsbS Dimer. The Journal of Physical
Chemistry Letters, 14, 905-911. https://doi.org/10.1021/acs.jpclett.2c03760
Borges-Araújo,
L., Patmanidis, I., Singh, A. P., Santos, L. H. S.,
Sieradzan, A. K., Vanni, S., Czaplewski, C., Pantano, S., Shinoda,
W., Monticelli, L., Liwo, A., Marrink, S. J., &
Souza, P. C. T. (2023). Pragmatic Coarse-Graining of
Proteins: Models and Applications. Journal of
Chemical Theory and Computation, 19(20),
7112-7135. Article e00733. https://doi.org/10.1021/acs.jctc.3c00733
Sami,
S., & Marrink, S. J. (2023). Reactive
Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics
Simulations. Journal of Chemical Theory and
Computation, 19(13), 4040-4046. https://doi.org/10.1021/acs.jctc.2c01186
Ramírez-Palacios,
C., & Marrink, S. J. (2023). Super
High-Throughput Screening of Enzyme Variants by Spectral Graph
Convolutional Neural Networks. Journal of Chemical
Theory and Computation, 19(14),
4668–4677. Article 1227. https://doi.org/10.1021/acs.jctc.2c01227
Manrho,
M., Krishnaswamy, S. R., Kriete,
B., Patmanidis, I., de Vries, A.
H., Marrink, S. J., Jansen, T. L.
C., Knoester, J., & Pshenichnikov, M.
S. (2023). Watching Molecular Nanotubes Self-Assemble
in Real Time. Journal of the American Chemical
Society, 145(41), 22494–22503. https://doi.org/10.1021/jacs.3c07103
Cebrián,
R., Martínez-García, M., Fernández, M., García,
F., Martínez-Bueno, M., Valdivia, E., Kuipers, O.
P., Montalbán-López, M., & Maqueda, M. (2023).
Advances in the preclinical characterization of the
antimicrobial peptide AS-48. Frontiers in
Microbiology, 14, Article 1110360. https://doi.org/10.3389/fmicb.2023.1110360
Fernandez-Cantos,
M. V., Garcia de la Morena, D., Yi,
Y., Liang, L., Gomez Vazquez, E., & Kuipers,
O. (2023). Bioinformatic mining for RiPP biosynthetic
gene clusters in Bacteroidales reveals possible new subfamily
architectures and novel natural products.
Frontiers in Microbiology, 14,
Article 1219272. https://doi.org/10.3389/fmicb.2023.1219272
Morawska,
L. P., & Kuipers, O. P. (2023).
Cell-to-cell non-conjugative plasmid transfer between
Bacillus subtilis and lactic acid bacteria.
Microbial Biotechnology, 16(4),
784-798. https://doi.org/10.1111/1751-7915.14195
Guo,
L., Wambui, J., Wang, C., Muchaamba, F.,
Fernandez-Cantos, M. V., Broos, J., Tasara,
T., Kuipers, O. P., & Stephan, R. (2023).
Cesin, a short natural variant of nisin, displays potent
antimicrobial activity against major pathogens despite lacking two
C-terminal macrocycles. Microbiology
Spectrum, 11(5), Article e0531922. https://doi.org/10.1128/spectrum.05319-22
Fu,
Y., Zhou, L., & Kuipers, O. P.
(2023). Discovery, biosynthesis, and characterization of a
lanthipeptide from Bacillus subtilis EH11 with a unique lanthionine
ring pattern. Cell Reports Physical
Science, 4(8), Article 101524. https://doi.org/10.1016/j.xcrp.2023.101524
Zhao,
X., Zhong, X., Yang, S., Deng, K., Liu, L., Song, X., Zou,
Y., Li, L., Zhou, X., Jia, R., Lin, J., Tang, H., Ye,
G., Yang, J., Zhao, S., Lang, Y., Wan, H., Yin,
Z., & Kuipers, O. P. (2023). Elucidating the
Mechanism of Action of the Gram-Negative-Pathogen-Selective Cyclic
Antimicrobial Lipopeptide Brevicidine.
Antimicrobial Agents and Chemotherapy,
67(5). https://doi.org/10.1128/aac.00010-23
Fu,
Y., Xu, Y., Ruijne, F.,
& Kuipers, O. P. (2023). Engineering
lanthipeptides by introducing a large variety of RiPP modifications
to obtain new-to-nature bioactive peptides. FEMS
Microbiology Reviews, 47(3), Article fuad017.
https://doi.org/10.1093/femsre/fuad017
Hammad,
M., Ali, H., Hassan, N., Tawab, A., Salman, M., Jawad, I., de
Jong, A., Moreno, C. M., Kuipers, O.
P., Feroz, Y., & Rashid, M. H. (2023). Food safety
and biological control; genomic insights and antimicrobial
potential of Bacillus velezensis FB2 against agricultural fungal
pathogens. PLoS ONE, 18(11),
Article e0291975. https://doi.org/10.1371/journal.pone.0291975
Liu,
F., van Heel, A. J., & Kuipers, O.
P. (2023). Leader- and Terminal Residue Requirements
for Circularin A Biosynthesis Probed by Systematic Mutational
Analyses. ACS Synthetic Biology,
12(3), 852-862. https://doi.org/10.1021/acssynbio.2c00661
Guo,
L., Wang, C., Broos, J.,
& Kuipers, O. P. (2023). Lipidated variants of the
antimicrobial peptide nisin produced via incorporation of
methionine analogs for click chemistry show improved
bioactivity. The Journal of Biological
Chemistry, 229(7), Article 104845. https://doi.org/10.1016/j.jbc.2023.104845
Li,
L., Zhang, L., Zhang, T., Liu, Y., Lü, X., Kuipers, O.
P., & Yi, Y. (2023). (Meta)genomics -assisted
screening of novel antibacterial lactic acid bacteria strains from
traditional fermented milk from Western China and their
bioprotective effects on cheese. LWT,
175, Article 114507. https://doi.org/10.1016/j.lwt.2023.114507
Cebrián
Castillo, R., Xia, Y., & Kuipers,
O. (2023). Synergistic composition
against pseudomonas aeruginosa. (Patent No.
WO2023063827).
Cebrián,
R., Lucas, R., Fernández-Cantos, M. V.,
Slot, K., Peñalver, P., Martínez-García, M.,
Párraga-Leo, A., de Paz, M. V., García, F.,
Kuipers, O. P., & Morales, J. C. (2023). Synthesis
and antimicrobial activity of aminoalkyl resveratrol derivatives
inspired by cationic peptides. Journal of enzyme
inhibition and medicinal chemistry, 38(1),
267-281. https://doi.org/10.1080/14756366.2022.2146685
Cacace,
E., Kim, V., Varik, V., Knopp, M., Tietgen, M.,
Brauer-Nikonow, A., Inecik, K., Mateus, A., Milanese, A.,
Mårli, M. T., Mitosch, K., Selkrig, J., Brochado, A. R.,
Kuipers, O. P., Kjos, M., Zeller, G., Savitski, M. M.,
Göttig, S., Huber, W., & Typas, A. (2023).
Systematic analysis of drug combinations against
Gram-positive bacteria. Nature
Microbiology, 8(11), 2196-2212. https://doi.org/10.1038/s41564-023-01486-9
Villela,
D. C., Namsolleck, P., Reichetzeder, C., & Moll, G.
N. (2023). AT2 receptor agonist LP2 restores
respiratory function in a rat model of bleomycin-induced lung
remodelling. Peptides, 170,
Article 171106. https://doi.org/10.1016/j.peptides.2023.171106
Wagenaar,
G. T. M., & Moll, G. N. (2023). Evolving
views on the first two ligands of the angiotensin II type 2
receptor. From putative antagonists to potential agonists?
European Journal of Pharmacology,
961, Article 176189. https://doi.org/10.1016/j.ejphar.2023.176189
Namsolleck,
P., Kofler, B., & Moll, G. N. (2023).
Galanin 2 Receptor: A Novel Target for a Subset of Pancreatic
Ductal Adenocarcinoma. International Journal of
Molecular Sciences, 24(12), Article 10193. https://doi.org/10.3390/ijms241210193
Namsolleck,
P., de Vries, L., & Moll, G. N.
(2023). LP2, a cyclic angiotensin-(1−7) analog extended
with an N-terminal D-lysine, impairs growth of patient-derived
xenografts of colorectal carcinoma in mice.
Peptides, 160, Article 170920. https://doi.org/10.1016/j.peptides.2022.170920
Namsolleck,
P., Rodgers, K. E., Franklin, R., & Moll, G. N.
(2023). LP2, a stable lanthipeptide derived from cAng-(1-7),
exerts myeloprotective action in mice. European
Journal of Haematology, 110(5), 534-539. https://doi.org/10.1111/ejh.13927
den
Uijl, M. J., & Driessen, A. J. M. (2024).
Phospholipid dependency of membrane protein insertion by the
Sec translocon. Biochimica et Biophysica Acta -
Biomembranes, 1866(1), Article 184232. https://doi.org/10.1016/j.bbamem.2023.184232
Nijland,
J. G., Zhang, X., & Driessen, A. J.
M. (2023). D-xylose accelerated death of pentose
metabolizing Saccharomyces cerevisiae.
Biotechnology for Biofuels and Bioproducts,
16(1), Article 67. https://doi.org/10.1186/s13068-023-02320-4
Peng,
B., Dai, L., Iacovelli, R.,
Driessen, A. J. M., & Haslinger, K. (2023).
Heterologous Naringenin Production in the Filamentous Fungus
Penicillium rubens. Journal of Agricultural and
Food Chemistry, 71(51), 20782-20792. https://doi.org/10.1021/acs.jafc.3c06755
Wolf,
I. R., Marques, L. F., de Almeida, L. F., Lázari, L. C., de
Moraes, L. N., Cardoso, L. H., Alves, C. C. D. O., Nakajima, R. T.,
Schnepper, A. P., Golim, M. D. A., Cataldi, T. R., Nijland,
J. G., Pinto, C. M., Fioretto, M. N., Almeida, R. O.,
Driessen, A. J. M., Simōes, R. P., Labate, M. V.,
Grotto, R. M. T., ... Valente, G. T. (2023). Integrative
Analysis of the Ethanol Tolerance of Saccharomyces
cerevisiae. International Journal of Molecular
Sciences, 24(6), Article 5646. https://doi.org/10.3390/ijms24065646
Rao,
A., de Kok, N. A. W., & Driessen, A.
J. M. (2023). Membrane Adaptations and Cellular
Responses of Sulfolobus acidocaldarius to the Allylamine
Terbinafine. International Journal of Molecular
Sciences, 24(8), Article 7328. https://doi.org/10.3390/ijms24087328
Nisa,
I., Driessen, A., Nijland, J., Rahman,
H., Mattner, J., & Qasim, M. (2023). Novel plasmids in
multidrug-resistant Shigella flexneri serotypes from
Pakistan. Archives of Microbiology,
205(5), 175. https://doi.org/10.1007/s00203-023-03523-x
Bramkamp,
M., & Scheffers, D.-J. (2023). Bacterial
membrane dynamics: Compartmentalization and repair.
Molecular Microbiology, 120(4),
Article 15077. https://doi.org/10.1111/mmi.15077
Ziylan,
Z. S., de Putter, G. J., Roelofs, M., van Dijl, J.
M., Scheffers, D. J., & Walvoort, M.
T. C. (2023). Evaluation of Kdo-8-N3
incorporation into lipopolysaccharides of various Escherichia
coli strains. RSC Chemical
Biology, 4(11), 884–893. https://doi.org/10.1039/d3cb00110e
Smith,
E. N., van Aalst, M., Tosens, T., Niinemets, Ü., Stich,
B., Morosinotto, T., Alboresi, A., Erb, T., Gómez-Coronado, P.
A., Tolleter, D., Finazzi, G., Curien, G., Heinemann,
M., Ebenhöh, O., Hibberd, J. M., Schlüter, U.,
Sun, T., & Weber, A. P. M. (2023). Improving
photosynthetic efficiency toward food security: Strategies,
advances, and perspectives. Molecular
Plant, 16(10), 1547-1563. https://doi.org/10.1016/j.molp.2023.08.017
Li,
X., & Heinemann, M. (2023).
Quantifying intracellular glucose levels when yeast is grown
in glucose media. Scientific Reports,
13(1), Article 17066. https://doi.org/10.1038/s41598-023-43602-z
Takhaveev,
V., Özsezen, S., Smith, E.
N., Zylstra, A., Chaillet, M. L., Chen,
H., Papagiannakis, A., Milias-Argeitis,
A., & Heinemann, M. (2023). Temporal
segregation of biosynthetic processes is responsible for metabolic
oscillations during the budding yeast cell cycle.
Nature Metabolism, 5(2), 294-313. https://doi.org/10.1038/s42255-023-00741-x
2022
de
Gonzalo, G., Loncar, N., & Fraaije,
M. (2024). Sulphoxidation reactions catalysed by the
Baeyer-Villiger monooxygenase OTEMO from Pseudomonas putida ATCC
17453. Biocatalysis and
Biotransformation, 42(1), 77-84. Article
2113519. https://doi.org/10.1080/10242422.2022.2113519
Boverio,
A., Widodo, W. S., Santema, L.
L., Rozeboom, H. J., Xiang, R., Guallar, V.,
Mattevi, A., & Fraaije, M. W. (2023).
Structural Elucidation and Engineering of a Bacterial
Carbohydrate Oxidase. Biochemistry,
62(2), 429-436. https://doi.org/10.1021/acs.biochem.2c00307
Partipilo,
M., Yang, G., Mascotti, L.,
Slotboom, D., & Fraaije, M. (2022). A
conserved sequence motif in the E. coli soluble FAD-containing
pyridine nucleotide transhydrogenase is important for reaction
efficiency. The Journal of Biological
Chemistry, 298(9), Article 102304. https://doi.org/10.1016/j.jbc.2022.102304
Tong,
Y., Loonstra, M. R., & Fraaije, M. (2022).
Broadening the scope of the Flavin-tag method by improving
flavin incorporation and incorporating flavin analogs.
ChemBioChem, 23(11), Article
e202200144. https://doi.org/10.1002/cbic.202200144
Venturi,
S., Trajkovic, M., Colombo, D., Brenna, E.,
Fraaije, M. W., Gatti, F. G., Macchi, P., & Zamboni, E.
(2022). Chemoenzymatic Synthesis of the Most Pleasant
Stereoisomer of Jessemal. The Journal of Organic
Chemistry, 87(9), 6499-6503. https://doi.org/10.1021/acs.joc.2c00427
de
Gonzalo, G., Lončar, N., & Fraaije,
M. (2022). Kinetic resolution of racemic benzofused
alcohols catalysed by HMFO variants in presence of natural deep
eutectic solvents. Biocatalysis and
Biotransformation, 41(2), 145-152. https://doi.org/10.1080/10242422.2022.2038582
Guo,
Y., Alvigini, L., Trajkovic, M.,
Alonso-Cotchico, L., Monza, E., Savino, S.,
Marić, I., Mattevi, A., & Fraaije, M.
W. (2022). Structure- and computational-aided
engineering of an oxidase to produce isoeugenol from a
lignin-derived compound. Nature
Communications, 13(1), Article 7195. https://doi.org/10.1038/s41467-022-34912-3
Ashworth,
M. A., Bombino, E., De Jong, R. M., Wijma, H.
J., Janssen, D. B., McLean, K. J., & Munro,
A. W. (2022). Computation-Aided Engineering of Cytochrome
P450 for the Production of Pravastatin. ACS
Catalysis, 12(24), 15028-15044. https://doi.org/10.1021/acscatal.2c03974
Marchand,
A., Sarchione, A., Athanasopoulos, P., Roy, H. B.-L.,
Goveas, L., Romain, MAGNEZ., Drouyer, M., Emanuele, M., Ho,
F. Y., Liberelle, M., Melnyk, P., Nicolas, LEBEGUE., Thuru,
X., Nichols, R. J., Greggio, E., kortholt, A., Galli,
T., chartier-harlin, M., & Taymans, J.-M. (2022). A
Phosphosite Mutant Approach on LRRK2 Links Phosphorylation and
Dephosphorylation to Protective and Deleterious Markers,
Respectively. Cells, 11(6),
Article 1018. https://doi.org/10.3390/cells11061018
Xu,
X., Pots, H., Gilsbach, B. K., Parsons, D., Veltman,
D. M., Ramachandra, S. G., Li, H., Kortholt, A., &
Jin, T. (2022). C2GAP2 is a common regulator of Ras signaling
for chemotaxis, phagocytosis, and macropinocytosis.
Frontiers in Immunology, 13, Article
1075386. https://doi.org/10.3389/fimmu.2022.1075386
Skakun,
V. V., Yatskou, M. M., Nederveen-Schippers, L.,
Kortholt, A., & Apanasovich, V. V. (2022).
Component Analysis of Photon Counting Histograms in
Fluorescence Fluctuation Spectroscopy Experiments.
Journal of applied spectroscopy,
89(5), 930-939. https://doi.org/10.1007/s10812-022-01450-1
Rideout,
H., Greggio, E., Kortholt, A., & Nichols, R. J.
(2022). Editorial: LRRK2-Fifteen Years From Cloning to the
Clinic. Frontiers in Neuroscience,
16, Article 880914. https://doi.org/10.3389/fnins.2022.880914
Oun,
A., Soliman, A., Trombetta-Lima,
M., Tzepapadaki, A., Tsagkari, D., Kortholt,
A., & Dolga, A. M. (2022). LRRK2
protects immune cells against erastin-induced ferroptosis.
Neurobiology of Disease, 175,
Article 105917. https://doi.org/10.1016/j.nbd.2022.105917
Singh,
R. K., Soliman, A., Guaitoli, G., Störmer, E.,
von Zweydorf, F., Dal Maso, T., Oun, A., Van Rillaer,
L., Schmidt, S. H., Chatterjee, D., David, J. A., Pardon, E.,
Schwartz, T. U., Knapp, S., Kennedy, E. J., Steyaert, J., Herberg,
F. W., Kortholt, A., Gloeckner, C. J., &
Versées, W. (2022). Nanobodies as allosteric modulators
of Parkinson's disease-associated LRRK2.
Proceedings of the National Academy of Sciences of the
United States of America, 119(9), Article
e2112712119. https://doi.org/10.1073/pnas.2112712119
Arenales
Arauz, Y. L., Ahuja, G., Kamsma, Y. P. T.,
Kortholt, A., van der Zee, E. A., &
van Heuvelen, M. J. G. (2022). Potential of Whole-Body
Vibration in Parkinson's disease: A systematic review and
meta-analysis of human and animal studies.
Biology, 11(8), Article 11081238. https://doi.org/10.3390/biology11081238
Cankara,
F. N., Kuş, M. S., Günaydın, C., Şafak, S.,
Bilge, S. S., Ozmen, O., Tural, E., & Kortholt, A.
(2022). The beneficial effect of salubrinal on
neuroinflammation and neuronal loss in intranigral LPS-induced
hemi-Parkinson disease model in rats.
Immunopharmacology and Immunotoxicology,
44(2), 168-177. https://doi.org/10.1080/08923973.2021.2023174
Oun,
A., Sabogal-Guaqueta, A. M., Galuh, S.,
Alexander, A., Kortholt, A., & Dolga, A.
M. (2022). The multifaceted role of LRRK2 in
Parkinson's disease: From human iPSC to organoids.
Neurobiology of Disease, 173,
Article 105837. https://doi.org/10.1016/j.nbd.2022.105837
Cogo,
S., Ho, F. Y., Tosoni, E., Tomkins, J. E., Tessari,
I., Iannotta, L., Montine, T. J., Manzoni, C., Lewis, P. A.,
Bubacco, L., Chartier Harlin, M.-C., Taymans, J.-M.,
Kortholt, A., Nichols, J., Cendron, L., Civiero, L., &
Greggio, E. (2022). The Roc domain of LRRK2 as a hub for
protein-protein interactions: a focus on PAK6 and its impact on RAB
phosphorylation. Brain Research,
1778, Article 147781. https://doi.org/10.1016/j.brainres.2022.147781
Kobauri,
P., Galenkamp, N. S., Schulte, A.
M., de Vries, J., Simeth, N. A., Maglia,
G., Thallmair, S., Kolarski,
D., Szymanski, W., & Feringa, B.
L. (2022). Hypothesis-Driven, Structure-Based Design
in Photopharmacology: The Case of eDHFR Inhibitors.
Journal of Medicinal Chemistry,
65(6), 4798-4817. Article 1c01962. https://doi.org/10.1021/acs.jmedchem.1c01962
Ying,
Y.-L., Hu, Z.-L., Zhang, S., Qing, Y., Fragasso,
A., Maglia, G., Meller, A., Bayley, H., Dekker, C.,
& Long, Y.-T. (2022). Nanopore-based technologies beyond
DNA sequencing. Nature Nanotechnology,
17, 1136-1146. https://doi.org/10.1038/s41565-022-01193-2
Lucas,
F. L. R., Versloot, R. C. R., &
Maglia, G. (2022). Nanopore
proteomics. (Patent No. WO2022245209).
Huang,
G., Voorspoels, A., Versloot, R. C. A.,
Van Der Heide, N. J., Carlon, E., Willems, K., &
Maglia, G. (2022). PlyAB Nanopores Detect Single Amino
Acid Differences in Folded Haemoglobin from Blood.
Angewandte Chemie (International ed. in
English), 61(34), Article e202206227. https://doi.org/10.1002/anie.202206227
Versloot,
R. C. A., Lucas, F. L. R., Yakovlieva,
L., Tadema, M. J., Zhang, Y., Wood, T. M.,
Martin, N. I., Marrink, S. J., Walvoort, M. T.
C., & Maglia, G. (2022).
Quantification of Protein Glycosylation Using
Nanopores. Nano Letters,
22(13), 5357-5364. Article 2c10338. https://doi.org/10.1021/acs.nanolett.2c01338
Galenkamp,
N. S., & Maglia, G. (2022).
Single-Molecule Sampling of Dihydrofolate Reductase Shows
Kinetic Pauses and an Endosteric Effect Linked to Catalysis.
ACS Catalysis, 12(2), 1228-1236.
Article 04388. https://doi.org/10.1021/acscatal.1c04388
Lucas,
F. L. R., Willems, K., Tadema, M. J.,
Tych, K. M., Maglia, G., & Wloka,
C. (2022). Unbiased Data Analysis for the
Parameterization of Fast Translocation Events through
Nanopores. ACS Omega, 7,
26040–26046. https://doi.org/10.1021/acsomega.2c00871
Versloot,
R. C. A., Straathof, S. A. P., Stouwie,
G., Tadema, M. J., & Maglia,
G. (2022). β-Barrel Nanopores with an
Acidic-Aromatic Sensing Region Identify Proteinogenic Peptides at
Low pH. Acs Nano, 16(5),
7258-7268. Article 1c11455. https://doi.org/10.1021/acsnano.1c11455
Bailoni,
E., & Poolman, B. (2022). ATP
Recycling Fuels Sustainable Glycerol 3-Phosphate Formation in
Synthetic Cells Fed by Dynamic Dialysis. ACS
Synthetic Biology, 11(7), 2348–2360.
Article 2c00075. https://doi.org/10.1021/acssynbio.2c00075
Frallicciardi,
J., Gabba, M., & Poolman, B. (2022).
Determining small-molecule permeation through lipid
membranes. Nature protocols,
17, 2620-2646. https://doi.org/10.1038/s41596-022-00734-2
Frallicciardi,
J., Melcr, J., Siginou, P.,
Marrink, S. J., & Poolman, B. (2022).
Membrane thickness, lipid phase and sterol type are
determining factors in the permeability of membranes to small
solutes. Nature Communications,
13(1), Article 1605. https://doi.org/10.1038/s41467-022-29272-x
Szomek,
M., Reinholdt, P., Walther, H. L., Scheidt, H. A., Müller,
P., Obermaier, S., Poolman, B., Kongsted,
J., & Wüstner, D. (2022). Natamycin sequesters
ergosterol and interferes with substrate transport by the lysine
transporter Lyp1 from yeast. Biochimica et
Biophysica Acta - Biomembranes, 1864(11),
Article 184012. https://doi.org/10.1016/j.bbamem.2022.184012
Smigiel,
W. M., Mantovanelli, L., Linnik, D.
S., Punter, M., Silberberg, J., Xiang, L., Xu,
K., & Poolman, B. (2022). Protein diffusion
in Escherichia coli cytoplasm scales with the mass ofthe complexes
and is location dependent. Science
Advances, 8(32), Article eabo5387. https://doi.org/10.1126/sciadv.abo5387
Aarts,
N., Bovenberg, R., Dogterom, M., van Est, R.,
Gerritsen, J., Macnaghten, P., Poolman, B., Robaey,
Z., Rasmussen, S., Ruivenkamp, G., Thole, E., Tremmel, G., van der
Vlugt, C., & Zwart, H. (2022). Society and synthetic
cells: A position paper by the Future Panel on Synthetic
Life. Rathenau Instituut.
Walter,
J. D., Scherer, M., Hutter, C. A. J., Garaeva, A. A.,
Zimmermann, I., Wyss, M., Rheinberger, J., Ruedin, Y.,
Earp, J. C., Egloff, P., Sorgenfrei, M., Hürlimann, L. M.,
Gonda, I., Meier, G., Remm, S., Thavarasah, S., van Geest, G.,
Bruggmann, R., Zimmer, G., ... Seeger, M. A. (2022).
Biparatopic sybodies neutralize SARS-CoV-2 variants of
concern and mitigate drug resistance. Embo
Reports, 23(4), Article e54199. https://doi.org/10.15252/embr.202154199
Zhou,
W., Trinco, G., Slotboom, D. J., Forrest,
L. R., & Faraldo-Gómez, J. D. (2022). Correction to:
On the Role of a Conserved Methionine in the Na+-Coupling Mechanism
of a Neurotransmitter Transporter Homolog (Neurochemical Research,
(2022), 47, 1, (163-175), 10.1007/s11064-021-03253-w).
NEUROCHEMICAL RESEARCH, 47(1), 176.
https://doi.org/10.1007/s11064-021-03420-z
Maity,
S., Trinco, G., Buzón,
P., Anshari, Z. R., Kodera, N., Ngo, K. X.,
Ando, T., Slotboom, D. J., & Roos, W.
H. (2022). High-speed atomic force microscopy reveals
a three-state elevator mechanism in the citrate transporter
CitS. Proceedings of the National Academy of
Sciences of the United States of America,
119(6), Article e2113927119. https://doi.org/10.1073/pnas.2113927119
Nijland,
M., Martínez Felices, J. M.,
Slotboom, D. J., & Thangaratnarajah, C.
(2022). Membrane transport of cobalamin. In G. Litwack
(Ed.), Vitamins and Hormones (pp. 121-148). (Vitamins and
Hormones; Vol. 119). ACADEMIC PRESS INC ELSEVIER SCIENCE. https://doi.org/10.1016/bs.vh.2022.01.008
Li,
X., Wang, Y., Wu, J., Jin, Z., Dijkhuizen,
L., Hachem, M. A., & Bai, Y. (2023). Thermoproteus
uzoniensis 4-α-glucanotransferase catalyzed production of a
thermo-reversible potato starch gel with superior rheological
properties and freeze-thaw stability. Food
hydrocolloids, 134, Article 108026. https://doi.org/10.1016/j.foodhyd.2022.108026
Meng,
X., Li, X., Pijning, T., Wang, X., van Leeuwen,
S. S., Dijkhuizen, L., Chen, G., & Liu, W.
(2022). Characterization of the (Engineered) Branching
Sucrase GtfZ-CD2 from Apilactobacillus kunkeei for Efficient
Glucosylation of Benzenediol Compounds. Applied
and environmental microbiology, 88(16),
Article e0103122. https://doi.org/10.1128/aem.01031-22
Pijning,
T., Te Poele, E. M., de Leeuw, T. C.,
Guskov, A., & Dijkhuizen, L. (2022).
Crystal Structure of 4,6-α-Glucanotransferase
GtfC-ΔC from Thermophilic Geobacillus 12AMOR1: Starch
Transglycosylation in Non-Permuted GH70 Enzymes.
Journal of Agricultural and Food Chemistry,
70(48), 15283–15295. Article 2c06394. https://doi.org/10.1021/acs.jafc.2c06394
Dobruchowska,
J. M., Bjornsdottir, B., Fridjonsson, O. H., Altenbuchner, J.,
Watzlawick, H., Gerwig, G. J., Dijkhuizen,
L., Kamerling, J. P., & Hreggvidsson, G. O. (2022).
Enzymatic depolymerization of alginate by two novel
thermostable alginate lyases from Rhodothermus marinus.
Frontiers in Plant Science , 13,
Article 981602. https://doi.org/10.3389/fpls.2022.981602
Haandrikman,
A. J., Happe, R. P., Pellis, E. P. M., Benjamins, F.,
Dijkhuizen, L., Chatziioannou, A. C., & van
Leeuwen, S. S. (2022). Increased 2'-fl
production by goats. (Patent No.
WO2022123036).
Bunt,
D. V., Aidy, S. E., & Minnaard, A.
J. (2023). Divergent Total Synthesis of Fornicin A,
Fornicin D, and Ganodercin D, Meroterpenoids from Ganoderma
Mushrooms. European Journal of Organic
Chemistry, 26(6), Article e202201446. https://doi.org/10.1002/ejoc.202201446
El
Aidy, S., & Waclawiková, B. (2022).
5-hydroxyindole and analogs thereof as
stimulants of gut motility. (Patent No.
WO2022010352).
González-Dávila,
P., Schwalbe, M., Danewalia, A., Dalile, B.,
Verbeke, K., Mahata, S. K., & El Aidy, S. (2022).
Catestatin selects for colonization of
antimicrobial-resistant gut bacterial communities.
The ISME journal, 16,
1873–1882. https://doi.org/10.1038/s41396-022-01240-9
Krieg,
C., Weber, L. M., Fosso, B., Marzano, M., Hardiman, G., Olcina, M.
M., Domingo, E., El Aidy, S., Mallah, K., Robinson, M.
D., & Guglietta, S. (2022). Complement downregulation
promotes an inflammatory signature that renders colorectal cancer
susceptible to immunotherapy. Journal for
immunotherapy of cancer, 10(9), Article
e004717. https://doi.org/10.1136/jitc-2022-004717
Waclawiková,
B., Codutti, A., Alim, K., & El Aidy, S.
(2022). Gut microbiota-motility interregulation: Insights
from in vivo, ex vivo and in silico studies. Gut
Microbes, 14(1), Article 1997296. https://doi.org/10.1080/19490976.2021.1997296
González-Dávila,
P., Schwalbe, M., Danewalia, A.,
Wardenaar, R., Dalile, B., Verbeke, K., Mahata, S. K.,
& El Aidy, S. (2022). Gut microbiota
transplantation drives the adoptive transfer of colonic
genotype-phenotype characteristics between mice lacking catestatin
and their wild type counterparts. Gut
Microbes, 14(1), Article e2081476. https://doi.org/10.1080/19490976.2022.2081476
Jansma,
J., van Essen, R., Haarman, B. C. M.,
Chatziioannou, A. C., Borkent, J., Ioannou,
M., van Hemert, S., Sommer, I. E. C.,
& El Aidy, S. (2022). Metabolic phenotyping
reveals a potential link between elevated faecal amino acids, diet
and symptom severity in individuals with severe mental
illness. Journal of Psychiatric
Research, 151, 507-515. https://doi.org/10.1016/j.jpsychires.2022.05.011
Maassen,
S., Warner, H., Ioannidis,
M., Jansma, J., Markus, H., El Aidy,
S., Chiara, M.-D., Chiara, J. L., Maierhofer, L., Weavers,
H., & van den Bogaart, G. (2022).
Mitochondrial interaction of fibrosis-protective 5-methoxy
tryptophan enhances collagen uptake by macrophages.
Free Radical Biology and Medicine,
188, 287-297. Article 202206235. https://doi.org/10.1016/j.freeradbiomed.2022.06.235
van
Kessel, S. P., Bullock, A., van Dijk, G.,
& El Aidy, S. (2022). Parkinson's disease
medication alters small intestinal motility and microbiota
composition in healthy rats. Msystems,
7(1), Article e0119121. https://doi.org/10.1128/msystems.01191-21
Rampelt,
H., Wollweber, F., Licheva, M., de Boer, R., Perschil,
I., Steidle, L., Becker, T., Bohnert, M., van der Klei,
I., Kraft, C., van der Laan, M., & Pfanner, N. (2022).
Dual role of Mic10 in mitochondrial cristae organization and
ATP synthase-linked metabolic adaptation and respiratory
growth. Cell reports, 38(4),
Article 110290. https://doi.org/10.1016/j.celrep.2021.110290
Wu,
F., & van der Klei, I. J. (2022).
Structure-function analysis of the ER-peroxisome contact site
protein Pex32. Frontiers in Cell and Developmental
Biology, 10, Article 957871. https://doi.org/10.3389/fcell.2022.957871
Yuan,
W., Akşit, A., de Boer, R., Krikken, A.
M., & van der Klei, I. J. (2022).
Yeast Vps13 is Crucial for Peroxisome Expansion in Cells With
Reduced Peroxisome-ER Contact Sites. Frontiers in
Cell and Developmental Biology, 10, Article
842285. https://doi.org/10.3389/fcell.2022.842285
De
Franceschi, N., Pezeshkian, W., Fragasso, A.,
Bruininks, B. M. H., Tsai, S., Marrink, S. J.,
& Dekker, C. (2023). Synthetic Membrane Shaper for
Controlled Liposome Deformation. Acs
Nano, 17(2), 966–978. https://doi.org/10.1021/acsnano.2c06125
Marrink,
S. J., Monticelli, L., Melo, M. N., Alessandri, R.,
Tieleman, D. P., & Souza, P. C. T. (2023).
Two decades of Martini: Better beads, broader scope.
Wiley Interdisciplinary Reviews: Computational Molecular
Science, 13(1), Article e1620. https://doi.org/10.1002/wcms.1620
Grünewald,
F., Punt, M. H., Jefferys, E. E., Vainikka, P.
A., König, M., Virtanen, V., Meyer, T.
A., Pezeshkian, W., Gormley, A. J., Karonen, M.,
Sansom, M. S. P., Souza, P. C. T., &
Marrink, S. J. (2022). Martini 3 Coarse-Grained Force
Field for Carbohydrates. Journal of Chemical
Theory and Computation, 18(12),
7555–7569. https://doi.org/10.1021/acs.jctc.2c00757
Patmanidis,
I., Souza, P. C. T., Sami,
S., Havenith, R. W. A., de Vries, A.
H., & Marrink, S. J. (2022).
Modelling structural properties of cyanine dye nanotubes at
coarse-grained level. Nanoscale
advances, 4(14), 3033-3042. https://doi.org/10.1039/d2na00158f
Losa,
J., Leupold, S., Alonso-Martinez, D., Vainikka,
P., Thallmair, S., Tych, K.
M., Marrink, S. J., & Heinemann,
M. (2022). Perspective: A stirring role for metabolism
in cells. Molecular Systems Biology,
18(4), Article e10822. https://doi.org/10.15252/msb.202110822
Grünewald,
F., Alessandri, R., Kroon, P. C., Monticelli, L.,
Souza, P. C. T., & Marrink, S. J. (2022).
Polyply: A python suite for facilitating simulations of
macromolecules and nanomaterials. Nature
Communications, 13(1), Article 68. https://doi.org/10.1038/s41467-021-27627-4
Sami,
S., Alessandri, R., Jeff, J. B., Grünewald,
F., De Vries, A. H., Marrink, S.
J., Broer, R., & Havenith, R. W.
A. (2022). Strategies for Enhancing the Dielectric
Constant of Organic Materials. Journal of Physical
Chemistry C, 126(45), 19462-19469. Article
2c05682. https://doi.org/10.1021/acs.jpcc.2c05682
Thallmair,
V., Schultz, L., Zhao, W., Marrink, S. J., Oliver,
D., & Thallmair, S. (2022). Two cooperative
binding sites sensitize PI(4,5)P2 recognition by the tubby
domain. Science Advances,
8(36), Article eabp9471. https://doi.org/10.1126/sciadv.abp9471
Krishnaswamy,
S. R., Gabrovski, I. A., Patmanidis,
I., Stuart, M. C. A., de Vries, A.
H., & Pshenichnikov, M. S. (2022).
Cryogenic TEM imaging of artificial light harvesting
complexes outside equilibrium. Scientific
Reports, 12(1), Article 5552. https://doi.org/10.1038/s41598-022-09496-z
Appukutti,
N., de Vries, A. H., Gudeangadi, P. G., Claringbold,
B. R., Garrett, M. D., Reithofer, M. R., & Serpell, C. J.
(2022). Sequence-complementarity dependent co-assembly of
phosphodiester-linked aromatic donor-acceptor trimers.
Chemical communications (Cambridge, England),
58(87), 12200-12203. https://doi.org/10.1039/d2cc00239f
Yu,
Y., van der Zwaag, M., Wedman, J.
J., Permentier, H., Plomp,
N., Jia, X., Kanon, B.,
Eggens-Meijer, E., Buist, G., Harmsen,
H., Kok, J., Salles, J. F.,
Wertheim, B., Hayflick, S. J., Strauss,
E., Grzeschik, N. A., Schepers, H.,
& Sibon, O. C. M. (2022). Coenzyme A precursors
flow from mother to zygote and from microbiome to host.
Molecular Cell, 82(14),
2650-2665.e12. https://doi.org/10.1016/j.molcel.2022.05.006
de
Jong, A., Kuipers, O. P., & Kok,
J. (2022). FUNAGE-Pro: comprehensive web server for
gene set enrichment analysis of prokaryotes.
Nucleic Acids Research, 50(W1),
330-336. Article gkac441. https://doi.org/10.1093/nar/gkac441
Pinto,
J. P. C., Brouwer, R., Zeyniyev, A., Kuipers, O.
P., & Kok, J. (2022). High-Resolution
Chrono-Transcriptome of Lactococcus lactis Reveals That It
Expresses Proteins with Adapted Size and pI upon Acidification and
Nutrient Starvation. Applied and environmental
microbiology, 88(9), Article e0247621. https://doi.org/10.1128/aem.02476-21
Kong,
C., de Jong, A., de Haan, B.
J., Kok, J., & de Vos, P.
(2022). Human milk oligosaccharides and non-digestible
carbohydrates reduce pathogen adhesion to intestinal epithelial
cells by decoy effects or by attenuating bacterial
virulence. Food Research
International, 151, Article 110867. https://doi.org/10.1016/j.foodres.2021.110867
Arias-Orozco,
P., Yi, Y., Ruijne, F., Cebrián, R.,
& Kuipers, OP. (2023). Investigating the
Specificity of the Dehydration and Cyclization Reactions in
Engineered Lanthipeptides by Synechococcal SyncM.
ACS Synthetic Biology, 12,
164–177. https://doi.org/10.1021/acssynbio.2c00455
Muñoz,
C. Y., Zhou, L., Yi, Y.,
& Kuipers, O. P. (2022). Biocontrol properties
from phyllospheric bacteria isolated from Solanum lycopersicum and
Lactuca sativa and genome mining of antimicrobial gene
clusters. BMC Genomics,
23(1), Article 152. https://doi.org/10.1186/s12864-022-08392-0
Cebrián,
R., Li, Q., Peñalver, P., Belmonte-Reche, E.,
Andrés-Bilbao, M., Lucas, R., de Paz, M. V., Kuipers, O.
P., & Morales, J. C. (2022). Chemically Tuning
Resveratrol for the Effective Killing of Gram-Positive
Pathogens. Journal of Natural
Products, 85(6), 1459-1473. Article 1c01107.
https://doi.org/10.1021/acs.jnatprod.1c01107
Farooq,
S. A., de Jong, A., Khaliq, S., & Kuipers,
O. P. (2022). Draft Genome Sequences of Bacillus
velezensis Strains AF_3B and OS2, Bacillus amyloliquefaciens Strain
BS9, Bacillus halotolerans Strain A1, and Bacillus sp. Strain BS3,
Producing Biosurfactants with Antimicrobial Potential.
Microbiology resource announcements,
11(10), Article e0048222. https://doi.org/10.1128/mra.00482-22
Bustamante
Ordonez, M., van Doorn, S., Weissing,
F., Daras, I., Kuipers, O.,
& de Vos, M. (2022). Eco-evolutionary
interactions and the spread of antimicrobial resistance in
pathogenic microbial communities. Poster session
presented at Netherlands Society for Evolutionary Biology Meeting
2022, Ede, Netherlands.
Mordhorst,
S., Ruijne, F., Vagstad, A. L., Kuipers, O.
P., & Piel, J. (2022). Emulating nonribosomal
peptides with ribosomal biosynthetic strategies.
RSC Chemical Biology, 4, 7-36. https://doi.org/10.1039/d2cb00169a
Liu,
F., van Heel, A. J., Chen,
J., & Kuipers, O. P. (2022).
Functional production of clostridial circularin A in
Lactococcus lactis NZ9000 and mutational analysis of its aromatic
and cationic residues. Frontiers in
Microbiology, 13, Article 1026290. https://doi.org/10.3389/fmicb.2022.1026290
Viel,
J. H., & Kuipers, O. P. (2022).
Modular Use of the Uniquely Small Ring A of Mersacidin
Generates the Smallest Ribosomally Produced Lanthipeptide.
ACS Synthetic Biology, 11(9),
3078-3087. Article 2c00343. https://doi.org/10.1021/acssynbio.2c00343
Viel,
J. H., & Kuipers, O. P. (2022).
Mutational Studies of the Mersacidin Leader Reveal the
Function of Its Unique Two-Step Leader Processing Mechanism.
ACS Synthetic Biology, 11(5),
1949–1957 . https://doi.org/10.1021/acssynbio.2c00088
Schouten,
G. K., Paulussen, F. M., Kuipers, O. P., Bitter, W.,
Grossmann, T. N., & van Ulsen, P. (2022). Stapling of
Peptides Potentiates the Antibiotic Treatment of Acinetobacter
baumannii In Vivo. Antibiotics ,
11(2), Article 11020273. https://doi.org/10.3390/antibiotics11020273
Morawska,
L. P., Detert Oude Weme, R. G. J., Frenzel, E., Dirkzwager,
M., Hoffmann, T., Bremer, E., & Kuipers, O. P.
(2022). Stress-induced activation of the proline biosynthetic
pathway in Bacillus subtilis: A population-wide and single-cell
study of the osmotically controlled proHJ promoter.
Microbial Biotechnology, 15(9),
2411-2425. https://doi.org/10.1111/1751-7915.14073
Ekkers,
D. M., Tusso, S., Moreno-Gamez, S., Rillo, M.
C., Kuipers, O. P., & van Doorn, G.
S. (2022). Trade-offs predicted by metabolic network
structure give rise to evolutionary specialization and phenotypic
diversification. Molecular Biology and
Evolution, 39(6), Article msac124. https://doi.org/10.1093/molbev/msac124
Morawska,
L. P., & Kuipers, O. P. (2022).
Transcriptome analysis and prediction of the metabolic state
of stress-induced viable but non-culturable Bacillus subtilis
cells. Scientific Reports,
12(1), Article 18015. https://doi.org/10.1038/s41598-022-21102-w
Iacovelli,
R., Bovenberg, R. A. L., & Driessen,
A. J. M. (2022). Correction to: Nonribosomal peptide
synthetases and their biotechnological potential in Penicillium
rubens. Journal of Industrial Microbiology and
Biotechnology, 49(3), Article kuac005. https://doi.org/10.1093/jimb/kuac005
Mózsik,
L., Iacovelli, R., Bovenberg, R. A.
L., & Driessen, A. J. M. (2022).
Transcriptional Activation of Biosynthetic Gene Clusters in
Filamentous Fungi. Frontiers in Bioengineering and
Biotechnology, 10, Article 901037. https://doi.org/10.3389/fbioe.2022.901037
Nisa,
I., Haroon, M., Driessen, A., Nijland,
J., Rahman, H., Yasin, N., Hussain, M., Khan, T. A., Ali,
A., Khan, S. A., & Qasim, M. (2022). Antimicrobial
Resistance of Shigella flexneri in Pakistani Pediatric Population
Reveals an Increased Trend of Third-Generation Cephalosporin
Resistance. Current Microbiology,
79(4), Article 118. https://doi.org/10.1007/s00284-022-02805-9
Zhang,
X., Nijland, J. G., & Driessen, A. J.
M. (2022). Combined roles of exporters in acetic acid
tolerance in Saccharomyces cerevisiae.
Biotechnology for Biofuels and Bioproducts,
15(1), Article 67. https://doi.org/10.1186/s13068-022-02164-4
de
Kok, N. A. W., & Driessen, A. J. M. (2022).
The catalytic and structural basis of archaeal
glycerophospholipid biosynthesis.
Extremophiles, 26(3), Article 29. https://doi.org/10.1007/s00792-022-01277-w
Zylstra,
A., & Heinemann, M. (2022). Metabolic
dynamics during the cell cycle. Current Opinion in
Systems Biology, 30, Article 100415. https://doi.org/10.1016/j.coisb.2022.100415
Van
den Bergh, B., Schramke, H., Michiels, J. E., Kimkes, T. E. P.,
Radzikowski, J. L., Schimpf, J., Vedelaar, S. R.,
Burschel, S., Dewachter, L., Lončar, N., Schmidt,
A., Meijer, T., Fauvart, M., Friedrich, T., Michiels, J.,
& Heinemann, M. (2022). Mutations in respiratory
complex I promote antibiotic persistence through alterations in
intracellular acidity and protein synthesis.
Nature Communications, 13(1),
Article 546. https://doi.org/10.1038/s41467-022-28141-x
Litsios,
A., Goswami, P., Terpstra, H. M., Coffin, C.,
Vuillemenot, L.-A., Rovetta, M., Ghazal,
G., Guerra, P., Buczak, K., Schmidt, A., Tollis, S.,
Tyers, M., Royer, C. A., Milias-Argeitis, A.,
& Heinemann, M. (2022). The timing of Start is
determined primarily by increased synthesis of the Cln3 activator
rather than dilution of the Whi5 inhibitor.
Molecular Biology of the Cell,
33(5), Article rp2. https://doi.org/10.1091/mbc.E21-07-0349
Marcondes,
M. F. M., Santos, G. S., Bronze, F., Machado, M. F. M., Perez, K.
R., Hesselink, R., de Vries, M. P., Broos,
J., & Oliveira, V. (2022). Probing the
Conformational States of Thimet Oligopeptidase in Solution.
International Journal of Molecular Sciences,
23(13), Article 7297. https://doi.org/10.3390/ijms23137297
Shao,
J., Kuiper, B. P., Thunnissen, A.-M. W.
H., Cool, R. H., Zhou, L., Huang, C., Dijkstra,
B. W., & Broos, J. (2022). The Role of
Tryptophan in π Interactions in Proteins: An Experimental
Approach. Journal of the American Chemical
Society, 144(30), 13815-13822. Article 04986.
https://doi.org/10.1021/jacs.2c04986
2021
Gran-Scheuch,
A., Parra, L., & Fraaije, M. W. (2023).
Systematic Assessment of Uncoupling in Flavoprotein Oxidases
and Monooxygenases. ACS Sustainable Chemistry and
Engineering, 4948–4959. https://doi.org/10.1021/acssuschemeng.1c02012
Rembeza,
E., Boverio, A., Fraaije, M. W., &
Engqvist, M. (2022). Discovery of two novel oxidases using a
high-throughput activity screen.
ChemBioChem, 23(2), Article
e202100510. https://doi.org/10.1002/cbic.202100510
Lee,
M., Drenth, J., Trajkovic, M., de
Jong, R. M., & Fraaije, M. W. (2022).
Introducing an Artificial Deazaflavin Cofactor in Escherichia
coli and Saccharomyces cerevisiae. ACS Synthetic
Biology, 11(2), 938-952. https://doi.org/10.1021/acssynbio.1c00552
Drenth,
J., Yang, G., Paul, C. E., & Fraaije,
M. W. (2021). A Tailor-Made Deazaflavin-Mediated
Recycling System for Artificial Nicotinamide Cofactor
Biomimetics. ACS Catalysis,
11, 11561-11569. https://doi.org/10.1021/acscatal.1c03033
Laura,
A., Gran-Scheuch, A., Guo, Y.,
Trajkovic, M., Saifuddin, M., Fraaije, M.
W., & Mattevi, A. (2021). Discovery, Biocatalytic
Exploration and Structural Analysis of a 4-Ethylphenol Oxidase from
Gulosibacter chungangensis.
ChemBioChem, 22(22), 3225-3233.
Article cbic.202100457. https://doi.org/10.1002/cbic.202100457
Tjallinks,
G., Martin, C., & Fraaije, M.
W. (2021). Enantioselective oxidation of secondary
alcohols by the flavoprotein alcohol oxidase from Phanerochaete
chrysosporium. Archives of Biochemistry and
Biophysics, 704, Article 108888. https://doi.org/10.1016/j.abb.2021.108888
Cibulka,
R., & Fraaije, M. W. (2021). Flavin-Based
Catalysis - Preface. In R. Cibulka, & M. Fraaije (Eds.),
Flavin-Based Catalysis: Principles and Applications (pp.
xi-xii). Wiley.
Tong,
Y., Lee, M., Drenth, J.,
& Fraaije, M. W. (2021). Flavin-Tag: A Facile
Method for Site-Specific Labeling of Proteins with a Flavin
Fluorophore. BIOCONJUGATE CHEMISTRY,
32(8), 1559-1563. https://doi.org/10.1021/acs.bioconjchem.1c00306
Savino,
S., Daniël‐Moráh Meijer, J., Rozeboom,
H. J., van Beek, H. L., & Fraaije, M.
W. (2021). Kinetic and structural properties of a
robust bacterial L-amino acid oxidase.
Catalysts, 11(11), Article 1309. https://doi.org/10.3390/catal11111309
Fraaije,
M. W., Trajkovic, M., & Martin,
C. (2021). Means and methods for
selective double diol oxidation. (Patent No.
WO2021071356).
Cibulka,
R., & Fraaije, M. W. (2021). Modes of
Flavin-Based Catalysis. In R. Cibulka, & M. W. Fraaije
(Eds.), Flavin-Based Catalysis: Principles and
Applications (pp. 97-124). Wiley. https://doi.org/10.1002/9783527830138.ch4
Purwani,
N. N., Martin, C., Savino,
S., & Fraaije, M. W. (2021). Modular
assembly of phosphite dehydrogenase and phenylacetone monooxygenase
for tuning cofactor regeneration.
Biomolecules, 11(6), Article 905. https://doi.org/10.3390/biom11060905
Drenth,
J., & Fraaije, M. W. (2021). Natural
Flavins: Occurrence, Role, and Noncanonical Chemistry. In R.
Cibulka, & M. W. F. (Eds.), Flavin-Based Catalysis:
Principles and Applications (pp. 29-65). Wiley. https://doi.org/10.1002/9783527830138.ch2
Mascotti,
M. L., Juri Ayub, M., & Fraaije, M. W.
(2021). On the diversity of F420 -dependent oxidoreductases:
A sequence- and structure-based classification.
Proteins, 89(11), 1497-1507. Article
26170. https://doi.org/10.1002/prot.26170
Gran-Scheuch,
A., Aalbers, F., Woudstra, Y., Parra, L.,
& Fraaije, M. W. (2021). Optimizing the linker
length for fusing an alcohol dehydrogenase with a cyclohexanone
monooxygenase. In M. Merkx (Ed.), Linkers in
Biomacromolecules (Vol. 647, pp. 107-143). (Methods in
Enzymology). Elsevier. https://doi.org/10.1016/bs.mie.2020.09.008
Lončar,
N., Konukoglu, F., Fraaije, M., Eryilmaz, J.,
& Tuncer, E. (2021). Process for dyeing
textiles. (Patent No. WO2021013371).
Zuccarello,
L., Barbosa, C., Galdino, E., Lončar,
N., Silveira, C. M., Fraaije, M. W., &
Todorovic, S. (2021). Serr spectroelectrochemistry as a guide
for rational design of dyp-based bioelectronics devices.
International Journal of Molecular Sciences,
22(15), Article 7998. https://doi.org/10.3390/ijms22157998
Kardashliev,
T., Weingartner, A., Romero, E., Schwaneberg, U., Fraaije,
M., Panke, S., & Held, M. (2021). Whole-cell
screening of oxidative enzymes using genetically encoded
sensors. Chemical Science,
12(44), 14766-14772. Article d1sc02578c. https://doi.org/10.1039/d1sc02578c
Marjanovic,
A., Rozeboom, H. J., de Vries, M. S., Mayer,
C., Otzen, M., Wijma, H. J.,
& Janssen, D. B. (2021). Catalytic and structural
properties of ATP-dependent caprolactamase from Pseudomonas
jessenii. Proteins, 89(9),
1079-1098. Article 26082. https://doi.org/10.1002/prot.26082
Ramírez-Palacios,
C., Wijma, H. J., Thallmair,
S., Marrink, S. J., & Janssen, D.
B. (2021). Computational Prediction of
ω-Transaminase Specificity by a Combination of Docking and
Molecular Dynamics Simulations. Journal of
chemical information and modeling, 61(11),
5569–5580. https://doi.org/10.1021/acs.jcim.1c00617
Meng,
Q., Ramírez-Palacios, C., Capra,
N., Hooghwinkel, M. E., Thallmair, S.,
Rozeboom, H. J., Thunnissen, A. M. W. H.,
Wijma, H. J., Marrink, S. J., &
Janssen, D. B. (2021). Computational Redesign of an
ω-Transaminase from Pseudomonas jessenii for Asymmetric
Synthesis of Enantiopure Bulky Amines. ACS
Catalysis, 11(17), 10733-10747. https://doi.org/10.1021/acscatal.1c02053
Doble,
M., Obrecht, L., Joosten, H.-J., Lee, M.,
Rozeboom, H. J., Branigan, E., Naismith, J. H.,
Janssen, D. B., Jarvis, A. G., & Kamer, P. C. J. (2021).
Engineering Thermostability in Artificial Metalloenzymes to
Increase Catalytic Activity. ACS
Catalysis, 11(6), 3620-3627. https://doi.org/10.1021/acscatal.0c05413
Toplak,
A., Oliveira, E. F. T. D., Schmidt, M.,
Rozeboom, H. J., Wijma, H. J., Meekels, L. K.
M., Visser, R. D., Janssen, D. B., & Nuijens, T.
(2021). From Thiol-Subtilisin to Omniligase: Design and
Structure of a Broadly Applicable Peptide Ligase.
Computational and Structural Biotechnology
Journal, 19, 1277-1287. https://doi.org/10.1016/j.csbj.2021.02.002
Marjanovic,
A., Ramírez-Palacios, C. J., Masman, M. F.,
Drenth, J., Otzen, M., Marrink,
S.-J., & Janssen, D. B. (2021).
Thermostable D-amino acid decarboxylases derived from
Thermotoga maritima diaminopimelate decarboxylase.
Protein Engineering, Design & Selection,
34, Article gzab016. https://doi.org/10.1093/protein/gzab016
Nederveen-Schippers,
L. M., Pathak, P., Keizer-Gunnink, I.,
Westphal, A. H., van Haastert, P. J. M., Borst, J.
W., Kortholt, A., & Skakun, V. (2021).
Combined FCS and PCH analysis to quantify protein
dimerization in living cells. International
Journal of Molecular Sciences, 22(14), Article
7300. https://doi.org/10.3390/ijms22147300
van
Haastert, P. J. M., Keizer-Gunnink, I.,
Pots, H., Ortiz-Mateos, C., Veltman, D.,
van Egmond, W., & Kortholt, A. (2021).
Forty-five years of cGMP research in Dictyostelium:
Understanding the regulation and function of the cGMP pathway for
cell movement and chemotaxis. Molecular Biology of
the Cell, 32(20), 1-14. Article mbcE21040171.
https://doi.org/10.1091/mbc.E21-04-0171
van
Haastert, P. J. M. (2021). Short- and long-term memory
of moving amoeboid cells. PLoS ONE,
16(2), Article e0246345. https://doi.org/10.1371/journal.pone.0246345
Rosenbusch,
I., Oun, A., Sanislav, O., Lay, S. T.,
Keizer-Gunnink, I., Annesley, S. J., Fisher, P. R.,
Dolga, A., & Kortholt, A. (2021). A
conserved role for LRRK2 and Roco proteins in the regulation of
mitochondrial activity. Frontiers in Cell and
Developmental Biology, 9, Article 734554. https://doi.org/10.3389/fcell.2021.734554
Helton,
L. G., Soliman, A., von Zweydorf, F., Kentros, M.,
Manschwetus, J. T., Hall, S., Gilsbach, B., Ho, F.
Y., Athanasopoulos, P. S., Singh, R. K.,
LeClair, T. J., Versées, W., Raimondi, F., Herberg, F. W.,
Gloeckner, C. J., Rideout, H., Kortholt, A., &
Kennedy, E. J. (2021). Allosteric Inhibition of
Parkinson's-Linked LRRK2 by Constrained Peptides.
ACS chemical biology, 16(11),
2326–2338. https://doi.org/10.1021/acschembio.1c00487
Kennedy,
E., Kortholt, A., & Helton, L. G. (2021). Chemically-stabilized allosteric modulators of
leucine-rich repeat kinase 2 (lrrk2). (Patent No.
WO2021173802).
Versees,
W., Singh, R. K., Kortholt, A., & Gloeckner, C. J.
(2021). Leucine-rich repeat kinase 2
allosteric modulators. (Patent No.
WO2021170540).
Wojewska,
D. N., & Kortholt, A. (2021). Lrrk2
targeting strategies as potential treatment of parkinson’s
disease. Biomolecules, 11(8),
Article 1101. https://doi.org/10.3390/biom11081101
Xu,
X., Bhimani, S., Pots, H., Wen, X., Jeon, T. J.,
Kortholt, A., & Jin, T. (2021). Membrane Targeting
of C2GAP1 Enables Dictyostelium discoideum to Sense Chemoattractant
Gradient at a Higher Concentration Range.
Frontiers in Cell and Developmental Biology,
9, Article 725073. https://doi.org/10.3389/fcell.2021.725073
Maglia,
G., & Zhang, S. (2021). Artificial nanopores and uses and methods relating
thereto. (Patent No. WO2021101378).
Lucas,
F. L. R., Piso, T. R. C., van der Heide, N.
J., Galenkamp, N. S., Hermans,
J., Wloka, C., & Maglia, G.
(2021). Automated Electrical Quantification of Vitamin B1 in
a Bodily Fluid using an Engineered Nanopore-Sensor.
Angewandte Chemie (International ed. in
English), 60(42), 22849-22855. https://doi.org/10.1002/anie.202107807
Zhang,
S., Huang, G., Versloot, R. C.
A., Bruininks, B. M. H., de Souza, P. C.
T., Marrink, S.-J., & Maglia,
G. (2021). Bottom-up fabrication of a
proteasome-nanopore that unravels and processes single
proteins. Nature Chemistry,
13(12), 1192–1199. https://doi.org/10.1038/s41557-021-00824-w
Maglia,
G., Huang, G., & Soskine, M. (2021). Engineered plyab nanopores and uses thereof.
(Patent No. WO2021182957).
de
Lannoy, C., Lucas, F. L. R., Maglia, G.,
& de Ridder, D. (2021). In silico assessment of a novel
single-molecule protein fingerprinting method employing
fragmentation and nanopore detection.
Iscience, 24(10), Article 103202. https://doi.org/10.1016/j.isci.2021.103202
Lauxen,
A. I., Kobauri, P., Wegener, M., Hansen, M.
J., Galenkamp, N. S., Maglia, G.,
Szymanski, W., Feringa, B. L., &
Kuipers, O. P. (2021). Mechanism of Resistance
Development in E. coli against TCAT, a Trimethoprim-Based
Photoswitchable Antibiotic.
Pharmaceuticals, 14(5), Article
ph14050392. https://doi.org/10.3390/ph14050392
Galenkamp,
N. S., Van Meervelt, V., Mutter, N. L.,
van der Heide, N. J., Wloka, C., &
Maglia, G. (2021). Preparation of Cytolysin A (ClyA)
Nanopores. In M. A. Fahie (Ed.), Nanopore Technology:
Methods in Molecular Biology (pp. 11-18). (Methods in
Molecular Biology; Vol. 2186). Humana Press. https://doi.org/10.1007/978-1-0716-0806-7_2
Mutter,
N. L., Huang, G., van der Heide, N.
J., Lucas, F. L. R., Galenkamp, N.
S., Maglia, G., & Wloka, C.
(2021). Preparation of Fragaceatoxin C (FraC)
Nanopores. In M. A. Fahie (Ed.), Nanopore Technology:
Methods in Molecular Biology (pp. 3-10). (Methods in Molecular
Biology; Vol. 2186). Humana Press. https://doi.org/10.1007/978-1-0716-0806-7_1
Lucas,
F. L. R., Versloot, R. C. A., Yakovlieva,
L., Walvoort, M. T. C., & Maglia,
G. (2021). Protein identification by nanopore peptide
profiling. Nature Communications,
12, Article 5795. https://doi.org/10.1038/s41467-021-26046-9
Maglia,
G., Mutter, N. L., Volaric,
J., Feringa, B. L., & Szymanski, W.
C. (2021). Reversible photo-controlled
frac nanopores, modified frac monomers, methods for preparing the
same, and uses thereof. (Patent No.
EP3771687).
Wloka,
C., Galenkamp, N. S., van der Heide, N.
J., Lucas, F. L. R., & Maglia,
G. (2021). Strategies for enzymological studies and
measurements of biological molecules with the cytolysin A
nanopore. Methods in Enzymology,
649, 567-585. https://doi.org/10.1016/bs.mie.2021.01.007
Alfaro,
J. A., Bohlander, P., Dai, M., Filius, M., Howard, C. J., van
Kooten, X. F., Ohayon, S., Pomorski, A., Schmid, S., Aksimentiev,
A., Anslyn, E. V., Bedran, G., Cao, C., Chinappi, M., Coyaud, E.,
Dekker, C., Dittmar, G., Drachman, N., Eelkema, R., ... Joo, C.
(2021). The emerging landscape of single-molecule protein
sequencing technologies. Nature
Methods, 18(6), 604-617. https://doi.org/10.1038/s41592-021-01143-1
Lucas,
F. L. R., Sarthak, K., Lenting, E. M., Coltan, D., van
der Heide, N. J., Versloot, R. C. A.,
Aksimentiev, A., & Maglia, G. (2021). The
Manipulation of the Internal Hydrophobicity of FraC Nanopores
Augments Peptide Capture and Recognition. Acs
Nano, 15(6), 9600-9613. Article
acsnano.0c09958. https://doi.org/10.1021/acsnano.0c09958
Iyer,
A., Baranov, M., Foster, A.
J., Chordia, S., Roelfes,
G., Vlijm, R., van den Bogaart,
G., & Poolman, B. (2021).
Chemogenetic Tags with Probe Exchange for Live-Cell
Fluorescence Microscopy. ACS chemical
biology, 16(5), 891-904. Article
acschembio.1c00100. https://doi.org/10.1021/acschembio.1c00100
Mantovanelli,
L., Gaastra, B. F., & Poolman,
B. (2021). Fluorescence-based sensing of the
bioenergetic and physicochemical status of the cell. In M.
A. Model, & I. Levitan (Eds.), Current Topics in Membranes:
New Methods and Sensors for Membrane and Cell Volume Research
(Vol. 88, pp. 1-54). (Current Topics in Membranes). ACADEMIC PRESS
INC ELSEVIER SCIENCE. https://doi.org/10.1016/bs.ctm.2021.10.002
Åberg,
C., & Poolman, B. (2021). Glass-Like
Characteristics of Intracellular Motion in Human Cells.
Biophysical Journal, 120(11),
2355-2366. https://doi.org/10.1016/j.bpj.2021.04.011
Alvarez-Sieiro,
P., Sikkema, H. R., & Poolman,
B. (2021). Heterodimer Formation of the Homodimeric
ABC Transporter OpuA. International Journal of
Molecular Sciences, 22(11), Article 5912. https://doi.org/10.3390/ijms22115912
Sikkema,
H. R., & Poolman, B. (2021). In
silico method for selecting residue pairs for single-molecule
microscopy and spectroscopy. Scientific
Reports, 11(1), Article 5756. https://doi.org/10.1038/s41598-021-85003-0
Tran,
B. M., Prabha, H., Iyer, A., O'Byrne, C., Abee,
T., & Poolman, B. (2021). Measurement of
Protein Mobility in Listeria monocytogenes Reveals a Unique
Tolerance to Osmotic Stress and Temperature Dependence of
Diffusion. Frontiers in Microbiology,
12, Article 640149. https://doi.org/10.3389/fmicb.2021.640149
Partipilo,
M., Ewins, E. J., Frallicciardi, J., Robinson,
T., Poolman, B., & Slotboom, D. J.
(2021). Minimal Pathway for the Regeneration of Redox
Cofactors. JACS Au, 1(12),
2280-2293. https://doi.org/10.1021/jacsau.1c00406
van
den Noort, M., de Boer, M., &
Poolman, B. (2021). Stability of Ligand-induced
Protein Conformation Influences Affinity in Maltose-binding
Protein. Journal of Molecular Biology,
433(15), Article 167036. https://doi.org/10.1016/j.jmb.2021.167036
Plötz,
E., Schuurman-Wolters, G., Zijlstra, N., Jager, A.,
Griffith, D., Guskov, A., Gouridis, G., Poolman,
B., & Cordes, T. (2021). Structural
and biophysical characterization of the tandem substrate-binding
domains of the ABC importer GlnPQ. Open
Biology, 11(4), Article 200406. https://doi.org/10.1098/rsob.200406
Zhou,
W., Trinco, G., Slotboom, D. J., Forrest,
L. R., & Faraldo-Gómez, J. D. (2022). On the Role of
a Conserved Methionine in the Na+-Coupling Mechanism of a
Neurotransmitter Transporter Homolog.
NEUROCHEMICAL RESEARCH, 47(1),
163-175. https://doi.org/10.1007/s11064-021-03253-w
Thangaratnarajah,
C., Rheinberger, J., Paulino,
C., & Slotboom, D. J. (2021).
Insights into the bilayer-mediated toppling mechanism of a
folate-specific ECF transporter by cryo-EM.
Proceedings of the National Academy of Sciences of the
United States of America, 118(34), Article
e2105014118. https://doi.org/10.1073/pnas.2105014118
Trinco,
G., Arkhipova, V., Garaeva, A., Hutter, C. A.
J., Seeger, M. A., Guskov, A., & Slotboom,
D. (2021). Kinetic mechanism of Na+-coupled aspartate
transport catalyzed by GltTk. Communications
biology, 4, Article 751. https://doi.org/10.1038/s42003-021-02267-y
Garibsingh,
R.-A. A., Ndaru, E., Garaeva, A. A., Shi, Y.,
Zielewicz, L., Zakrepine, P., Bonomi, M., Slotboom, D.
J., Paulino, C., Grewer, C., &
Schlessinger, A. (2021). Rational design of ASCT2 inhibitors
using an integrated experimental-computational approach.
Proceedings of the National Academy of Sciences of the
United States of America, 118(37), Article
e2104093118. https://doi.org/10.1073/pnas.2104093118
Arkhipova,
V., Fu, H., Hoorens, M., Trinco,
G., Lameijer, L., Marin, E., Feringa, B.
L., Poelarends, G., Szymanski,
W., Slotboom, D., & Guskov, A.
(2021). Structural Aspects of Photopharmacology: Insight into
the Binding of Photoswitchable and Photocaged Inhibitors to the
Glutamate Transporter Homologue. Journal of the
American Chemical Society, 143(3), 1513-1520.
https://doi.org/10.1021/jacs.0c11336
Li,
X., Meng, X., de Leeuw, T. C., Te Poele, E. M.,
Pijning, T., Dijkhuizen, L., & Liu, W.
(2023). Enzymatic glucosylation of polyphenols using
glucansucrases and branching sucrases of glycoside hydrolase family
70. Critical Reviews in Food Science and
Nutrition, 63(21), 5247–5267. Article
2016598. https://doi.org/10.1080/10408398.2021.2016598
Jiang,
Y., Li, X., Pijning, T., Bai, Y., &
Dijkhuizen, L. (2022). Mutations in Amino Acid
Residues of Limosilactobacillus reuteri 121 GtfB
4,6-α-Glucanotransferase that Affect Reaction and Product
Specificity. Journal of Agricultural and Food
Chemistry, 70(6), 1952-1961. Article 1c07618.
https://doi.org/10.1021/acs.jafc.1c07618
Figueroa
Lozano, S., Akkerman, R., Beukema,
M., van Leeuwen, S., Dijkhuizen,
L., & de Vos, P. (2021). 2
'-Fucosyllactose impacts the expression of mucus-related genes in
goblet cells and maintains barrier function of gut epithelial
cells. Journal of Functional Foods,
85, 1-8. Article 104630. https://doi.org/10.1016/j.jff.2021.104630
Chatziioannou,
A. C., Benjamins, E., Pellis, L., Haandrikman, A.,
Dijkhuizen, L., & van Leeuwen, S. S.
(2021). Extraction and Quantitative Analysis of Goat Milk
Oligosaccharides: Composition, Variation, Associations, and 2 '-FL
Variability. Journal of Agricultural and Food
Chemistry, 69(28), 7851-7862. https://doi.org/10.1021/acs.jafc.1c00499
Te
Poele, E. M., Van Der Hoek, S. E., Chatziioannou, A.
C., Gerwig, G. J., Duisterwinkel, W. J., Oudhuis, L.
A. A. C. M., Gangoiti, J., Dijkhuizen,
L., & Leemhuis, H. (2021). GtfC
Enzyme of Geobacillus sp. 12AMOR1 Represents a Novel Thermostable
Type of GH70 4,6-α-Glucanotransferase That Synthesizes a
Linear Alternating (α1 → 6)/(α1 → 4)
α-Glucan and Delays Bread Staling. Journal of
Agricultural and Food Chemistry, 69(34),
9859-9868. https://doi.org/10.1021/acs.jafc.1c03475
Pijning,
T., Gangoiti, J., Te Poele, E. M.,
Börner, T., & Dijkhuizen, L. (2021).
Insights into Broad-Specificity Starch Modification from the
Crystal Structure of Limosilactobacillus Reuteri NCC 2613
4,6-α-Glucanotransferase GtfB. Journal of
Agricultural and Food Chemistry, 69(44),
13235-13245. Article 05657. https://doi.org/10.1021/acs.jafc.1c05657
Valk-Weeber,
R. L., Nichols, K., Dijkhuizen, L., Bijl, E.,
& van Leeuwen, S. S. (2021). Variations in
N-linked glycosylation of glycosylation-dependent cell adhesion
molecule 1 (GlyCAM-1) whey protein: Intercow differences and
dietary effects. Journal of dairy
science, 104(4), 5056-5068. https://doi.org/10.3168/jds.2020-19297
Muntjewerff,
E. M., Tang, K., Lutter, L., Christoffersson, G., Nicolasen, M. J.
T., Gao, H., Katkar, G. D., Das, S., Ter Beest, M., Ying, W.,
Ghosh, P., Aidy, S. E., Oldenburg, B., van den
Bogaart, G., & Mahata, S. K. (2021). Chromogranin
A regulates gut permeability via the antagonistic actions of its
proteolytic peptides. Acta
physiologica, 232(2), Article e13655. https://doi.org/10.1111/apha.13655
Waclawiková,
B., Bullock, A., Schwalbe, M.,
Aranzamendi, C., Nelemans, S. A., van Dijk,
G., & El Aidy, S. (2021). Gut
bacteria-derived 5-hydroxyindole is a potent stimulant of
intestinal motility via its action on L-type calcium
channels. PLOS BIOLOGY,
19(1), Article e3001070. https://doi.org/10.1371/journal.pbio.3001070
van
Kessel, S. P., Auvinen, P., Scheperjans, F., & El
Aidy, S. (2021). Gut bacterial tyrosine decarboxylase
associates with clinical variables in a longitudinal cohort study
of Parkinsons disease. NPJ Parkinson's
disease, 7(1), Article 115. https://doi.org/10.1038/s41531-021-00260-0
Bunt,
D. V., Minnaard, A. J., & El Aidy,
S. (2021). Potential Modulatory Microbiome Therapies
for Prevention or Treatment of Inflammatory Bowel Diseases.
Pharmaceuticals, 14(6), Article 506.
https://doi.org/10.3390/ph14060506
Aresti-Sanz,
J., Schwalbe, M., Pereira, R. R.,
Permentier, H., & El Aidy, S. (2021).
Stability of methylphenidate under various ph conditions in
the presence or absence of gut microbiota.
Pharmaceuticals, 14(8), Article 733.
https://doi.org/10.3390/ph14080733
Jansma,
J., & El Aidy, S. (2021).
Understanding the host-microbe interactions using metabolic
modeling. Microbiome, 9(1),
Article 16. https://doi.org/10.1186/s40168-020-00955-1
Jansen,
R. L. M., Santana-Molina, C., van den Noort,
M., Devos, D. P., & van der Klei, I. J.
(2021). Comparative Genomics of Peroxisome Biogenesis
Proteins: Making Sense of the PEX Proteins.
Frontiers in Cell and Developmental Biology,
9, Article 654163. https://doi.org/10.3389/fcell.2021.654163
Machado,
N., Bruininks, B. M. H., Singh, P., Dos Santos, L.,
Dal Pizzol, C., Dieamant, G. D. C., Kruger, O., Martin, A.
A., Marrink, S. J., Souza, P. C. T.,
& Favero, P. P. (2022). Complex nanoemulsion for vitamin
delivery: Droplet organization and interaction with skin
membranes. Nanoscale, 14(2),
506-514. https://doi.org/10.1039/d1nr04610a
Alessandri,
R., Barnoud, J., Gertsen, A. S., Patmanidis, I.,
de Vries, A. H., Souza, P. C. T., &
Marrink, S. J. (2022). Martini 3 Coarse-Grained Force
Field: Small Molecules. Advanced theory and
simulations, 5(1), Article 2100391. https://doi.org/10.1002/adts.202100391
Azadi-Chegeni,
F., Thallmair, S., Ward, M. E., Perin, G.,
Marrink, S. J., Baldus, M., Morosinotto, T., & Pandit,
A. (2022). Protein dynamics and lipid affinity of monomeric,
zeaxanthin-binding LHCII in thylakoid membranes.
Biophysical Journal, 121(3),
396-409. Article bpj.2021.12.039. https://doi.org/10.1016/j.bpj.2021.12.039
Stehantsev,
P., Stetsenko, A., Nemchinova, M.,
Aduri, N. G., Marrink, S., Gati, C., &
Guskov, A. (2021). A structural view onto
disease-linked mutations in the human neutral amino acid exchanger
ASCT1. Computational and Structural Biotechnology
Journal, 19, 5246-5254. https://doi.org/10.1016/j.csbj.2021.09.015
Nemchinova,
M., Melcr, J., Wassenaar,
T., Marrink, S., & Guskov, A.
(2021). Asymmetric CorA Gating Mechanism as Observed by
Molecular Dynamics Simulations. Journal of
chemical information and modeling, 61(5),
2407-2417. https://doi.org/10.1021/acs.jcim.1c00261
Kobauri,
P., Szymanski, W., Cao, F.,
Thallmair, S., Marrink, S. J., Witte, M.
D., Dekker, F. J., & Feringa, B.
L. (2021). Biaryl sulfonamides as cisoid azosteres for
photopharmacology. Chemical
Communications, 57(34), 4126-4129. https://doi.org/10.1039/d1cc00950h
Liu,
Y., de Vries, A. H., Pezeshkian,
W., & Marrink, S. J. (2021).
Capturing Membrane Phase Separation by Dual Resolution
Molecular Dynamics Simulations. Journal of
Chemical Theory and Computation, 17(9),
5876-5884. Article 00151. https://doi.org/10.1021/acs.jctc.1c00151
Tsanai,
M., Frederix, PW. J. M., Schroer, C. F.
E., Souza, P. C. T., & Marrink, S.
J. (2021). Coacervate formation studied by explicit
solvent coarse-grain molecular dynamics with the Martini
model. Chemical Science,
12(24), 8521-8530. https://doi.org/10.1039/d1sc00374g
Patmanidis,
I., Alessandri, R., de Vries, A. H.,
& Marrink, S. J. (2021). Comparing Dimerization
Free Energies and Binding Modes of Small Aromatic Molecules with
Different Force Fields. Molecules,
26(19), Article 6069. https://doi.org/10.3390/molecules26196069
Dong,
J., Sami, S., Balazs, D. M., Alessandri, R.,
Jahani, F., Qiu, L., Marrink, S. J., Havenith,
R. W. A., Hummelen, J. C., Loi, M.
A., & Portale, G. (2021). Fullerene
derivatives with oligoethylene-glycol side chains: An investigation
on the origin of their outstanding transport properties.
Journal of Materials Chemistry C,
9(45), 16217-16225. https://doi.org/10.1039/d1tc02753k
Kjølbye,
L. R., De Maria, L., Wassenaar, T. A.,
Abdizadeh, H., Marrink, S. J.,
Ferkinghoff-Borg, J., & Schiøtt, B. (2021). General
Protocol for Constructing Molecular Models of Nanodiscs.
Journal of chemical information and modeling,
61(6), 2869-2883. Article acs.jcim.1c00157. https://doi.org/10.1021/acs.jcim.1c00157
Souza,
P. C. T., Alessandri, R., Barnoud, J., Thallmair,
S., Faustino, I., Grünewald,
F., Patmanidis, I., Abdizadeh,
H., Bruininks, B. M. H., Wassenaar, T.
A., Kroon, P. C., Melcr, J., Nieto, V.,
Corradi, V., Khan, H. M., Domański, J., Javanainen, M.,
Martinez-Seara, H., Reuter, N., ... Marrink, S. J.
(2021). Martini 3: A general purpose force field for
coarse-grained molecular dynamics. Nature
Methods, 18, 382-388. https://doi.org/10.1038/s41592-021-01098-3
Vainikka,
P., Thallmair, S., Souza, P. C.
T., & Marrink, S. J. (2021). Martini
3 Coarse-Grained Model for Type III Deep Eutectic Solvents:
Thermodynamic, Structural, and Extraction Properties.
ACS Sustainable Chemistry and Engineering,
9(51), 17338-17350. https://doi.org/10.1021/acssuschemeng.1c06521
Thallmair,
S., Javanainen, M., Fábián, B., Martinez-Seara,
H., & Marrink, S. J. (2021). Nonconverged
Constraints Cause Artificial Temperature Gradients in Lipid Bilayer
Simulations. Journal of Physical Chemistry
B, 125(33), 9537-9546. https://doi.org/10.1021/acs.jpcb.1c03665
Souza,
P. C. T., Limongelli, V., Wu, S., Marrink, S.
J., & Monticelli, L. (2021). Perspectives on
High-Throughput Ligand/Protein Docking With Martini MD
Simulations. Frontiers in Molecular
Biosciences, 8, Article 657222. https://doi.org/10.3389/fmolb.2021.657222
Grünewald,
F., Kroon, P. C., Souza, P. C. T., &
Marrink, S. J. (2021). Protocol for Simulations of
PEGylated Proteins with Martini 3. In Y. W. Chen , & CP.
B. Yiu (Eds.), Structural Genomics (pp. 315-335). (Methods
in Molecular Biology; Vol. 2199). Humana Press. https://doi.org/10.1007/978-1-0716-0892-0_18
Yakovlieva,
L., Ramírez-Palacios, C., Marrink,
S. J., & Walvoort, M. T. C. (2021).
Semiprocessive Hyperglycosylation of Adhesin by Bacterial
Protein N-Glycosyltransferases. ACS chemical
biology, 16(1), 165-175. https://doi.org/10.1021/acschembio.0c00848
Bruininks,
B. M. H., Thie, A. S., Souza, P. C.
T., Wassenaar, T. A., Faraji,
S., & Marrink, S. J. (2021).
Sequential Voxel-Based Leaflet Segmentation of Complex Lipid
Morphologies. Journal of Chemical Theory and
Computation, 17(12), 7873–7885. https://doi.org/10.1021/acs.jctc.1c00446
Pezeshkian,
W., & Marrink, S. J. (2021).
Simulating realistic membrane shapes.
Current Opinion in Cell Biology, 71,
103-111. Article j.ceb.2021.02.009. https://doi.org/10.1016/j.ceb.2021.02.009
Liaci,
A. M., Steigenberger, B., Telles de Souza, P. C.,
Tamara, S., Gröllers-Mulderij, M., Ogrissek, P.,
Marrink, S. J., Scheltema, R. A., & Förster, F.
(2021). Structure of the human signal peptidase complex
reveals the determinants for signal peptide cleavage.
Molecular Cell, 81(19),
3934-3948.e11. https://doi.org/10.1016/j.molcel.2021.07.031
Alessandri,
R., Grünewald, F., & Marrink, S.
J. (2021). The Martini Model in Materials
Science. Advanced materials,
33(24), Article e2008635. https://doi.org/10.1002/adma.202008635
Piskorz,
T. K., de Vries, A. H., & van Esch, J. H. (2022).
How the Choice of Force-Field Affects the Stability and
Self-Assembly Process of Supramolecular CTA Fibers.
Journal of Chemical Theory and Computation,
18(1), 431-440. Article acs.jctc.1c00257. https://doi.org/10.1021/acs.jctc.1c00257
Hernández-Ortega,
E. P., van der Meulen, S., Kuijpers, L. J., & Kok,
J. (2022). Riboswitch RSthiT as a molecular tool in
Lactococcus lactis. Applied and environmental
microbiology, 88(4), Article e01764-21. https://doi.org/10.1128/AEM.01764-21
Wakai,
T., Kano, C., Karsens, H., Kok, J., &
Yamamoto, N. (2021). Functional role of surface layer
proteins of Lactobacillus acidophilus L-92 in stress tolerance and
binding to host cell proteins. Bioscience of
Microbiota, Food and Health, 40(1), 33-42. https://doi.org/10.12938/BMFH.2020-005
Chen,
J., & Kuipers, O. P. (2022). Analysis
of cross-functionality within LanBTC synthetase complexes from
different bacterial sources with respect to production of fully
modified lanthipeptides. Applied and environmental
microbiology, 88(2), Article AEM0161821. https://doi.org/10.1128/AEM.01618-21
Morawska,
L. P., Hernandez-Valdes, J. A., &
Kuipers, O. P. (2022). Diversity of bet-hedging
strategies in microbial communities-Recent cases and
insights. Wires mechanisms of disease,
14(2), Article e1544. https://doi.org/10.1002/wsbm.1544
Cebrián,
R., Belmonte-Reche, E., Pirota, V., de Jong,
A., Morales, J. C., Freccero, M., Doria, F., &
Kuipers, O. P. (2022). G-Quadruplex DNA as a Target in
Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide
Ligand and Its Mode of Action. Journal of
Medicinal Chemistry, 65(6), 4752-4766. https://doi.org/10.1021/acs.jmedchem.1c01905
van
Tilburg, A. Y., Warmer, P., van Heel, A. J.,
Sauer, U., & Kuipers, O. P. (2022). Membrane
composition and organization of Bacillus subtilis 168 and its
genome-reduced derivative miniBacillus PG10.
Microbial Biotechnology, 15(5),
1633-1651. Article 13978. https://doi.org/10.1111/1751-7915.13978
Zhou,
L., Song, C., Li, Z., & Kuipers, O. P.
(2021). Antimicrobial activity screening of rhizosphere soil
bacteria from tomato and genome-based analysis of their
antimicrobial biosynthetic potential. BMC
Genomics, 22(1), Article 29. https://doi.org/10.1186/s12864-020-07346-8
Fu,
Y., Jaarsma, A. H., & Kuipers, O. P.
(2021). Antiviral activities and applications of ribosomally
synthesized and post-translationally modified peptides
(RiPPs). Cellular and molecular life
sciences, 78, 3921–3940 . https://doi.org/10.1007/s00018-021-03759-0
Zhou,
L., Song, C., Muñoz, C. Y., &
Kuipers, O. P. (2021). Bacillus cabrialesii BH5
Protects Tomato Plants Against Botrytis cinerea by Production of
Specific Antifungal Compounds. Frontiers in
Microbiology, 12, Article 707609. https://doi.org/10.3389/fmicb.2021.707609
Zhao,
X., Wang, X., Shukla, R., Kumar, R., Weingarth, M.,
Breukink, E., & Kuipers, O. P. (2021).
Brevibacillin 2V, a Novel Antimicrobial Lipopeptide With an
Exceptionally Low Hemolytic Activity. Frontiers in
Microbiology, 12, Article 693725. https://doi.org/10.3389/fmicb.2021.693725
Zhao,
X., Wang, X., Shukla, R., Kumar, R., Weingarth, M.,
Breukink, E., & Kuipers, O. P. (2021).
Brevibacillin 2V Exerts Its Bactericidal Activity via Binding
to Lipid II and Permeabilizing Cellular Membranes.
Frontiers in Microbiology, 12,
Article 694847. https://doi.org/10.3389/fmicb.2021.694847
Zhao,
X., & Kuipers, O. P. (2021).
BrevicidineB, a New Member of the Brevicidine Family,
Displays an Extended Target Specificity. Frontiers
in Microbiology, 12, Article 693117. https://doi.org/10.3389/fmicb.2021.693117
Viel,
J. H., van Tilburg, A. Y., & Kuipers,
O. P. (2021). Characterization of Leader Processing
Shows That Partially Processed Mersacidin Is Activated by AprE
After Export. Frontiers in
Microbiology, 12, Article 765659. https://doi.org/10.3389/fmicb.2021.765659
Ruijne,
F., & Kuipers, O. P. (2021).
Combinatorial biosynthesis for the generation of
new-to-nature peptide antimicrobials. Biochemical
Society Transactions, 49(1), 203-215. Article
BST20200425. https://doi.org/10.1042/BST20200425
Muñoz,
C. Y., de Jong, A., & Kuipers, O.
P. (2021). Draft Genome Sequences of a Bacillus
subtilis Strain, a Bacillus velezensis Strain, a Paenibacillus
Strain, and an Acinetobacter baumannii Strain, All Isolated from
the Phyllosphere of Lactuca sativa or Solanum lycopersicum.
Microbiology resource announcements,
10(4), Article e01092-20. https://doi.org/10.1128/MRA.01092-20
Arias-Orozco,
P., Yi, Y., & Kuipers, O. P.
(2021). Draft Genome Sequences of Four Bacterial Strains of
Heterotrophic Alteromonas macleodii and Marinobacter, Isolated from
a Nonaxenic Culture of Two Marine Synechococcus Strains.
Microbiology resource announcements,
10(19), Article e00116-21. https://doi.org/10.1128/MRA.00116-21
Xia,
Y., Cebrián, R., Xu, C., Jong, A.
D., Wu, W., & Kuipers, O. P. (2021).
Elucidating the mechanism by which synthetic helper peptides
sensitize Pseudomonas aeruginosa to multiple antibiotics.
PLoS Pathogens, 17(9), Article
e1009909. https://doi.org/10.1371/journal.ppat.1009909
Arias-Orozco,
P., Inklaar, M., Lanooij, J., Cebrián,
R., & Kuipers, O. P. (2021).
Functional Expression and Characterization of the Highly
Promiscuous Lanthipeptide Synthetase SyncM, Enabling the Production
of Lanthipeptides with a Broad Range of Ring Topologies.
ACS Synthetic Biology, 10(10),
2579-2591. Article acssynbio.1c00224. https://doi.org/10.1021/acssynbio.1c00224
Gazioglu,
O., Kareem, B. O., Afzal, M., Shafeeq, S., Kuipers, O.
P., Ulijasz, A. T., Andrew, P. W., & Yesilkaya, H.
(2021). Glutamate Dehydrogenase (GdhA) of Streptococcus
pneumoniae Is Required for High Temperature Adaptation.
Infection and Immunity, 89(12),
Article IAI0040021. https://doi.org/10.1128/IAI.00400-21
Viel,
J. H., Jaarsma, A. H., & Kuipers, O. P.
(2021). Heterologous Expression of Mersacidin in Escherichia
coli Elucidates the Mode of Leader Processing. ACS
Synthetic Biology, 10(3), 600-608. Article
acssynbio.0c00601. https://doi.org/10.1021/acssynbio.0c00601
Zhou,
L., de Jong, A., Yi, Y.,
& Kuipers, O. P. (2021). Identification,
Isolation, and Characterization of Medipeptins, Antimicrobial
Peptides From Pseudomonas mediterranea EDOX.
Frontiers in Microbiology, 12,
Article 732771. https://doi.org/10.3389/fmicb.2021.732771
Chen,
J., & Kuipers, O. P. (2021).
Isolation and Analysis of the Nisin Biosynthesis Complex
NisBTC: Further Insights into Their Cooperative Action.
mBio, 12(5), Article e02585-21. https://doi.org/10.1128/mBio.02585-21
Zhao,
X., & Kuipers, O. P. (2021). Nisin-
and Ripcin-Derived Hybrid Lanthipeptides Display Selective
Antimicrobial Activity against Staphylococcus aureus.
ACS Synthetic Biology, 10(7),
1703–1714. https://doi.org/10.1021/acssynbio.1c00080
Li,
Q., Cebrián, R., Montalbán-López, M., Ren, H., Wu,
W., & Kuipers, O. P. (2021).
Outer-membrane-acting peptides and lipid II-targeting
antibiotics cooperatively kill Gram-negative pathogens.
Communications biology, 4(1),
Article 31. https://doi.org/10.1038/s42003-020-01511-1
Luo,
Y., Korza, G., DeMarco, A. M., Kuipers, O. P., Li,
Y.-Q., & Setlow, P. (2021). Properties of spores of
Bacillus subtilis with or without a transposon that decreases spore
germination and increases spore wet heat resistance.
Journal of Applied Microbiology,
131(6), 2918-2928. https://doi.org/10.1111/jam.15163
Fernandez-Cantos,
M. V., Garcia-Morena, D., Iannone, V.,
El-Nezami, H., Kolehmainen, M., & Kuipers, O. P.
(2021). Role of microbiota and related metabolites in
gastrointestinal tract barrier function in NAFLD.
Tissue Barriers, 9(3), Article
e1879719. https://doi.org/10.1080/21688370.2021.1879719
Zhao,
X., Xu, Y., Viel, J. H.,
& Kuipers, O. P. (2021). Semisynthetic Macrocyclic
Lipo-lanthipeptides Display Antimicrobial Activity Against
Bacterial Pathogens. ACS Synthetic
Biology, 10(8), 1980-1991. https://doi.org/10.1021/acssynbio.1c00161
Zhao,
X., & Kuipers, O. P. (2021).
Synthesis of silver-nisin nanoparticles with low cytotoxicity
as antimicrobials against biofilm-forming pathogens.
Colloids and Surfaces B: Biointerfaces,
206, Article 111965. https://doi.org/10.1016/j.colsurfb.2021.111965
Michalik,
S., Reder, A., Richts, B., Faßhauer, P., Mäder, U.,
Pedreira, T., Poehlein, A., van Heel, A. J., van
Tilburg, A. Y., Altenbuchner, J., Klewing, A., Reuß, D.
R., Daniel, R., Commichau, F. M., Kuipers, O. P.,
Hamoen, L. W., Völker, U., & Stülke, J. (2021).
The Bacillus subtilis Minimal Genome Compendium.
ACS Synthetic Biology, 10(10),
2767-2771. Article acssynbio.1c00339. https://doi.org/10.1021/acssynbio.1c00339
Cebrián,
R., Xu, C., Xia, Y., Wu, W., &
Kuipers, O. P. (2021). The cathelicidin-derived
close-to-nature peptide D-11 sensitizes Klebsiella pneumoniae to a
range of antibiotics in vitro, ex vivo and in vivo.
International journal of antimicrobial
agents, 58(5), Article 106434. https://doi.org/10.1016/j.ijantimicag.2021.106434
Shlla,
B., Gazioglu, O., Shafeeq, S., Manzoor, I., Kuipers, O.
P., Ulijasz, A., Hiller, N. L., Andrew, P. W., &
Yesilkaya, H. (2021). The Rgg1518 transcriptional regulator
is a necessary facet of sugar metabolism and virulence in
Streptococcus pneumoniae. Molecular
Microbiology, 116(3), 996-1008. https://doi.org/10.1111/mmi.14788
van
Tilburg, A. Y., Fülleborn, J. A., Reder,
A., Völker, U., Stülke, J., van Heel, A.
J., & Kuipers, O. P. (2021).
Unchaining miniBacillus PG10: Relief of FlgM-mediated
repression of autolysin genes. Applied and
environmental microbiology, 87(18), Article
e01123-21. https://doi.org/10.1128/AEM.01123-21
Chen,
J., van Heel, A. J., & Kuipers, O.
P. (2021). Visualization and Analysis of the Dynamic
Assembly of a Heterologous Lantibiotic Biosynthesis Complex in
Bacillus subtilis. mBio,
12(4), Article e01219-21. https://doi.org/10.1128/mBio.01219-21
Kuipers,
A., Balaskó, M., Pétervári, E., Koller, A.,
Brunner, S. M., Moll, G. N., & Kofler, B. (2021).
Intranasal Delivery of a Methyllanthionine-Stabilized Galanin
Receptor-2-Selective Agonist Reduces Acute Food Intake.
Neurotherapeutics : the journal of the American Society
for Experimental NeuroTherapeutics, 18,
2737–2752. https://doi.org/10.1007/s13311-021-01155-x
Mózsik,
L., Hoekzema, M., de Kok, N. A.
W., Bovenberg, R. A. L., Nygård, Y.,
& Driessen, A. J. M. (2021). Author Correction:
CRISPR-based transcriptional activation tool for silent genes in
filamentous fungi (Scientific Reports, (2021), 11, 1, (1118),
10.1038/s41598-020-80864-3). Scientific
Reports, 11(1), Article 20129. https://doi.org/10.1038/s41598-021-99654-6
Mózsik,
L., Hoekzema, M., de Kok, N. A.
W., Bovenberg, R. A. L., Nygård, Y.,
& Driessen, A. J. M. (2021). CRISPR-based
transcriptional activation tool for silent genes in filamentous
fungi. Scientific Reports,
11(1), Article 1118. https://doi.org/10.1038/s41598-020-80864-3
Mackelprang,
R., Aurand, E. R., Bovenberg, R. A. L., Brink, K. R.,
Charo, R. A., Delborne, J. A., Diggans, J., Ellington, A. D.,
Fortman, J. L. C., Isaacs, F. J., Medford, J. I., Murray, R. M.,
Noireaux, V., Palmer, M. J., Zoloth, L., & Friedman, D. C.
(2021). Guiding Ethical Principles in Engineering Biology
Research. ACS Synthetic Biology,
10(5), 907-910. https://doi.org/10.1021/acssynbio.1c00129
Iacovelli,
R., Mózsik, L., Bovenberg, R. A.
L., & Driessen, A. J. M. (2021).
Identification of a conserved N-terminal domain in the first
module of ACV synthetases.
MicrobiologyOpen, 10(1), Article
e1145. https://doi.org/10.1002/mbo3.1145
Mózsik,
L., Pohl, C., Meyer, V., Bovenberg, R. A. L.,
Nygård, Y., & Driessen, A. J. M. (2021).
Modular Synthetic Biology Toolkit for Filamentous
Fungi. ACS Synthetic Biology,
10(11), 2850–2861. https://doi.org/10.1021/acssynbio.1c00260
Iacovelli,
R., Bovenberg, R. A. L., & Driessen,
A. J. M. (2021). Nonribosomal peptide synthetases and
their biotechnological potential in Penicillium rubens.
Journal of Industrial Microbiology &
Biotechnology, 48(7-8), Article kuab045. https://doi.org/10.1093/jimb/kuab045
Nass,
K. J., Ilie, I. M., Saller, M. J., Driessen, A. J. M.,
Caflisch, A., Kammerer, R. A., & Li, X. (2022). The role
of the N-terminal amphipathic helix in bacterial YidC: Insights
from functional studies, the crystal structure and molecular
dynamics simulations. Biochimica et Biophysica
Acta - Biomembranes, 1864(3), Article 183825.
https://doi.org/10.1016/j.bbamem.2021.183825
Exterkate,
M., de Kok, N. A. W., Andringa, R. L.
H., Wolbert, N. H. J., Minnaard, A. J.,
& Driessen, A. J. M. (2021). A promiscuous
archaeal cardiolipin synthase enables construction of diverse
natural and unnatural phospholipids. The Journal
of Biological Chemistry, 296, Article 100691.
https://doi.org/10.1016/j.jbc.2021.100691
Andringa,
R. L. H., de Kok, N. A. W., Driessen, A.
J. M., & Minnaard, A. J. (2021). A
Unified Approach for the Total Synthesis of cyclo-Archaeol,
iso-Caldarchaeol, Caldarchaeol, and Mycoketide.
Angewandte Chemie (International ed. in
English), 60(32), 17497-17503. https://doi.org/10.1002/anie.202104759
de
Kok, N. A. W., Exterkate, M., Andringa,
R. L. H., Minnaard, A. J., &
Driessen, A. J. M. (2021). A versatile method to
separate complex lipid mixtures using 1-butanol as eluent in a
reverse-phase UHPLC-ESI-MS system. Chemistry and
physics of lipids, 240, Article 105125. https://doi.org/10.1016/j.chemphyslip.2021.105125
Seinen,
A.-B., Spakman, D., van Oijen, A. M., & Driessen, A. J.
M. (2021). Cellular dynamics of the SecA ATPase at the
single molecule level. Scientific
Reports, 11(1), Article 1433. https://doi.org/10.1038/s41598-021-81081-2
Ren,
S., de Kok, N. A. W., Gu, Y., Yan, W., Sun, Q., Chen,
Y., He, J., Tian, L., Andringa, R. L. H., Zhu, X.,
Tang, M., Qi, S., Xu, H., Ren, H., Fu, X., Minnaard, A.
J., Yang, S., Zhang, W., Li, W., ... Cheng, W. (2021).
Correction: Structural and Functional Insights into an
Archaeal Lipid Synthase. Cell reports,
35(7), Article 109182. https://doi.org/10.1016/j.celrep.2021.109182
Nisa,
I., Qasim, M., Driessen, A., Nijland, J.,
Rafiullah, Ali, A., Mirza, M. R., Khan, M. A., Khan, T. A., Jalal,
A., & Rahman, H. (2021). Prevalence and associated risk
factors of Shigella flexneri isolated from drinking water
and retail raw foods in Peshawar, Pakistan.
Journal of food science, 86(6),
2579-2589. https://doi.org/10.1111/1750-3841.15777
Koch,
S., Seinen, A. B., Kamel, M., Kuckla, D., Monzel, C., Kedrov,
A., & Driessen, A. J. M. (2021).
Single-molecule analysis of dynamics and interactions of the
SecYEG translocon. Febs Journal,
288(7), 2203-2221. https://doi.org/10.1111/febs.15596
Nisa,
I., Qasim, M., Driessen, A., Nijland, J.,
Adnan, F., Shuja, M. N., & Rahman, H. (2021). Virulence
profiling of Shigella flexneri and emergence of serotype 2b as a
highly virulent shigellosis causing strain in Pakistan.
Infection genetics and evolution,
93, Article 104922. https://doi.org/10.1016/j.meegid.2021.104922
Chakraborty,
P., Oosterhuis, D., Bonsignore, R., Casini,
A., Olinga, P., & Scheffers, D.-J.
(2021). An organogold compound as potential antimicrobial
agent against drug resistant bacteria: Initial mechanistic
insights. ChemMedChem,
16(19), 3060-3070. https://doi.org/10.1002/cmdc.202100342
Polaquini,
C. R., Marques, B. C., Ayusso, G. M., Morão, L. G., Sardi, J.
C. O., Campos, D. L., Silva, I. C., Cavalca, L.
B., Scheffers, D.-J., Rosalen, P. L., Pavan, F.
R., Ferreira, H., & Regasini, L. O. (2021). Antibacterial
activity of a new monocarbonyl analog of curcumin MAC 4 is
associated with divisome disruption. Bioorganic
Chemistry, 109, Article 104668. https://doi.org/10.1016/j.bioorg.2021.104668
Cavalca,
L. B., Lahive, C. W., Gijsbers, F., Pavan, F.
R., Scheffers, D.-J., & Deuss, P. J.
(2021). Benzenetriol-Derived Compounds against Citrus
Canker. Molecules, 26(5),
Article 1436. https://doi.org/10.3390/molecules26051436
Sellner,
B., Prakapaitė, R., van Berkum, M., Heinemann,
M., Harms, A., & Jenal, U. (2021). A New Sugar for
an Old Phage: a c-di-GMP-Dependent Polysaccharide Pathway
Sensitizes Escherichia coli for Bacteriophage Infection.
mBio, 12(6), Article e03246-21. https://doi.org/10.1128/mbio.03246-21
Vedelaar,
S. R., Radzikowski, J. L., & Heinemann, M.
(2021). A Robust Method for Generating, Quantifying, and
Testing Large Numbers of Escherichia coli Persisters.
Methods in molecular biology (Clifton, N.J.),
2357, 41-62. https://doi.org/10.1007/978-1-0716-1621-5_3
Ortega,
A. D., Takhaveev, V., Vedelaar, S. R.,
Long, Y., Mestre-Farràs, N., Incarnato, D.,
Ersoy, F., Olsen, L. F., Mayer, G., & Heinemann,
M. (2021). A synthetic RNA-based biosensor for
fructose-1,6-bisphosphate that reports glycolytic flux.
Cell Chemical Biology, 28(11),
1554-1568.e8. Article j.chembiol.2021.04.006. https://doi.org/10.1016/j.chembiol.2021.04.006
Alseekh,
S., Aharoni, A., Brotman, Y., Contrepois, K., D'Auria, J., Ewald,
J., C Ewald, J., Fraser, P. D., Giavalisco, P., Hall, R. D.,
Heinemann, M., Link, H., Luo, J., Neumann, S., Nielsen, J.,
Perez de Souza, L., Saito, K., Sauer, U., Schroeder, F. C., ...
Fernie, A. R. (2021). Mass spectrometry-based metabolomics: A
guide for annotation, quantification and best reporting
practices. Nature Methods,
18(7), 747-756. https://doi.org/10.1038/s41592-021-01197-1
Yang,
X., Heinemann, M., Howard, J., Huber, G., Iyer-Biswas,
S., Le Treut, G., Lynch, M., Montooth, K. L., Needleman, D. J.,
Pigolotti, S., Rodenfels, J., Ronceray, P., Shankar, S., Tavassoly,
I., Thutupalli, S., Titov, D. V., Wang, J., & Foster, P. J.
(2021). Physical bioenergetics: Energy fluxes, budgets, and
constraints in cells. Proceedings of the National
Academy of Sciences of the United States of America,
118(26), Article e2026786118. https://doi.org/10.1073/pnas.2026786118
Xu,
G., Kunzendorf, A., Crotti,
M., Rozeboom, H. J., Thunnissen, A. W.
H., & Poelarends, G. J. (2022). Gene
Fusion and Directed Evolution to Break Structural Symmetry and
Boost Catalysis by an Oligomeric C‐C Bond‐Forming
Enzyme. Angewandte Chemie International
Edition, 61(8), Article e202113970. https://doi.org/10.1002/anie.202113970
Abidin,
M. M., Thangavelu, S., Bothof, L.,
Tepper, P., Thunnissen, A., &
Poelarends, G. J. (2021). Biocatalytic
Enantioselective Hydroaminations Enabling Synthesis of
N-Arylalkyl-Substituted L-Aspartic Acids. Organic
& Biomolecular Chemistry, 19(29),
6407–6411 . https://doi.org/10.1039/D1OB00748C
Kunzendorf,
A., Xu, G., Van Der Velde, J. J. H.,
Rozeboom, H. J., Thunnissen, A. W. H.,
& Poelarends, G. J. (2021). Unlocking Asymmetric
Michael Additions in an Archetypical Class I Aldolase by Directed
Evolution. ACS Catalysis,
11(21), 13236-13243. https://doi.org/10.1021/acscatal.1c03911
2020
Bailleul,
G., Nicoll, C. R., Mascotti, M. L., Mattevi,
A., & Fraaije, M. W. (2021). Ancestral
reconstruction of mammalian FMO1 enables structural determination,
revealing unique features that explain its catalytic
properties. The Journal of Biological
Chemistry, 296, Article 100221. https://doi.org/10.1074/jbc.RA120.016297
Martin,
C., Tjallinks, G., Trajkovic,
M., & Fraaije, M. (2021). Facile
Stereoselective Reduction of Prochiral Ketones by using an F
420-dependent alcohol dehydrogenase.
ChemBioChem, 22(1), 156-159. Article
cbic.202000651. https://doi.org/10.1002/cbic.202000651
Zitare,
U. A., Habib, M. H., Rozeboom, H.,
Mascotti, M. L., Todorovic, S., & Fraaije, M.
W. (2021). Mutational and structural analysis of an
ancestral fungal dye decolorizing peroxidase. The
FEBS Journal, 288(11), 3602-3618. Article
febs.15687. https://doi.org/10.1111/febs.15687
Savino,
S., Jensen, S., Terwisscha van Scheltinga, A., &
Fraaije, M. W. (2020). Analysis of the structure and
substrate scope of chitooligosaccharide oxidase reveals high
affinity for C2-modified glucosamines. FEBS
Letters, 594(17), 2819-2828. https://doi.org/10.1002/1873-3468.13854
Aalbers,
F. S., Fürst, M. J., Rovida, S.,
Trajkovic, M., Gómez Castellanos, J. R., Bartsch, S.,
Vogel, A., Mattevi, A., & Fraaije, M. W. (2020).
Approaching boiling point stability of an alcohol
dehydrogenase through computationally-guided enzyme
engineering. eLife, 9,
Article e54639. https://doi.org/10.7554/eLife.54639
Ueoka,
R., Meoded, R. A., Gran-Scheuch, A., Bhushan,
A., Fraaije, M. W., & Piel, J. (2020).
Corrigendum to: Genome Mining of Oxidation Modules in trans
-Acyltransferase Polyketide Synthases Reveals a Culturable Source
for Lobatamides (Angewandte Chemie International Edition, (2020),
59, 20, (7761-7765), 10.1002/anie.201916005).
Angewandte Chemie-International Edition,
59(29), 11698-11698. https://doi.org/10.1002/anie.202007393
Ueoka,
R., Meoded, R., Gran-Scheuch, A., Bhushan, A.,
Fraaije, M., & Piel, J. (2020). Genome mining of
oxidation modules in trans-acyltransferase polyketide synthases
reveals a culturable source for lobatamides.
Angewandte Chemie (International ed. in
English), 59(20), 7761-7765. https://doi.org/10.1002/anie.201916005
Román,
R., Lončar, N., Casablancas, A., Fraaije,
M. W., & Gonzalez, G. (2020). High-level
production of industrially relevant oxidases by a two-stage
fed-batch approach: Overcoming catabolite repression in
arabinose-inducible Escherichia coli systems.
Applied Microbiology and Biotechnology,
104(12), 5337-5345. https://doi.org/10.1007/s00253-020-10622-y
Romero,
E., Savino, S., Fraaije, M. W.,
& Loncar, N. (2020). Mechanistic and
Crystallographic Studies of Azoreductase AzoA from Bacillus
wakoensis A01. ACS chemical biology,
15(2), 504-512. Article acschembio.9b00970. https://doi.org/10.1021/acschembio.9b00970
Venturi,
S., Brenna, E., Colombo, D., Fraaije, M. W., Gatti, F.
G., Macchi, P., Monti, D., Trajkovic, M., &
Zamboni, E. (2020). Multienzymatic Stereoselective Reduction
of Tetrasubstituted Cyclic Enones to Halohydrins with Three
Contiguous Stereogenic Centers. ACS
Catalysis, 10(21), 13050-13057. https://doi.org/10.1021/acscatal.0c04097
de
Gonzalo, G., Martin, C., & Fraaije, M.
W. (2020). Positive Impact of Natural Deep Eutectic
Solvents on the Biocatalytic Performance of
5-Hydroxymethyl-Furfural Oxidase.
Catalysts, 10(4), Article 447. https://doi.org/10.3390/catal10040447
Lončar,
N., Eryilmaz, J., Senel, E., Kaplan, G., Fraaije,
M., & Cobanoglu, O. (2020). Process
and apparatus for dyeing textiles. (Patent No.
WO2020015839).
Martin,
C., Trajkovic, M., & Fraaije,
M. (2020). Production of Hydroxy Acids: Selective
Double Oxidation of Diols by Flavoprotein Alcohol Oxidase.
Angewandte Chemie (International ed. in
English), 59(12), 4869-4872. https://doi.org/10.1002/anie.201914877
Fabara,
A. N., & Fraaije, M. W. (2020).
Production of indigo through the use of a dual-function
substrate and a bifunctional fusion enzyme. Enzyme
and Microbial Technology, 142, Article 109692.
https://doi.org/10.1016/j.enzmictec.2020.109692
Nicoll,
C. R., Bailleul, G., Fiorentini, F., Mascotti,
M. L., Fraaije, M. W., & Mattevi, A.
(2020). Publisher Correction: Ancestral-sequence
reconstruction unveils the structural basis of function in
mammalian FMOs (Nature Structural & Molecular Biology, (2020),
27, 1, (14-24), 10.1038/s41594-019-0347-2). Nature
Structural & Molecular Biology, 27(2),
222. https://doi.org/10.1038/s41594-020-0378-8
Silveira,
C. M., Moe, E., Fraaije, M., Martins, L. O., &
Todorovic, S. (2020). Resonance Raman view of the active site
architecture in bacterial DyP-type peroxidases.
RSC Advances, 10(19), 11095-11104.
https://doi.org/10.1039/d0ra00950d
Lončar,
N., Rozeboom, H. J., Franken, L. E.,
Stuart, M. C. A., & Fraaije, M. W. (2020).
Structure of a robust bacterial protein cage and its
application as a versatile biocatalytic platform through enzyme
encapsulation. Biochemical and Biophysical
Research Communications, 529(3), 548-553.
Article j.bbrc.2020.06.059. https://doi.org/10.1016/j.bbrc.2020.06.059
Tong,
Y., Trajkovic, M., Savino, S., van
Berkel, W. J. H., & Fraaije, M. W. (2020).
Substrate binding tunes the reactivity of hispidin
3-hydroxylase, a flavoprotein monooxygenase involved in fungal
bioluminescence. The Journal of Biological
Chemistry, 295(47), 16013-16022. https://doi.org/10.1074/jbc.RA120.014996
Martin,
C., Binda, C., Fraaije, M. W., & Mattevi,
A. (2020). The multipurpose family of flavoprotein
oxidases. In P. Chaiyen, & F. Tamanoi (Eds.),
Flavin-Dependent Enzymes : Mechanisms, Structures and
Applications (Vol. 47, pp. 63-86). (The Enzymes). Elsevier. https://doi.org/10.1016/bs.enz.2020.05.002
Savino,
S., & Fraaije, M. W. (2020). The vast
repertoire of carbohydrate oxidases: An overview.
Biotechnology Advances, 51, Article
107634. https://doi.org/10.1016/j.biotechadv.2020.107634
Niero,
M., Righetto, I., Beneventi, E., de Laureto, P. P., Fraaije,
M. W., Filippini, F., & Bergantino, E. (2020).
Unique Features of a New Baeyer-Villiger Monooxygenase from a
Halophilic Archaeon. Catalysts,
10(1), Article 128. https://doi.org/10.3390/catal10010128
Ewing,
T. A., Gygli, G., Fraaije, M. W., & van Berkel, W.
J. H. (2020). Vanillyl alcohol oxidase. In P. Chaiyen,
& F. Tamanoi (Eds.), Flavin-Dependent Enzymes : Mechanisms,
Structures and Applications (Vol. 47, pp. 87-116). (The
Enzymes). Elsevier. https://doi.org/10.1016/bs.enz.2020.05.003
Bracco,
P., Wijma, H. J., Nicolai, B., Rodriguez Buitrago, J.
A., Klünemann, T., Vila, A., Schrepfer, P., Blankenfeldt,
W., Janssen, D. B., & Schallmey, A. (2021).
CYP154C5 Regioselectivity in Steroid Hydroxylation Explored
by Substrate Modifications and Protein Engineering.
ChemBioChem, 22(6), 1099-1110. https://doi.org/10.1002/cbic.202000735
Wullich,
S. C., Wijma, H. J., Janssen, D. B.,
& Fetzner, S. (2021). Stabilizing AqdC, a Pseudomonas
Quinolone Signal-Cleaving Dioxygenase from Mycobacteria, by
FRESCO-Based Protein Engineering.
ChemBioChem, 22(4), 733-742. https://doi.org/10.1002/cbic.202000641
Dong,
L., Meng, Q., Ramirez-Palacios, C.,
Wijma, H. J., Marrink, S. J., &
Janssen, D. B. (2020). Asymmetric synthesis of
optically pure aliphatic amines with an engineered robust
ω-transaminase. Catalysts,
10(11), 1-14. Article 1310. https://doi.org/10.3390/catal10111310
Božić,
N., Rozeboom, H. J., Lončar, N.,
Slavić, M. Š., Janssen, D. B., &
Vujčić, Z. (2020). Characterization of the starch
surface binding site on Bacillus paralicheniformis
α-amylase. International Journal of
Biological Macromolecules, 165(Pt A),
1529-1539. https://doi.org/10.1016/j.ijbiomac.2020.10.025
Arabnejad,
H., Bombino, E., Colpa, D. I.,
Jekel, P. A., Trajkovic, M., Wijma, H.
J., & Janssen, D. B. (2020).
Computational Design of Enantiocomplementary Epoxide
Hydrolases for Asymmetric Synthesis of Aliphatic and Aromatic
Diols. ChemBioChem, 21(13),
1893-1904. https://doi.org/10.1002/cbic.201900726
Janssen,
D. B., & Stucki, G. (2020). Perspectives of
genetically engineered microbes for groundwater
bioremediation. Environmental science. Processes
& impacts, 22(3), 487-499. Article
c9em00601j. https://doi.org/10.1039/c9em00601j
Meng,
Q., Capra, N., Palacio, C. M., Lanfranchi,
E., Otzen, M., Van Schie, L. Z., Rozeboom, H.
J., Thunnissen, A. M. W. H., Wijma, H.
J., & Janssen, D. B. (2020). Robust
ω-Transaminases by Computational Stabilization of the Subunit
Interface. ACS Catalysis,
10(5), 2915-2928. https://doi.org/10.1021/acscatal.9b05223
Lee,
M., Rozeboom, H. J., Keuning, E., de Waal,
P., & Janssen, D. B. (2020). Structure-based
directed evolution improves S. cerevisiae growth on xylose by
influencing in vivo enzyme performance.
Biotechnology for Biofuels, 13(1),
Article 5. https://doi.org/10.1186/s13068-019-1643-0
van
Haastert, P. J. M. (2020). Symmetry Breaking during
Cell Movement in the Context of Excitability, Kinetic Fine-Tuning
and Memory of Pseudopod Formation.
Cells, 9(8), Article 1809. https://doi.org/10.3390/cells9081809
van
Haastert, P. J. M. (2020). Unified control of amoeboid
pseudopod extension in multiple organisms by branched F-actin in
the front and parallel F-actin/myosin in the cortex.
PLoS ONE, 15(12), Article e0243442.
https://doi.org/10.1371/journal.pone.0243442
Konstantinidou,
M., Oun, A., Pathak, P.,
Zhang, B., Wang, Z., ter Brake, F.,
Dolga, A., Kortholt, A., & Doemling,
A. (2021). The tale of proteolysis targeting chimeras
(PROTACs) for leucine-rich repeat kinase 2 (LRRK2).
ChemMedChem, 16(6), 959-965. https://doi.org/10.1002/cmdc.202000872
Soliman,
A., Cankara, F. N., & Kortholt, A. (2020).
Allosteric inhibition of LRRK2, where are we now.
Biochemical Society Transactions,
48(5), 2185-2194. Article BST20200424. https://doi.org/10.1042/BST20200424
Leemans,
M., Galicia, C., Deyaert, E., Daems, E., Krause, L., Paesmans, J.,
Pardon, E., Steyaert, J., Kortholt, A., Sobott, F.,
Klostermeier, D., & Versées, W. (2020). Allosteric
modulation of the GTPase activity of a bacterial LRRK2 homolog by
conformation-specific Nanobodies. Biochemical
Journal, 477(7), 1203-1218. https://doi.org/10.1042/BCJ20190843
Yatskou,
M. M., Skakun, V. V., Nederveen-Schippers, L.,
Kortholt, A., & Apanasovich, V. V. (2020). Complex
Analysis of Fluorescence Intensity Fluctuations of Molecular
Compounds. Journal of applied
spectroscopy, 87(4), 685-692. https://doi.org/10.1007/s10812-020-01055-6
Buckley,
C. M., Pots, H., Gueho, A., Vines, J. H., Munn, C. J.,
Phillips, B. A., Gilsbach, B., Traynor, D., Nikolaev, A., Soldati,
T., Parnell, A. J., Kortholt, A., & King, J. S.
(2020). Coordinated Ras and Rac Activity Shapes
Macropinocytic Cups and Enables Phagocytosis of Geometrically
Diverse Bacteria. Current Biology,
30(15), 2912-2926.e5. https://doi.org/10.1016/j.cub.2020.05.049
Cankara,
F. N., Günaydın, C., Bilge, S. S., Özmen,
Ö., & Kortholt, A. (2020). The
neuroprotective action of lenalidomide on rotenone model of
Parkinson's Disease: Neurotrophic and supportive actions in the
substantia nigra pars compacta. Neuroscience
Letters, 738, Article 135308. https://doi.org/10.1016/j.neulet.2020.135308
Bayoumi,
M., Nomidis, S. K., Willems, K., Carlon, E., & Maglia,
G. (2021). Autonomous and Active Transport Operated by
an Entropic DNA Piston. Nano Letters,
21(1), 762-768. Article acs.nanolett.0c04464. https://doi.org/10.1021/acs.nanolett.0c04464
Willems,
K., Ruić, D., L R Lucas, F., Barman, U.,
Verellen, N., Hofkens, J., Maglia, G., & Van
Dorpe, P. (2020). Accurate modeling of a biological nanopore
with an extended continuum framework.
Nanoscale, 12(32), 16775-16795. https://doi.org/10.1039/d0nr03114c
Ciudad,
S., Puig, E., Botzanowski, T., Meigooni, M., Arango, A. S., Do, J.,
Mayzel, M., Bayoumi, M., Chaignepain, S., Maglia, G.,
Cianferani, S., Orekhov, V., Tajkhorshid, E., Bardiaux, B., &
Carulla, N. (2020). Aβ(1-42) tetramer and octamer
structures reveal edge conductivity pores as a mechanism for
membrane damage. Nature
Communications, 11(1), Article 3014. https://doi.org/10.1038/s41467-020-16566-1
Huang,
K., & Maglia, G. (2020). Biological nanopores having tunable pore diameters
and uses thereof as analytical tools. (Patent No.
WO2020055246).
Restrepo-Pérez,
L., Huang, G., Bohländer, P. R., Worp, N.,
Eelkema, R., Maglia, G., Joo, C., & Dekker, C.
(2020). Correction to Resolving Chemical Modifications to a
Single Amino Acid within a Peptide Using a Biological
Nanopore. Acs Nano, 14(4),
5148. Article acsnano.0c01699. https://doi.org/10.1021/acsnano.0c01699
Zernia,
S., van der Heide, N. J., Galenkamp, N.
S., Gouridis, G., & Maglia, G. (2020).
Current Blockades of Proteins Inside Nanopores for Real-Time
Metabolome Analysis. Acs Nano,
14(2), 2296-2307. Article acsnano.9b09434. https://doi.org/10.1021/acsnano.9b09434
Galenkamp,
N. S., Biesemans, A., & Maglia, G. (2020).
Directional conformer exchange in dihydrofolate reductase
revealed by single-molecule nanopore recordings.
Nature Chemistry, 12(5), 481-488. https://doi.org/10.1038/s41557-020-0437-0
Huang,
G., Willems, K., Bartelds, M., van Dorpe, P., Soskine,
M., & Maglia, G. (2020). Electro-Osmotic
Vortices Promote the Capture of Folded Proteins by PlyAB
Nanopores. Nano Letters,
20(5), 3819-3827. https://doi.org/10.1021/acs.nanolett.0c00877
Willems,
K., Ruic, D., Biesemans, A., Galenkamp, N., Van Dorpe,
P., & Maglia, G. (2020). Electrophoretic
Trapping of a Single Protein Inside a Nanopore.
Biophysical Journal, 118(3),
305A-305A.
Henderson,
R. K., de Valk, S. C., Poolman, B., & Mans, R.
(2021). Energy coupling of membrane transport and efficiency
of sucrose dissimilation in yeast. Metabolic
Engineering, 65, 243-254. https://doi.org/10.1016/j.ymben.2020.11.014
Pols,
T., Singh, S., Deelman-Driessen, C., Gaastra, B.
F., & Poolman, B. (2021). Enzymology
of the pathway for ATP production by arginine breakdown.
The FEBS Journal, 288(1), 293-309.
Article febs.15337. https://doi.org/10.1111/febs.15337
Liu,
B., Mavrova, S. N., van den Berg, J., Kristensen, S.
K., Mantovanelli, L., Veenhoff, L.
M., Poolman, B., & Boersma, A. J. (2020).
Erratum. ACS Sensors,
5(5), 1500-1500. https://doi.org/10.1021/acssensors.0c00744
Van't
Klooster, J. S., Bianchi, F., Doorn, R. B.,
Lorenzon, M., Lusseveld, J. H., Punter, C. M.,
& Poolman, B. (2020). Extracellular loops matter:
Subcellular location and function of the lysine transporter Lyp1
from Saccharomyces cerevisiae. The FEBS
Journal, 287(20), 4401-4414. Article
febs.15262. https://doi.org/10.1111/febs.15262
Sikkema,
H. R., van den Noort, M., Rheinberger,
J., de Boer, M., Krepel, S. T.,
Schuurman-Wolters, G. K., Paulino, C., &
Poolman, B. (2020). Gating by ionic strength and
safety check by cyclic-di-AMP in the ABC transporter OpuA.
Science Advances, 6(47), Article
eabd7697. https://doi.org/10.1126/sciadv.abd7697
Ruiz,
S. J., van 't Klooster, J. S., Bianchi,
F., & Poolman, B. (2020). Growth
Inhibition by Amino Acids in Saccharomyces cerevisiae.
Microorganisms, 9(1), 1-17. Article
9010007. https://doi.org/10.3390/microorganisms9010007
de
Boer, M., Cordes, T., & Poolman,
B. (2020). Kinetic Modelling of Transport Inhibition
by Substrates in ABC Importers. Journal of
Molecular Biology, 432(20), 5565-5576. https://doi.org/10.1016/j.jmb.2020.08.008
van
't Klooster, J. S., Cheng, T.-Y., Sikkema, H.
R., Jeucken, A., Moody, D. B., &
Poolman, B. (2020). Membrane Lipid Requirements of the
Lysine Transporter Lyp1 from Saccharomyces cerevisiae.
Journal of Molecular Biology,
432(14), 4023-4031. https://doi.org/10.1016/j.jmb.2020.04.029
van
't Klooster, J. S., Cheng, T.-Y., Sikkema, H.
R., Jeucken, A., Moody, B., &
Poolman, B. (2020). Periprotein lipidomes of
Saccharomyces cerevisiae provide a flexible environment for
conformational changes of membrane proteins.
eLife, 9, Article e57003. https://doi.org/10.7554/eLife.57003
Marinus,
N., Tahiri, N., Duca, M., Mouthaan, L. M. C.
M., Bianca, S., van den Noort,
M., Poolman, B., Witte, M.
D., & Minnaard, A. J. (2020).
Stereoselective Protection-Free Modification of
3-Keto-saccharides. Organic letters,
22(14), 5622-5626. https://doi.org/10.1021/acs.orglett.0c01986
Thomas,
C., Aller, S. G., Beis, K., Carpenter, E. P., Chang, G., Chen, L.,
Dassa, E., Dean, M., Duong Van Hoa, F., Ekiert, D., Ford, R.,
Gaudet, R., Gong, X., Holland, I. B., Huang, Y., Kahne, D. K.,
Kato, H., Koronakis, V., Koth, C. M., ... Tampé, R. (2020).
Structural and functional diversity calls for a new
classification of ABC transporters. FEBS
Letters, 594(23), 3767-3775. Article
1873-3468.13935. https://doi.org/10.1002/1873-3468.13935
van
der Zouwen, A. J. N., Jeucken, A., Steneker,
R., Hohmann, K. F., Lohse, J., Slotboom, D. J.,
& Witte, M. (2021). Iminoboronates as Dual-Purpose
Linkers in Chemical Probe Development.
Chemistry, 27(10), 3292-3296. https://doi.org/10.1002/chem.202005115
Rempel,
S., Gati, C., Nijland, M., Thangaratnarajah,
C., Karyolaimos, A., Gier, J.-W. L. D., Guskov,
A., & Slotboom, D. (2020). A
mycobacterial ABC transporter mediates the uptake of hydrophilic
compounds. Nature, 580(7803),
409-412. https://doi.org/10.1038/s41586-020-2072-8
Jochim,
A., Adolf, L., Belikova, D., Schilling, N. A., Setyawati,
I., Chin, D., Meyers, S., Verhamme, P., Heinrichs, D.
E., Slotboom, D. J., & Heilbronner, S. (2020).
An ECF-type transporter scavenges heme to overcome
iron-limitation in Staphylococcus lugdunensis.
eLife, 9, Article e57322. https://doi.org/10.7554/eLife.57322
Slotboom,
D. J., Ettema, T. W., Nijland,
M., & Thangaratnarajah, C. (2020).
Bacterial multi-solute transporters. FEBS
Letters, 594(23), 3898-3907. https://doi.org/10.1002/1873-3468.13912
Garaeva,
A. A., & Slotboom, D. J. (2020).
Elevator-type mechanisms of membrane transport.
Biochemical Society Transactions,
48(3), 1227-1241. Article BST20200290. https://doi.org/10.1042/BST20200290
Walter,
J. D., Hutter, C. A., Garaeva, A. A., Scherer, M.,
Zimmermann, I., Wyss, M., Rheinberger, J., Ruedin, Y.,
Earp, J. C., Egloff, P., Sorgenfrei, M., Hürlimann, L. M.,
Gonda, I., Meier, G., Remme, S., Thavarasah, S., van der Geest, G.,
Bruggman, R., Zimmer, G., ... Seeger, M. A. (2020).
Highly potent bispecific sybodies neutralize
SARS-CoV-2. BioRxiv. https://doi.org/10.1101/2020.11.10.376822
Setyawati,
I., Stanek, W. K., Dosz-Majsnerowska, M., Ziel-Swier,
L., Pardon, E., Steyaert, J., Guskov, A.,
& Slotboom, D. (2020). In vitro reconstitution of
dynamically interacting integral membrane subunits of
energy-coupling factor transporters.
eLife, 9, 1-21. Article e64389. https://doi.org/10.7554/eLife.64389
Faustino,
I., Abdizadeh, H., Souza, P. C.
T., Jeucken, A., Stanek, W. K., Guskov,
A., Slotboom, D., & Marrink,
S. (2020). Membrane mediated toppling mechanism of the
folate energy coupling factor transporter. Nature
Communications, 11(1), Article 1763. https://doi.org/10.1038/s41467-020-15554-9
Stetsenko,
A., Singh, R., Jähme, M., Guskov,
A., & Slotboom, D. (2020). Structural
and Functional Characterization of NadR from Lactococcus
lactis. Molecules, 25(8),
Article 1940. https://doi.org/10.3390/molecules25081940
Arkhipova,
V., Guskov, A., & Slotboom, D.
(2020). Structural ensemble of a glutamate transporter
homologue in lipid nanodisc environment. Nature
Communications, 11(1), Article 998. https://doi.org/10.1038/s41467-020-14834-8
Hartman,
A. M., Jumde, V. R., Elgaher, W. A. M., Te Poele, E.
M., Dijkhuizen, L., & Hirsch, A. K.
H. (2021). Potential Dental Biofilm Inhibitors:
Dynamic Combinatorial Chemistry Affords Sugar-Based Molecules that
Target Bacterial Glucosyltransferase.
ChemMedChem, 16(1), 113-123. Article
cmdc.202000222. https://doi.org/10.1002/cmdc.202000222
Te
Poele, E., Corwin, S., Hamaker, B. R., Lamothe, L.,
Vafeiadi, C., & Dijkhuizen, L. (2020).
Development of Slowly Digestible Starch Derived
α-Glucans with 4,6-α-Glucanotransferase and Branching
Sucrase Enzymes. Journal of Agricultural and Food
Chemistry, 68(24), 6664-6671. Article
acs.jafc.0c01465. https://doi.org/10.1021/acs.jafc.0c01465
Knight,
J., Branneby, C. K., Dijkhuizen, L., Petrusma, M.,
& Fernández de las Heras, L. (2020). Genetically-modified bacteria and uses
thereof. (Patent No. WO2020030799).
van
Leeuwen, S. S., Te Poele, E. M., Chatziioannou,
A. C., Benjamins, E., Haandrikman, A., & Dijkhuizen,
L. (2020). Goat Milk Oligosaccharides: Their
Diversity, Quantity, and Functional Properties in Comparison to
Human Milk Oligosaccharides. Journal of
Agricultural and Food Chemistry, 68(47),
13469-13485. https://doi.org/10.1021/acs.jafc.0c03766
Valk-Weeber,
R. L., Deelman-Driessen, C., Dijkhuizen,
L., Eshuis-de Ruiter, T., & van Leeuwen, S.
(2020). In depth analysis of the contribution of specific
glycoproteins to the overall bovine whey N-linked
glycoprofile. Journal of Agricultural and Food
Chemistry, 68(24), 6544-6553. Article
acs.jafc.0c00959. https://doi.org/10.1021/acs.jafc.0c00959
Figueroa-Lozano,
S., Valk-Weeber, R. L., Akkerman, R.,
Abdulahad, W., van Leeuwen, S. S.,
Dijkhuizen, L., & de Vos, P. (2020).
Inhibitory Effects of Dietary N-Glycans From Bovine
Lactoferrin on Toll-Like Receptor 8; Comparing Efficacy With
Chloroquine. Frontiers in Immunology,
11, Article 790. https://doi.org/10.3389/fimmu.2020.00790
Valk-Weeber,
R. L., Eshuis-de Ruiter, T., Dijkhuizen, L.,
& van Leeuwen, S. S. (2020). Quantitative analysis
of bovine whey glycoproteins using the overall N-linked whey
glycoprofile. International Dairy
Journal, 110, Article 104814. https://doi.org/10.1016/j.idairyj.2020.104814
Kittibunchakul,
S., van Leeuwen, S. S., Dijkhuizen, L.,
Haltrich, D., & Thu-Ha Nguyen (2020). Structural
Comparison of Different Galacto-oligosaccharide Mixtures Formed by
beta-Galactosidases from Lactic Acid Bacteria and
Bifidobacteria. Journal of Agricultural and Food
Chemistry, 68(15), 4437-4446. https://doi.org/10.1021/acs.jafc.9b08156
Li,
X., Wang, X., Meng, X., Dijkhuizen, L., & Liu, W.
(2020). Structures, physico-chemical properties, production
and (potential) applications of sucrose-derived α-d-glucans
synthesized by glucansucrases. Carbohydrate
Polymers, 249, Article 116818. https://doi.org/10.1016/j.carbpol.2020.116818
Figueroa-Lozano,
S., Ren, C., Yin, H., Pham,
H., van Leeuwen, S., Dijkhuizen,
L., & de Vos, P. (2020). The impact
of oligosaccharide content, glycosidic linkages and lactose content
of galacto-oligosaccharides (GOS) on the expression of
mucus-related genes in goblet cells. Food &
Function, 11(4), 3506-3515. https://doi.org/10.1039/d0fo00064g
Kiewiet,
M. B. G., Elderman, M. E., Aidy, S.
E., Burgerhof, J. G. M., Visser,
H., Vaughan, E. E., Faas, M. M., & de
Vos, P. (2021). Flexibility of Gut Microbiota in
Ageing Individuals during Dietary Fiber Long-Chain Inulin
Intake. Molecular Nutrition & Food
Research, Article e2000390. https://doi.org/10.1002/mnfr.202000390
Jansma,
J., Brinkman, F., van Hemert, S., & El Aidy,
S. (2021). Targeting the endocannabinoid system with
microbial interventions to improve gut integrity.
Progress in Neuro-Psychopharmacology and Biological
Psychiatry, 106, Article 110169. https://doi.org/10.1016/j.pnpbp.2020.110169
Morais,
L. H., Golubeva, A. V., Moloney, G. M., Moya-Pérez, A.,
Ventura-Silva, A. P., Arboleya, S., Bastiaanssen, T. F. S.,
O'Sullivan, O., Rea, K., Borre, Y., Scott, K. A., Patterson, E.,
Cherry, P., Stilling, R., Hoban, A. E., El Aidy, S.,
Sequeira, A. M., Beers, S., Moloney, R. D., ... Cryan, J. F.
(2020). Enduring Behavioral Effects Induced by Birth by
Caesarean Section in the Mouse. Current
Biology, 30(19), 3761-3774. https://doi.org/10.1016/j.cub.2020.07.044
van
Kessel, S. P., de Jong, H. R., Winkel, S. L., van
Leeuwen, S. S., Nelemans, S. A., Permentier,
H., Keshavarzian, A., & El Aidy, S. (2020).
Gut bacterial deamination of residual levodopa medication for
Parkinson's disease. BMC Biology,
18(1), Article 137. https://doi.org/10.1186/s12915-020-00876-3
Haarman,
B., El Aidy, S., van Hemert, S., Fu,
J., Festen, N., & Sommer, I. E.
C. (2020). The gut-brain axis in bipolar disorder
and schizophrenia – a target for precision
psychiatry?. Abstract from Digitaal NVVP
voorjaarscongres , Netherlands.
Haarman,
B., Ioannou, M., Borkent,
J., Doorduin, J., Fu, J., El
Aidy, S., & Sommer, I. E. C. (2020).
The impact of intestinal permeability and intestinal
microbiome on cerebral immunological activity and myelination in
bipolar disorder. Poster session presented at 22nd
Annual Conference of the International Society for Bipolar
Disorders.
Haarman,
B. C. M., Ioannou, M., Borkent,
J., Doorduin, J., Fu, J., El
Aidy, S., & Sommer, I. E. C. (2020).
The impact of intestinal permeability and intestinal
microbiome on cerebral immunological activity and myelination in
bipolar disorder. Bipolar Disorders,
22, 84-85.
Zielińska,
A., Savietto, A., de Sousa Borges, A., Martinez, D., Berbon,
M., Roelofsen, J. R., Hartman, A. M., de Boer,
R., Van der Klei, I. J., Hirsch, A.
K., Habenstein, B., Bramkamp, M., & Scheffers,
D.-J. (2020). Flotillin-mediated membrane fluidity
controls peptidoglycan synthesis and MreB movement.
eLife, 9, 1-21. Article e57179. https://doi.org/10.7554/eLife.57179
Singh,
R., Wróblewska, J., de Boer, R., & van
der Klei, I. J. (2020). Hansenula Polymorpha
Vac8: A Vacuolar Membrane Protein Required for Vacuole
Inheritance and Nucleus-Vacuole Junction Formation.
Contact, 3, 1-8. https://doi.org/10.1177/2515256420974928
Krikken,
A. M., Wu, H., de Boer, R., Devos,
D. P., Levine, T. P., & van der Klei, I. J.
(2020). Peroxisome retention involves Inp1-dependent
peroxisome-plasma membrane contact sites in yeast.
The Journal of Cell Biology,
219(10), Article e201906023. https://doi.org/10.1083/jcb.201906023
Wu,
F., de Boer, R., Krikken, A. M.,
Akşit, A., Bordin, N., Devos, D. P., & van der Klei,
I. J. (2020). Pex24 and Pex32 are required to tether
peroxisomes to the ER for organelle biogenesis, positioning and
segregation in yeast. Journal of Cell
Science, 133(16), Article jcs.246983. https://doi.org/10.1242/jcs.246983
Bruininks,
B. M., Souza, P. C., Ingolfsson, H.,
& Marrink, S. J. (2020). A molecular view on the
escape of lipoplexed DNA from the endosome.
eLife, 9, Article e52012. https://doi.org/10.7554/eLife.52012
Thallmair,
V., Schultz, L., Marrink, S., Oliver, D., &
Thallmair, T. (2020). A second
PI(4,5)P2 binding site determines PI(4,5)P2
sensitivity of the tubby domain. BioRxiv. https://doi.org/10.1101/2020.09.23.309492
Pezeshkian,
W., König, M., Wassenaar, T.
A., & Marrink, S. J. (2020).
Backmapping triangulated surfaces to coarse-grained membrane
models. Nature Communications,
11(1), Article 2296. https://doi.org/10.1038/s41467-020-16094-y
Khan,
H. M., Telles de Souza, P. C., Thallmair,
S., Barnoud, J., De Vries, A. H.,
Marrink, S. J., & Reuter, N. (2020). Capturing
Choline–Aromatics Cation−π Interactions in the
MARTINI Force Field. Journal of Chemical Theory
and Computation, 16(4), 2550-2560. https://doi.org/10.1021/acs.jctc.9b01194
Maity,
S., Ottelé, J., Santiago, G.
M., Frederix, P. W. J. M., Kroon, P.,
Markovitch, O., Stuart, M. C. A.,
Marrink, S. J., Otto, S., & Roos, W.
H. (2020). Caught in the Act: Mechanistic Insight into
Supramolecular Polymerization-Driven Self-Replication from
Real-Time Visualization. Journal of the American
Chemical Society, 142(32), 13709-13717. https://doi.org/10.1021/jacs.0c02635
Schroer,
C. F. E., Baldauf, L., van Buren, L., Wassenaar, T.
A., Melo, M. N., Koenderink, G. H., & Marrink, S.
J. (2020). Charge-dependent interactions of monomeric
and filamentous actin with lipid bilayers.
Proceedings of the National Academy of Sciences of the
United States of America, 117(11), 5861-5872.
Article pnas.1914884117. https://doi.org/10.1073/pnas.1914884117
Marrink,
S. J., & Levental, I. (2020). Computational and
Experimental Advances in Biomembranes: Resolving Their
Complexity. The Journal of Physical Chemistry. B:
Materials, Surfaces, Interfaces, & Biophysical,
124(45), 9975-9976. https://doi.org/10.1021/acs.jpcb.0c09401
Liu,
Y., Pezeshkian, W., Barnoud, J., De Vries, A.
H., & Marrink, S. J. (2020). Coupling
Coarse-Grained to Fine-Grained Models via Hamiltonian Replica
Exchange. Journal of Chemical Theory and
Computation, 16(8), 5313-5322. Article
acs.jctc.0c00429. https://doi.org/10.1021/acs.jctc.0c00429
Liu,
Y., De Vries, A. H., Barnoud, J., Pezeshkian,
W., Melcr, J., & Marrink, S.
J. (2020). Dual Resolution Membrane Simulations Using
Virtual Sites. The Journal of Physical Chemistry.
B: Materials, Surfaces, Interfaces, & Biophysical,
124(19), 3944-3953. https://doi.org/10.1021/acs.jpcb.0c01842
Su,
J., Marrink, S. J., & Melo, M. N. (2020).
Localization Preference of Antimicrobial Peptides on
Liquid-Disordered Membrane Domains. Frontiers in
Cell and Developmental Biology, 8, Article
350. https://doi.org/10.3389/fcell.2020.00350
Vazquez-Salazar,
L. I., Selle, M., de Vries, A. H., Marrink, S.
J., & Souza, P. C. T. (2020). Martini
coarse-grained models of imidazolium-based ionic liquids: from
nanostructural organization to liquid-liquid extraction.
Green Chemistry, 22(21), 7376-7386.
https://doi.org/10.1039/d0gc01823f
Liguori,
N., Croce, R., Marrink, S. J., & Thallmair,
S. (2020). Molecular dynamics simulations in
photosynthesis. Photosynthesis
Research, 144(2), 273-295. https://doi.org/10.1007/s11120-020-00741-y
Sun,
F., Schroer, C. F. E., Palacios, C. R.,
Xu, L., Luo, S.-Z., & Marrink, S. J. (2020).
Molecular mechanism for bidirectional regulation of CD44 for
lipid raft affiliation by palmitoylations and PIP2.
PLoS Computational Biology, 16(4),
Article e1007777. https://doi.org/10.1371/journal.pcbi.1007777
Kriete,
B., Bondarenko, A. S., Alessandri, R., Patmanidis,
I., Krasnikov, V. V., Jansen, T. L. C.,
Marrink, S. J., Knoester, J., &
Pshenichnikov, M. S. (2020). Molecular versus
excitonic disorder in individual artificial light-harvesting
systems. Journal of the American Chemical
Society, 142(42), 18073-18085. Article
jacs.0c07392. https://doi.org/10.1021/jacs.0c07392
Bondarenko,
A. S., Patmanidis, I., Alessandri, R., Souza, P.
C. T., Jansen, T. L. C., de Vries, A.
H., Marrink, S. J., & Knoester,
J. (2020). Multiscale modeling of molecular structure
and optical properties of complex supramolecular aggregates.
Chemical Science, 11(42),
11514-11524. https://doi.org/10.1039/d0sc03110k
Liu,
J., van der Zee, B., Alessandri, R., Sami,
S., Dong, J., Nugraha, M. I., Barker, A.
J., Rousseva, S., Qiu, L., Qiu, X.,
Klasen, N., Chiechi, R. C., Baran, D., Caironi, M.,
Anthopoulos, T. D., Portale, G., Havenith, R. W.
A., Marrink, S. J., Hummelen, J.
C., & Koster, L. J. A. (2020). N-type
organic thermoelectrics: demonstration of ZT > 0.3.
Nature Communications, 11(1),
Article 5694. https://doi.org/10.1038/s41467-020-19537-8
Alessandri,
R., Sami, S., Barnoud, J., de Vries, A.
H., Marrink, S. J., & Havenith, R. W.
A. (2020). Resolving Donor-Acceptor Interfaces and
Charge Carrier Energy Levels of Organic Semiconductors with Polar
Side Chains. Advanced Functional
Materials, 30(46), Article 2004799. https://doi.org/10.1002/adfm.202004799
Patmanidis,
I., de Vries, A. H., Wassenaar, T.
A., Wang, W., Portale, G., & Marrink,
S. J. (2020). Structural characterization of
supramolecular hollow nanotubes with atomistic simulations and
SAXS. PPCP : Physical Chemistry Chemical
Physics, 22(37), 21083-21093. Article
D0CP03282D. https://doi.org/10.1039/d0cp03282d
Grünewald,
F., Souza, P. C. T., Abdizadeh,
H., Barnoud, J., de Vries, A. H., &
Marrink, S. J. (2020). Titratable Martini model for
constant pH simulations. The Journal of Chemical
Physics, 153(2), Article 024118. https://doi.org/10.1063/5.0014258
Vaishampayan,
A., Ahmed, R., Wagner, O., de Jong, A., Haag,
R., Kok, J., & Grohmann, E. (2021).
Transcriptomic analysis of stress response to novel
antimicrobial coatings in a clinical MRSA strain.
Materials science & engineering c-Biomimetic and
supramolecular systems, 119, Article 111578.
https://doi.org/10.1016/j.msec.2020.111578
Hernandez-Valdes,
J. A., Huang, C., Kok, J., & Kuipers,
O. P. (2020). Another Breaker of the Wall: the
Biological Function of the Usp45 Protein of Lactococcus
lactis. Applied and environmental
microbiology, 86(16), 1-14. Article e00903-20.
https://doi.org/10.1128/AEM.00903-20
Marcelli,
B., de Jong, A., Janzen, T., Serrano, M., Kok,
J., & Kuipers, O. P. (2020). Complete
Genome Sequences of 28 Lactococcal Bacteriophages Isolated from
Failed Dairy Fermentation Processes. Microbiology
resource announcements, 9(12), Article
e01535-19. https://doi.org/10.1128/MRA.01535-19
Hernandez-Valdes,
J. A., de Jong, A., Kok, J.,
& Kuipers, O. P. (2020). Draft Genome Sequences of
Three Amino Acid-Secreting Lactococcus lactis Strains.
Microbiology resource announcements,
9(16), Article e00158. https://doi.org/10.1128/MRA.00158-20
Huang,
C., & Kok, J. (2020). Editing of the
proteolytic system of Lactococcus lactis increases its bioactive
potential. Applied and environmental
microbiology, 86(18), Article e01319. https://doi.org/10.1128/AEM.01319-20
Papadimitriou,
K., Kline, K., Renault, P., & Kok, J. (2020).
Editorial: Omics and Systems Approaches to Study the Biology
and Applications of Lactic Acid Bacteria.
Frontiers in Microbiology, 11,
Article 1786. https://doi.org/10.3389/fmicb.2020.01786
Marcelli,
B., Karsens, H., Nijland, M., Oudshoorn,
R., Kuipers, O. P., & Kok, J. (2020).
Employing lytic phage-mediated horizontal gene transfer in
Lactococcus lactis. PLoS ONE,
15(9 ), Article e0238988. https://doi.org/10.1371/journal.pone.0238988
Huang,
C., Hernandez-Valdes, J. A., Kuipers, O.
P., & Kok, J. (2020). Lysis of a
Lactococcus lactis dipeptidase mutant and rescue by mutation in the
pleiotropic regulator cody. Applied and
environmental microbiology, 86(8), Article
2937. https://doi.org/10.1128/AEM.02937-19
van
Tatenhove-Pel, R. J., Rijavec, T., Lapanje, A., van Swam, I.,
Zwering, E., Hernandez-Valdes, J. A., Kuipers,
O. P., Picioreanu, C., Teusink, B., & Bachmann, H.
(2021). Microbial competition reduces metabolic interaction
distances to the low µm-range. The ISME
journal, 15, 688–701. https://doi.org/10.1038/s41396-020-00806-9
Montalbán-López,
M., Scott, T. A., Ramesh, S., Rahman, I. R., van Heel, A.
J., Viel, J. H., Bandarian, V., Dittmann, E.,
Genilloud, O., Goto, Y., Grande Burgos, M. J., Hill, C., Kim, S.,
Koehnke, J., Latham, J. A., Link, A. J., Martínez, B., Nair,
S. K., Nicolet, Y., ... van der Donk, W. A. (2021). New
developments in RiPP discovery, enzymology and engineering.
Natural product reports, 38(1),
130-239. Article D0NP00027B. https://doi.org/10.1039/d0np00027b
de
Vries, R. H., Viel, J. H., Kuipers, O.
P., & Roelfes, G. (2021). Rapid and
selective chemical editing of Ribosomally synthesized and
Post-translationally modified Peptides (RiPPs) via Cu(II)-catalyzed
β-borylation of dehydroamino acids.
Angewandte Chemie (International ed. in
English), 60(8), 3946-3950. https://doi.org/10.1002/anie.202011460
Teusink,
B., Kuipers, O. P., & Moineau, S. (2021).
Symposium on Lactic Acid Bacteria-reading while waiting for a
meeting. FEMS Microbiology Reviews,
45(2), Article fuaa049. https://doi.org/10.1093/femsre/fuaa049
Xia,
Y., Xu, C., Wang, D., Weng, Y., Jin, Y., Bai,
F., Cheng, Z., Kuipers, O. P., & Wu, W. (2021).
YbeY controls the type III and type VI secretion systems and
biofilm formation through RetS in Pseudomonas aeruginosa.
Applied and environmental microbiology,
87(5). https://doi.org/10.1128/AEM.02171-20
Boonstra,
M., Schaffer, M., Sousa, J., Morawska, L.,
Holsappel, S., Hildebrandt, P., Sappa, P. K., Rath,
H., de Jong, A., Lalk, M., Mäder, U.,
Völker, U., & Kuipers, O. P. (2020).
Analyses of competent and non-competent subpopulations of
Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in
competence. Environmental
Microbiology, 22(6), 2312-2328. https://doi.org/10.1111/1462-2920.15005
Zhao,
X., Yin, Z., Breukink, E., Moll, G. N.,
& Kuipers, O. P. (2020). An Engineered Double
Lipid II Binding Motifs-Containing Lantibiotic Displays Potent and
Selective Antimicrobial Activity against Enterococcus
faecium. Antimicrobial Agents and
Chemotherapy, 64(6), Article e02050-19. https://doi.org/10.1128/AAC.02050-19
Hernandez-Valdes,
J. A., van Gestel, J., & Kuipers, O. P.
(2020). A riboswitch gives rise to multi-generational
phenotypic heterogeneity in an auxotrophic bacterium.
Nature Communications, 11(1),
Article 1203. https://doi.org/10.1038/s41467-020-15017-1
Caro-Astorga,
J., Frenzel, E., Perkins, J. R., Álvarez-Mena, A., de Vicente,
A., Ranea, J. A. G., Kuipers, O. P., & Romero, D.
(2020). Biofilm formation displays intrinsic offensive and
defensive features of Bacillus cereus. NPJ
biofilms and microbiomes, 6(1), Article 3. https://doi.org/10.1038/s41522-019-0112-7
Li,
Z., Song, C., Yi, Y., & Kuipers, O. P. (2020).
Characterization of plant growth-promoting rhizobacteria from
perennial ryegrass and genome mining of novel antimicrobial gene
clusters. BMC Genomics,
21(1), Article 157. https://doi.org/10.1186/s12864-020-6563-7
Li,
Z., Chakraborty, P., de Vries, R. H.,
Song, C., Zhao, X., Roelfes, G.,
Scheffers, D.-J., & Kuipers, O. P. (2020).
Characterization of two relacidines belonging to a novel
class of circular lipopeptides that act against Gram-negative
bacterial pathogens. Environmental
Microbiology, 22(12), 5125-5136. https://doi.org/10.1111/1462-2920.15145
Deng,
J., Viel, J. H., Kubyshkin, V., Budisa, N.,
& Kuipers, O. P. (2020). Conjugation of Synthetic
Polyproline Moietes to Lipid II Binding Fragments of Nisin Yields
Active and Stable Antimicrobials. Frontiers in
Microbiology, 11, Article 575334. https://doi.org/10.3389/fmicb.2020.575334
Hernandez-Valdes,
J. A., Solopova, A., & Kuipers, O. P.
(2020). Development of Lactococcus lactis Biosensors for
Detection of Diacetyl. Frontiers in
Microbiology, 11, Article 1032. https://doi.org/10.3389/fmicb.2020.01032
Hernandez-Valdes,
J. A., Dalglish, M. M., Hermans, J.,
& Kuipers, O. P. (2020). Development of
Lactococcus lactis Biosensors for Detection of Sulfur-Containing
Amino Acids. Frontiers in
Microbiology, 11, Article 1654. https://doi.org/10.3389/fmicb.2020.01654
Namsolleck,
P., Richardson, A., Moll, G. N., & Mescheder, A.
(2021). LP2, the first lanthipeptide GPCR agonist in a human
pharmacokinetics and safety study.
Peptides, 136, Article 170468. https://doi.org/10.1016/j.peptides.2020.170468
Moll,
G. N., Kuipers, A., Rink, R., Bosma, T.,
de Vries, L., & Namsolleck, P. (2020).
Biosynthesis of lanthionine-constrained agonists of G
protein-coupled receptors. Biochemical Society
Transactions, 48(5), 2195-2203. https://doi.org/10.1042/BST20200427
Namsolleck,
P., & Moll, G. N. (2020). Does activation of
the protective Renin-Angiotensin System have therapeutic potential
in COVID-19? Molecular medicine,
26(1), Article 80. https://doi.org/10.1186/s10020-020-00211-0
Zhao,
X., Cebrian, R., Fu, Y., Rink, R., Bosma,
T., Moll, G. N., & Kuipers, O. P.
(2020). High-throughput screening for substrate
specificity-adapted mutants of the nisin dehydratase NisB.
ACS Synthetic Biology, 9(6),
1468-1478. https://doi.org/10.1021/acssynbio.0c00130
Pohl,
C., Polli, F., Schütze, T., Viggiano, A., Mózsik,
L., Jung, S., de Vries, M., Bovenberg, R. A.
L., Meyer, V., & Driessen, A. J. M. (2020).
A Penicillium rubens platform strain for secondary metabolite
production. Scientific Reports,
10(1), Article 7630. https://doi.org/10.1038/s41598-020-64893-6
Iacovelli,
R., Zwahlen, R. D., Bovenberg, R. A. L.,
& Driessen, A. J. M. (2020). Biochemical
characterization of the Nocardia lactamdurans ACV
synthetase. PLoS ONE, 15(4),
Article e0231290. https://doi.org/10.1371/journal.pone.0231290
Nijland,
J. G., Shin, H. Y., Dore, E., Rudinatha, D., de Waal, P.
P., & Driessen, A. J. M. (2021). D-glucose
overflow metabolism in an evolutionary engineered high-performance
D-xylose consuming Saccharomyces cerevisiae strain.
Fems Yeast Research, 21(1), Article
foaa062. https://doi.org/10.1093/femsyr/foaa062
Driessen,
A. J. M., & Wei, Y.-Q. (2020). Announcing
Molecular Biomedicine. Molecular
biomedicine, 1(1), Article 1. https://doi.org/10.1186/s43556-020-00003-2
Nisa,
I., Haroon, M., Qasim, M., Driessen, A.,
Nijland, J., Yasin, N., Jalal, A., Ali, N., Ullah, W., Khan,
T. A., Begum, A., & Rahman, H. (2020). Association of
Serotype With Antimicrobial Resistance Patterns Among Shigella
flexneri Isolates From Pakistan: The Importance of Serotype
2b. Pediatric infectious disease
journal, 39(11), E352-E358. https://doi.org/10.1097/INF.0000000000002791
Nijland,
J. G., & Driessen, A. J. M. (2020).
Engineering of Pentose Transport in Saccharomyces cerevisiae
for Biotechnological Applications. Frontiers in
Bioengineering and Biotechnology, 7, Article
464. https://doi.org/10.3389/fbioe.2019.00464
Nisa,
I., Qasim, M., Driessen, A., Nijland, J.,
Bari, F., Haroon, M., Rahman, H., Yasin, N., Khan, T. A., Hussain,
M., & Hussain, W. (2020). Molecular epidemiology of
Shigella flexneri isolated from pediatrics in a diarrhea-endemic
area of Khyber Pakhtunkhwa, Pakistan. European
Journal of Clinical Microbiology & Infectious
Diseases, 39(5), 971-985. https://doi.org/10.1007/s10096-020-03811-0
Ren,
S., de Kok, N. A. W., Gu, Y., Yan, W., Sun, Q., Chen,
Y., He, J., Tian, L., Andringa, R. L. H., Zhu, X.,
Tang, M., Qi, S., Xu, H., Ren, H., Fu, X., Minnaard, A.
J., Yang, S., Zhang, W., Li, W., ... Cheng, W. (2020).
Structural and Functional Insights into an Archaeal Lipid
Synthase. Cell reports,
33(3), Article 108294. https://doi.org/10.1016/j.celrep.2020.108294
Morao,
L. G., Lorenzoni, A. S. G., Chakraborty, P., Ayusso,
G. M., Cavalca, L. B., Santos, M. B., Marques, B. C.,
Dilarri, G., Zamuner, C., Regasini, L. O., Ferreira, H.,
& Scheffers, D.-J. (2020). Investigating the Modes
of Action of the Antimicrobial Chalcones BC1 and T9A.
Molecules, 25(20), Article 4596. https://doi.org/10.3390/molecules25204596
Li,
Z., de Vries, R. H., Chakraborty, P.,
Song, C., Zhao, X., Scheffers,
D.-J., Roelfes, G., & Kuipers, O.
P. (2020). Novel modifications of nonribosomal
peptides from Brevibacillus laterosporus MG64 and investigation of
their mode of action. Applied and environmental
microbiology, 86(24), 1-14. Article e01981-20.
https://doi.org/10.1128/AEM.01981-20
Morales
Angeles, D., & Scheffers, D.-J. (2020). The
Cell Wall of Bacillus subtilis. Current Issues in
Molecular Biology, 41, 539-596. https://doi.org/10.21775/cimb.041.539
Heinemann,
M., Basan, M., & Sauer, U. (2020). Implications of
initial physiological conditions for bacterial adaptation to
changing environments. Molecular Systems
Biology, 16(9), Article e9965. https://doi.org/10.15252/msb.20209965
Guo,
C., Ni, Y., Biewenga, L., Pijning, T.,
Thunnissen, A.-M. W. H., & Poelarends, G.
J. (2021). Using Mutability Landscapes To Guide Enzyme
Thermostabilization. ChemBioChem,
22(1), 170-175. https://doi.org/10.1002/cbic.202000442
Villarino,
L., Chordia, S., Alonso-Cotchico, L.,
Reddem, E., Zhou, Z., Thunnissen, A. M. W.
H., Maréchal, J.-D., & Roelfes, G.
(2020). Cofactor Binding Dynamics Influence the Catalytic
Activity and Selectivity of an Artificial Metalloenzyme.
ACS Catalysis, 10(20), 11783-11790.
https://doi.org/10.1021/acscatal.0c01619
2019
Zych,
K., Gort, G., Maliepaard, C. A., Jansen, R. C., &
Voorrips, R. E. (2019). FitTetra 2.0-improved genotype
calling for tetraploids with multiple population and parental data
support. Bmc Bioinformatics,
20, Article 148. https://doi.org/10.1186/s12859-019-2703-y
Prins,
P., Smant, G., Arends, D., Mulligan, M. K., Williams, R.
W., & Jansen, R. C. (2019). Systems Genetics
for Evolutionary Studies. In M. Anisimova (Ed.),
Evolutionary Genomics (pp. 635-652). (Methods in Molecular
Biology; Vol. 1910). Springer. https://doi.org/10.1007/978-1-4939-9074-0_21
Fabara,
A. N., & Fraaije, M. W. (2020). An
overview of microbial indigo-forming enzymes.
Applied Microbiology and Biotechnology,
104(3), 925-933. https://doi.org/10.1007/s00253-019-10292-5
Maenpuen,
S., Pongsupasa, V., Pensook, W., Anuwan, P., Kraivisitkul, N.,
Pinthong, C., Phonbuppha, J., Luanloet, T., Wijma, H.
J., Fraaije, M. W., Lawan, N., Chaiyen, P.,
Wongnate, T., & Kraivisitkul, N. (2020). Creating Flavin
Reductase Variants with Thermostable and Solvent‐Tolerant
Properties by Rational‐Design Engineering.
ChemBioChem, 21(10), 1481-1491. https://doi.org/10.1002/cbic.201900737
Nicoll,
C. R., Bailleul, G., Fiorentini, F., Mascotti,
M. L., Fraaije, M. W., & Mattevi, A.
(2019). Ancestral-sequence reconstruction unveils the
structural basis of function in mammalian FMOs.
Nature Structural & Molecular Biology,
27(1), 14-24. https://doi.org/10.1038/s41594-019-0347-2
Furst,
M. J. L. J., Gran-Scheuch, A., Aalbers,
F. S., & Fraaije, M. W. (2019).
Baeyer-Villiger Monooxygenases: Tunable Oxidative
Biocatalysts. ACS Catalysis,
9(12), 11207-11241. https://doi.org/10.1021/acscatal.9b03396
Fürst,
M. J. L. J., Fiorentini, F., & Fraaije, M.
W. (2019). Beyond active site residues: overall
structural dynamics control catalysis in flavin-containing and
heme-containing monooxygenases. Current Opinion in
Structural Biology, 59, 29-37. https://doi.org/10.1016/j.sbi.2019.01.019
Gandomkar,
S., Jost, E., Loidolt, D., Swoboda, A., Pickl, M., Elaily, W.,
Daniel, B., Fraaije, M. W., Macheroux, P., &
Kroutil, W. (2019). Biocatalytic Enantioselective Oxidation
of Sec-Allylic Alcohols with Flavin-Dependent Oxidases.
Advanced Synthesis & Catalysis,
361(22), 5264-5271. https://doi.org/10.1002/adsc.201900921
Habib,
M. H., Rozeboom, H. J., & Fraaije, M.
W. (2019). Characterization of a New DyP-Peroxidase
from the Alkaliphilic Cellulomonad, Cellulomonas
bogoriensis. Molecules,
24(7), Article 1208. https://doi.org/10.3390/molecules24071208
Lončar,
N., Fiorentini, F., Bailleul, G., Savino,
S., Romero, E., Mattevi, A., & Fraaije, M.
W. (2019). Characterization of a thermostable
flavin-containing monooxygenase from Nitrincola lacisaponensis
(NiFMO). Applied Microbiology and
Biotechnology, 103(4), 1755-1764. https://doi.org/10.1007/s00253-018-09579-w
Drenth,
J., Trajkovic, M., & Fraaije, M.
W. (2019). Chemoenzymatic Synthesis of an Unnatural
Deazaflavin Cofactor That Can Fuel F-420-Dependent Enzymes.
ACS Catalysis, 9(7), 6435-6443. https://doi.org/10.1021/acscatal.9b01506
Huang,
L., Aalbers, F. S., Tang, W., Röllig, R.,
Fraaije, M. W., & Kara, S. (2019). Convergent
cascade catalyzed by monooxygenase - alcohol dehydrogenase fusion
applied in organic media. ChemBioChem,
20(13), 1653-1658. https://doi.org/10.1002/cbic.201800814
Tischler,
D., van Berkel, W. J. H., & Fraaije, M. W. (2019).
Editorial: Actinobacteria, a Source of Biocatalytic
Tools. Frontiers in Microbiology,
10, Article 800. https://doi.org/10.3389/fmicb.2019.00800
Palacio,
C. M., Rozeboom, H. J., Lanfranchi, E., Meng,
Q., Otzen, M., & Janssen, D.
B. (2019). Biochemical properties of a Pseudomonas
aminotransferase involved in caprolactam metabolism.
The FEBS Journal, 286(20),
4086-4102. Article 14950. https://doi.org/10.1111/febs.14950
Lanfranchi,
E., Trajković, M., Barta, K., de
Vries, J. G., & Janssen, D. B. (2019). Cover
Feature: Exploring the Selective Demethylation of Aryl Methyl
Ethers with a Pseudomonas Rieske Monooxygenase (ChemBioChem
1/2019). Digital or Visual Products, Wiley. https://doi.org/10.1002/cbic.201800747
Schmidt,
M., Huang, Y.-H., Texeira de Oliveira, E. F., Toplak,
A., Wijma, H. J., Janssen, D. B., van
Maarseveen, J. H., Craik, D. J., & Nuijens, T. (2019).
Efficient Enzymatic Cyclization of Disulfide-rich Peptides
using Peptide Ligases. ChemBioChem,
20(12), 1524-1529. https://doi.org/10.1002/cbic.201900033
Sabogal-Guáqueta,
A. M., Hobbie, F., Keerthi, A., Oun, A.,
Kortholt, A., Boddeke, E., & Dolga,
A. (2019). Linalool attenuates oxidative stress and
mitochondrial dysfunction mediated by glutamate and NMDA
toxicity. Biomedicine & pharmacotherapy =
Biomedecine & pharmacotherapie, 118,
Article 109295. https://doi.org/10.1016/j.biopha.2019.109295
Wauters,
L., Versées, W., & Kortholt, A. (2019).
Roco Proteins: GTPases with a Baroque Structure and
Mechanism. International Journal of Molecular
Sciences, 20(1), Article ijms20010147. https://doi.org/10.3390/ijms20010147
Maglia,
G., & Browne, W. (2019). Editorial
overview: Reprogramming biology: from biopolymers to complex
systems. Current Opinion in
Biotechnology, 58, v-vi. https://doi.org/10.1016/j.copbio.2019.08.002
Zhao,
S., Restrepo-Pérez, L., Soskine, M., Maglia, G.,
Joo, C., Dekker, C., & Aksimentiev, A. (2019).
Electro-Mechanical Conductance Modulation of a Nanopore Using
a Removable Gate. Acs Nano,
13(2), 2398-2409. https://doi.org/10.1021/acsnano.8b09266
Willems,
K., Ruić, D., Biesemans, A., Galenkamp, N. S.,
Van Dorpe, P., & Maglia, G. (2019).
Engineering and Modeling the Electrophoretic Trapping of a
Single Protein Inside a Nanopore. Acs
Nano, 13(9), 9980-9992. https://doi.org/10.1021/acsnano.8b09137
Huang,
G., Voet, A., & Maglia, G. (2019).
FraC nanopores with adjustable diameter identify the mass of
opposite-charge peptides with 44 dalton resolution.
Nature Communications, 10, Article
835. https://doi.org/10.1038/s41467-019-08761-6
Restrepo-Pérez,
L., Wong, C. H., Maglia, G., Dekker, C., & Joo, C.
(2019). Label-Free Detection of Post-translational
Modifications with a Nanopore. Nano
Letters, 19(11), 7957-7964. https://doi.org/10.1021/acs.nanolett.9b03134
Restrepo-Pérez,
L., Huang, G., Bohländer, P. R., Worp, N.,
Eelkema, R., Maglia, G., Joo, C., & Dekker, C.
(2019). Resolving Chemical Modifications to a Single Amino
Acid within a Peptide Using a Biological Nanopore.
Acs Nano, 13(12), 13668-13676. https://doi.org/10.1021/acsnano.9b05156
Mutter,
N. L., Volarić, J., Szymanski,
W., Feringa, B. L., & Maglia,
G. (2019). Reversible Photocontrolled Nanopore
Assembly. Journal of the American Chemical
Society, 141(36), 14356-14363. https://doi.org/10.1021/jacs.9b06998
Syga,
L., De Vries, R. H., van Oosterhout, H., Bartelds, R.,
Boersma, A. J., Roelfes, G., & Poolman,
B. (2020). A trifunctional linker for palmitoylation
and peptide and protein localization in biological
membranes. ChemBioChem,
21(9), 1320-1328. https://doi.org/10.1002/cbic.201900655
Rempel,
I. L., Popken, P., Ghavami, A., Mishra, A., Hapsari,
R. A., Wolters, A. H. G., Veldsink, A.
C., Klaassens, M., Meinema, A. C., Poolman,
B., Giepmans, B. N. G., Onck, P.
R., Steen, A., & Veenhoff, L.
M. (2020). Flexible and Extended Linker Domains
Support Efficient Targeting of Heh2 to the Inner Nuclear
Membrane. Structure, 28(2),
185-195.e5. https://doi.org/10.1016/j.str.2019.11.003
Gabba,
M., & Poolman, B. (2020). Physiochemical
Modeling of Vesicle Dynamics upon Osmotic Upshift.
Biophysical Journal, 118(2),
435-447. Article bpj.2019.11.3383. https://doi.org/10.1016/j.bpj.2019.11.3383
Gabba,
M., Frallicciardi, J., van 't Klooster,
J., Henderson, R., Syga, Ł., Mans, R., van Maris, A. J.
A., & Poolman, B. (2020). Weak Acid
Permeation in Synthetic Lipid Vesicles and Across the Yeast Plasma
Membrane. Biophysical Journal,
118(2), 422-434. https://doi.org/10.1016/j.bpj.2019.11.3384
Price,
C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J.,
Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F.
J., Marrink, S.-J., Montalban-Lopez, M., de
Jong, A., Kok, J., Molenaar, D., Poolman,
B., Teusink, B., & Kuipers, O. P. (2019).
Adaption to glucose limitation is modulated by the pleotropic
regulator CcpA, independent of selection pressure strength.
BMC Evolutionary Biology, 19(1),
Article 15. https://doi.org/10.1186/s12862-018-1331-x
Pols,
T., Sikkema, H. R., Gaastra, B. F.,
Frallicciardi, J., Śmigiel, W. M., Singh, S.,
& Poolman, B. (2019). A synthetic metabolic
network for physicochemical homeostasis. Nature
Communications, 10(1), Article 4239. https://doi.org/10.1038/s41467-019-12287-2
Sikkema,
H. R., Gaastra, B. F., Pols, T., &
Poolman, B. (2019). Cell fueling and metabolic energy
conservation in synthetic cells.
ChemBioChem, 20(20 SI),
2581–2592. https://doi.org/10.1002/cbic.201900398
de
Boer, M., Gkouridis, G., Vietrov, R., Begg, S. L.,
Schuurman-Wolters, G. K., Husada, F., Eleftheriadis, N.,
Poolman, B., McDevitt, C. A., & Cordes, T.
(2019). Conformational and dynamical plasticity in
substrate-binding proteins underlies selective transport in ABC
importers. eLife, 8, Article
e44652. https://doi.org/10.7554/eLife.44652
Liu,
B., Hasrat, Z., Poolman, B., & Boersma, A. J.
(2019). Decreased Effective Macromolecular Crowding in
Escherichia coli Adapted to Hyperosmotic Stress.
Journal of Bacteriology, 201(10),
Article e00708-18. https://doi.org/10.1128/JB.00708-18
Smigiel,
W. M., Lefrancois, P., & Poolman, B.
(2019). Physicochemical considerations for bottom-up
synthetic biology. Emerging topics in life
sciences, 3(5), 445-458. Article ETLS20190017.
https://doi.org/10.1042/ETLS20190017
Bianchi,
F., Van't Klooster, J. S., Ruiz, S. J., & Poolman,
B. (2019). Regulation of Amino Acid Transport in
Saccharomyces cerevisiae. Microbiology and
Molecular Biology Reviews, 83(4), Article
e00024-19. https://doi.org/10.1128/MMBR.00024-19
Leth,
M. L., Ejby, M., Madland, E., Kitaoku, Y., Slotboom, D.
J., Guskov, A., Aachmann, F. L., & Abou
Hachem, M. (2020). Molecular insight into a new low affinity
xylan binding module from the xylanolytic gut symbiont Roseburia
intestinalis. The FEBS Journal,
287(10), 2105-2117. https://doi.org/10.1111/febs.15117
Garaeva,
A. A., Guskov, A., Slotboom, D.
J., & Paulino, C. (2019). A one-gate
elevator mechanism for the human neutral amino acid transporter
ASCT2. Nature Communications,
10, Article 3427. https://doi.org/10.1038/s41467-019-11363-x
Arkhipova,
V. I., Trinco, G., Thijs, E., Jensen, S.,
Slotboom, D., & Guskov, A. (2019).
Binding and transport of D-aspartate by the glutamate
transporter homologue GltTk. eLife,
8, Article e45286. https://doi.org/10.7554/eLife.45286
Bousis,
S., Setyawati, I., Diamanti, E.,
Slotboom, D. J., & Hirsch, A. K. H. (2019).
Energy-Coupling Factor Transporters as Novel Antimicrobial
Targets. Advanced Therapeutics,
2(2), Article 1800066. https://doi.org/10.1002/adtp.201800066
Lolkema,
J. S., & Slotboom, D. J. (2019). Models to
determine the kinetic mechanisms of ion-coupled
transporters. The Journal of General
Physiology, 151(3), 369-380. https://doi.org/10.1085/jgp.201812055
Ejby,
M., Guskov, A., Pichler, M. J., Zanten, G. C., Schoof,
E., Saburi, W., Slotboom, D. J., & Abou Hachem, M.
(2019). Two binding proteins of the ABC transporter that
confers growth of Bifidobacterium animalis subsp. lactis ATCC27673
on β-mannan possess distinct manno-oligosaccharide binding
profiles. Molecular Microbiology,
112(1), 114-130. Article 14257. https://doi.org/10.1111/mmi.14257
Valk-Weeber,
R. L., Eshuis-de Ruiter, T., Dijkhuizen, L.,
& van Leeuwen, S. S. (2020). Dynamic temporal
variations in bovine lactoferrin glycan structures.
Journal of Agricultural and Food Chemistry,
68(2), 549-560. Article acs.jafc.9b06762. https://doi.org/10.1021/acs.jafc.9b06762
Valk-Weeber,
R. L., Dijkhuizen, L., & van Leeuwen, S.
S. (2019). Large-scale quantitative isolation of pure
protein N-linked glycans. Carbohydrate
Research, 479, 13-22. https://doi.org/10.1016/j.carres.2019.04.011
Böger,
M., Hekelaar, J., van Leeuwen, S.
S., Dijkhuizen, L., & Lammerts van Bueren,
A. (2019). Structural and functional characterization of a
family GH53 β-1,4-galactanase from Bacteroides
thetaiotaomicron that facilitates degradation of prebiotic
galactooligosaccharides. Journal of Structural
Biology, 205(1), 1-10. Article
j.jsb.2018.12.002. https://doi.org/10.1016/j.jsb.2018.12.002
Boger,
M., van Leeuwen, S. S., van Bueren, A. L., &
Dijkhuizen, L. (2019). Structural Identity of
Galactooligosaccharide Molecules Selectively Utilized by Single
Cultures of Probiotic Bacterial Strains. Journal
of Agricultural and Food Chemistry, 67(50),
13969-13977. https://doi.org/10.1021/acs.jafc.9b05968
Pham,
H., Ten Kate, G. A., Dijkhuizen, L., & van
Leeuwen, S. S. (2019). Synthesis and characterization
of sialylated lactose- and lactulose-derived oligosaccharides by
Trypanosoma cruzi trans-sialidase. Journal of
Agricultural and Food Chemistry, 67(12),
3469–3479. https://doi.org/10.1021/acs.jafc.8b06974
Devlamynck,
T., Te Poele, E. M., Quataert, K., Gerwig, G.
J., Van de Walle, D., Dewettinck, K., Kamerling, J. P.,
Soetaert, W., & Dijkhuizen, L. (2019).
Trans-α-glucosylation of stevioside by the mutant
glucansucrase enzyme Gtf180-ΔN-Q1140E improves its taste
profile. Food Chemistry, 272,
653-662. https://doi.org/10.1016/j.foodchem.2018.08.025
El
Aidy, S., Bolsius, Y. G., Raven,
F., & Havekes, R. (2020). A brief
period of sleep deprivation leads to subtle changes in mouse gut
microbiota. Journal of Sleep Research,
29(6), Article e12920. https://doi.org/10.1111/jsr.12920
Bugda
Gwilt, K., González, D. P., Olliffe, N., Oller,
H., Hoffing, R., Puzan, M., El Aidy, S., & Miller,
G. M. (2020). Actions of Trace Amines in the
Brain-Gut-Microbiome Axis via Trace Amine-Associated Receptor-1
(TAAR1). Cellular and molecular
neurobiology, 40(2), 191-201. https://doi.org/10.1007/s10571-019-00772-7
van
Kessel, S. P., & El Aidy, S. (2019).
Bacterial Metabolites Mirror Altered Gut Microbiota
Composition in Patients with Parkinson's Disease.
Journal of Parkinson's Disease,
9(2), S359-S370. https://doi.org/10.3233/JPD-191780
van
Kessel, S. P., & El Aidy, S. (2019).
Contributions of Gut Bacteria and Diet to Drug
Pharmacokinetics in the Treatment of Parkinson's Disease.
Frontiers in Neurology, 10, Article
1087. https://doi.org/10.3389/fneur.2019.01087
van
Kessel, S. P., Frye, A. K., El-Gendy, A. O., Castejon, M.,
Keshavarzian, A., van Dijk, G., & El Aidy,
S. (2019). Gut bacterial tyrosine decarboxylases
restrict levels of levodopa in the treatment of Parkinson's
disease. Nature Communications,
10(1), Article 310. https://doi.org/10.1038/s41467-019-08294-y
Aarts,
E., & El Aidy, S. (2019). Increasing
reproducibility and interpretability of microbiota-gut-brain
studies on human neurocognition and intermediary microbial
metabolites. Behavioral and Brain
Sciences, 42, Article e61. https://doi.org/10.1017/S0140525X18002777
Sanz,
J. A., & El Aidy, S. (2019).
Microbiota and gut neuropeptides: a dual action of
antimicrobial activity and neuroimmune response.
Psychopharmacology, 236(5),
1597-1609. https://doi.org/10.1007/s00213-019-05224-0
Torres-Fuentes,
C., Golubeva, A. V., Zhdanov, A. V., Wallace, S., Arboleya, S.,
Papkovsky, D. B., El Aidy, S., Ross, P., Roy, B. L.,
Stanton, C., Dinan, T. G., Cryan, J. F., & Schellekens, H.
(2019). Short-chain fatty acids and microbiota metabolites
attenuate ghrelin receptor signaling. The FASEB
Journal, 33(12), 13546-13559. https://doi.org/10.1096/fj.201901433R
Singh,
R., Manivannan, S., Krikken, A. M., de Boer,
R., Bordin, N., Devos, D. P., & van der Klei, I.
J. (2020). Hansenula polymorpha Pex37 is a peroxisomal
membrane protein required for organelle fission and
segregation. The FEBS Journal,
287(9), 1742-1757. https://doi.org/10.1111/febs.15123
Wu,
H., & van der Klei, I. J. (2019).
Novel Peroxisome–Vacuole Contacts in Yeast.
Contact, 2, 1-3. https://doi.org/10.1177/2515256419829623
Wu,
H., de Boer, R., Krikken, A. M.,
Akşit, A., Yuan, W., & van der Klei, I. J.
(2019). Peroxisome development in yeast is associated with
the formation of Pex3-dependent peroxisome-vacuole contact
sites. Biochimica et Biophysica Acta (BBA) -
Molecular Cell Research, 1866(3), 349-359. https://doi.org/10.1016/j.bbamcr.2018.08.021
Wróblewska,
J. P., & van der Klei, I. J. (2019).
Peroxisome Maintenance Depends on De Novo Peroxisome
Formation in Yeast Mutants Defective in Peroxisome Fission and
Inheritance. International Journal of Molecular
Sciences, 20(16), Article 4023. https://doi.org/10.3390/ijms20164023
Costello,
J. L., Zalckvar, E., Kemp, S., di Cara, F., Kim, P. K., Linka,
N., & van der Klei, I. J. (2019).
Peroxisomes: New insights into protein sorting, dynamics,
quality control, signalling and roles in health and disease.
Histochemistry and cell biology,
151(4), 283-289. https://doi.org/10.1007/s00418-019-01780-w
Jansen,
R. L. M., & van der Klei, I. J. (2019).
The peroxisome biogenesis factors Pex3 and Pex19:
Multitasking proteins with disputed functions.
FEBS Letters, 593(5), 457-474. https://doi.org/10.1002/1873-3468.13340
Gholamjani
Moghaddam, K., de Vries, A., Marrink, S.
J., & Faraji, S. (2019). Binding of
quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen
bonding and π-π stacking. Biophysical
Chemistry, 253, Article 106220. https://doi.org/10.1016/j.bpc.2019.106220
Verkhnyatskaya,
S. A., de Vries, A. H., Douma-de Vries,
E., Sneep, R. J. L., & Walvoort, M. T.
C. (2019). Direct and Regioselective
Di-alpha-fucosylation on the Secondary Rim of beta-Cyclodextrin:
Cover Profile. Chemistry,
25(27), 6649-6649. https://doi.org/10.1002/chem.201901257
Verkhnyatskaya,
S. A., de Vries, A. H., Douma-de Vries,
E., Sneep, E. J. L., & Walvoort, M. T.
C. (2019). Direct and Regioselective
Di-alpha-fucosylation on the Secondary Rim of
beta-Cyclodextrin. Chemistry,
25(27), 6722-6727. https://doi.org/10.1002/chem.201806090
Piskorz,
T. K., Gobbo, C., Marrink, S. J., De Feyter, S.,
de Vries, A. H., & van Esch, J. H. (2019).
Nucleation Mechanisms of Self-Assembled Physisorbed
Monolayers on Graphite. Journal of Physical
Chemistry C, 123(28), 17510-17520. https://doi.org/10.1021/acs.jpcc.9b01234
Alessandri,
R., Souza, P. C. T., Thallmair, S., Melo,
M. N., De Vries, A. H., & Marrink, S.
J. (2019). Pitfalls of the Martini Model.
Journal of Chemical Theory and Computation,
15(10), 5448-5460. https://doi.org/10.1021/acs.jctc.9b00473
Marcelli,
B., de Jong, A., Karsens, H., Janzen,
T., Kok, J., & Kuipers, O. P. (2019).
A specific sugar moiety in the Lactococcus lactis cell wall
pellicle is required for infection by CHPC971, a member of the rare
1706 phage species. Applied and environmental
microbiology, 85(19), Article e01224-19. https://doi.org/10.1128/AEM.01224-19
Perez,
M., Calles-Enríquez, M., Del Rio, B., Redruello, B., de
Jong, A., Kuipers, O. P., Kok, J.,
Martin, M. C., Ladero, V., Fernandez, M., & Alvarez, M. A.
(2019). Construction and characterization of a double mutant
of Enterococcus faecalis that does not produce biogenic
amines. Scientific Reports,
9(1), Article 16881. https://doi.org/10.1038/s41598-019-53175-5
Kasuga,
G., Tanaka, M., Harada, Y., Nagashima, H., Yamato, T., Wakimoto,
A., Arakawa, K., Ito, Y., Kawai, Y., Kok, J., &
Masuda, T. (2019). Homologous expression and characterization
of gassericin T and gassericin S, a novel class IIb bacteriocin
produced by LA327. Applied and environmental
microbiology, 85(6), Article e02815-18. https://doi.org/10.1128/AEM.02815-18
Omony,
J., de Jong, A., Kok, J., & van
Hijum, S. A. F. T. (2019). Reconstruction and inference of
the Lactococcus lactis MG1363 gene co-expression network.
PLoS ONE, 14(5), Article e0214868.
https://doi.org/10.1371/journal.pone.0214868
van
der Meulen, S. B., Hesseling-Meinders, A., de Jong,
A., & Kok, J. (2019). The protein
regulator ArgR and the sRNA derived from the 3'-UTR region of its
gene, ArgX, both regulate the arginine deiminase pathway in
Lactococcus lactis. PLoS ONE,
14(6), Article e0218508. https://doi.org/10.1371/journal.pone.0218508
Tarazanova,
M., Starrenburg, M., Todt, T., van Hijum, S., Kok, J.,
& Bachmann, H. (2019). Transcriptional response of
Lactococcus lactis during bacterial emulsification.
PLoS ONE, 14(7), Article e0220048.
https://doi.org/10.1371/journal.pone.0220048
Kuipers,
A., Moll, G. N., Levy, A., Krakovsky, M., &
Franklin, R. (2020). Cyclic angiotensin-(1-7) contributes to
rehabilitation of animal performance in a rat model of cerebral
stroke. Peptides, 123,
Article 170193. https://doi.org/10.1016/j.peptides.2019.170193
Bosma,
T., Rink, R., Moosmeier, M. A., & Moll, G. (2019).
Genetically Encoded Libraries of Constrained Peptides.
ChemBioChem, 20(14), 1754-1758. https://doi.org/10.1002/cbic.201900031
Wu,
M., Crismaru, C. G., Salo, O., Bovenberg, R. A.
L., & Driessen, A. J. M. (2020).
Impact of classical strain improvement of penicillium rubens
on amino acid metabolism during β-Lactam production.
Applied and environmental microbiology,
86(3), Article e01561. https://doi.org/10.1128/AEM.01561-19
Zwahlen,
R., Pohl, C., Bovenberg, R. A. L., &
Driessen, A. J. M. (2019). Bacterial MbtH-like
proteins stimulate nonribosomal peptide synthetase-derived
secondary metabolism in the filamentous fungi. ACS
Synthetic Biology, 8(8), 1776-1787. https://doi.org/10.1021/acssynbio.9b00106
Mózsik,
L., Büttel, Z., Bovenberg, R. A. L.,
Driessen, A. J. M., & Nygård, Y. (2019).
Synthetic control devices for gene regulation in Penicillium
chrysogenum. Microbial Cell Factories,
18(1), Article 203. https://doi.org/10.1186/s12934-019-1253-3
Exterkate,
M., & Driessen, A. J. M. (2019).
Continuous expansion of a synthetic minimal cellular
membrane. Emerging topics in life
sciences, 3(5), 543-549. https://doi.org/10.1042/ETLS20190020
Hansen,
M., Hille, J., Szymanski, W., Driessen,
A., & Feringa, B. L. (2019). Easily
Accessible, Highly Potent, Photocontrolled Modulators of Bacterial
Communication. Chem, 5(5),
1293-1301. https://doi.org/10.1016/j.chempr.2019.03.005
Nijland,
J. G., Li, X., Shin, H. Y., de Waal, P.
P., & Driessen, A. J. M. (2019). Efficient,
D-glucose insensitive, growth on D-xylose by an evolutionary
engineered Saccharomyces cerevisiae strain. Fems
Yeast Research, 19(8), Article foz083. https://doi.org/10.1093/femsyr/foz083
Komarudin,
A. G., & Driessen, A. J. M. (2019).
SecA-Mediated Protein Translocation through the SecYEG
Channel. Microbiology Spectrum,
7(4). https://doi.org/10.1128/microbiolspec.PSIB-0028-2019
Seinen,
A.-B., & Driessen, A. J. M. (2019).
Single-Molecule Studies on the Protein Translocon.
Annual Review of Biophysics, 48,
185-207. https://doi.org/10.1146/annurev-biophys-052118-115352
Exterkate,
M., & Driessen, A. J. M. (2019).
Synthetic Minimal Cell: Self-Reproduction of the Boundary
Layer. ACS Omega, 4(3),
5293-5303. Article 02955. https://doi.org/10.1021/acsomega.8b02955
Koch,
S., Exterkate, M., López, C. A., Patro, M.,
Marrink, S. J., & Driessen, A. J. M.
(2019). Two distinct anionic phospholipid-dependent events
involved in SecA-mediated protein translocation.
Biochimica et Biophysica Acta - Biomembranes,
1861(11), Article 183035. https://doi.org/10.1016/j.bbamem.2019.183035
Morales
Angeles, D., Macia Valero, A., Bohorquez Suarez,
L., & Scheffers, D.-J. (2020). The PASTA
domains of Bacillus subtilis PBP2B stabilize the interaction of
PBP2B with DivIB. Microbiology,
166(9), 826–836. Article 000957. https://doi.org/10.1099/mic.0.000957
Polaquini,
C. R., Morão, L. G., Nazaré, A. C., Torrezan, G. S.,
Dilarri, G., Cavalca, L. B., Campos, D. L., Silva, I.
C., Pereira, J. A., Scheffers, D.-J., Duque, C.,
Pavan, F. R., Ferreira, H., & Regasini, L. O. (2019).
Antibacterial activity of 3,3'-dihydroxycurcumin (DHC) is
associated with membrane perturbation. Bioorganic
Chemistry, 90, Article 103031. https://doi.org/10.1016/j.bioorg.2019.103031
Kimkes,
T. E. P., & Heinemann, M. (2020). How
bacteria recognise and respond to surface contact.
FEMS Microbiology Reviews, 44(1),
106-122. https://doi.org/10.1093/femsre/fuz029
Niebel,
B., Leupold, S., & Heinemann, M. (2019). An
upper limit on Gibbs energy dissipation governs cellular
metabolism. Nature Metabolism,
1, 125-131. https://doi.org/10.1038/s42255-018-0006-7
Balaban,
N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B.,
Andersson, D. I., Brynildsen, M. P., Bumann, D., Camilli, A.,
Collins, J. J., Dehio, C., Fortune, S., Ghigo, J.-M., Hardt, W.-D.,
Harms, A., Heinemann, M., Hung, D. T., Jenal, U.,
Levin, B. R., ... Zinkernagel, A. (2019). Definitions and
guidelines for research on antibiotic persistence.
Nature Reviews Microbiology, 17(7),
441-448. https://doi.org/10.1038/s41579-019-0196-3
Litsios,
A., Huberts, D. H. E. W., Terpstra, H. M.,
Guerra, P., Schmidt, A., Buczak, K., Papagiannakis,
A., Rovetta, M., Hekelaar, J., Hubmann,
G., Exterkate, M., Milias-Argeitis,
A., & Heinemann, M. (2019).
Differential scaling between G1 protein production and cell
size dynamics promotes commitment to the cell division cycle in
budding yeast. Nature Cell Biology,
21(11), 1382-1392. https://doi.org/10.1038/s41556-019-0413-3
Ozsezen,
S., Papagiannakis, A., Chen, H., Niebel,
B., Milias-Argeitis, A., & Heinemann,
M. (2019). Inference of the High-Level Interaction
Topology between the Metabolic and Cell-Cycle Oscillators from
Single-Cell Dynamics. Cell systems,
9(4), 354-365. https://doi.org/10.1016/j.cels.2019.09.003
Zhang,
Z., Kimkes, T. E. P., & Heinemann, M. (2019).
Manipulating rod-shaped bacteria with optical
tweezers. Scientific Reports,
9(1), Article 19086. https://doi.org/10.1038/s41598-019-55657-y
Monteiro,
F., Hubmann, G., Takhaveev, V., Vedelaar, S.
R., Norder, J., Hekelaar, J., Saldida,
J., Litsios, A., Wijma, H. J., Schmidt,
A., & Heinemann, M. (2019). Measuring
glycolytic flux in single yeast cells with an orthogonal synthetic
biosensor. Molecular Systems Biology,
15(12), Article e9071. https://doi.org/10.15252/msb.20199071
Balaban,
N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B.,
Andersson, D. I., Brynildsen, M. P., Bumann, D., Camilli, A.,
Collins, J. J., Dehio, C., Fortune, S., Ghigo, J.-M., Hardt, W.-D.,
Harms, A., Heinemann, M., Hung, D. T., Jenal, U.,
Levin, B. R., ... Zinkernagel, A. (2019). Publisher
Correction: Definitions and guidelines for research on antibiotic
persistence. Nature Reviews
Microbiology, 17(7), 460-460. https://doi.org/10.1038/s41579-019-0207-4
Leupold,
S., Hubmann, G., Litsios, A., Meinema, A. C., Takhaveev,
V., Papagiannakis, A., Niebel, B., Janssens, G., Siegel,
D., & Heinemann, M. (2019). Saccharomyces
cerevisiae goes through distinct metabolic phases during its
replicative lifespan. eLife,
8, Article e41046. https://doi.org/10.7554/eLife.41046
Yang,
Y.-S., Kato, M., Wu, X., Litsios, A., Sutter, B. M., Wang, Y., Hsu,
C.-H., Wood, N. E., Lemoff, A., Mirzaei, H., Heinemann,
M., & Tu, B. P. (2019). Yeast Ataxin-2 Forms an
Intracellular Condensate Required for the Inhibition of TORC1
Signaling during Respiratory Growth.
Cell, 177(3), 697-710. https://doi.org/10.1016/j.cell.2019.02.043
Zhang,
J., Grandi, E., Fu, H., Thangavelu, S.,
Bothof, L., Tepper, P. G., Thunnissen, A.-M. W.
H., & Poelarends, G. J. (2020).
Engineered C–N Lyase: Enantioselective Synthesis of
Chiral Synthons for Artificial Dipeptide Sweeteners .
Angewandte Chemie International Edition,
59(1), 429-435. https://doi.org/10.1002/anie.201910704
Mayer,
C., Dulson, C., Reddem, E., Thunnissen, A.-M. W.
H., & Roelfes, G. (2019). Directed
Evolution of a Designer Enzyme Featuring an Unnatural Catalytic
Amino Acid. Angewandte Chemie-International
Edition, 58(7), 2083-2087. https://doi.org/10.1002/anie.201813499
Biewenga,
L., Thangavelu, S., Kunzendorf, A., Van
Der Meer, J., Pijning, T., Tepper,
P., Van Merkerk, R., Charnock, S. J.,
Thunnissen, A. W. H., & Poelarends, G. J.
(2019). Enantioselective Synthesis of Pharmaceutically Active
γ-Aminobutyric Acids Using a Tailor-Made Artificial Michaelase
in One-Pot Cascade Reactions. ACS
Catalysis, 9, 1503-1513. https://doi.org/10.1021/acscatal.8b04299
Franceus,
J., Capra, N., Desmet, T., & Thunnissen,
A.-M. W. H. (2019). Structural Comparison of a
Promiscuous and a Highly Specific Sucrose 6F-Phosphate
Phosphorylase. International Journal of Molecular
Sciences, 20(16). https://doi.org/10.3390/ijms20163906
2018
Aalbers,
F., & Fraaije, M. (2019). Design of
artificial alcohol oxidases: alcohol dehydrogenase - NADPH oxidase
fusions for continuous oxidations.
ChemBioChem, 20(1), 51-56. Article
cbic.201800421. https://doi.org/10.1002/cbic.201800421
Lanfranchi,
E., Trajković, M., Barta, K., de
Vries, J. G., & Janssen, D. B. (2019).
Exploring the selective demethylation of aryl-methyl ethers
by a Pseudomonas Rieske monooxygenase.
ChemBioChem, 20(1), 118-125. Article
cbic.201800594. https://doi.org/10.1002/cbic.201800594
Otzen,
M., Palacio, C., & Janssen, D. B. (2018).
Characterization of the caprolactam degradation pathway in
Pseudomonas jessenii using mass spectrometry-based
proteomics. Applied Microbiology and
Biotechnology, 15, 6699-6711. https://doi.org/10.1007/s00253-018-9073-7
Li,
R., Wijma, H. J., Song, L., Cui, Y., Otzen,
M., Tian, Y., Du, J., Li, T., Niu, D., Chen, Y., Feng, J.,
Han, J., Chen, H., Tao, Y., Janssen, D. B., & Wu,
B. (2018). Computational redesign of enzymes for regio- and
enantioselective hydroamination. Nature Chemical
Biology, 14, 664-670. https://doi.org/10.1038/s41589-018-0053-0
Schmidt,
M., Toplak, A., Rozeboom, H. J., Wijma, H.
J., Quaedflieg, P. J. L. M., van Maarseveen, J. H.,
Janssen, D. B., & Nuijens, T. (2018). Design of a
substrate-tailored peptiligase variant for the efficient synthesis
of thymosin-alpha(1). Organic & Biomolecular
Chemistry, 16(4), 609-618. https://doi.org/10.1039/c7ob02812a
Verhoeven,
M. D., Lee, M., van den Broek, M., Janssen, D.
B., Daran, J.-M. G., van Maris, A. J. A., Pronk, J. T.,
Bracher, J. M., De Waal, P. P., & de Bruijn, H. M. C. J.
(2018). Eukaryotic cell comprising xylose
isomerase. (Patent No. WO2018073107). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2018073107A1&KC=A1&FT=D&ND=3&date=20180426&DB=&locale=en_EP
De
Vries, J., Lanfranchi, E., Deuss, P., Janssen,
D., & Barta, K. (2018). Making single
monomeric building blocks from lignin and theri further conversion
into useful products. Abstracts of Papers of the
American Chemical Society, 255.
Atashgahi,
S., Liebensteiner, M. G., Janssen, D. B., Smidt, H.,
Stams, A. J. M., & Sipkema, D. (2018). Microbial
Synthesis and Transformation of Inorganic and Organic Chlorine
Compounds. Frontiers in Microbiology,
9, Article 3079. https://doi.org/10.3389/fmicb.2018.03079
van
Haastert, P. J. M., Keizer-Gunnink, I.,
& Kortholt, A. (2018). The cytoskeleton regulates
symmetry transitions in moving amoeboid cells.
Journal of Cell Science, 131(7),
Article UNSP jcs208892. https://doi.org/10.1242/jcs.208892
Deyaert,
E., Leemans, M., Singh, R. K., Gallardo, R., Steyaert, J.,
Kortholt, A., Lauer, J., & Versées, W. (2019).
Structure and nucleotide-induced conformational dynamics of
the Chlorobium tepidum Roco protein. Biochemical
Journal, 476(1), 51-66. https://doi.org/10.1042/BCJ20180803
Wauters,
L., Terheyden, S., Gilsbach, B. K., Leemans, M.,
Athanasopoulos, P. S., Guaitoli, G., Wittinghofer, A.,
Gloeckner, C. J., Versées, W., & Kortholt, A.
(2018). Biochemical and kinetic properties of the complex
Roco G-protein cycle. Biological
Chemistry, 399(12), 1447-1456. https://doi.org/10.1515/hsz-2018-0227
Athanasopoulos,
P. S., Heumann, R., & Kortholt, A. (2018).
The role of (auto)-phosphorylation in the complex activation
mechanism of LRRK2. Biological
Chemistry, 399(7), 643-647. https://doi.org/10.1515/hsz-2017-0332
Geuverink,
E., Kraaijeveld, K., van Leussen, M.,
Chen, F., Pijpe, J., Linskens, M. H. K.,
Beukeboom, L. W., & van de Zande, L.
(2018). Evidence for involvement of a transformer paralog in
sex determination of the wasp Leptopilina clavipes.
Insect Molecular Biology, 27(6),
780-795. Article imb.12522. https://doi.org/10.1111/imb.12522
Maglia,
G., Wloka, C., Mutter, N. L.,
Soskine, M., & Huang, G. (2018). Biological nanopores for biopolymer sensing and
sequencing based on frac actinoporin. (Patent No.
WO2018012963). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2018012963A1&KC=A1&FT=D&ND=3&date=20180118&DB=&locale=en_EP
Galenkamp,
N. S., Soskine, M., Hermans, J., Wloka,
C., & Maglia, G. (2018). Direct
electrical quantification of glucose and asparagine from bodily
fluids using nanopores. Nature
Communications, 9(1), Article 4085. https://doi.org/10.1038/s41467-018-06534-1
Nomidis,
S. K., Hooyberghs, J., Maglia, G., & Carlon, E.
(2018). DNA capture into the ClyA nanopore: Diffusion-limited
versus reaction-limited processes. Journal of
Physics-Condensed Matter, 30(30), Article
304001. https://doi.org/10.1088/1361-648X/aacc01
Mutter,
N. L., Soskine, M., Huang, G., Albuquerque, I.
S., Bernardes, G. J. L., & Maglia, G. (2018).
Modular pore-forming immunotoxins with caged cytotoxicity
tailored by directed evolution. ACS chemical
biology, 13(11), 3153–3160. Article
8b00720. https://doi.org/10.1021/acschembio.8b00720
Wilmaerts,
D., Bayoumi, M., Dewachter, L., Knapen, W., Mika, J. T., Hofkens,
J., Dedecker, P., Maglia, G., Verstraeten, N., &
Michiels, J. (2018). The Persistence-Inducing Toxin HokB
Forms Dynamic Pores That Cause ATP Leakage.
mBio, 9(4), Article ARTN e00744-18.
https://doi.org/10.1128/mBio.00744-18
Henderson,
R. K., Fendler, K., & Poolman, B. (2019).
Coupling efficiency of secondary active transporters.
Current Opinion in Biotechnology,
58, 62-71. https://doi.org/10.1016/j.copbio.2018.11.005
Marques,
W. L., Mans, R., Henderson, R. K., Marella, E. R., Horst, J. T.,
Hulster, E. D., Poolman, B., Daran, J.-M., Pronk, J.
T., Gombert, A. K., & van Maris, A. J. A. (2018).
Combined engineering of disaccharide transport and
phosphorolysis for enhanced ATP yield from sucrose fermentation in
Saccharomyces cerevisiae. Metabolic
Engineering, 45, 121-133. https://doi.org/10.1016/j.ymben.2017.11.012
Lycklama
A Nijeholt, J. A., Vietrov, R., Schuurman-Wolters, G.
K., & Poolman, B. (2018). Energy
coupling efficiency in the Type I ABC transporter GlnPQ.
Journal of Molecular Biology,
430(6), 853-866. https://doi.org/10.1016/j.jmb.2018.02.001
Schavemaker,
P. E., Boersma, A. J., & Poolman, B. (2018).
How Important Is Protein Diffusion in Prokaryotes?
Frontiers in Molecular Biosciences,
5, Article fmolb.2018.00093. https://doi.org/10.3389/fmolb.2018.00093
Schavemaker,
P. E., & Poolman, B. (2018). (Membrane)
Protein Production in Context. Trends in
Biochemical Sciences, 43(11), 858-868. https://doi.org/10.1016/j.tibs.2018.08.009
Syga,
Ł., Spakman, D., Punter, C. M., &
Poolman, B. (2018). Method for immobilization of
living and synthetic cells for high-resolution imaging and
single-particle tracking. Scientific
Reports, 8(1), Article 13789. https://doi.org/10.1038/s41598-018-32166-y
Bartelds,
R., Nematollahi, M. H., Pols, T., Stuart, M. C. A.,
Pardakhty, A., Asadikaram, G., & Poolman, B.
(2018). Niosomes, an alternative for liposomal
delivery. PLoS ONE, 13(4),
Article e0194179. https://doi.org/10.1371/journal.pone.0194179
Schuurman-Wolters,
G. K., de Boer, M., Pietrzyk, M. K.,
& Poolman, B. (2018). Protein linkers provide
limits on the domain interactions in the ABC importer GlnPQ and
determine the rate of transport. Journal of
Molecular Biology, 430(8), 1249-1262. Article
j.jmb.2018.02.014. https://doi.org/10.1016/j.jmb.2018.02.014
Bianchi,
F., Syga, Ł., Moiset, G., Spakman, D., Schavemaker, P.
E., Punter, C. M., Seinen, A.-B., van Oijen, A.
M., Robinson, A., & Poolman, B. (2018).
Steric exclusion and protein conformation determine the
localization of plasma membrane transporters.
Nature Communications, 9(1), Article
501. https://doi.org/10.1038/s41467-018-02864-2
Liu,
B., Mavrova, S. N., van den Berg, J., Kristensen, S.
K., Mantovanelli, L., Veenhoff, L.
M., Poolman, B., & Boersma, A. J. (2018).
The influence of fluorescent protein maturation on FRET
measurements in living cells. ACS
Sensors, 3(9), 1735-1742. https://doi.org/10.1021/acssensors.8b00473
Rempel,
S., Stanek, W. K., & Slotboom, D. J. (2019).
ECF-Type ATP-Binding Cassette Transporters.
Annual Review of Biochemistry, 88,
551-576. Article annurev-biochem-013118-111705. https://doi.org/10.1146/annurev-biochem-013118-111705
Garaeva,
A., Oostergetel, G., Gati, C., Guskov,
A., Batista Paulino, C., & Slotboom,
D. (2018). Cryo-EM structure of the human neutral
amino acid transporter ASCT2. Nature Structural
& Molecular Biology, 25, 515-521. https://doi.org/10.1038/s41594-018-0076-y
Rempel,
S., Colucci, E., Gier, J.-W. D., Guskov,
A., & Slotboom, D. (2018).
Cysteine-mediated decyanation of vitamin B12 by the predicted
membrane transporter BtuM. Nature
Communications, 9(1), Article 3038. https://doi.org/10.1038/s41467-018-05441-9
Luís
da Silva Santos Guimarães, J. A., Rempel, S., Mous, S. T. M.,
Tambascia Pereira, C., ter Beek, J., Gier, J.-W. D., Guskov,
A., & Slotboom, D. (2018). Functional
and structural characterization of an ECF-type ABC transporter for
vitamin B12. eLife, 7,
Article e35828. https://doi.org/10.7554/eLife.35828
Hoorens,
M. W. H., Fu, H., Duurkens, R. H., Trinco, G.,
Arkhipova, V., Feringa, B. L., Poelarends, G.
J., Slotboom, D. J., & Szymanski,
W. (2018). Glutamate Transporter Inhibitors with
Photo-Controlled Activity. Advanced
Therapeutics, 1(2), Article 1800028. https://doi.org/10.1002/adtp.201800028
Gangoiti,
J., Corwin, S. F., Lamothe, L. M., Vafiadi, C., Hamaker, B.
R., & Dijkhuizen, L. (2020). Synthesis of
novel α-glucans with potential health benefits through
controlled glucose release in the human gastrointestinal
tract. Critical Reviews in Food Science and
Nutrition, 60(1), 123-146. https://doi.org/10.1080/10408398.2018.1516621
Pham,
H. T. T., Boger, M. C. L., Dijkhuizen, L., &
van Leeuwen, S. S. (2019). Stimulatory effects of
novel glucosylated lactose derivatives GL34 on growth of selected
gut bacteria. Applied Microbiology and
Biotechnology, 103(2), 707-718. https://doi.org/10.1007/s00253-018-9473-8
Meng,
X., Gangoiti, J., Wang, X., Grijpstra, P., van
Leeuwen, S. S., Pijning, T., &
Dijkhuizen, L. (2018). Biochemical characterization of
a GH70 protein from Lactobacillus kunkeei DSM 12361 with two
catalytic domains involving branching sucrase activity.
Applied Microbiology and Biotechnology,
102(18), 7935-7950. https://doi.org/10.1007/s00253-018-9236-6
Meng,
X., Gangoiti, J., de Kok, N., van
Leeuwen, S. S., Pijning, T., &
Dijkhuizen, L. (2018). Biochemical characterization of
two GH70 family 4,6-α-glucanotransferases with distinct
product specificity from Lactobacillus aviarius subsp. aviarius DSM
20655. Food Chemistry, 253,
236-246. Article j.foodchem.2018.01.154. https://doi.org/10.1016/j.foodchem.2018.01.154
Gangoiti
Muñecas, J., van Leeuwen, S. S.,
Pijning, T., Dijkhuizen, L., Vafeiadi, C.,
& Duboux, S. (2018). Branched alpha
glucans. (Patent No. WO2018167032). https://nl.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2018167032A1&KC=A1&FT=D&ND=3&date=20180920&DB=&locale=nl_NL
Boger,
M. C. L., van Bueren, A. L., & Dijkhuizen, L.
(2018). Cross-Feeding among Probiotic Bacterial Strains on
Prebiotic Inulin Involves the Extracellular exo-Inulinase of
Lactobacillus paracasei Strain W20. Applied and
environmental microbiology, 84(21), Article
e01539-18. https://doi.org/10.1128/AEM.01539-18
Te
Poele, E. M., Devlamynck, T., Jäger, M., Gerwig,
G. J., Van de Walle, D., Dewettinck, K., Hirsch, A. K.
H., Kamerling, J. P., Soetaert, W., & Dijkhuizen,
L. (2018). Glucansucrase (mutant) enzymes from
Lactobacillus reuteri 180 efficiently transglucosylate Stevia
component rebaudioside A, resulting in a superior taste.
Scientific Reports, 8(1), Article
1516. https://doi.org/10.1038/s41598-018-19622-5
Pham,
H., Pijning, T., Dijkhuizen, L.,
& van Leeuwen, S. S. (2018). Mutational Analysis
of the Role of the Glucansucrase Gtf180-Delta N Active Site
Residues in Product and Linkage Specificity with Lactose as
Acceptor Substrate. Journal of Agricultural and
Food Chemistry, 66(47), 12544-12554. Article
acs.jafc.8b04486. https://doi.org/10.1021/acs.jafc.8b04486
Lammerts
van Bueren-Brandt, A., & Dijkhuizen, L.
(2018). Prebiotic branched
galacto-oligosaccharides (gos). (Patent No.
WO2018048305). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2018048305A1&KC=A1&FT=D&ND=3&date=20180315&DB=&locale=en_EP
van
Leeuwen, S. S., Stoutjesdijk, E., ten Kate, G. A.,
Schaafsma, A., Dijck-Brouwer, J., Muskiet, F. A.
J., & Dijkhuizen, L. (2018). Regional
variations in human milk oligosaccharides in Vietnam suggest FucTx
activity besides FucT2 and FucT3. Scientific
Reports, 8(1), Article 16790. https://doi.org/10.1038/s41598-018-34882-x
Pham,
H. T., Dijkhuizen, L., & van Leeuwen, S.
S. (2018). Structural characterization of glucosylated
GOS derivatives synthesized by the Lactobacillus reuteri GtfA and
Gtf180 glucansucrase enzymes. Carbohydrate
Research, 470, 57-63. https://doi.org/10.1016/j.carres.2018.10.003
Yin,
H., Dijkhuizen, L., & van Leeuwen, S.
(2018). Synthesis of galacto-oligosaccharides derived from
lactulose by wild-type and mutant β-galactosidase enzymes from
Bacillus circulans ATCC 31382. Carbohydrate
Research, 465, 58-65. Article
j.carres.2018.06.009. https://doi.org/10.1016/j.carres.2018.06.009
Waclawikova,
B., & El Aidy, S. (2018). Role of
Microbiota and Tryptophan Metabolites in the Remote Effect of
Intestinal Inflammation on Brain and Depression.
Pharmaceuticals, 11(3), Article 63.
https://doi.org/10.3390/ph11030063
Bears,
A., Oosting, A., Lohuis, M., Koehorse, M., El Aidy,
S., Hugenholtz, F., Smidt, H., Mischke, M., Boekschoten, M.
V., Verkade, H. J., Garssen, J., van der Beek,
E. M., Knol, J., de Vos, P., van
Bergenhenegouwen, J., & Fransen, F. (2018). Sex
differences in lipid metabolism are affected by presence of the gut
microbiota. Scientific Reports,
8, Article 13426. https://doi.org/10.1038/s41598-018-31695-w
Rampelt,
H., Wollweber, F., Gerke, C., de Boer, R., van
der Klei, I. J., Bohnert, M., Pfanner, N., & van der
Laan, M. (2018). Assembly of the Mitochondrial Cristae
Organizer Mic10 is Regulated by Mic26-Mic27 Antagonism and
Cardiolipin. Journal of Molecular
Biology, 430(13), 1883-1890. https://doi.org/10.1016/j.jmb.2018.04.037
Aksit,
A., & van der Klei, I. J. (2018). Yeast
peroxisomes: How are they formed and how do they grow?
International journal of biochemistry & cell
biology, 105, 24-34. https://doi.org/10.1016/j.biocel.2018.09.019
Grunewald,
F., Rossi, G., De Vries, A. H., Marrink,
S. J., & Monticelli, L. (2018). A Transferable
MARTINI Model of Polyethylene Oxide. The Journal
of Physical Chemistry. B: Materials, Surfaces, Interfaces, &
Biophysical, 122(29), 7436-7449. https://doi.org/10.1021/acs.jpcb.8b04760
Piskorz,
T. K., de Vries, A. H., De Feyter, S., & van Esch,
J. H. (2018). Mechanism of Ostwald Ripening in 2D Physisorbed
Assemblies at Molecular Time and Length Scale by Molecular Dynamics
Simulations. Journal of Physical Chemistry
C, 122(42), 24380-24385. https://doi.org/10.1021/acs.jpcc.8b06432
Lubbe,
A. S., Liu, Q., Smith, S. J., de Vries, J. W., Kistemaker,
J. C. M., De Vries, A. H., Faustino, I.,
Meng, Z., Szymanski, W., Herrmann,
A., & Feringa, B. L. (2018).
Photoswitching of DNA Hybridization Using a Molecular
Motor. Journal of the American Chemical
Society, 140(15), 5069-5076. Article
jacs.7b09476. https://doi.org/10.1021/jacs.7b09476
Bron,
P. A., Marcelli, B., Mulder, J., van der Els, S., Morawska,
L. P., Kuipers, O. P., Kok, J.,
& Kleerebezem, M. (2019). Renaissance of traditional DNA
transfer strategies for improvement of industrial lactic acid
bacteria. Current Opinion in
Biotechnology, 56, 61-68. https://doi.org/10.1016/j.copbio.2018.09.004
Tarazanova,
M., Huppertz, T., Kok, J., & Bachmann, H. (2018).
Altering textural properties of fermented milk by using
surface-engineered Lactococcus lactis. Microbial
Biotechnology, 11(4), 770-780. https://doi.org/10.1111/1751-7915.13278
Vaishampayan,
A., de Jong, A., Wight, D. J., Kok, J.,
& Grohmann, E. (2018). A Novel Antimicrobial Coating
Represses Biofilm and Virulence-Related Genes in
Methicillin-Resistant Staphylococcus aureus.
Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.00221
van
Heel, A. J., de Jong, A., Song, C., Viel,
J. H., Kok, J., & Kuipers, O.
P. (2018). BAGEL4: a user-friendly web server to
thoroughly mine RiPPs and bacteriocins. Nucleic
Acids Research, 46(W1), W278-W281. https://doi.org/10.1093/nar/gky383
Solopova,
A., Bachmann, H., Teusink, B., Kok, J., &
Kuipers, O. P. (2018). Further Elucidation of
Galactose Utilization in MG1363. Frontiers in
Microbiology, 9, Article 1803. https://doi.org/10.3389/fmicb.2018.01803
Tarazanova,
M., Huppertz, T., Kok, J., & Bachmann, H. (2018).
Influence of lactococcal surface properties on cell retention
and distribution in cheese curd. International
Dairy Journal, 85, 73-78. https://doi.org/10.1016/j.idairyj.2018.05.003
Siroli,
L., Braschi, G., de Jong, A., Kok, J.,
Patrignani, F., & Lanciotti, R. (2018). Transcriptomic
approach and membrane fatty acid analysis to study the response
mechanisms of Escherichia coli to thyme essential oil, carvacrol,
2-(E)-hexanal and citral exposure. Journal of
Applied Microbiology, 125(5), 1308-1320.
Article jam.14048. https://doi.org/10.1111/jam.14048
Kuipers,
A., Moll, G. N., Wagner, E., & Franklin, R.
(2019). Efficacy of lanthionine-stabilized angiotensin-(1-7)
in type I and type II diabetes mouse models.
Peptides, 112, 78-84. https://doi.org/10.1016/j.peptides.2018.10.015
Guzman-Chavez,
F., Salo, O., Samol, M., Ries, M., Kuipers, J.,
Bovenberg, R. A. L., Vreeken, R. J., & Driessen,
A. J. M. (2018). Deregulation of secondary metabolism
in a histone deacetylase mutant of Penicillium chrysogenum.
MicrobiologyOpen, 7(5), Article
e00598. https://doi.org/10.1002/mbo3.598
Guzman-Chavez,
F., Zwahlen, R. D., Bovenberg, R. A. L., &
Driessen, A. J. M. (2018). Engineering of the
Filamentous Fungus Penicillium chrysogenum as Cell Factory for
Natural Products. Frontiers in
Microbiology, 9, Article 2768. https://doi.org/10.3389/fmicb.2018.02768
Pohl,
C., Mózsik, L., Driessen, A. J.
M., Bovenberg, R. A. L., & Nygård, Y.
I. (2018). Genome Editing in Penicillium chrysogenum Using
Cas9 Ribonucleoprotein Particles. In J. C. Braman (Ed.),
Synthetic biology: Methods and Protocols (pp. 213-232).
(Methods in Molecular Biology; Vol. 1772). Humana Press. https://doi.org/10.1007/978-1-4939-7795-6_12
Koch,
S., Driessen, A., & Kedrov, A. (2018).
Biophysical Analysis of Sec-Mediated Protein Translocation in
Nanodiscs. In Advances in Biomembranes and Lipid
Self-Assembly (Advances in Biomembranes and Lipid
Self-Assembly; Vol. 27). Elsevier. https://doi.org/10.1016/bs.abl.2018.05.003
Baker,
L. A., Sinnige, T., Schellenberger, P., de Keyzer, J., Siebert, C.
A., Driessen, A. J. M., Baldus, M., &
Grünewald, K. (2018). Combined 1H-Detected Solid-State
NMR Spectroscopy and Electron Cryotomography to Study Membrane
Proteins across Resolutions in Native Environments.
Structure, 26(1), 161-170. Article
j.str.2017.11.011. https://doi.org/10.1016/j.str.2017.11.011
Caforio,
A., Siliakus, M. F., Exterkate, M., Jain, S., Jumde,
V. R., Andringa, R. L. H., Kengen, S. W. M.,
Minnaard, A. J., Driessen, A. J. M., & van
der Oost, J. (2018). Converting into an archaebacterium with
a hybrid heterochiral membrane. Proceedings of the
National Academy of Sciences of the United States of
America, 115(14), 3704-3709. Article
pnas.1721604115. https://doi.org/10.1073/pnas.1721604115
Grijseels,
S., Pohl, C., Nielsen, J. C., Wasil, Z., Nygård, Y., Nielsen,
J., Frisvad, J. C., Nielsen, K. F., Workman, M., Larsen, T.
O., Driessen, A. J. M., & Frandsen, R. J. N.
(2018). Identification of the decumbenone biosynthetic gene
cluster in and the importance for production of calbistrin.
Fungal Biology and Biotechnology, 5,
Article 18. https://doi.org/10.1186/s40694-018-0063-4
Verhoeven,
M. D., Bracher, J. M., Nijland, J. G., Bouwknegt, J.,
Daran, J.-M. G., Driessen, A. J. M., van Maris, A. J.
A., & Pronk, J. T. (2018). Laboratory evolution of a
glucose-phosphorylation-deficient, arabinose-fermenting S.
cerevisiae strain reveals mutations in GAL2 that enable
glucose-insensitive l-arabinose uptake. Fems Yeast
Research, 18(6). https://doi.org/10.1093/femsyr/foy062
Bracher,
J. M., Verhoeven, M. D., Wisselink, H. W., Crimi, B.,
Nijland, J. G., Driessen, A. J. M., Klaassen,
P., van Maris, A. J. A., Daran, J.-M. G., & Pronk, J. T.
(2018). The Penicillum chrysogenum transporter PcAraT enables
high-affinity, glucose-insensitive L-arabinose transport in
Saccharomyces cerevisiae. Biotechnology for
Biofuels, 11, Article 63. https://doi.org/10.1186/s13068-018-1047-6
Morão,
L. G., Polaquini, C. R., Kopacz, M., Torrezan, G. S., Ayusso, G.
M., Dilarri, G., Cavalca, L. B., Zielińska, A.,
Scheffers, D.-J., Regasini, L. O., & Ferreira, H.
(2019). A simplified curcumin targets the membrane of
Bacillus subtilis. MicrobiologyOpen,
8(4), Article 683. https://doi.org/10.1002/mbo3.683
Kopacz,
M. M., Lorenzoni, A. S. G., Polaquini, C. R., Regasini, L.
O., & Scheffers, D.-J. (2019). Purification
and characterization of FtsZ from the citrus canker pathogen
Xanthomonas citri subsp. citri.
MicrobiologyOpen, 8(5), Article
e00706. https://doi.org/10.1002/mbo3.706
Savietto,
A., Polaquini, C. R., Kopacz, M., Scheffers, D.-J.,
Marques, B. C., Regasini, L. O., & Ferreira, H. (2018).
Antibacterial activity of monoacetylated alkyl gallates
against Xanthomonas citri subsp citri. Archives of
Microbiology, 200(6), 929-937. https://doi.org/10.1007/s00203-018-1502-6
Nazaré,
A. C., Polaquini, C. R., Cavalca, L. B., Anselmo, D.
B., Saiki, M. D. F. C., Monteiro, D. A., Zielinska,
A., Rahal, P., Gomes, E., Scheffers, D.-J.,
Ferreira, H., & Regasini, L. O. (2018). Design of
Antibacterial Agents: Alkyl Dihydroxybenzoates against Xanthomonas
citri subsp. citri. International Journal of
Molecular Sciences, 19(10), 1-15. https://doi.org/10.3390/ijms19103050
von
Borzyskowski, L. S., Carrillo, M., Leupold, S., Glatter, T.,
Kiefer, P., Weishaupt, R., Heinemann, M., & Erb,
T. J. (2018). An engineered Calvin-Benson-Bassham cycle for
carbon dioxide fixation in Methylobacterium extorquens AM1.
Metabolic Engineering, 47, 423-433.
https://doi.org/10.1016/j.ymben.2018.04.003
Bley
Folly, B., Ortega, A. D., Hubmann, G., Bonsing-Vedelaar,
S., Wijma, H. J., van der Meulen,
P., Milias-Argeitis, A., & Heinemann,
M. (2018). Assessment of the interaction between the
flux-signaling metabolite fructose-1,6-bisphosphate and the
bacterial transcription factors CggR and Cra.
Molecular Microbiology, 109(3),
278-290. https://doi.org/10.1111/mmi.14008
Zhang,
Z., Milias-Argeitis, A., & Heinemann,
M. (2018). Dynamic single-cell NAD(P)H measurement
reveals oscillatory metabolism throughout the E. coli cell division
cycle. Scientific Reports,
8(1), Article 2162. https://doi.org/10.1038/s41598-018-20550-7
Takhaveev,
V., & Heinemann, M. (2018). Metabolic
heterogeneity in clonal microbial populations.
Current Opinion in Microbiology, 45,
30-38. https://doi.org/10.1016/j.mib.2018.02.004
Kimkes,
T. E. P., & Heinemann, M. (2018).
Reassessing the role of the Escherichia coli CpxAR system in
sensing surface contact. PLoS ONE,
13(11), Article e0207181. https://doi.org/10.1371/journal.pone.0207181
van
Wilderen, L. J. G. W., Brunst, H., Gustmann, H., Wachtveitl,
J., Broos, J., & Bredenbeck, J. (2018).
Cyano-tryptophans as dual infrared and fluorescence
spectroscopic labels to assess structural dynamics in
proteins. PPCP : Physical Chemistry Chemical
Physics, 20(30), 19906-19915. Article
C8CP00846A. https://doi.org/10.1039/c8cp00846a
Villarino,
L., Splan, K. E., Reddem, E., Alonso-Cotchico,
L., Gutiérrez de Souza, C., Lledós,
A., Maréchal, J.-D., Thunnissen, A.-M. W.
H., & Roelfes, G. (2018). An
Artificial Heme Enzyme for Cyclopropanation Reactions.
Angewandte Chemie - International Edition,
57(26), 7785-7789. https://doi.org/10.1002/anie.201802946
Poddar,
H., De Villiers, J., Zhang, J., Puthan Veetil, V., Raj,
H., Thunnissen, A. W. H., & Poelarends, G.
J. (2018). Structural basis for the catalytic
mechanism of ethylenediamine-N,N′-disuccinic acid lyase, a
carbon-nitrogen bond-forming enzyme with broad substrate
scope. Biochemistry, 57(26),
3752-3763. https://doi.org/10.1021/acs.biochem.8b00406
Jóźwik,
I. K., Litzenburger, M., Khatri, Y., Schifrin, A., Girhard, M.,
Urlacher, V., Thunnissen, A.-M. W. H., &
Bernhardt, R. (2018). Structural insights into oxidation of
medium-chain fatty acids and flavanone by
myxobacterial cytochrome P450 CYP267B1.
Biochemical Journal, 475(17),
2801-2817. https://doi.org/10.1042/BCJ20180402
Khatri,
Y., Jóźwik, I. K., Ringle, M., Ionescu, I. A.,
Litzenburger, M., Hutter, M. C., Thunnissen, A.-M. W.
H., & Bernhardt, R. (2018). Structure-based
engineering of steroidogenic CYP260A1 for stereo- and
regioselective hydroxylation of progesterone. ACS
chemical biology, 13(4), 1021-1028. https://doi.org/10.1021/acschembio.8b00026
2017
Zych,
K., Snoek, L. B., Elvin, M., Rodriguez, M., van der Velde, K.
J., Arends, D., Westra, H.-J., Swertz, M.
A., Poulin, G., Kammenga, J. E., Breitling, R.,
Jansen, R. C., & Li, Y. (2017).
reGenotyper: Detecting mislabeled samples in genetic
data. PLoS ONE, 12(2),
Article e0171324. https://doi.org/10.1371/journal.pone.0171324
Beyer,
N., Kulig, J. K., Fraaije, M. W., Hayes, M.
A., & Janssen, D. B. (2018). Exploring
PTDH-P450BM3 variants for the synthesis of drug metabolites.
ChemBioChem, 19(4), 326-337. Article
cbic.201700470. https://doi.org/10.1002/cbic.201700470
Wijma,
H., Fürst, M., & Janssen,
D. (2017). A Computational Library Design Protocol for
Rapid Improvement of Protein Stability: FRESCO. In N. J.
Clifton (Ed.), Protein Engineering: Methods and Protocols
(Vol. 1685, pp. 69-85). Humana Press. https://doi.org/10.1007/978-1-4939-7366-8_5
Wijma,
H. J., Janssen, D. B., & van Leeuwen, J. G.
E. (2017). Beta-glucosidase and uses
thereof. (Patent No. WO2017097897). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2017097897A1&KC=A1&FT=D&ND=3&date=20170615&DB=&locale=en_EP
Bringel,
F., Postema, C. P., Mangenot, S., Bibi-Triki, S.,
Chaignaud, P., Farhan Ul Haque, M., Gruffaz, C., Hermon, L.,
Louhichi, Y., Maucourt, B., Muller, E. E. L., Nadalig, T., Lajus,
A., Rouy, Z., Médigue, C., Barbe, V., Janssen, D.
B., & Vuilleumier, S. (2017). Genome Sequence of
the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain
GJ21. Genome Announcements,
5(30), 1-3. Article e00622-17. https://doi.org/10.1128/genomeA.00622-17
Lee,
M., Rozeboom, H. J., de Waal, P., de Jong, R.,
Dudek, H. M., & Janssen, D. B. (2017).
Metal-dependence of xylose isomerase from Piromyces sp. E2
explored by activity profiling and protein crystallography.
Biochemistry, 56(45), 5991-6005. https://doi.org/10.1021/acs.biochem.7b00777
Verhoeven,
M. D., Lee, M., Kamoen, L., van den Broek, M.,
Janssen, D. B., Daran, J.-M. G., van Maris, A. J. A., &
Pronk, J. T. (2017). Mutations in PMR1 stimulate xylose
isomerase activity and anaerobic growth on xylose of engineered
Saccharomyces cerevisiae by influencing manganese
homeostasis. Scientific Reports,
7, Article 46155. https://doi.org/10.1038/srep46155
Deyaert,
E., Wauters, L., Guaitoli, G., Konijnenberg, A., Leemans, M.,
Terheyden, S., Petrovic, A., Gallardo, R.,
Nederveen-Schippers, L. M., Athanasopoulos, P.
S., Pots, H., Van Haastert, P. J.
M., Sobott, F., Gloeckner, C. J., Efremov, R.,
Kortholt, A., & Versées, W. (2017). A
homologue of the Parkinson's disease-associated protein LRRK2
undergoes a monomer-dimer transition during GTP turnover.
Nature Communications, 8(1), 1-12.
Article 1008. https://doi.org/10.1038/s41467-017-01103-4
van
Haastert, P. J. M., Keizer-Gunnink, I.,
& Kortholt, A. (2017). Coupled Excitable Ras and
F-actin activation mediate spontaneous pseudopod formation and
directed cell movement. Molecular Biology of the
Cell, 28(7), 922-934. https://doi.org/10.1091/mbc.E16-10-0733
Liu,
Y., Lacal, J., Firtel, R. A., & Kortholt, A.
(2018). Connecting G protein signaling to
chemoattractant-mediated cell polarity and cytoskeletal
reorganization. Small GTPases,
9(4), 360-364. https://doi.org/10.1080/21541248.2016.1235390
Xu,
X., Wen, X., Veltman, D. M., Keizer-Gunnink, I.,
Pots, H., Kortholt, A., & Jin, T. (2017).
GPCR-controlled membrane recruitment of negative regulator
C2GAP1 locally inhibits Ras signaling for adaptation and long-range
chemotaxis. Proceedings of the National Academy of
Sciences of the United States of America,
114(47), 10092-10101. https://doi.org/10.1073/pnas.1703208114
Hilbi,
H., & Kortholt, A. (2017). Role of the small
GTPase Rap1 in signal transduction, cell dynamics and bacterial
infection. Small GTPases,
10(5), 336-342. https://doi.org/10.1080/21541248.2017.1331721
Deyaert,
E., Kortholt, A., & Versées, W. (2017).
The LRR-Roc-COR module of the Chlorobium tepidum Roco
protein: crystallization and X-ray crystallographic
analysis. Acta Crystallographica Section F:
Structural Biology Communications , 73(9),
520-524. https://doi.org/10.1107/S2053230X17011955
Huang,
G., Willems, K., Soskine, M., Wloka, C.,
& Maglia, G. (2017). Electro-osmotic capture and
ionic discrimination of peptide and protein biomarkers with FraC
nanopores. Nature Communications,
8, 1-11. Article 935. https://doi.org/10.1038/s41467-017-01006-4
Aminipour,
Z., Khorshid, M., Bayoumi, M., Losada-Perez, P., Thoelen, R.,
Bonakdar, S., Keshvari, H., Maglia, G., Wagner, P.,
& Van der Bruggen, B. (2017). Formation and electrical
characterization of black lipid membranes in porous filter
materials. Physica Status Solidi A-Applications
and materials science, 214(9), Article
1700104. https://doi.org/10.1002/pssa.201700104
Wloka,
C., Van Meervelt, V., van Gelder, D., Danda, N., Jager, N.,
Williams, C. P., & Maglia, G. (2017).
Label-Free and Real-Time Detection of Protein Ubiquitination
with a Biological Nanopore. Acs Nano,
11(5), 4387-4394. Article acsnano.6b07760. https://doi.org/10.1021/acsnano.6b07760
Bayoumi,
M., Bayley, H., Maglia, G., & Sapra, K. T. (2017).
Multi-compartment encapsulation of communicating droplets and
droplet networks in hydrogel as a model for artificial
cells. Scientific Reports, 7,
1-11. Article 45167. https://doi.org/10.1038/srep45167
Van
Meervelt, V., Soskine, M., Singh, S., Schuurman-Wolters,
G., Wijma, H. J., Poolman,
B., & Maglia, G. (2017). Real-time
conformational changes and controlled orientation of native
proteins inside a protein nanoreactor. Journal of
the American Chemical Society, 139(51),
18640-18646. Article jacs.7b10106. https://doi.org/10.1021/jacs.7b10106
Loveridge,
E. J., Hroch, L., Hughes, R. L., Williams, T., Davies, R. L.,
Angelastro, A., Luk, L. Y. P., Maglia, G., &
Allemann, R. K. (2017). Reduction of Folate by Dihydrofolate
Reductase from Thermotoga maritima.
Biochemistry, 56(13), 1879-1886.
Article acs.biochem.6b01268. https://doi.org/10.1021/acs.biochem.6b01268
Willems,
K., Van Meervelt, V., Wloka, C., & Maglia,
G. (2017). Single-molecule nanopore enzymology.
Philosophical Transactions of the Royal Society of
London. Series B: Biological Sciences,
372(1726), Article 20160230. https://doi.org/10.1098/rstb.2016.0230
Cozzoli,
L., Gjonaj, L., Stuart, M. C. A., Poolman,
B., & Roelfes, G. (2018). Responsive
DNA G-quadruplex micelles. Chemical communications
(Cambridge, England), 54, 260-263. https://doi.org/10.1039/c7cc07899d
Franken,
L., Oostergetel, G., Pijning, T., Puri, P., Arkhipova,
V. I., Boekema, E., Poolman, B., & Guskov,
A. (2017). A general mechanism of ribosome
dimerization revealed by single-particle cryo-electron
microscopy. Nature Communications,
8, Article 722. https://doi.org/10.1038/s41467-017-00718-x
Liu,
B., Åberg, C., van Eerden, F. J., Marrink,
S., Poolman, B., & Boersma, A. J. (2017).
Design and Properties of Genetically Encoded Probes for
Sensing Macromolecular Crowding. Biophysical
Journal, 112(9), 1929-1939. https://doi.org/10.1016/j.bpj.2017.04.004
Liu,
B., Poolman, B., & Boersma, A. J. (2017).
Ionic strength sensing in living cells. ACS
chemical biology, 12(10), 2510-2514. Article
acschembio.7b00348. https://doi.org/10.1021/acschembio.7b00348
Bartelds,
R., Barnoud, J., J. Boersma, A., J. Marrink, S.,
& Poolman, B. (2017). Lipid phase separation in
the presence of hydrocarbons in giant unilamellar vesicles.
AIMS Biophysics, 4(4), 528-542. https://doi.org/10.3934/biophy.2017.4.528
van
den Berg, J., Boersma, A. J., & Poolman, B.
(2017). Microorganisms maintain crowding homeostasis.
Nature Reviews Microbiology, 15,
309-318. Article nrmicro.2017.17. https://doi.org/10.1038/nrmicro.2017.17
Henderson,
R., & Poolman, B. (2017). Proton-solute
coupling mechanism of the maltose transporter from Saccharomyces
cerevisiae. Scientific Reports,
7(1), 1-12. Article 14375. https://doi.org/10.1038/s41598-017-14438-1
Schavemaker,
P. E., Śmigiel, W. M., & Poolman, B. (2017).
Ribosome surface properties may impose limits on the nature
of the cytoplasmic proteome. eLife,
6, Article eLife.30084. https://doi.org/10.7554/eLife.30084
Poolman,
B., & Noireaux, V. (2017). Synthetic Biology: From
engineering living systems to the bottom=up construction of
synthetic cells. In J. van Doorn, J. Luirink, J. van der
Oost, B. Oudega, L. Robertson, H. Smit, P. Willemsen, & C.
Biemans (Eds.), Mighty Microbes: the amazing world of
microorganisms (1 ed., Vol. 1, pp. 215-217). Microcanon
Foundation. https://www.noireauxlab.org/
Arkhipova,
V. I., Guskov, A., & Slotboom, D.
(2017). Analysis of the quality of crystallographic data and
the limitations of structural models. The Journal
of General Physiology, 149(12). https://doi.org/10.1085/jgp.201711852
Monjas,
L., Swier, L. J. Y. M., Setyawati,
I., Slotboom, D. J., & Hirsch, A. K.
H. (2017). Dynamic combinatorial chemistry to identify
binders of ThiT, an S-component of the energy-coupling factor
transporter for thiamine. ChemMedChem,
12(20), 1693-1696. https://doi.org/10.1002/cmdc.201700440
Swier,
L. J. Y. M., Monjas, L., Reeßing, F., Oudshoorn, R. C.,
Aisyah, A., Primke, T., Bakker, M. M., Van Olst, E., Ritschel,
T., Faustino, I., Marrink, S. J.,
Hirsch, A. K. H., & Slotboom, D. J. (2017).
Insight into the complete substrate-binding pocket of ThiT by
chemical and genetic mutations.
MedChemCommun, 8(5), 1121-1130. https://doi.org/10.1039/C7MD00079K
Baumgarten,
T., Schlegel, S., Wagner, S., Löw, M., Eriksson, J., Bonde,
I., Herrgård, M. J., Heipieper, H. J., Nørholm, M. H.
H., Slotboom, D. J., & de Gier, J.-W. (2017).
Isolation and characterization of the E. coli membrane
protein production strain Mutant56(DE3).
Scientific Reports, 7, 1-14. Article
45089. https://doi.org/10.1038/srep45089
Jaehme,
M., Singh, R., Garaeva, A. A., Duurkens, R. H.,
& Slotboom, D.-J. (2017). PnuT uses a facilitated
diffusion mechanism for thiamine uptake. Journal
of general physiology, 150(1), 41-50. Article
jgp.201711850. https://doi.org/10.1085/jgp.201711850
Goudsmits,
J. M. H., van Oijen, A. M., & Slotboom, D.
J. (2017). Single-Molecule Fluorescence Studies of
Membrane Transporters Using Total Internal Reflection
Microscopy. Methods in Enzymology,
594, 101-121. https://doi.org/10.1016/bs.mie.2017.05.009
Goudsmits,
J. M. H., Slotboom, D. J., & van Oijen, A.
M. (2017). Single-molecule visualization of
conformational changes and substrate transport in the vitamin B-12
ABC importer BtuCD-F. Nature
Communications, 8, Article 1652. https://doi.org/10.1038/s41467-017-01815-7
Lolkema,
J., & Slotboom, D. (2017). Structure and
elevator mechanism of the Na+-citrate transporter CitS.
Current Opinion in Structural Biology,
45, 1-9. https://doi.org/10.1016/j.sbi.2016.10.004
Hjelm,
A., Karyolaimos, A., Zhang, Z., Rujas, E., Vikström, D.,
Slotboom, D. J., & de Gier, J.-W. (2017).
Tailoring Escherichia coli for the L-rhamnose PBAD
promoter-based production of membrane and secretory
proteins. ACS Synthetic Biology,
6(6), 985-994. Article acssynbio.6b00321. https://doi.org/10.1021/acssynbio.6b00321
Lohse,
J., Swier, L. J. Y. M., Oudshoorn, R. C., Médard,
G., Kuster, B., Slotboom, D. J., & Witte, M.
D. (2017). Targeted Diazotransfer Reagents Enable
Selective Modification of Proteins with Azides.
BIOCONJUGATE CHEMISTRY, 28(4),
913-917. https://doi.org/10.1021/acs.bioconjchem.7b00110
Gati,
C., Stetsenko, A., Slotboom, D., Scheres,
S., & Guskov, A. (2017). The structural
basis of proton driven zinc transport by ZntB.
Nature Communications, 8, Article
1313. https://doi.org/10.1038/s41467-017-01483-7
Kuipers,
G., Karyolaimos, A., Zhang, Z., Ismail, N., Trinco,
G., Vikstrom, D., Slotboom, D. J., & de
Gier, J.-W. (2017). The tunable pReX expression vector
enables optimizing the T7-based production of membrane and
secretory proteins in E. coli. Microbial Cell
Factories, 16, Article 226. https://doi.org/10.1186/s12934-017-0840-4
Gangoiti,
J., Pijning, T., & Dijkhuizen,
L. (2018). Biotechnological potential of novel
glycoside hydrolase family 70 enzymes synthesizing α-glucans
from starch and sucrose. Biotechnology
Advances, 36, 196-207. https://doi.org/10.1016/j.biotechadv.2017.11.001
Figueroa-Lozano,
S., Valk-Weeber, R. L., van Leeuwen, S.
S., Dijkhuizen, L., & de Vos,
P. (2018). Dietary N-glycans from Bovine Lactoferrin
and TLR Modulation. Molecular Nutrition & Food
Research, 62(2), Article 1700389. https://doi.org/10.1002/mnfr.201700389
Montersino,
S., te Poele, E., Orru, R., Westphal, A. H.,
Barendregt, A., Heck, A. J. R., van der Geize, R.,
Dijkhuizen, L., Mattevi, A., & van Berkel, W. J. H.
(2017). 3-Hydroxybenzoate 6-Hydroxylase from Rhodococcus
jostii RHA1 Contains a Phosphatidylinositol Cofactor.
Frontiers in Microbiology, 8, 1-11.
Article 1110. https://doi.org/10.3389/fmicb.2017.01110
Gangoiti
Muñecas, J., van Leeuwen, S. S.,
Gerwig, G. J., Duboux, S., Vafiadi, C., Pijning,
T., & Dijkhuizen, L. (2017).
4,3-α-Glucanotransferase, a novel reaction specificity
in glycoside hydrolase family 70 and clan GH-H.
Scientific Reports, 7, 1-15. Article
39761. https://doi.org/10.1038/srep39761
Dijkhuizen,
L., Gangoiti Muñecas, J., van
Leeuwen, S. S., Vafeiadi, C., & Duboux, S. (2017). Alpha glucans. (Patent No.
WO2017207663). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2017207663A1&KC=A1&FT=D&ND=3&date=20171207&DB=&locale=en_EP
Sarian,
F. D., Janeček, Š., Pijning, T., Ihsanawati,
Nurachman, Z., Radjasa, O. K., Dijkhuizen, L.,
Natalia, D., & van der Maarel, M. J. E. C. (2017).
A new group of glycoside hydrolase family 13 α-amylases
with an aberrant catalytic triad. Scientific
Reports, 7, Article 44230. https://doi.org/10.1038/srep44230
Yin,
H., Pijning, T., Meng, X., Dijkhuizen,
L., & van Leeuwen, S. S. (2017).
Biochemical characterization of the functional roles of
residues in the active site of the β-galactosidase from
Bacillus circulans ATCC 31382.
Biochemistry, 56(24), 3109-3118. https://doi.org/10.1021/acs.biochem.7b00207
Gangoiti
Muñecas, J., van Leeuwen, S. S.,
Dijkhuizen, L., Vafeiadi, C., & Lamothe, L. (2017).
Branched alpha glucans. (Patent No.
WO2017046040). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2017046040A1&KC=A1&FT=D&ND=3&date=20170323&DB=&locale=en_EP
te
Poele, E. M., Valk, V., Devlamynck, T., van Leeuwen,
S. S., & Dijkhuizen, L. (2017).
Catechol glucosides act as donor/acceptor substrates of
glucansucrase enzymes of Lactobacillus reuteri.
Applied Microbiology and Biotechnology,
101(11), 4495-4505. https://doi.org/10.1007/s00253-017-8190-z
Meng,
X., Pijning, T., Tietema, M., Dobruchowska, J. M.,
Yin, H., Gerwig, G. J., Kralj, S., &
Dijkhuizen, L. (2017). Characterization of the
glucansucrase GTF180 W1065 mutant enzymes producing polysaccharides
and oligosaccharides with altered linkage composition.
Food Chemistry, 217, 81-90. https://doi.org/10.1016/j.foodchem.2016.08.087
Gangoiti,
J., Lamothe, L., van Leeuwen, S. S., Vafiadi,
C., & Dijkhuizen, L. (2017).
Characterization of the Paenibacillus beijingensis DSM 24997
GtfD and its glucan polymer products representing a new glycoside
hydrolase 70 subfamily of 4,6-α-glucanotransferase
enzymes. PLoS ONE, 12(4),
Article e0172622. https://doi.org/10.1371/journal.pone.0172622
Gangoiti
Muñecas, J., Meng, X., Lamerts van Bueren,
A., & Dijkhuizen, L. (2017). Draft
Genome Sequence of Lactobacillus reuteri 121, a Source of
α-Glucan and β-Fructan Exopolysaccharides.
Genome Announcements, 5(10), 1-2.
Article e01691-16. https://doi.org/10.1128/genomeA.01691-16
Yin,
H., Pijning, T., Meng, X., Dijkhuizen,
L., & van Leeuwen, S. S. (2017).
Engineering of the Bacillus circulans β-galactosidase
product specificity. Biochemistry,
56(5), 704-711. https://doi.org/10.1021/acs.biochem.7b00032
Ceniceros,
A., Dijkhuizen, L., Petrusma, M., & Medema, M. H.
(2017). Genome-based exploration of the specialized metabolic
capacities of the genus Rhodococcus. BMC
Genomics, 18(1), 1-16. Article 593. https://doi.org/10.1186/s12864-017-3966-1
Gangoiti,
J., van Leeuwen, S. S., Meng, X., Duboux, S.,
Vafiadi, C., Pijning, T., & Dijkhuizen,
L. (2017). Mining novel starch-converting Glycoside
Hydrolase 70 enzymes from the Nestlé Culture Collection genome
database: The Lactobacillus reuteri NCC 2613 GtfB.
Scientific Reports, 7(1), Article
9947. https://doi.org/10.1038/s41598-017-07190-z
Frasch,
H.-J., Leeuwen, S. S. V., & Dijkhuizen,
L. (2017). Molecular and biochemical characteristics
of the inulosucrase HugO from Streptomyces viridochromogenes
DSM40736 (Tü494).
Microbiology-Reading, 163(7),
1030-1041. https://doi.org/10.1099/mic.0.000493
Ceniceros,
A., Dijkhuizen, L., & Petrusma, M. (2017).
Molecular characterization of a Rhodococcus jostii RHA1
γ-butyrolactone(-like) signalling molecule and its main
biosynthesis gene gblA. Scientific
Reports, 7(1), 1-13. Article 17743. https://doi.org/10.1038/s41598-017-17853-6
Lammerts
van Bueren, A., Mulder, M., Leeuwen, S.
V., & Dijkhuizen, L. (2017).
Prebiotic galactooligosaccharides activate mucin and pectic
galactan utilization pathways in the human gut symbiont Bacteroides
thetaiotaomicron. Scientific Reports,
7, 1-13. Article 40478. https://doi.org/10.1038/srep40478
Yin,
H., Bultema, J. B., Dijkhuizen, L., & van
Leeuwen, S. S. (2017). Reaction kinetics and
galactooligosaccharide product profiles of the
β-galactosidases from Bacillus circulans, Kluyveromyces lactis
and Aspergillus oryzae. Food
Chemistry, 225, 230-238. Article
j.foodchem.2017.01.030. https://doi.org/10.1016/j.foodchem.2017.01.030
Gerwig,
G. J., Te Poele, E. M., Dijkhuizen,
L., & Kamerling, J. P. (2017). Structural analysis
of rebaudioside A derivatives obtained by Lactobacillus reuteri 180
glucansucrase-catalyzed trans-α-glucosylation.
Carbohydrate Research, 440-441,
51-62. https://doi.org/10.1016/j.carres.2017.01.008
Pham,
H. T. T., Dijkhuizen, L., & van Leeuwen, S.
S. (2017). Structural characterization of glucosylated
lactose derivatives synthesized by the Lactobacillus reuteri GtfA
and Gtf180 glucansucrase enzymes. Carbohydrate
Research, 449, 59-64. https://doi.org/10.1016/j.carres.2017.07.002
Fransen,
F., van Beek, A. A., Borghuis, T., El Aidy,
S., Hugenholtz, F., van der Gaast-de Jongh, C., Savelkoul,
H. F. J., De Jonge, M. I., Boekschoten, M. V., Smidt, H.,
Faas, M. M., & de Vos, P. (2017).
Aged Gut Microbiota Contributes to Systemical Inflammaging
after Transfer to Germ-Free Mice. Frontiers in
Immunology, 8, Article 1385. https://doi.org/10.3389/fimmu.2017.01385
Koopman,
M., El Aidy, S., & MIDtrauma Consortium (2017).
Depressed gut? The microbiota-diet-inflammation trialogue in
depression. Current opinion in
psychiatry, 30(5), 369-377. https://doi.org/10.1097/YCO.0000000000000350
El
Aidy, S., Ramsteijn, A. S., Dini-Andreote,
F., van Eijk, R., Houwing, D. J., Salles, J.
F., & Olivier, J. D. A. (2017).
Serotonin transporter genotype modulates the gut microbiota
composition in young rats, an effect augmented by early life
stress. Frontiers in cellular
neuroscience, 11, Article 222. https://doi.org/10.3389/fncel.2017.00222
Fransen,
F., van Beek, A. A., Borghuis, T., Meijer, B.,
Hugenholtz, F., van der Gaast-de Jongh, C., Savelkoul, H. F., de
Jonge, M. I., Faas, M. M., Boekschoten, M. V., Smidt,
H., El Aidy, S., & de Vos, P. (2017).
The Impact of Gut Microbiota on Gender-Specific Differences
in Immunity. Frontiers in Immunology,
8, Article 754. https://doi.org/10.3389/fimmu.2017.00754
Vinke,
P. C., El Aidy, S., & van Dijk,
G. (2017). The role of supplemental complex dietary
carbohydrates and gut microbiota in promoting cardiometabolic and
immunological health in obesity: Lessons from healthy non-obese
individuals. Frontiers in nutrition,
4, Article 34. https://doi.org/10.3389/fnut.2017.00034
Fransen,
F., Sahasrabudhe, N. M., Elderman, M., Bosveld,
M., El Aidy, S., Hugenholtz, F., Borghuis,
T., Kousemaker, B., Winkel, S., Gaast-de Jongh, C. E.,
Jonge, M. I. D., Boekschoten, M. V., Smidt, H., Schols, H.
A., & de Vos, P. (2017). β2→
1-fructans modulate the immune system in vivo by direct interaction
with the mucosa in a microbiota-independent fashion.
Frontiers in Immunology, 8, Article
154. https://doi.org/10.3389/fimmu.2017.00154
Kumar,
S., de Boer, R., & van der Klei, I.
J. (2018). Yeast cells contain a heterogeneous
population of peroxisomes that segregate asymmetrically during cell
division. Journal of Cell Science,
131(3), Article jcs.207522. https://doi.org/10.1242/jcs.207522
van
der Klei, I., & Veenhuis, M. (2017). Microscopes:
Essential instruments in microbiology research. In J. van
Doorn, J. Luirink, J. van der Oost, B. Oudega, L. Robertson, H.
Smit, P. Willemsen, & C. Biemans (Eds.), Mighty microbes:
the amazing world of microorganisms (1 ed., Vol. 1, pp.
41-44). Microcanon Foundation.
Wroblewska,
J. P., Cruz-Zaragoza, L. D., Yuan, W., Schummer, A., Chuartzman, S.
G., de Boer, R., Oeljeklaus, S., Schuldiner, M.,
Zalckvar, E., Warscheid, B., Erdmann, R., & van der Klei,
I. J. (2017). Saccharomyces cerevisiae cells lacking
Pex3 contain membrane vesicles that harbor a subset of peroxisomal
membrane proteins. Biochimica et Biophysica Acta -
Molecular Cell Research, 1864(10), 1656-1667.
Article bbamcr.2017.05.021. https://doi.org/10.1016/j.bbamcr.2017.05.021
Alessandri,
R., Uusitalo, J. J., De Vries, A. H., Havenith,
R. W. A., & Marrink, S. J. (2017).
Bulk Heterojunction Morphologies with Atomistic Resolution
from Coarse-Grain Solvent Evaporation Simulations.
Journal of the American Chemical Society,
139 (10), 3697–3705. Article jacs.6b11717. https://doi.org/10.1021/jacs.6b11717
Gu,
R.-X., Ingólfsson, H. I., De Vries, A. H.,
Marrink, S. J., & Tieleman, D. P. (2017).
Ganglioside-Lipid and Ganglioside-Protein Interactions
Revealed by Coarse-Grained and Atomistic Molecular Dynamics
Simulations. Journal of Physical Chemistry
B, 121(15), 3262–3275. Article
jpcb.6b07142. https://doi.org/10.1021/acs.jpcb.6b07142
Kanduc,
M., Schlaich, A., de Vries, A. H., Jouhet, J.,
Marechal, E., Deme, B., Netz, R. R., & Schneck, E. (2017).
Tight cohesion between glycolipid membranes results from
balanced water-headgroup interactions. Nature
Communications, 8, Article 14899. https://doi.org/10.1038/ncomms14899
Clauss-Lendzian,
E., Vaishampayan, A., de Jong, A., Landau, U., Meyer,
C., Kok, J., & Grohmann, E. (2018). Stress
response of a clinical Enterococcus faecalis isolate subjected to a
novel antimicrobial surface coating.
Microbiological Research, 207,
53-64. https://doi.org/10.1016/j.micres.2017.11.006
Tarazanova,
M., Huppertz, T., Beerthuyzen, M., van Schalkwijk, S., Janssen, P.,
Wels, M., Kok, J., & Bachmann, H. (2017).
Cell Surface Properties of Lactococcus lactis Reveal Milk
Protein Binding Specifically Evolved in Dairy Isolates.
Frontiers in Microbiology, 8,
Article 1691. https://doi.org/10.3389/fmicb.2017.01691
Solopova,
A., Kok, J., & Kuipers, O. P. (2017).
Disruption of a transcriptional repressor by an IS-element
integration leads to the activation of a novel silent cellobiose
transporter in Lactococcus lactis MG1363. Applied
and environmental microbiology, 83(23),
Article e01279-17. https://doi.org/10.1128/AEM.01279-17
van
der Meulen, S. B., de Jong, A., & Kok,
J. (2017). Early Transcriptome Response of Lactococcus
lactis to Environmental Stresses Reveals Differentially Expressed
Small Regulatory RNAs and tRNAs. Frontiers in
Microbiology, 8, Article 1704. https://doi.org/10.3389/fmicb.2017.01704
Visweswaran,
G. R. R., Kurek, D., Szeliga, M., Pastrana, F.
R., Kuipers, O. P., Kok, J.,
& Buist, G. (2017). Expression of prophage-encoded
endolysins contributes to autolysis of Lactococcus lactis.
Applied Microbiology and Biotechnology,
101(3), 1099-1110. https://doi.org/10.1007/s00253-016-7822-z
van
Gijtenbeek, L. A., & Kok, J. (2017).
Illuminating Messengers: An Update and Outlook on RNA
Visualization in Bacteria. Frontiers in
Microbiology, 8, Article 1161. https://doi.org/10.3389/fmicb.2017.01161
Kok,
J., van Gijtenbeek, L. A., de Jong, A., van der
Meulen, S. B., Solopova, A., & Kuipers, O. P.
(2017). The evolution of gene regulation research in
Lactococcus lactis. FEMS Microbiology
Reviews, 41(Supp_1), S220-S243. https://doi.org/10.1093/femsre/fux028
Perez,
M., Ladero, V., del Rio, B., Redruello, B., de Jong,
A., Kuipers, O., Kok, J., Martin,
M. C., Fernandez, M., & Alvarez, M. A. (2017). The
Relationship among Tyrosine Decarboxylase and Agmatine Deiminase
Pathways in Enterococcus faecalis. Frontiers in
Microbiology, 8, 1-9. Article 2107. https://doi.org/10.3389/fmicb.2017.02107
Urban,
J. H., Moosmeier, M. A., Aumüller, T., Thein, M., Bosma, T.,
Rink, R., Groth, K., Zulley, M., Siegers, K., Tissot, K.,
Moll, G. N., & Prassler, J. (2017). Phage display
and selection of lanthipeptides on the carboxy-terminus of the
gene-3 minor coat protein. Nature
Communications, 8(1), Article 1500. https://doi.org/10.1038/s41467-017-01413-7
Kuipers,
A., de Vries, L., de Vries, M. P., Rink, R., Bosma,
T., & Moll, G. N. (2017).
Semi-microbiological synthesis of an active
lysinoalanine-bridged analog of glucagon-like-peptide-1.
Peptides, 91, 33-39. https://doi.org/10.1016/j.peptides.2017.03.004
Viggiano,
A., Salo, O., Ali, H., Szymanski, W., Lankhorst, P.
P., Nygård, Y., Bovenberg, R. A. L., &
Driessen, A. J. M. (2018). Pathway for the
Biosynthesis of the Pigment Chrysogine by Penicillium
chrysogenum. Applied and environmental
microbiology, 84(4), Article e02246-17. https://doi.org/10.1128/AEM.02246-17
Bovenberg,
R. A. L., Muller, U. M., Driessen, A. J. M.,
Pohl, C., & Zwahlen, R. D. (2017). Mbth-like proteins in eukaryotic nrps-catalyzed
processes. (Patent No. WO2017178624). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2017178624A1&KC=A1&FT=D&ND=3&date=20171019&DB=&locale=en_EP
Guzmán-Chávez,
F., Salo, O., Nygård, Y., Lankhorst, P. P., Bovenberg,
R. A. L., & Driessen, A. J. M. (2017).
Mechanism and regulation of sorbicillin biosynthesis by
Penicillium chrysogenum. Microbial
Biotechnology, 10(4), 958-968. https://doi.org/10.1111/1751-7915.12736
Exterkate,
M., Caforio, A., Stuart, M. C. A., &
Driessen, A. J. M. (2018). Growing membranes in vitro
by continuous phospholipid biosynthesis from free fatty
acids. ACS Synthetic Biology,
7(1), 153-165. Article acssynbio.7b00265. https://doi.org/10.1021/acssynbio.7b00265
Nijland,
J. G., Shin, H. Y., de Waal, P. P., Klaassen, P.,
& Driessen, A. J. M. (2018). Increased xylose
affinity of Hxt2 through gene shuffling of hexose transporters in
Saccharomyces cerevisiae. Journal of Applied
Microbiology, 124(2), 503-510. Article
jam.13670. https://doi.org/10.1111/jam.13670
Caforio,
A., & Driessen, A. J. M. (2017). Archaeal
phospholipids: Structural properties and biosynthesis.
Biochimica et Biophysica Acta - Molecular and Cell
Biology of Lipids, 1862(11), 1325-1339. https://doi.org/10.1016/j.bbalip.2016.12.006
Nijland,
J. G., Shin, H. Y., Boender, L. G. M., de Waal, P. P.,
Klaassen, P., & Driessen, A. J. M. (2017).
Improved xylose metabolism by a CYC8 mutant of Saccharomyces
cerevisiae. Applied and environmental
microbiology, 83(11), Article e00095-17. https://doi.org/10.1128/AEM.00095-17
Derntl,
C., Guzmán-Chávez, F., Mello-de-Sousa, T. M., Busse,
H.-J., Driessen, A. J. M., Mach, R. L., &
Mach-Aigner, A. R. (2017). In Vivo Study of the
Sorbicillinoid Gene Cluster in Trichoderma reesei.
Frontiers in Microbiology, 8,
Article 2037. https://doi.org/10.3389/fmicb.2017.02037
Wegener,
M., Hansen, M. J., Driessen, A. J. M.,
Szymanski, W., & Feringa, B. L. (2017).
Photocontrol of Antibacterial Activity: Shifting from UV to
Red Light Activation. Journal of the American
Chemical Society, 139(49), 17979-17986. https://doi.org/10.1021/jacs.7b09281
Ren,
S., Caforio, A., Yang, Q., Sun, B., Yu, F., Zhu, X., Wang, J., Dou,
C., Fu, Q., Huang, N., Sun, Q., Nie, C., Qi, S., Gong, X., He, J.,
Wei, Y., Driessen, A. J. M., & Cheng, W. (2017).
Structural and mechanistic insights into the biosynthesis of
CDP-archaeol in membranes. Cell
research, 27, 1378-1391. Article cr.2017.122.
https://doi.org/10.1038/cr.2017.122
Shin,
H. Y., Nijland, J. G., de Waal, P. P., &
Driessen, A. J. M. (2017). The Amino-Terminal Tail of
Hxt11 Confers Membrane Stability to the Hxt2 Sugar Transporter and
Improves Xylose Fermentation in the Presence of Acetic Acid.
Biotechnology and Bioengineering,
114(9), 1937-1945. https://doi.org/10.1002/bit.26322
Prabudiansyah,
I., & Driessen, A. J. M. (2017). The
Canonical and Accessory Sec System of Gram-positive
Bacteria. In F. Bagnoli, & R. Rappuoli (Eds.),
Protein and Sugar Export and Assembly in Gram-positive
Bacteria (pp. 45-67). (Current Topics in Microbiology and
Immunology; Vol. 404). Springer. https://doi.org/10.1007/82_2016_9
Dockerty,
P., Edens, J. G., Tol, M. B., Morales Angeles, D., Domenech Pena,
A., Liu, Y., Hirsch, A. K. H., Veening, J.-W.,
Scheffers, D.-J., & Witte, M. D. (2017).
Bicyclic enol cyclocarbamates inhibit penicillin-binding
proteins. Organic & Biomolecular
Chemistry, 15(4), 894-910. https://doi.org/10.1039/c6ob01664b
Król,
E., de Sousa Borges, A., Kopacz, M., & Scheffers,
D.-J. (2017). Metal-dependent SpoIIE oligomerization
stabilizes FtsZ during asymmetric division in Bacillus
subtilis. PLoS ONE, 12(3),
Article e0174713. https://doi.org/10.1371/journal.pone.0174713
Morales
Angeles, D., Liu, Y., Hartman, A. M., Borisova, M., de
Sousa Borges, A., de Kok, N., Beilharz, K., Veening,
J.-W., Mayer, C., Hirsch, A. K. H., &
Scheffers, D.-J. (2017). Pentapeptide-rich
peptidoglycan at the Bacillus subtilis cell-division site.
Molecular Microbiology, 104(2),
319-333. https://doi.org/10.1111/mmi.13629
Soibelmann
Glock Lorenzoni, A., Dantas, G., Bergsma, T., Ferreira, H.,
& Scheffers, D. (2017). Xanthomonas citri MinC
Oscillates from Pole to Pole to Ensure Proper Cell Division and
Shape. Frontiers in Microbiology,
8, 1-12. Article 1352. https://doi.org/10.3389/fmicb.2017.01352
Litsios,
A., Ortega, Á. D., Wit, E. C., &
Heinemann, M. (2018). Metabolic-flux dependent
regulation of microbial physiology. Current
Opinion in Microbiology, 42, 71-78. https://doi.org/10.1016/j.mib.2017.10.029
Papagiannakis,
A., Niebel, B., Wit, E., & Heinemann,
M. (2017). A CDK-independent metabolic oscillator
orchestrates the budding yeast cell cycle. Febs
Journal, 284(S1), 54. Article S.5.4-002. https://doi.org/10.1111/febs.14170
Radzikowski,
J. L., Schramke, H., & Heinemann, M. (2017).
Bacterial persistence from a system-level perspective.
Current Opinion in Biotechnology,
46, 98-105. https://doi.org/10.1016/j.copbio.2017.02.012
Heinemann,
M., & Pilpel, Y. (2017). Editorial overview:
Systems biology for biotechnology. Current Opinion
in Biotechnology, 46, iv-v. https://doi.org/10.1016/j.copbio.2017.07.001
Papagiannakis,
A., de Jonge, J. J., Zhang, Z., & Heinemann, M.
(2017). Quantitative characterization of the auxin-inducible
degron: a guide for dynamic protein depletion in single yeast
cells. Scientific Reports, 7,
Article 4704. https://doi.org/10.1038/s41598-017-04791-6
Filer,
D., Thompson, M. A., Takhaveev, V., Dobson, A. J.,
Kotronaki, I., Green, J. W. M., Heinemann, M., Tullet,
J. M. A., & Alic, N. (2017). RNA polymerase III limits
longevity downstream of TORC1. Nature,
552(7684), 263-267. https://doi.org/10.1038/nature25007
Oliveira-Souza,
W. P., Bronze, F., Broos, J., Marcondes, M. F. M.,
& Oliveira, V. (2017). On the efficient bio-incorporation
of 5-hydroxy-tryptophan in recombinant proteins expressed in
Escherichia coli with T7 RNA polymerase-based vectors.
Biochemical and Biophysical Research
Communications, 492(3), 343-348. Article
j.bbrc.2017.08.111. https://doi.org/10.1016/j.bbrc.2017.08.111
Abdulmughni,
A., Jóźwik, I. K., Brill, E., Hannemann, F.,
Thunnissen, A.-M. W. H., & Bernhardt, R. (2017).
Biochemical and structural characterization of CYP109A2, a
vitamin D3 25-hydroxylase from Bacillus megaterium.
Febs Journal, 284(22), 3881-3894. https://doi.org/10.1111/febs.14276
Borner,
T., Ramisch, S., Reddem, E. R., Bartsch, S., Vogel, A.,
Thunnissen, A.-M. W. H., Adlercreutz, P., & Grey, C.
(2017). Explaining Operational Instability of Amine
Transaminases: Substrate-Induced Inactivation Mechanism and
Influence of Quaternary Structure on Enzyme-Cofactor Intermediate
Stability. ACS Catalysis,
7(2), 1259-1269. https://doi.org/10.1021/acscatal.6b02100
van
Bezouwen, L. S., Caffarri, S., Kale, R. S., Kouřil, R.,
Thunnissen, A.-M. W. H., Oostergetel, G. T., & Boekema,
E. J. (2017). Subunit and chlorophyll organization of the
plant photosystem II supercomplex. Nature
Plants, 3, Article 17080. https://doi.org/10.1038/nplants.2017.80
2016
Arabnejad,
H., Dal Lago, M., Jekel, P. A., Floor, R. J.,
Thunnissen, A.-M. W. H., Terwisscha van Scheltinga, A.
C., Wijma, H. J., & Janssen, D. B.
(2017). A robust cosolvent-compatible halohydrin dehalogenase
by computational library design. Protein
Engineering, Design & Selection, 30(3),
175-189. https://doi.org/10.1093/protein/gzw068
Beyer,
N., Kulig, J. K., Bartsch, A., Hayes, M. A., Janssen,
D. B., & Fraaije, M. W. (2017).
P450BM3 fused to phosphite dehydrogenase allows
phosphite-driven selective oxidations. Applied
Microbiology and Biotechnology, 101,
2319-2331. https://doi.org/10.1007/s00253-016-7993-7
Nuijens,
T., Toplak, A., Van de Meulenreek , M. B. A. C., Schmidt, M.,
Goldbach, M., Janssen , D. B., & Quaedflieg, P. J.
L. M. (2016). Chemo-enzymatic peptide synthesis (CEPS) using
omniligases and selective peptiligases Efficient biocatalysts for
assembling linear and cyclic peptides and protein
conjugates. Chimica Oggi-Chemistry
Today, 34(6A), 16-19.
Toplak,
A., Arif, M. I., Wu, B., & Janssen, D. B. (2016).
Discovery and Engineering of Enzymes for Peptide Synthesis
and Activation. In R. N. Patel (Ed.), Green
Biocatalysis (pp. 397-420). Wiley. https://doi.org/10.1002/9781118828083.ch15
Nuijens,
T., Toplak, A., Quaedflieg, P. J. L. M., Drenth, J.,
Wu, B., & Janssen, D. B. (2016). Engineering
a Diverse Ligase Toolbox for Peptide Segment Condensation.
Advanced Synthesis & Catalysis,
358(24), 4041-4048. https://doi.org/10.1002/adsc.201600774
Palacio,
C. M., Crismaru, G. C., Bartsch, S., Navickas, V., Ditrich, K.,
Breuer, M., Abu, R., Woodley, J., Baldenius, K.-U., Wu, B.,
& Janssen, D. (2016). Enzymatic Network for
Production of Ether Amines From Alcohols.
Biotechnology and Bioengineering,
113(9), 1853-1861. https://doi.org/10.1002/bit.25954
Quaedflieg,
P. J. L. M., Nuijens, T., van der Laan, J. M., Janssen, D.
B., Toplak, A., & Wu, B. (2016). Peptide fragment condensation and cyclisation using
a subtilisin variant with improved synthesis over hydrolysis
ratio. (Patent No. WO2016056913). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2016056913A1&KC=A1&FT=D&ND=3&date=20160414&DB=&locale=en_EP
Toplak,
A., Nuijens, T., Quaedflieg, P. J. L. M., Wu, B., &
Janssen, D. B. (2016). Peptiligase, an Enzyme for
Efficient Chemoenzymatic Peptide Synthesis and Cyclization in
Water. Advanced Synthesis &
Catalysis, 358(13), 2140-2147. https://doi.org/10.1002/adsc.201600017
Gross,
J., Prokop, Z., Janssen, D., Faber, K., & Hall, M.
(2016). Regio- and Enantioselective Sequential Dehalogenation
of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB.
ChemBioChem, 17(15), 1437-1441. https://doi.org/10.1002/cbic.201600227
Wu,
B., Wijma, H. J., Song, L., Rozeboom, H.
J., Poloni, C., Tian, Y., Arif, M. I., Nuijens, T.,
Quaedflieg, P. J. L. M., Szymanski, W., Feringa,
B. L., & Janssen, D. B. (2016).
Versatile Peptide C-Terminal Functionalization via a
Computationally Engineered Peptide Amidase. ACS
Catalysis, 6(8), 5405-5414. https://doi.org/10.1021/acscatal.6b01062
Liu,
Y., Lacal, J., Veltman, D. M., Fusetti, F., van Haastert, P.
J. M., Firtel, R. A., & Kortholt, A.
(2016). A Gα-Stimulated RapGEF Is a Receptor-Proximal
Regulator of Dictyostelium Chemotaxis.
Developmental Cell, 37(5), 458-472.
https://doi.org/10.1016/j.devcel.2016.05.001
Skoge,
M., Wong, E., Hamza, B., Bae, A., Martel, J., Kataria, R.,
Keizer-Gunnink, I., Kortholt, A., Van
Haastert, P. J. M., Charras, G., Janetopoulos, C., &
Irimia, D. (2016). A Worldwide Competition to Compare the
Speed and Chemotactic Accuracy of Neutrophil-Like Cells.
PLoS ONE, 11(6), Article e0154491.
https://doi.org/10.1371/journal.pone.0154491
Plak,
K., Pots, H., Van Haastert, P. J.
M., & Kortholt, A. (2016). Direct
Interaction between TalinB and Rap1 is necessary for adhesion of
Dictyostelium cells. BMC Cell Biology,
17(1), 1-8. https://doi.org/10.1186/s12860-015-0078-0
Postma,
M., & van Haastert, P. J. M. (2016).
Mathematics of Experimentally Generated Chemoattractant
Gradients. Methods in Molecular
Biology, 1407, 381-396. https://doi.org/10.1007/978-1-4939-3480-5_26
Khanna,
A., Lotfi, P., Chavan, A. J., Montaño, N. M., Bolourani, P.,
Weeks, G., Shen, Z., Briggs, S. P., Pots, H.,
Van Haastert, P. J. M., Kortholt, A., &
Charest, P. G. (2016). The small GTPases Ras and Rap1 bind to
and control TORC2 activity. Scientific
Reports, 6, 1-9. Article 25823. https://doi.org/10.1038/srep25823
Rosenbusch,
K. E., & Kortholt, A. (2016).
Activation Mechanism of LRRK2 and Its Cellular Functions in
Parkinson's Disease. Parkinsons
disease, 2016, Article ID 7351985. https://doi.org/10.1155/2016/7351985
Kamp,
M. E., Liu, Y., & Kortholt, A. (2016).
Function and Regulation of Heterotrimeric G Proteins during
Chemotaxis. International Journal of Molecular
Sciences, 17(1), Article 90. https://doi.org/10.3390/ijms17010090
Guaitoli,
G., Raimondi, F., Gilsbach, B. K., Gómez-Llorente, Y.,
Deyaert, E., Renzi, F., Li, X., Schaffner, A., Jagtap, P. K. A.,
Boldt, K., von Zweydorf, F., Gotthardt, K., Lorimer, D. D., Yue,
Z., Burgin, A., Janjic, N., Sattler, M., Versées, W., Ueffing,
M., ... Gloeckner, C. J. (2016). Structural model of the
dimeric Parkinson's protein LRRK2 reveals a compact architecture
involving distant interdomain contacts.
Proceedings of the National Academy of Sciences of the
United States of America, 113(30),
E4357-E4366. https://doi.org/10.1073/pnas.1523708113
Terheyden,
S., Nederveen-Schippers, L. M., & Kortholt,
A. (2016). The unconventional G-protein cycle of LRRK2
and Roco proteins. Biochemical Society
Transactions, 44(6), 1611-1616. https://doi.org/10.1042/BST20160224
Wloka,
C., Mutter, N. L., Soskine, M., &
Maglia, G. (2016). Alpha-Helical Fragaceatoxin C
Nanopore Engineered for Double-Stranded and Single-Stranded Nucleic
Acid Analysis. Angewandte Chemie - International
Edition, 55(40), 12494-12498. https://doi.org/10.1002/anie.201606742
Serra-Batiste,
M., Ninot-Pedrosa, M., Bayoumi, M., Gairí, M., Maglia,
G., & Carulla, N. (2016). Aβ42 assembles into
specific β-barrel pore-forming oligomers in membrane-mimicking
environments. Proceedings of the National Academy
of Sciences of the United States of America,
113(39), 10866-10871. https://doi.org/10.1073/pnas.1605104113
Biesemans,
A., Soskine, M., & Maglia, G. (2016).
Controlling the Nanoscopic Confinement of Enzymes Inside ClyA
Nanopores for Single-Protein Studies. Biophysical
Journal, 110(3, Supplement 1), 518A-518A. https://doi.org/10.1016/j.bpj.2015.11.2769
Maglia,
G. (2016). Design and Engineering of Nanopores with
Emergent Functions. Biophysical
Journal, 110(3), 536A-536A. https://doi.org/10.1016/j.bpj.2015.11.2871
Franceschini,
L., Brouns, T., Willems, K., Carlon, E., & Maglia,
G. (2016). DNA Translocation through Nanopores at
Physiological Ionic Strengths Requires Precise Nanoscale
Engineering. Acs Nano, 10(9),
8394-8402. https://doi.org/10.1021/acsnano.6b03159
Vega,
M., Perez, M. S., Granell, P., Golmar, F., Wloka,
C., Maglia, G., Dieguez, M. J., Del Valle, E.
M., Lasorsa, C., & Lerner, B. (2016). Effect of butanol
and salt concentration on solid-state nanopores resistance.
Cogent chemistry, 2, Article
1225345. https://doi.org/10.1080/23312009.2016.1225345
Maglia,
G., Soskine, M., Biesemans, A., Meervelt, V., &
Poolman, B. (2016). Nanopores with
internal protein adaptors. (Patent No.
WO2016166232). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2016166232A1&KC=A1&FT=D&ND=3&date=20161020&DB=&locale=en_EP
Scheepers,
G. H., Lycklama A Nijeholt, J. A., & Poolman, B.
(2016). An updated structural classification of
substrate-binding proteins. FEBS
Letters, 590(23), 4393-4401. https://doi.org/10.1002/1873-3468.12445
Popov-Čeleketić,
D., Bianchi, F., Ruiz, S. J., Meutiawati, F.,
& Poolman, B. (2016). A Plasma Membrane
Association Module in Yeast Amino Acid Transporters.
The Journal of Biological Chemistry,
291(31), 16024-16037. https://doi.org/10.1074/jbc.M115.706770
Bianchi,
F., Klooster, J. S. V. ., Ruiz, S. J., Luck,
K., Pols, T., Urbatsch, I. L., & Poolman, B.
(2016). Asymmetry in inward- and outward-affinity constant of
transport explain unidirectional lysine flux in Saccharomyces
cerevisiae. Scientific Reports,
6, 1-13. Article 31443. https://doi.org/10.1038/srep31443
van
den Berg, J., & Poolman, B. (2016).
Compartmental Volume Regulation of E. Coli under Various
Growth Conditions. Biophysical
Journal, 110(3), 35A-35A. https://doi.org/10.1016/j.bpj.2015.11.259
Ruiz,
S. J., Schuurman-Wolters, G. K., & Poolman, B.
(2016). Crystal Structure of the Substrate-Binding Domain
from Listeria monocytogenes Bile-Resistance Determinant
BilE. Liquid Crystals, 6(12),
1-16. Article cryst6120162. https://doi.org/10.3390/cryst6120162
van
den Berg, J., Galbiati, H., Rasmussen, A., Miller, S., &
Poolman, B. (2016). On the mobility, membrane location
and functionality of mechanosensitive channels in Escherichia
coli. Scientific Reports, 6,
Article 32709 . https://doi.org/10.1038/srep32709
van
Gijtenbeek, L. A., Robinson, A., van Oijen , A.,
Poolman, B., & Kok, J. (2016). On the Spatial
Organization of mRNA, Plasmids, and Ribosomes in a Bacterial Host
Overexpressing Membrane Proteins. PLoS
genetics, 12(12), 1-28. Article e1006523. https://doi.org/10.1371/journal.pgen.1006523
Boersma,
A., Liu, B., Åberg, C., & Poolman,
B. (2016). Quantification of Macromolecular Crowding
in Living Cells. Biophysical Journal,
110(3), 368A-368A. https://doi.org/10.1016/j.bpj.2015.11.1984
Ejby,
M., Fredslund, F., Andersen, J. M., Zagar, A. V., Henriksen, J. R.,
Andersen, T. L., Svensson, B., Slotboom, D. J., &
Abou Hachem, M. (2016). An ATP Binding Cassette Transporter
Mediates the Uptake of alpha-(1,6)-Linked Dietary Oligosaccharides
in Bifidobacterium and Correlates with Competitive Growth on These
Substrates. The Journal of Biological
Chemistry, 291(38), 20220-20231. https://doi.org/10.1074/jbc.M116.746529
Guskov,
A., Jensen, S., Faustino, I., Marrink, S.
J., & Slotboom, D. J. (2016). Coupled
binding mechanism of three sodium ions and aspartate in the
glutamate transporter homologue GltTk. Nature
Communications, 7, 1-6. Article 13420. https://doi.org/10.1038/ncomms13420
Monjas
, L., Swier, L. J. Y. M., de Voogd, A. R., Oudshoorn,
R. C., Hirsch, A. K. H., & Slotboom, D.
J. (2016). Design and synthesis of thiamine analogues
to study their binding to the ECF transporter for thiamine in
bacteria. MedChemCommun,
7(5), 966-971. https://doi.org/10.1039/c6md00022c
Jähme,
M., Guskov, A., & Slotboom, D. J.
(2016). Pnu Transporters: Ain't They SWEET?
Trends in Biochemical Sciences,
41(2), 117-118. https://doi.org/10.1016/j.tibs.2015.11.013
Guskov,
A., & Slotboom, D. (2016). Size
exclusion chromatography with multi-angle laser light scattering
(SEC-MALLS) to determine protein oligomeric states. In E.
Pebay-Peyroula, H. Nury, F. Parcy, R. W. H. Ruigrok, C. Ziegler,
& L. F. Cugliandolo (Eds.), From molecules to living
organisms: an interplay between biology and physics: Lecture Notes
of the Les Houches School of Physics: Volume 102, July 2014
(pp. 169-183). (Lecture Notes of the Les Houches School of Physics;
Vol. 102). Oxford University Press. https://doi.org/10.1093/acprof:oso/9780198752950.003.0006
Swier,
L. J. Y. M., Guskov, A., & Slotboom,
D. J. (2016). Structural insight in the toppling
mechanism of an energy-coupling factor transporter.
Nature Communications, 7, 1-11.
Article 11072. https://doi.org/10.1038/ncomms11072
Bai,
Y., Gangoiti , J., Dijkstra, B. W., Dijkhuizen,
L., & Pijning, T. (2017). Crystal
Structure of 4,6-α-Glucanotransferase Supports Diet-Driven
Evolution of GH70 Enzymes from α-Amylases in Oral
Bacteria. Structure, 25(2),
231-242. https://doi.org/10.1016/j.str.2016.11.023
Valk,
V., Lammerts van Bueren, A., van der Kaaij, R.
M., & Dijkhuizen, L. (2016).
Carbohydrate Binding Module 74 is a novel starch binding
domain associated with large and multi-domain α-amylase
enzymes. Febs Journal,
283(12), 2354-2368. Article 13745. https://doi.org/10.1111/febs.13745
Valk,
V., van der Kaaij, R. M., & Dijkhuizen,
L. (2016). Characterization of the starch-acting
MaAmyB enzyme from Microbacterium aurum B8.A representing the novel
subfamily GH13_42 with an unusual, multi-domain
organization. Scientific Reports,
6, 1-12. Article srep36100. https://doi.org/10.1038/srep36100
van
Leeuwen, S. S., Kuipers, B. J. H., Dijkhuizen,
L., & Kamerling, J. P. (2016). Comparative
structural characterization of 7 commercial galacto-oligosaccharide
(GOS) products. Carbohydrate Research,
425, 48-58. https://doi.org/10.1016/j.carres.2016.03.006
van
Leeuwen, S. S., Kuipers, B. J. H., Dijkhuizen,
L., & Kamerling, J. P. (2016). Corrigendum to
“1H NMR analysis of the lactose/β-galactosidase-derived
galacto-oligosaccharide components of Vivinal® GOS up to
DP5” [Carbohydr. Res. 400 (2014) 59–73].
Carbohydrate Research, 419, 69-70.
https://doi.org/10.1016/j.carres.2015.12.004
Pijning,
T., Bai, Y., Gangoiti Muñecas, J.,
& Dijkhuizen, L. (2016). Crystal Structure of
a 4,6-α-Glucanotransferase Supports Diet-Driven Evolution of
GH70 Enzymes from α-Amylases in Oral Bacteria.
Poster session presented at ALAMY, Smolenice, Slovakia.
Figueroa,
S., Dijkhuizen, L., Valk, R., van Leeuwen,
S., & de Vos, P. (2016). Dietary N- and O-glycans
from cow milk and TLR modulation. European Journal
of Immunology, 46, 479-479.
Devlamynck,
T., Te Poele, E. M., Meng, X., van Leeuwen, S.
S., & Dijkhuizen, L. (2016).
Glucansucrase Gtf180-Delta N of Lactobacillus reuteri 180:
enzyme and reaction engineering for improved glycosylation of
non-carbohydrate molecules. Applied Microbiology
and Biotechnology, 100(17), 7529-7539. https://doi.org/10.1007/s00253-016-7476-x
Te
Poele, E. M., Grijpstra, P., van Leeuwen,
S. S., & Dijkhuizen, L. (2016).
Glucosylation of catechol with the GTFA glucansucrase enzyme
from Lactobacillus reuteri and sucrose as donor substrate.
BIOCONJUGATE CHEMISTRY, 27(4),
937-946. https://doi.org/10.1021/acs.bioconjchem.6b00018
Bai,
Y., Böger, M., van der Kaaij, R. M.,
Woortman, A. J. J., Pijning, T., van
Leeuwen, S. S., Lammerts van Bueren, A.,
& Dijkhuizen, L. (2016). Lactobacillus reuteri
strains convert starch and maltodextrins into
homo-exopolysaccharides using an extracellular and cell-associated
4,6-α-glucanotransferase. Journal of
Agricultural and Food Chemistry, 64(14),
2941-2952. https://doi.org/10.1021/acs.jafc.6b00714
te
Poele, E. M., Dijkhuizen, L., Gerwig, G.
J., & Kamerling, J. P. (2016). Methods for the enzymatic modification of steviol
glycosides, modified steviol glycosides obtainable thereby, and the
use thereof as sweeteners. (Patent No.
WO2016144175). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2016144175A1&KC=A1&FT=D&ND=3&date=20160915&DB=EPODOC&locale=en_EP
Dobruchowska,
J. M., Jonsson, J. O., Fridjonsson, O. H., Aevarsson, A.,
Kristjansson, J. K., Altenbuchner, J., Watzlawick, H.,
Gerwig, G. J., Dijkhuizen, L., Kamerling, J.
P., & Hreggvidsson, G. O. (2016). Modification of linear
(β1→3)-linked gluco-oligosaccharides with a novel
recombinant β-glucosyltransferase (trans-β-glucosidase)
enzyme from Bradyrhizobium diazoefficiens.
Glycobiology, 26(11), 1157-1170. https://doi.org/10.1093/glycob/cww074
Gerwig,
G. J., Te Poele, E. M., Dijkhuizen,
L., & Kamerling, J. P. (2016). Stevia Glycosides:
Chemical and Enzymatic Modifications of Their Carbohydrate Moieties
to Improve the Sweet-Tasting Quality. Advances in
carbohydrate chemistry and biochemistry, 73,
1-72. https://doi.org/10.1016/bs.accb.2016.05.001
Bai,
Y., Dobruchowska, J. M., van der Kaaij, R. M.,
Gerwig, G. J., & Dijkhuizen, L. (2016).
Structural basis for the roles of starch and sucrose in
homo-exopolysaccharide formation by Lactobacillus reuteri
35-5. Carbohydrate Polymers,
151, 29-39. https://doi.org/10.1016/j.carbpol.2016.05.048
Meng,
X., Pijning, T., Dobruchowska, J. M., Yin, H.,
Gerwig, G. J., & Dijkhuizen, L. (2016).
Structural determinants of alternating
(α1 → 4) and (α1 → 6)
linkage specificity in reuteransucrase of Lactobacillus
reuteri. Scientific Reports,
6, Article 35261. https://doi.org/10.1038/srep35261
Meng,
X., Gangoiti, J., Bai, Y., Pijning, T., Van
Leeuwen, S. S., & Dijkhuizen, L. (2016).
Structure-function relationships of family GH70 glucansucrase
and 4,6-α-glucanotransferase enzymes, and their evolutionary
relationships with family GH13 enzymes. Cellular
and molecular life sciences, 73(14),
2681-2706. https://doi.org/10.1007/s00018-016-2245-7
Gangoiti,
J., van Leeuwen, S. S., Vafiadi, C., &
Dijkhuizen, L. (2016). The gram-negative bacterium
Azotobacter chroococcum NCIMB 8003 employs a new glycoside
hydrolase family 70 4,6-α-glucanotransferase enzyme (GtfD) to
synthesize a reuteran like polymer from maltodextrins and
starch. Biochimica et biophysica acta,
1860(6), 1224-1236. https://doi.org/10.1016/j.bbagen.2016.02.005
El
Aidy, S. (2016). De invloed op ons brein. In M.
Kleerebezem, W. Hoekstra, & A. van de Graaf (Eds.), Ons
microbioom: Wat betekenen bacteriën voor onze gezondheid?
(4 ed., Vol. 35, pp. 54-57). (Cahier Biowetenschappen en
Maatschappij). Stichting Biowetenschappen en Maatschappij. http://www.biomaatschappij.nl/wordpress/wp-content/uploads/2016/12/Ons-microbioom.pdf?utm_source=cahier&utm_medium=pdf%20button&utm_campaign=cahier%20download
El
Aidy, S., Stilling, R., Dinan, T. G., & Cryan, J. F.
(2016). Microbiome to Brain: Unravelling the Multidirectional
Axes of Communication. In M. Lyte (Ed.), Microbial
Endocrinology: Interkingdom Signalling in Infectious Diseases and
Health (2 ed., Vol. 874, pp. 301-336). (Advances in
Experimental Medicine and Biology; Vol. 874). Springer
International Publishing AG. https://doi.org/10.1007/978-3-319-20215-0_15
Sarker,
S. A., Sultana, S., Reuteler, G., Moine, D., Descombes, P.,
Charton, F., Bourdin, G., Mccallin, S., Ngom-bru, C., Neville, T.,
Akter, M., Huq, S., Qadri, F., Talukdar, K., Kassam, M., Delley,
M., Loiseau, C., Deng, Y., El Aidy, S., ...
Brüssow, H. (2016). Oral Phage Therapy of Acute
Bacterial Diarrhea With Two Coliphage Preparations: A Randomized
Trial in Children From Bangladesh.
EBioMedicine, 124-137. https://doi.org/10.1016/j.ebiom.2015.12.023
Kelly,
J. R., Borre, Y., O' Brien, C., Patterson, E., El Aidy,
S., Deane, J., Kennedy, P. J., Beers, S., Scott, K.,
Moloney, G., Hoban, A. E., Scott, L., Fitzgerald, P., Ross, P.,
Stanton, C., Clarke, G., Cryan, J. F., & Dinan, T. G. (2016).
Transferring the blues: Depression-associated gut microbiota
induces neurobehavioural changes in the rat.
Journal of Psychiatric Research, 82,
109-118. https://doi.org/10.1016/j.jpsychires.2016.07.019
Kawalek,
A., Jagadeesan, C., & van der Klei, I. J. (2016).
Impaired biosynthesis of the non-bilayer lipids
phosphatidylethanolamine or cardiolipin does not affect peroxisome
biogenesis and proliferation in Saccharomyces cerevisiae.
Biochemical and Biophysical Research
Communications, 480(2), 228-233. https://doi.org/10.1016/j.bbrc.2016.10.033
Antillón,
A., De Vries, A. H., Espinosa-caballero, M.,
Falcón-gonzález, J. M., Flores Romero, D.,
González–damián, J., Jiménez-montejo, F. E.,
León-buitimea, A., López-ortiz, M., Magaña,
R., Marrink, S. J., Morales-nava, R., Periole, X.,
Reyes-esparza, J., Rodríguez Lozada, J., Santiago-angelino, T.
M., Vargas González, M. C., Regla, I., Carrillo-tripp, M., ...
Ortega-blake, I. (2016). An Amphotericin B Derivative Equally
Potent to Amphotericin B and with Increased Safety.
PLoS ONE, 11(9), Article e0162171.
https://doi.org/10.1371/journal.pone.0162171
Gu,
R.-X., Ingolfsson, H. I., de Vries, A. H.,
Marrink, S. J., & Tieleman, D. P. (2016).
Ganglioside and Protein-Ganglioside Interactions in Martini
and Atomistic Molecular Dynamics Simulations.
Biophysical Journal, 110(3),
254A-254A. https://doi.org/10.1016/j.bpj.2015.11.1395
Ingolfsson,
H. I., Melo, M. N., Baoukina, S., Wassenaar, T. A.,
Periole, X., de Vries, A. H., Tieleman, D. P.,
& Marrink, S. J. (2016). In Silico Modeling of
Biologically Complex Membranes. Biophysical
Journal, 110(3), 83A-83A. https://doi.org/10.1016/j.bpj.2015.11.505
Solopova,
A., Formosa-Dague, C., Courtin, P., Furlan, S., Veiga, P.,
Péchoux, C., Armalyte, J., Sadauskas, M., Kok,
J., Hols, P., Dufrêne, Y. F., Kuipers, O.
P., Chapot-Chartier, M.-P., & Kulakauskas, S. (2016).
Regulation of cell wall plasticity by nucleotide metabolism
in Lactococcus lactis. The Journal of Biological
Chemistry, 291(21), 11323-11336. https://doi.org/10.1074/jbc.M116.714303
Papadimitriou,
K., Alegría, Á., Bron, P. A., de Angelis, M., Gobbetti,
M., Kleerebezem, M., Lemos, J. A., Linares, D. M., Ross, P.,
Stanton, C., Turroni, F., van Sinderen, D., Varmanen, P., Ventura,
M., Zúñiga, M., Tsakalidou, E., & Kok,
J. (2016). Stress Physiology of Lactic Acid
Bacteria. Microbiology and Molecular Biology
Reviews, 80(3), 837-890. https://doi.org/10.1128/MMBR.00076-15
van
der Meulen, S. B., de Jong, A., & Kok,
J. (2016). Transcriptome landscape of Lactococcus
lactis reveals many novel RNAs including a small regulatory RNA
involved in carbon uptake and metabolism. RNA
Biology, 13(3), 353-366. https://doi.org/10.1080/15476286.2016.1146855
Perez,
M., Ladero, V., Del Rio, B., Redruello, B., Jong, de,
A., Kuipers, O. P., Kok, J.,
Martin, M. C., Fernandez, M., & Alvarez, M. A. (2016).
Transcriptome profiling of TDC cluster deletion mutant of
Enterococcus faecalis V583. Genomics
Data, 9, 67-69. https://doi.org/10.1016/j.gdata.2016.06.012
Plat,
A., Kuipers, A., Crabb, J., Rink, R.,
& Moll, G. N. (2017). Mutagenesis of nisin's
leader peptide proline strongly modulates export of precursor
nisin. Antonie Van Leeuwenhoek: International
Journal of General and Molecular Microbiology,
110(3), 321-330. https://doi.org/10.1007/s10482-016-0802-6
van
Heel, A. J., Kloosterman, T. G., Montalban-Lopez, M., Deng,
J., Plat, A., Baudu, B., Hendriks, D., Moll, G.
N., & Kuipers, O. P. (2016).
Discovery, production and modification of 5 novel
lantibiotics using the promiscuous nisin modification
machinery. ACS Synthetic Biology,
5(10), 1146-1154. Article 6b00033. https://doi.org/10.1021/acssynbio.6b00033
Meijrink,
B., Verwaal, R., Gielesen, B. E. M., Roubos, J. A., Nygård, Y.
I., Bovenberg, R., Driessen, A. J. M.,
& Pohl, C. (2016). A CRISPR-CAS system for
a filamentous fungal host cell. (Patent No.
WO2016110453). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2016110453A1&KC=A1&FT=D&ND=3&date=20160714&DB=&locale=en_EP
Gorochowski,
T. E., Avcilar-Kucukgoze, I., Bovenberg, R. A. L.,
Roubos, J. A., & Ignatova, Z. (2016). A Minimal Model of
Ribosome Allocation Dynamics Captures Trade-offs in Expression
between Endogenous and Synthetic Genes. ACS
Synthetic Biology, 5(7), 710-720. Article
6b00040. https://doi.org/10.1021/acssynbio.6b00040
Pohl,
C., Kiel, J. A. K. W., Driessen, A. J.
M., Bovenberg, R. A. L., & Nygård, Y.
(2016). CRISPR/Cas9 based genome editing of Penicillium
chrysogenum. ACS Synthetic Biology,
5(7), 754-764. Article 6b00082. https://doi.org/10.1021/acssynbio.6b00082
Salo,
O., Guzmán-Chávez, F., Ries, M. I., Lankhorst, P.
P., Bovenberg, R. A. L., Vreeken, R. J., &
Driessen, A. J. M. (2016). Identification of a
polyketide synthase involved in sorbicillin biosynthesis by
Penicillium chrysogenum. Applied and environmental
microbiology, 82(13), 3971-3978. Article
00350-00316. https://doi.org/10.1128/AEM.00350-16
Turk,
S. C. H. J., Kloosterman, W. P., Ninaber, D. K., Kolen, K. P. A.
M., Knutova, J., Suir, E., Schurmann, M., Raemakers-Franken, P. C.,
Muller, M., de Wildeman, S. M. A., Raamsdonk, L. M., van der Pol,
R., Wu, L., Temudo, M. F., van der Hoeven, R. A. M., Akeroyd, M.,
van der Stoel, R. E., Noorman, H. J., Bovenberg, R. A.
L., & Trefzer, A. C. (2016). Metabolic Engineering
toward Sustainable Production of Nylon-6. ACS
Synthetic Biology, 5(1), 65-73. https://doi.org/10.1021/acssynbio.5b00129
van
Wolferen, M., Ajon, M., Driessen, A. J. M., &
Albers, S.-V. (2016). Corrigendum: Molecular analysis of the
UV-inducible pili operon from Sulfolobus acidocaldarius (vol 2, pg
928, 2013). MicrobiologyOpen,
5(6), 1085-1085. https://doi.org/10.1002/mbo3.426
Nijland,
J. G., Vos, E., Shin, H. Y., de Waal, P. P., Klaassen,
P., & Driessen, A. J. M. (2016). Improving
pentose fermentation by preventing ubiquitination of hexose
transporters in Saccharomyces cerevisiae.
Biotechnology for Biofuels, 9(158),
Article 158. https://doi.org/10.1186/s13068-016-0573-3
Koch,
S., de Wit, J. G., Vos, I., Birkner, J.
P., Gordiichuk, P., Herrmann, A., van
Oijen, A. M., & Driessen, A. J. M. (2016).
Lipids activate SecA for high affinity binding to the SecYEG
complex. The Journal of Biological
Chemistry, 291(43), 22534-22543. https://doi.org/10.1074/jbc.M116.743831
de
Sousa Borges, A., & Scheffers, D.-J. (2016).
Bacterial dynamin as a membrane puncture repair kit.
Environmental Microbiology, 18(8),
2298-2301. https://doi.org/10.1111/1462-2920.13218
Pereira,
A. R., Hsin, J., Król, E., Tavares, A. C.,
Flores, P., Hoiczyk, E., Ng, N., Dajkovic, A., Brun, Y. V.,
VanNieuwenhze, M. S., Roemer, T., Carballido-Lopez, R.,
Scheffers, D.-J., Huang, K. C., & Pinho, M. G. (2016).
FtsZ-Dependent Elongation of a Coccoid Bacterium.
mBio, 7(5), 1-9. Article e00908-16 .
https://doi.org/10.1128/mBio.00908-16
Papagiannakis,
A., Niebel, B., Wit, E. C., & Heinemann,
M. (2017). Autonomous Metabolic Oscillations Robustly
Gate the Early and Late Cell Cycle. Molecular
Cell, 65(2), 285-295. https://doi.org/10.1016/j.molcel.2016.11.018
Radzikowski,
J. L., Vedelaar, S., Siegel, D., Ortega, Á. D.,
Schmidt, A., & Heinemann, M. (2016).
Bacterial persistence is an active σS stress response to
metabolic flux limitation. Molecular Systems
Biology, 12(9), 1-18. Article 882. https://doi.org/10.15252/msb.20166998
van
Rijsewijk, B. R. B. H., Kochanowski, K., Heinemann,
M., & Sauer, U. (2016). Distinct transcriptional
regulation of the two Escherichia coli transhydrogenases PntAB and
UdhA. Microbiology-Reading,
162(9), 1672-1679. https://doi.org/10.1099/mic.0.000346
Heinemann,
M. (2016). Flux Controls Flux – a Key Challenge
for Metabolic Engineering.
Chemie-Ingenieur-Technik, 88(9),
1392. https://doi.org/10.1002/cite.201650531
Shao,
J., Thunnissen, A.-M. W. H., & Broos,
J. (2016). A Protein Expression System for Evaluating
Cation-PI And PI-PI Interaction in Proteins.
Biophysical Journal, 110(3),
51A-51A. https://doi.org/10.1016/j.bpj.2015.11.339
Shao,
J., Marcondes, M. F. M., Oliveira, V., & Broos, J.
(2016). Development of Chemically Defined Media to Express
Trp-Analog-Labeled Proteins in a Lactococcus lactis Trp
Auxotroph. Journal of Molecular Microbiology and
Biotechnology, 26(4), 269-276. https://doi.org/10.1159/000445687
Zhou,
L., Shao, J., Li, Q., van Heel, A. J., de Vries,
M. P., Broos, J., & Kuipers, O.
P. (2016). Incorporation of tryptophan analogues into
the lantibiotic nisin. Amino Acids,
48(5), 1309-1318. https://doi.org/10.1007/s00726-016-2186-3
Abdulmughni,
A., Jozwik, I. K., Putkaradze, N., Brill, E., Zapp, J.,
Thunnissen, A.-M. W. H., Hannemann, F., & Bernhardt, R.
(2017). Characterization of cytochrome P450 CYP109E1 from
Bacillus megaterium as a novel vitamin D3 hydroxylase.
Journal of Biotechnology, 243,
38-47. https://doi.org/10.1016/j.jbiotec.2016.12.023
Jozwik,
I., Kiss, F. M., Gricman, Ł., Abdulmughni, A., Brill, E.,
Zapp, J., Pleiss, J., Bernhardt, R., & Thunnissen, A.-M.
W. H. (2016). Structural basis of steroid binding and
oxidation by the cytochrome P450 CYP109E1 from Bacillus
megaterium. Febs Journal,
283(22), 4128-4148. https://doi.org/10.1111/febs.13911
van
der Meer, J.-Y., Poddar, H., Baas, B.-J., Miao, Y.,
Rahimi, M., Kunzendorf, A., van Merkerk, R.,
Tepper, P. G., Geertsema, E. M., Thunnissen, A.-M. W.
H., Quax, W. J., & Poelarends, G.
J. (2016). Using mutability landscapes of a
promiscuous tautomerase to guide the engineering of
enantioselective Michaelases. Nature
Communications, 7, Article 10911. https://doi.org/10.1038/ncomms10911
2015
Westra,
H.-J., Arends, D., Esko, T., Peters, M. J., Schurmann, C.,
Schramm, K., Kettunen, J., Yaghootkar, H., Fairfax, B. P.,
Andiappan, A. K., Li, Y., Fu, J.,
Karjalainen, J., Platteel, M., Visschedijk,
M., Weersma, R. K., Kasela, S., Milani, L.,
Tserel, L., ... Franke, L. (2015). Cell Specific
eQTL Analysis without Sorting Cells. PLoS
genetics, 11(5), Article 1005223. https://doi.org/10.1371/journal.pgen.1005223
Fehrmann,
R. S. N., Karjalainen, J. M., Krajewska, M., Westra,
H.-J., Maloney, D., Simeonov, A., Pers, T. H., Hirschhorn,
J. N., Jansen, R. C., Schultes, E. A., van Haagenl, H.
H. H. B. M., de Vries, E. G. E., te Meerman,
G., Wijmenga, C., van Vugt, M. A. T.
M., & Franke, L. (2015). Gene
expression analysis identifies global gene dosage sensitivity in
cancer. Nature Genetics,
47(2), 115-125. https://doi.org/10.1038/ng.3173
Zych,
K., Li, Y., van der Velde, J. K., Joosen,
R. V. L., Ligterink, W., Jansen, R. C., & Arends,
D. (2015). Pheno2Geno: High-throughput generation of genetic
markers and maps from molecular phenotypes for crosses between
inbred strains. Bmc Bioinformatics,
16(1), Article 51. https://doi.org/10.1186/s12859-015-0475-6
van
der Graaf, A., Wardenaar, R., Neumann, D. A.,
Taudt, A., Shaw, R. G., Jansen, R. C., Schmitz, R.
J., Colome-Tatche, M., & Johannes, F. (2015).
Rate, spectrum, and evolutionary dynamics of spontaneous
epimutations. Proceedings of the National Academy
of Sciences of the United States of America,
112(21), 6676-6681. https://doi.org/10.1073/pnas.1424254112
Prins,
P., de Ligt, J., Tarasov, A., Jansen, R. C.,
Cuppen, E., & Bourne, P. E. (2015). Toward effective
software solutions for big biology. Nature
Biotechnology, 33(7), 686-687. https://doi.org/10.1038/nbt.3240
Schallmey,
M., Jekel, P., Tang, L., Majeric Elenkov, M., Höffken, H. W.,
Hauer, B., & Janssen, D. B. (2015). A single
point mutation enhances hydroxynitrile synthesis by halohydrin
dehalogenase. Enzyme and Microbial
Technology, 70, 50-57. https://doi.org/10.1016/j.enzmictec.2014.12.009
Wijma,
H. J., Floor, R. J., Bjelic, S., Marrink, S.
J., Baker, D., & Janssen, D. B. (2015).
Enantioselective Enzymes by Computational Design and In
Silico Screening. Angewandte Chemie -
International Edition, 54(12), 3726-3730. https://doi.org/10.1002/anie.201411415
Diez,
V., Loznik, M., Taylor, S., Winn, M., Rattray, N. J. W., Podmore,
H., Micklefield, J., Goodacre, R., Medema, M. H., Müller,
U., Bovenberg, R. A. L., Janssen, D. B.,
& Takano, E. (2015). Functional exchangeability of
oxidase and dehydrogenase reactions in the biosynthesis of
hydroxyphenylglycine, a non-ribosomal peptide building
block. ACS Synthetic Biology,
4(7), 796-807. https://doi.org/10.1021/sb500368w
Heberling,
M. M., Masman, M. F., Bartsch, S., Wybenga, G. G., Dijkstra, B.
W., Marrink, S. J., & Janssen, D. B.
(2015). Ironing out Their Differences: Dissecting the
Structural Determinants of a Phenylalanine Aminomutase and Ammonia
Lyase. ACS chemical biology,
10(4), 989-997. https://doi.org/10.1021/cb500794h
van
Beek, H. L., Beyer, N., Janssen, D.
B., & Fraaije, M. W. (2015).
Lyophilization conditions for the storage of
monooxygenases. Journal of
Biotechnology, 203, 41-44. https://doi.org/10.1016/j.jbiotec.2015.03.010
Otzen,
M., Crismaru, C. G., Postema, C. P.,
Wijma, H. J., Heberling, M. M., Szymanski, W.,
de Wildeman, S., & Janssen, D. B. (2015).
Metabolism of β-valine via a CoA-dependent ammonia lyase
pathway. Applied Microbiology and
Biotechnology, 99(21), 8987-8998. https://doi.org/10.1007/s00253-015-6551-z
Mikleusevic,
A., Hamersak, Z., Salopek-Sondi, B., Tang, L., Janssen, D.
B., & Elenkov, M. M. (2015). Oxazolidinone
Synthesis through Halohydrin Dehalogenase-Catalyzed Dynamic Kinetic
Resolution. Advanced Synthesis &
Catalysis, 357(8), 1709-1714. https://doi.org/10.1002/adsc.201500111
Toplak,
A., Nuijens, T., Quaedflieg, P. J. L. M., Wu, B., &
Janssen, D. B. (2015). Peptide synthesis in neat
organic solvents with novel thermostable proteases.
Enzyme and Microbial Technology,
73-74, 20-28. https://doi.org/10.1016/j.enzmictec.2015.03.003
Colin,
P.-Y., Kintses, B., Gielen, F., Miton, C. M., Fischer, G., Mohamed,
M. F., Hyvönen, M., Morgavi, D. P., Janssen, D.
B., & Hollfelder, F. (2015). Ultrahigh-throughput
discovery of promiscuous enzymes by picodroplet functional
metagenomics. Nature Communications,
6, 1-12. Article 10008. https://doi.org/10.1038/ncomms10008
Floor,
R. J., Wijma, H. J., Jekel, P. A., Terwisscha van
Scheltinga, A. C., Dijkstra, B. W., & Janssen, D.
B. (2015). X-ray crystallographic validation of
structure predictions used in computational design for protein
stabilization. Proteins, 83,
940-951. https://doi.org/10.1002/prot.24791
Rudi,
K., Ho, F. Y., Gilsbach, B. K., Pots, H.,
Wittinghofer, A., Kortholt, A., & Klare, J. P.
(2015). Conformational heterogeneity of the Roc domains in C.
tepidum Roc-COR and implications for human LRRK2 Parkinson
mutations. Bioscience reports,
35(5), 1-12. Article e00254. https://doi.org/10.1042/BSR20150128
Wu,
J., Pipathsouk, A., Keizer-Gunnink, A., Fusetti, F.,
Alkema, W., Liu, S., Altschuler, S., Wu, L., Kortholt,
A., & Weiner, O. D. (2015). Homer3 regulates the
establishment of neutrophil polarity. Molecular
Biology of the Cell, 26(9), 1629-1639. https://doi.org/10.1091/mbc.E14-07-1197
Terheyden,
S., Ho, F. Y., Gilsbach, B. K., Wittinghofer,
A., & Kortholt, A. (2015). Revisiting the
Roco G-protein cycle. Biochemical
Journal, 465(1), 139-147. https://doi.org/10.1042/BJ20141095
Gilsbach,
B. K., Messias, A. C., Ito, G., Sattler, M., Alessi, D. R.,
Wittinghofer, A., & Kortholt, A. (2015).
Structural Characterization of LRRK2 Inhibitors.
Journal of Medicinal Chemistry,
58(9), 3751−3756. https://doi.org/10.1021/jm5018779
McGinn,
S., Bauer, D., Brefort, T., Dong, L., El-Sagheer, A., Elsharawy,
A., Evans, G., Falk-Sörqvist, E., Forster, M., Fredriksson,
S., Freeman, P., Freitag, C., Fritzsche, J., Gibson, S., Gullberg,
M., Gut, M., Heath, S., Heath-Brun, I., Heron, A. J., ... Gut, I.
G. (2016). New Technologies for DNA analysis-A review of the
READNA Project. New Biotechnology,
33(3), 311-330. https://doi.org/10.1016/j.nbt.2015.10.003
Biesemans,
A., Soskine, M., & Maglia, G. (2015). A
Protein Rotaxane Controls the Translocation of Proteins Across a
ClyA Nanopore. Nano Letters,
15(9), 6076-6081. https://doi.org/10.1021/acs.nanolett.5b02309
Stoddart,
D., Franceschini, L., Heron, A., Bayley, H., & Maglia,
G. (2015). DNA stretching and optimization of
nucleobase recognition in enzymatic nanopore sequencing.
Nanotechnology, 26(8), Article
084002. https://doi.org/10.1088/0957-4484/26/8/084002
Ho,
C.-W., Meervelt, V., Tsai, K.-C., De Temmerman, P.-J., Mast,
J., & Maglia, G. (2015). Engineering a
nanopore with co-chaperonin function. Science
Advances, 1(11), Article e1500905. https://doi.org/10.1126/sciadv.1500905
Soskine,
M., Biesemans, A., & Maglia, G. (2015).
Single-Molecule Analyte Recognition with ClyA Nanopores
Equipped with Internal Protein Adaptors. Journal
of the American Chemical Society, 137(17),
5793-7. https://doi.org/10.1021/jacs.5b01520
Fulyani,
F., Schuurman-Wolters, G., Slotboom,
D.-J., & Poolman, B. (2016). Relative
rates of amino acid import via the ABC transporter GlnPQ determine
the growth performance of Lactococcus lactis.
Journal of Bacteriology, 198(3),
477-485. Article JB.00685-15. https://doi.org/10.1128/JB.00685-15
Swier,
L. J. Y. M., Slotboom, D., & Poolman,
B. (2015). ABC Importers. In A. M. George
(Ed.), ABC Transporters - 40 Years on (1 ed., Vol. 1, pp.
3-36). Springer. https://doi.org/10.1007/978-3-319-23476-2_1
Laba,
J. K., Steen, A., Popken, P., Chernova, A.,
Poolman, B., & Veenhoff, L. M. (2015).
Active Nuclear Import of Membrane Proteins Revisited.
Cells, 4(4), 653-673. https://doi.org/10.3390/cells4040653
Boersma,
A. J., Zuhorn, I. S., & Poolman, B.
(2015). A sensor for quantification of macromolecular
crowding in living cells. Nature
Methods, 12(3), 227-229. https://doi.org/10.1038/nmeth.3257
Gouridis,
G., Schuurman-Wolters, G., Ploetz, E., Husada, F.,
Vietrov, R., de Boer, M., Cordes,
T., & Poolman, B. (2015).
Conformational dynamics in substrate-binding domains
influences transport in the ABC importer GlnPQ.
Nature Structural & Molecular Biology,
22(1), 57-64. https://doi.org/10.1038/nsmb.2929
Spitzer,
J., Pielak, G. J., & Poolman, B. (2015).
Emergence of life: Physical chemistry changes the
paradigm. Biology Direct,
10(33). https://doi.org/10.1186/s13062-015-0060-y
Ho,
F. Y., & Poolman, B. (2015).
Engineering Escherichia coli for Functional Expression of
Membrane Proteins. Methods in
Enzymology, 556, 3-21. https://doi.org/10.1016/bs.mie.2015.01.003
Driessen,
A. J. M., & Poolman, B. (2015). In
memoriam: Wilhelmus Nicolaas Konings (1937-2014).
Extremophiles, 19, 233-234. https://doi.org/10.1007/s00792-015-0736-3
Kralt,
A., Carretta, M., Mari, M., Reggiori,
F., Steen, A., Poolman, B.,
& Veenhoff, L. M. (2015). Intrinsically disordered
linker and plasma membrane-binding motif sort ist2 and ssy1 to
junctions. Traffic, 16(2),
135-147. https://doi.org/10.1111/tra.12243
Goel,
A., Eckhardt, T. H., Puri, P., de Jong, A., Branco dos
Santos, F., Giera, M., Fusetti, F., de Vos, W. M., Kok,
J., Poolman, B., Molenaar, D., Kuipers,
O. P., & Teusink, B. (2015). Protein costs do not
explain evolution of metabolic strategies and regulation of
ribosomal content: does protein investment explain an anaerobic
bacterial Crabtree effect? Molecular
Microbiology, 97(1), 77-92. https://doi.org/10.1111/mmi.13012
Zollmann,
T., Moiset Coll, G., Tumulka, F., Tampé, R., Poolman,
B., & Abele, R. (2015). Single liposome analysis
of peptide translocation by the ABC transporter TAPL.
Proceedings of the National Academy of Sciences of the
United States of America, 112(7), 2046-2051.
https://doi.org/10.1073/pnas.1418100112
Popken,
P., Ghavami, A., Onck, P. R., Poolman,
B., & Veenhoff, L. M. (2015).
Size-dependent leak of soluble and membrane proteins through
the yeast nuclear pore complex. Molecular Biology
of the Cell, 26(7), 1386-1394. https://doi.org/10.1091/mbc.E14-07-1175
Husada,
F., Gouridis, G., Vietrov, R., Schuurman-Wolters, G.
K., Ploetz, E., de Boer, M., Poolman,
B., & Cordes, T. (2015). Watching
conformational dynamics of ABC transporters with single-molecule
tools. Biochemical Society
Transactions, 43(5), 1041-1047. https://doi.org/10.1042/BST20150140
Majsnerowska,
M., Ter Beek, J., Stanek, W. K., Duurkens, R., &
Slotboom, D. J. (2015). Competition between Different
S-Components for the Shared Energy Coupling Factor Module in Energy
Coupling Factor Transporters.
Biochemistry, 54, 4763-4766. https://doi.org/10.1021/acs.biochem.5b00609
Zhang,
Z., Kuipers, G., Niemiec, Ł., Baumgarten, T., Slotboom,
D. J., de Gier, J.-W., & Hjelm, A. (2015).
High-level production of membrane proteins in E. coli
BL21(DE3) by omitting the inducer IPTG. Microbial
Cell Factories, 14(1), 1-11. Article 142. https://doi.org/10.1186/s12934-015-0328-z
Hänelt,
I., Jensen, S., Wunnicke, D., & Slotboom, D. J.
(2015). Low affinity and slow Na+-binding precedes high
affinity aspartate binding in GltPh. The Journal
of Biological Chemistry, 290(26), 15962-15972.
https://doi.org/10.1074/jbc.M115.656876
Swier,
L. J. Y. M., Monjas, L., Guskov, A., de Voogd,
A. R., Erkens, G. B., Slotboom, D. J., &
Hirsch, A. K. H. (2015). Structure-Based Design of
Potent Small-Molecule Binders to the S-Component of the ECF
Transporter for Thiamine. ChemBioChem,
16(5), 819-826. https://doi.org/10.1002/cbic.201402673
Jähme,
M., & Slotboom, D. J. (2015). Structure,
function, evolution, and application of bacterial Pnu-type vitamin
transporters. Biological Chemistry,
396(9-10), 955-966. https://doi.org/10.1515/hsz-2015-0113
Lolkema,
J. S., & Slotboom, D.-J. (2015). The Hill
analysis and co-ion-driven transporter kinetics.
Journal of general physiology,
145(6), 565-574. https://doi.org/10.1085/jgp.201411332
Jähme,
M., Guskov, A., & Slotboom, D.
(2015). The twisted relation between Pnu and SWEET
transporters. Trends in Biochemical
Sciences, 40(4), 183-188. https://doi.org/10.1016/j.tibs.2015.02.002
Meng,
X., Dobruchowska, J. M., Pijning, T., Gerwig, G.
J., & Dijkhuizen, L. (2016).
Synthesis of New Hyper-Branched α-Glucans from Sucrose
by Lactobacillus reuteri 180 Glucansucrase Mutants.
Journal of Agricultural and Food Chemistry,
64(2), 433-442. https://doi.org/10.1021/acs.jafc.5b05161
Paul,
C. J., Leemhuis, H., Dobruchowska, J. M., Grey, C.,
Onnby, L., van Leeuwen, S. S., Dijkhuizen,
L., & Karlsson, E. N. (2015). A GH57
4-alpha-glucanotransferase of hyperthermophilic origin with
potential for alkyl glycoside production. Applied
Microbiology and Biotechnology, 99(17),
7101-7113. https://doi.org/10.1007/s00253-015-6435-2
Bai,
Y., van der Kaaij, R. M., Leemhuis,
H., Pijning, T., van Leeuwen, S.
S., Jin, Z., & Dijkhuizen, L. (2015).
Biochemical characterization of Lactobacillus reuteri
Glycoside Hydrolase family 70 GTFB type of
4,6-α-Glucanotransferase enzymes that synthesize soluble
dietary starch fibers. Applied and environmental
microbiology, 81(20), 7223-7232. https://doi.org/10.1128/AEM.01860-15
Bai,
Y., van der Kaaij, R. M., Woortman, A. J.
J., Jin, Z., & Dijkhuizen, L. (2015).
Characterization of the 4,6-α-glucanotransferase GTFB
enzyme of Lactobacillus reuteri 121 isolated from inclusion
bodies. BMC Biotechnology,
15, Article 49. https://doi.org/10.1186/s12896-015-0163-7
Meng,
X., Pijning, T., Dobruchowska, J. M., Gerwig, G.
J., & Dijkhuizen, L. (2015).
Characterization of the functional roles of amino acid
residues in acceptor binding subsite +1 in the active site of the
glucansucrase GTF180 enzyme of Lactobacillus reuteri 180.
The Journal of Biological Chemistry,
290(50), 30131-30141. https://doi.org/10.1074/jbc.M115.687558
van
Munster, J. M., Dobruchowska, J. M., Veloo, R., Dijkhuizen,
L., & van der Maarel, M. J. E. C. (2015).
Characterization of the starvation-induced chitinase CfcA and
α-1,3-glucanase AgnB of Aspergillus niger.
Applied Microbiology and Biotechnology,
99, 2209-2223. https://doi.org/10.1007/s00253-014-6062-3
Valk,
V., Eeuwema, W., Sarian, F. D., van der Kaaij, R.
M., & Dijkhuizen, L. (2015).
Degradation of granular starch by the bacterium
Microbacterium aurum B8.A involves a novel modular α-amylase
enzyme system with FNIII and CBM25 domains.
Applied and environmental microbiology,
81(19), 6610-6620. https://doi.org/10.1128/AEM.01029-15
Lammerts
van Bueren, A., Saraf, A., Martens, E. C., &
Dijkhuizen, L. (2015). Differential metabolism of
Exopolysaccharides from probiotic Lactobacilli by the human gut
symbiont Bacteroides thetaiotaomicron. Applied and
environmental microbiology, 81(12), 3973-3983.
https://doi.org/10.1128/AEM.00149-15
Wilbrink,
M. H., Ten Kate, G. A., Sanders, P., Gerwig, G.
J., van Leeuwen, S. S., Sallomons, E.,
Klarenbeek, B., Hage, J. H., van Vuure, C. A., Dijkhuizen,
L., & Kamerling, J. P. (2015). Enzymatic
Decoration of Prebiotic Galacto-oligosaccharides (Vivinal®
GOS) with Sialic Acid using Trypanosoma cruzi Trans-Sialidase and
Two Bovine Sialoglycoconjugates as Donor Substrates.
Journal of Agricultural and Food Chemistry,
63(25), 5976-5984. https://doi.org/10.1021/acs.jafc.5b01505
van
Munster, J. M., Sanders, P., ten Kate, G. A.,
Dijkhuizen, L., & van der Maarel, M. J. E.
C. (2015). Kinetic characterization of Aspergillus
niger chitinase CfcI using a HPAEC-PAD method for native chitin
oligosaccharides. Carbohydrate
Research, 407, 73-78. https://doi.org/10.1016/j.carres.2015.01.014
Aalbers,
F., Turkenburg, J. P., Davies, G. J., Dijkhuizen,
L., & Lammerts van Bueren, A. (2015).
Structural and Functional Characterization of a Novel Family
GH115 4-O-Methyl-α-Glucuronidase with Specificity for
Decorated Arabinogalactans. Journal of Molecular
Biology, 427(24), 3935-3946. https://doi.org/10.1016/j.jmb.2015.07.006
Meng,
X., Dobruchowska, J. M., Gerwig, G. J., Kamerling, J.
P., & Dijkhuizen, L. (2015). Synthesis of
oligo- and polysaccharides by Lactobacillus reuteri 121
reuteransucrase at high concentrations of sucrose.
Carbohydrate Research, 414, 85-92.
https://doi.org/10.1016/j.carres.2015.07.011
van
Munster, J. M., Nitsche, B. M., Akeroyd, M., Dijkhuizen,
L., van der Maarel, M. J. E. C., & Ram, A.
F. J. (2015). Systems Approaches to Predict the Functions of
Glycoside Hydrolases during the Life Cycle of Aspergillus niger
Using Developmental Mutants ∆brlA and ∆flbA.
PLoS ONE, 10(1), Article e0116269.
https://doi.org/10.1371/journal.pone.0116269
Fransen,
F., Zagato, E., Mazzini, E., Fosso, B., Manzari, C., El Aidy,
S., Chiavelli, A., D'Erchia, A. M., Sethi, M. K., Pabst, O.,
Marzano, M., Moretti, S., Romani, L., Penna, G., Pesole, G., &
Rescigno, M. (2015). BALB/c and C57BL/6 Mice Differ in
Polyreactive IgA Abundance, which Impacts the Generation of
Antigen-Specific IgA and Microbiota Diversity.
Immunity, 43(3), 527-540. https://doi.org/10.1016/j.immuni.2015.08.011
Pusceddu,
M. M., El Aidy, S., Crispie, F., O'Sullivan, O.,
Cotter, P., Stanton, C., Kelly, P., Cryan, J. F., & Dinan, T.
G. (2015). Correction: N-3 Polyunsaturated Fatty Acids
(PUFAs) Reverse the Impact of Early-Life Stress on the Gut
Microbiota. PLoS ONE, 10(10),
Article e0142228. https://doi.org/10.1371/journal.pone.0142228
El
Aidy, S., Dinan, T. G., & Cryan, J. F. (2015). Gut
Microbiota: The conductor in the Orchestra of immune-neuroendocrine
communication. Clinical Therapeutics,
37(5), 954-967. https://doi.org/10.1016/j.clinthera.2015.03.002
Menckeberg,
C. L., Hol, J., Simons-Oosterhuis, Y., Raatgeep, H. R. C., de
Ruiter, L. F., Lindenbergh-Kortleve, D. J., Korteland-van Male, A.
M., El Aidy, S., van Lierop, P. P. E., Kleerebezem,
M., Groeneweg, M., Kraal, G., Elink-Schuurman, B. E., de Jongste,
J. C., Nieuwenhuis, E. E. S., & Samsom, J. N. (2015).
Human buccal epithelium acquires microbial hyporesponsiveness
at birth, a role for secretory leukocyte protease inhibitor.
Gut, 64(6), 884-893. https://doi.org/10.1136/gutjnl-2013-306149
Pusceddu,
M. M., El Aidy, S., Crispie, F., O'Sullivan, O.,
Cotter, P., Stanton, C., Kelly, P., Cryan, J. F., & Dinan, T.
G. (2015). N-3 Polyunsaturated Fatty Acids (PUFAs) Reverse
the Impact of Early-Life Stress on the Gut Microbiota.
PLoS ONE, 10(10), Article e0139721.
https://doi.org/10.1371/journal.pone.0139721
El
Aidy, S., van den Bogert, B., & Kleerebezem, M. (2015).
The small intestine microbiota, nutritional modulation and
relevance for health. Current Opinion in
Biotechnology, 32, 14-20. https://doi.org/10.1016/j.copbio.2014.09.005
Kumar,
S., Singh, R., Williams, C. P., & van der Klei, I.
J. (2016). Stress exposure results in increased
peroxisomal levels of yeast Pnc1 and Gpd1, which are imported via a
piggy-backing mechanism. Biochimica et Biophysica
Acta-Molecular Cell Research, 1863(1),
148-156. https://doi.org/10.1016/j.bbamcr.2015.10.017
Yuan,
W., Veenhuis, M., & van der Klei, I. J. (2016).
The birth of yeast peroxisomes. Biochimica
et biophysica acta, 1863(5), 902-910. Article
17661. https://doi.org/10.1016/j.bbamcr.2015.09.008
Bohnert,
M., Zerbes, R. M., Davies, K. M., Mühleip, A. W., Rampelt, H.,
Horvath, S. E., Boenke, T., Kram, A., Perschil, I.,
Veenhuis, M., Kühlbrandt, W., van der Klei, I.
J., Pfanner, N., & van der Laan, M. (2015).
Central role of mic10 in the mitochondrial contact site and
cristae organizing system. Cell
Metabolism, 21(5), 747-755. https://doi.org/10.1016/j.cmet.2015.04.007
Lefevre,
S. D., Kumar, S., & van der Klei, I. J. (2015).
Inhibition of peroxisome fission, but not mitochondrial
fission, increases yeast chronological lifespan.
Cell Cycle, 14(11), 1698-1703. https://doi.org/10.1080/15384101.2015.1029685
Thomas,
A. S., Krikken, A. M., van der Klei, I.
J., & Williams, C. P. (2015). Phosphorylation of
Pex11p does not regulate peroxisomal fission in the yeast Hansenula
polymorpha. Scientific Reports,
5, 1-11. Article 11493. https://doi.org/10.1038/srep11493
Williams,
C., Opalinski, L., Landgraf, C., Costello, J., Schrader, M.,
Krikken, A. M., Knoops, K., Kram, A. M.,
Volkmer, R., & van der Klei, I. J. (2015).
The membrane remodeling protein Pex11p activates the GTPase
Dnm1p during peroxisomal fission. Proceedings of
the National Academy of Sciences of the United States of
America, 112(20), 6377-6382. https://doi.org/10.1073/pnas.1418736112
Knoops,
K., de Boer, R., Kram, A., &
van der Klei, I. J. (2015). Yeast pex1 cells contain
peroxisomal ghosts that import matrix proteins upon reintroduction
of Pex1. The Journal of Cell Biology,
211(5), 955-962. https://doi.org/10.1083/jcb.201506059
Goga,
N., Melo, M. N., Rzepiela, A. J., de Vries, A.,
Hadar, A., Marrink, S. J., & Berendsen, H. (2015).
Benchmark of Schemes for Multiscale Molecular Dynamics
Simulations. Journal of Chemical Theory and
Computation, 11(4), 1389-1398. https://doi.org/10.1021/ct501102b
van
Eerden, F. J., de Jong, D. H., de Vries, A. H.,
Wassenaar, T. A., & Marrink, S. J. (2015).
Characterization of thylakoid lipid membranes from
cyanobacteria and higher plants by molecular dynamics
simulations. Biochimica et Biophysica
Acta-Biomembranes, 1848(6), 1319-1330. https://doi.org/10.1016/j.bbamem.2015.02.025
Ingolfsson,
H. I., Melo, M. N., Wassenaar, T. A., Periole,
X., de Vries, A. H., Tieleman, D. P., &
Marrink, S. J. (2015). Computational Lipidomics and
the Lipid Organization of Cell Envelopes.
Biophysical Journal, 108(2),
342A-342A.
Arnarez,
C., Uusitalo, J. J., Masman, M. F., Ingolfsson, H. I., de Jong, D.
H., Melo, M. N., Periole, X., de Vries, A. H.,
& Marrink, S. J. (2015). Dry Martini, a
Coarse-Grained Force Field for Lipid Membrane Simblations with
Implicit Solvent. Journal of Chemical Theory and
Computation, 11(1), 260-275. https://doi.org/10.1021/ct500477k
de
Jong, A., van der Meulen, S., Kuipers, O.
P., & Kok, J. (2015). T-REx:
Transcriptome analysis webserver for RNA-seq Expression
data. BMC Genomics, 16(1),
Article 663. https://doi.org/10.1186/s12864-015-1834-4
Carlucci,
G., Kuipers, A., Ananias, H. J. K., Faria, D. D. P., Dierckx,
R. A. J. O., Helfrich, W., Rink, R.,
Moll, G. N., de Jong, I. J., &
Elsinga, P. H. (2015). GRPR-selective PET imaging of
prostate cancer using [F-18]-bombesin analogs.
Peptides, 67, 45-54. https://doi.org/10.1016/j.peptides.2015.03.004
Khusainov,
R., van Heel, A. J., Lubelski, J., Moll, G.
N., & Kuipers, O. P. (2015).
Identification of essential amino acid residues in the nisin
dehydratase NisB. Frontiers in
Microbiology, 6, Article 102. https://doi.org/10.3389/fmicb.2015.00102
Polli,
F., Meijrink, B., Bovenberg, R. A. L., &
Driessen, A. J. M. (2016). New promoters for strain
engineering of Penicillium chrysogenum. Fungal
Genetics and Biology, 89, 62-71. https://doi.org/10.1016/j.fgb.2015.12.003
Zhou,
H., Vonk, B., Roubos, J. A., Bovenberg, R. A. L.,
& Voigt, C. A. (2015). Algorithmic co-optimization of
genetic constructs and growth conditions: application to 6-ACA, a
potential nylon-6 precursor. Nucleic Acids
Research. https://doi.org/10.1093/nar/gkv1071
Ouchaou,
K., Maire, F., Salo, O., Ali, H., Hankemeier, T., van der Marel, G.
A., Filippov, D. V., Bovenberg, R. A. L., Vreeken, R.
J., Driessen, A. J. M., & Overkleeft, H. S.
(2015). A Mutasynthesis Approach with a Penicillium
chrysogenum ΔroqA Strain Yields New Roquefortine D
Analogues. ChemBioChem, 16,
915-923. https://doi.org/10.1002/cbic.201402686
Salo,
O. V., Ries, M., Medema, M. H., Lankhorst, P. P., Vreeken, R.
J., Bovenberg, R. A. L., & Driessen, A. J.
M. (2015). Genomic mutational analysis of the impact
of the classical strain improvement program on β-lactam
producing Penicillium chrysogenum. BMC
Genomics, 16(1), Article 937. https://doi.org/10.1186/s12864-015-2154-4
Shin,
H. Y., Nijland, J. G., de Waal, P. P., de Jong, R. M.,
Klaassen, P., & Driessen, A. J. M. (2015).
An engineered cryptic Hxt11 sugar transporter facilitates
glucose-xylose co-consumption in Saccharomyces cerevisiae.
Biotechnology for Biofuels, 8(176).
https://doi.org/10.1186/s13068-015-0360-6
Velema,
W. A., van der Berg, J. P., Szymanski, W.,
Driessen, A. J. M., & Feringa, B. L.
(2015). Bacterial patterning controlled by light
exposure. Organic & Biomolecular
Chemistry, 13(6), 1639-1642. https://doi.org/10.1039/c4ob02483d
van
der Berg, J. P., Madoori, P. K., Komarudin, A. G.,
Thunnissen, A.-M., & Driessen, A. J. M.
(2015). Binding of the Lactococcal Drug Dependent
Transcriptional Regulator LmrR to Its Ligands and Responsive
Promoter Regions. PLoS ONE,
10(8), Article e0135467. https://doi.org/10.1371/journal.pone.0135467
Prabudiansyah,
I., Kusters, I., Caforio, A., & Driessen, A. J. M.
(2015). Characterization of the annular lipid shell of the
Sec translocon. Biochimica et biophysica
acta, 1848(10, Part A), 2050-2056. https://doi.org/10.1016/j.bbamem.2015.06.024
Velema,
W. A., Hansen, M. J., Lerch, M. M., Driessen, A.
J. M., Szymanski, W., & Feringa, B.
L. (2015). Ciprofloxacin-Photoswitch Conjugates: A
Facile Strategy for Photopharmacology.
BIOCONJUGATE CHEMISTRY, 26(12),
2592-2597. https://doi.org/10.1021/acs.bioconjchem.5b00591
Van
der Berg, J. P., Velema, W. A., Szymanski, W.,
Driessen, A. J. M., & Feringa, B. L.
(2015). Controlling the activity of quorum sensing
autoinducers with light. Chemical
Science, 6(6), 3593-3598. https://doi.org/10.1039/c5sc00215j
Caforio,
A., Jain, S., Fodran, P., Siliakus, M.,
Minnaard, A. J., van der Oost, J., & Driessen, A.
J. M. (2015). Formation of the ether lipids
archaetidylglycerol and archaetidylethanolamine in Escherichia
coli. Biochemical Journal,
470(3), 343-355. Article 20150626. https://doi.org/10.1042/BJ20150626
Reznicek,
O., Facey, S. J., de Waal, P. P., Teunissen, A. W. R. H., de Bont,
J. A. M., Nijland, J. G., Driessen, A. J.
M., & Hauer, B. (2015). Improved xylose uptake in
Saccharomyces cerevisiae due to directed evolution of
galactose permease Gal2 for sugar co-consumption.
Journal of Applied Microbiology,
119(1), 99-111. https://doi.org/10.1111/jam.12825
Prabudiansyah,
I., Kusters, I., & Driessen, A. J. M. (2015).
In Vitro Interaction of the Housekeeping SecA1 with the
Accessory SecA2 Protein of Mycobacterium tuberculosis.
PLoS ONE, 10(6), Article e0128788.
https://doi.org/10.1371/journal.pone.0128788
Medema,
M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B.,
Blin, K., de Bruijn, I., Chooi, Y. H., Claesen, J., Coates, R. C.,
Cruz-Morales, P., Duddela, S., Düsterhus, S., Edwards, D. J.,
Fewer, D. P., Garg, N., Geiger, C., Gomez-Escribano, J. P., Greule,
A., ... Glöckner, F. O. (2015). Minimum Information
about a Biosynthetic Gene cluster. Nature Chemical
Biology, 11(9), 625-631. https://doi.org/10.1038/nchembio.1890
Geng,
Y., Kedrov, A., Caumanns, J. J., Crevenna, A. H., Lamb, D. C.,
Beckmann, R., & Driessen, A. J. M. (2015).
Role of the cytosolic loop C2 and the C-terminus of YidC in
ribosome binding and insertion activity. The
Journal of Biological Chemistry, 290,
17250-17261. https://doi.org/10.1074/jbc.M115.650309
Bos,
J., Browne, W. R., Driessen, A. J.
M., & Roelfes, G. (2015).
Supramolecular Assembly of Artificial Metalloenzymes Based on
the Dimeric Protein LmrR as Promiscuous Scaffold.
Journal of the American Chemical Society,
137(31), 9796-9799. https://doi.org/10.1021/jacs.5b05790
de
Sousa Borges, A., de Keyzer, J., Driessen, A. J.
M., & Scheffers, D.-J. (2015). The
Escherichia coli membrane protein insertase YidC assists in the
biogenesis of Penicillin Binding Proteins. Journal
of Bacteriology, 197, 1444-1450. https://doi.org/10.1128/JB.02556-14
Yang,
N., & Driessen, A. J. M. (2015). The
saci_2123 gene of the hyperthermoacidophile Sulfolobus
acidocaldarius encodes an ATP-binding cassette multidrug
transporter. Extremophiles,
19(1), 101-108. https://doi.org/10.1007/s00792-014-0688-z
Trip,
E. N., & Scheffers, D.-J. (2015). A
1 MDa protein complex containing critical components of the
Escherichia coli divisome. Scientific
Reports, 5, Article 18190. https://doi.org/10.1038/srep18190
Krol,
E., de Sousa Borges, A., da Silva, I., Polaquini, C.,
Regasini, L., Ferreira, H., & Scheffers, D.
(2015). Antibacterial activity of alkyl gallates is a
combination of direct targeting of FtsZ and permeabilization of
bacterial membranes. Frontiers in
Microbiology, 6, Article 390. https://doi.org/10.3389/fmicb.2015.00390
Silva,
I., Pavan, F. R., Polaquini, C., Regasini, L. O., Scheffers,
D. .-J., & Ferreira, H. (2015). Assessment of
cyto/genotoxicity of the antibacterial heptyl gallate in HepG2
cells and the possible target in bacteria.
Toxicology Letters, 238(2,
Supplement), S328-S328. https://doi.org/10.1016/j.toxlet.2015.08.935
Tol,
M. B., Angeles, D. M., & Scheffers, D.-J. (2015).
In vivo cluster formation of nisin and Lipid II is correlated
with membrane depolarization. Antimicrobial Agents
and Chemotherapy, 59(6), 3683-3686. https://doi.org/10.1128/AAC.04781-14
Scheffers,
D.-J., & Tol, M. B. (2015). LipidII: Just Another
Brick in the Wall? PLoS Pathogens,
11(12), Article e1005213. https://doi.org/10.1371/journal.ppat.1005213
Schmidt,
A., Kochanowski, K., Vedelaar, S., Ahrné, E.,
Volkmer, B., Callipo, L., Knoops, K., Bauer, M., Aebersold,
R., & Heinemann, M. (2016). The quantitative
and condition-dependent Escherichia coli proteome.
Nature Biotechnology, 34(1),
104-110. https://doi.org/10.1038/nbt.3418
Janssens,
G. E., Meinema, A. C., Gonzalez, J., Wolters, J. C.,
Schmidt, A., Guryev, V., Bischoff,
R., Wit, E. C., Veenhoff, L.
M., & Heinemann, M. (2015). Protein
biogenesis machinery is a driver of replicative aging in
yeast. eLife, 4, Article
e08527. https://doi.org/10.7554/eLife.08527
Shao,
J., Korendovych, I. V., & Broos, J. (2015).
Biosynthetic incorporation of the azulene moiety in proteins
with high efficiency. Amino Acids,
47(1), 213-216. https://doi.org/10.1007/s00726-014-1870-4
Xu,
J., Chen, B., Callis, P. R., Muiño, P. L., Rozeboom, H.
J., Broos, J., Toptygin, D., Brand, L., &
Knutson, J. R. (2015). Picosecond Fluorescence Dynamics of
Tryptophan and 5-Fluorotryptophan in Monellin: Slow Water-Protein
Relaxation Unmasked. The Journal of Physical
Chemistry. B: Materials, Surfaces, Interfaces, &
Biophysical, 119(11), 4230-4239. https://doi.org/10.1021/acs.jpcb.5b01651
Poddar,
H., Rahimi, M., Geertsema, E., Thunnissen,
A., & Poelarends, G. (2015). Evidence
for the Formation of an Enamine Species during Aldol and
Michael-type Addition Reactions Promiscuously Catalyzed by
4-Oxalocrotonate Tautomerase.
ChemBioChem, 16(5), 738-741. https://doi.org/10.1002/cbic.201402687
Baas,
B.-J., Poddar, H., Geertsema, E. M., Rozeboom,
H. J., de Vries, M., Permentier, H.
P., Thunnissen, A.-M. W. H., &
Poelarends, G. J. (2015). Functional and Structural
Characterization of an Unusual Cofactor-Independent
Oxygenase. Biochemistry,
54(5), 1219-1232. https://doi.org/10.1021/bi501200j
2014
Cortijo,
S., Wardenaar, R., Colome-Tatche, M.,
Gilly, A., Etcheverry, M., Labadie, K., Caillieux, E., Hospital,
F., Aury, J.-M., Wincker, P., Roudier, F., Jansen, R.
C., Colot, V., & Johannes, F. (2014). Mapping the
Epigenetic Basis of Complex Traits.
Science, 343(6175), 1145-1148. https://doi.org/10.1126/science.1248127
Rintisch,
C., Heinig, M., Bauerfeind, A., Schafer, S., Mieth, C., Patone, G.,
Hummel, O., Chen, W., Cook, S., Cuppen, E., Colomé
Tatché, M., Johannes, F., Jansen, R. C.,
Neil, H., Werner, M., Pravenec, M., Vingron, M., & Hubner, N.
(2014). Natural variation of histone modification and its
impact on gene expression in the rat genome.
Genome Research, 24(6), 942-953. https://doi.org/10.1101/gr.169029.113
Pino
Del Carpio, D., Basnet, R. K., Arends, D., Lin, K., De Vos, R. C.
H., Muth, D., Kodde, J., Boutilier, K., Bucher, J., Wang, X.,
Jansen, R., & Bonnema, G. (2014). Regulatory
network of secondary metabolism in Brassica rapa: insight into the
glucosinolate pathway. PLoS ONE,
9(9), Article e107123. https://doi.org/10.1371/journal.pone.0107123
Velde,
K. J. V. D., Haan, M. D., Zych, K., Arends, D., Snoek, L.
B., Kammenga, J. E., Jansen, R. C., Swertz, M.
A., & Li, Y. (2014). WormQTL(HD)-a
web database for linking human disease to natural variation data in
C. elegans. Nucleic Acids Research,
42(D1), D794-D801. https://doi.org/10.1093/nar/gkt1044
Snoek,
L. B., Joeri van der Velde, K., Li,
Y., Jansen, R. C., Swertz, M. A.,
& Kammenga, J. E. (2014). Worm variation made accessible:
Take your shopping cart to store, link, and investigate!
Worm, 3(2), Article e28357. https://doi.org/10.4161/worm.28357
Samin,
G., Pavlova, M., Arif, M., Postema, C. P., Damborsky,
J., & Janssen, D. B. (2014). A Pseudomonas
putida strain genetically engineered for 1,2,3-trichloropropane
bioremediation. Applied and environmental
microbiology, 80(17), 5467-5476. https://doi.org/10.1128/AEM.01620-14
Floor,
R. J., Wijma, H. J., Colpa, D. I.,
Ramos-Silva, A., Jekel, P. A., Szymanski, W.,
Feringa, B. L., Marrink, S. J., &
Janssen, D. B. (2014). Computational Library Design
for Increasing Haloalkane Dehalogenase Stability.
ChemBioChem, 15(11), 1659-1671. https://doi.org/10.1002/cbic.201402128
Wijma,
H. J., Floor, R. J., Jekel, P. A., Baker, D., Marrink,
S. J., & Janssen, D. B. (2014).
Computationally designed libraries for rapid enzyme
stabilization. Protein Engineering, Design &
Selection, 27(2), 49-58. https://doi.org/10.1093/protein/gzt061
Wijma,
H. J., Marrink, S. J., & Janssen, D.
B. (2014). Computationally Efficient and Accurate
Enantioselectivity Modeling by Clusters of Molecular Dynamics
Simulations. Journal of chemical information and
modeling, 54(7), 2079-2092. https://doi.org/10.1021/ci500126x
Masman,
M. F., Heberling, M. M., & Janssen, D. B. (2014).
From Aminomutases to Ammonia Lyases: A Protein Engineering
Study. Biophysical Journal,
106(2), 655a-655a. https://doi.org/10.1016/j.bpj.2013.11.3623
Baldenius,
K.-U., Ditrich, K., Breurer, M., Navickas, V., Janssen,
D., Bartsch, S., & Crismaru, C. (2014). Method for the production of primary amines.
(Patent No. WO2014041011). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2014041011A2&KC=A2&FT=D&ND=3&date=20140320&DB=&locale=en_EP
Arif,
M. I., Toplak, A., Szymanski, W., Feringa, B.
L., Nuijens, T., Quaedflieg, P. J. L. M., Wu, B.,
& Janssen, D. B. (2014). One-Step C-Terminal
Deprotection and Activation of Peptides with Peptide Amidase from
Stenotrophomonas maltophilia in Neat Organic Solvent.
Advanced Synthesis & Catalysis,
356(10), 2197-2202. https://doi.org/10.1002/adsc.201400109
Beek,
H. L. V., Wijma, H. J., Fromont, L.,
Janssen, D. B., & Fraaije, M. W. (2014).
Stabilization of cyclohexanone monooxygenase by a
computationally designed disulfide bond spanning only one
residue. FEBS Open Bio, 4,
168-174. https://doi.org/10.1016/j.fob.2014.01.009
Wybenga,
G. G., Szymanski, W., Wu, B., Feringa, B.
L., Janssen, D. B., & Dijkstra, B. W.
(2014). Structural Investigations into the Stereochemistry
and Activity of a Phenylalanine-2,3-aminomutase from Taxus
chinensis. Biochemistry,
53(19), 3187-3198. https://doi.org/10.1021/bi500187a
Plak,
K., Keizer-Gunnink, I., van Haastert, P. J.
M., & Kortholt, A. (2014).
Rap1-dependent pathways coordinate cytokinesis in
Dictyostelium. Molecular Biology of the
Cell, 25(25), 4195-4204. https://doi.org/10.1091/mbc.E14-08-1285
Gilsbach,
B. K., & Kortholt, A. (2014). Structural
biology of the LRRK2 GTPase and kinase domains: implications for
regulation. Frontiers in Molecular
Neuroscience, 7, Article 32. https://doi.org/10.3389/fnmol.2014.00032
Ho,
F. Y., Rosenbusch, K. E., & Kortholt,
A. (2014). The Potential of Targeting LRRK2 in
Parkinson’s Disease. In A. Qayyum Rana (Ed.), A
Synopsis of Parkinson's Disease (pp. 161-192). IntechOpen. https://doi.org/10.5772/57362
Van
Meervelt, V., Soskine, M., & Maglia, G. (2014).
Detection of Two Isomeric Binding Configurations in a
Protein-Aptamer Complex with a Biological Nanopore.
Acs Nano, 8(12), 12826-12835. https://doi.org/10.1021/nn506077e
Stoddart,
D., Ayub, M., Hoefler, L., Raychaudhuri, P., Klingelhoefer, J.
W., Maglia, G., Heron, A., & Bayley, H. (2014).
Functional truncated membrane pores.
Proceedings of the National Academy of Science of the
United States of America, 111(7), 2425-2430.
https://doi.org/10.1073/pnas.1312976111
Maglia,
G., & Soskine, M. (2014). Nanopore
biosensors for detection of proteins and nucleic acids.
(Patent No. WO2014153625). https://nl.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2014153625A1&KC=A1&FT=D&ND=3&date=20141002&DB=&locale=nl_NL
Jähme,
M., & Slotboom, D. J. (2015). Diversity of
membrane transport proteins for vitamins in bacteria and
archaea. Biochimica et biophysica
acta, 1850(3), 565-576. https://doi.org/10.1016/j.bbagen.2014.05.006
Jähme,
M., Guskov, A., & Slotboom, D. J.
(2014). Crystal structure of the vitamin B3 transporter PnuC,
a full-length SWEET homolog. Nature Structural
& Molecular Biology, 21(11), 1013-1015. https://doi.org/10.1038/nsmb.2909
Slotboom,
D. J. (2014). Structural and mechanistic insights into
prokaryotic energy-coupling factor transporters.
Nature Reviews Microbiology, 12(2),
79-87. https://doi.org/10.1038/nrmicro3175
ter
Beek, J., Guskov, A., & Slotboom, D.
J. (2014). Structural diversity of ABC
transporters. Journal of general
physiology, 143(4), 419-435. https://doi.org/10.1085/jgp.201411164
Venkataraman,
H., Te Poele, E. M., Rosłoniec, K. Z., Vermeulen,
N., Commandeur, J. N. M., van der Geize, R., &
Dijkhuizen, L. (2015). Biosynthesis of a steroid
metabolite by an engineered Rhodococcus erythropolis strain
expressing a mutant cytochrome P450 BM3 enzyme.
Applied Microbiology and Biotechnology,
99(11), 4713-4721. https://doi.org/10.1007/s00253-014-6281-7
El
Aidy, S., Dinan, T. G., & Cryan, J. F. (2014).
Immune modulation of the brain-gut-microbe axis.
Frontiers in Microbiology, 5,
Article 146. https://doi.org/10.3389/fmicb.2014.00146
El
Aidy, S., Derrien, M., Aardema, R., Hooiveld, G., Richards,
S. E., Dane, A., Dekker, J., Vreeken, R., Levenez, F., Doré,
J., Zoetendal, E. G., van Baarlen, P., & Kleerebezem, M.
(2014). Transient inflammatory-like state and microbial
dysbiosis are pivotal in establishment of mucosal homeostasis
during colonisation of germ-free mice. Beneficial
microbes, 5(1), 67-77. https://doi.org/10.3920/BM2013.0018
Veenhuis,
M., & van der Klei, I. J. (2014). A critical
reflection on the principles of peroxisome formation in
yeast. Frontiers in Physiology,
5, Article 110. https://doi.org/10.3389/fphys.2014.00110
Kawalek,
A., & van der Klei, I. (2014). At neutral pH
the chronological lifespan of Hansenula polymorpha increases upon
enhancing the carbon source concentration.
Microbial Cell, 1(6), 189-202. https://doi.org/10.15698/mic2014.06.149
Veenhuis,
M., & van der Klei, I. J. (2014). De novo
peroxisome biogenesis revisited. Microbial
Cell, 1(4), 128-130. https://doi.org/10.15698/mic2014.04.138
Hettema,
E. H., Erdmann, R., van der Klei, I., & Veenhuis,
M. (2014). Evolving models for peroxisome biogenesis.
Current Opinion in Cell Biology,
29C, 25-30. https://doi.org/10.1016/j.ceb.2014.02.002
Scheckhuber,
C. Q., & van der Klei, I. J. (2014). Improved penicillin production. (Patent No.
WO2014003555). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2014003555A1&KC=A1&FT=D&ND=3&date=20140103&DB=&locale=en_EP
van
Zutphen, T., Todde, V., de Boer, R., Kreim, M.,
Hofbauer, H. F., Wolinski, H., Veenhuis, M., Klei, I. J. V.
D., & Kohlwein, S. D. (2014). Lipid droplet
autophagy in the yeast Saccharomyces cerevisiae.
Molecular Biology of the Cell,
25(2), 290-301. https://doi.org/10.1091/mbc.E13-08-0448
Kumar,
S., Kawalek, A., & van der Klei, I. J. (2014).
Peroxisomal quality control mechanisms.
Current Opinion in Microbiology, 22,
30-37. https://doi.org/10.1016/j.mib.2014.09.009
van
der Klei, I. J. (2014). Peroxisomes. In L. M.
McManus, & R. N. Mitchell (Eds.), Pathobiology of Human
Disease: A Dynamic Encyclopedia of Disease Mechanisms (pp.
108-113). Elsevier. https://doi.org/10.1016/B978-0-12-386456-7.01407-6
Knoops,
K., Manivannan, S., Cepinska, M. N., Krikken, A.
M., Kram, A. M., Veenhuis, M., & van
der Klei, I. J. (2014). Preperoxisomal vesicles can
form in the absence of Pex3. The Journal of Cell
Biology, 204(5), 659-668. https://doi.org/10.1083/jcb.201310148
Williams,
C., & van der Klei, I. (2014). The Functions
of Pex11 Family Proteins in Peroxisome Biology: Molecular Machines
Involved in Peroxisome Biogenesis and Maintenance. In C.
Brocard, & A. Hartig (Eds.), Molecular Machines Involved in
Peroxisome Biogenesis and Maintenance (pp. 425-437). Springer.
https://doi.org/10.1007/978-3-7091-1788-0_19
Saraya,
R., Gidijala, L., Veenhuis, M., & van der Klei, I.
J. (2014). Tools for genetic engineering of the yeast
Hansenula polymorpha. In V. Mapelli (Ed.), Yeast
Metabolic Engineering: Methods and Protocols (Vol. 1152, pp.
43-62). (Methods in Molecular Biology ; Vol. 1152). Springer. https://doi.org/10.1007/978-1-4939-0563-8_3
Pfanner,
N., van der Laan, M., Amati, P., Capaldi, R. A., Caudy, A. A.,
Chacinska, A., Darshi, M., Deckers, M., Hoppins, S., Icho, T.,
Jakobs, S., Ji, J., Kozjak-Pavlovic, V., Meisinger, C., Odgren, P.
R., Park, S. K., Rehling, P., Reichert, A. S., Sheikh, M. S., ...
Nunnari, J. (2014). Uniform nomenclature for the
mitochondrial contact site and cristae organizing system.
The Journal of Cell Biology, 204(7),
1083-1086. https://doi.org/10.1083/jcb.201401006
Zavadlav,
J., Melo, M. N., Cunha, A. V., de Vries, A. H.,
Marrink, S. J., & Praprotnik, M. (2014). Adaptive
Resolution Simulation of MARTINI Solvents. Journal
of Chemical Theory and Computation, 10(6),
2591-2598. https://doi.org/10.1021/ct5001523
Negro,
E., Latsuzbaia, R., de Vries, A. H., & Koper, G.
J. M. (2014). Experimental and molecular dynamics
characterization of dense micro emulsion systems morphology,
conductivity and SAXS. Soft Matter,
10(43), 8685-8697. https://doi.org/10.1039/c4sm01763c
Haverkort,
F., Stradomska, A., Vries, A. H. D., &
Knoester, J. (2014). First-Principles Calculation of
the Optical Properties of an Amphiphilic Cyanine Dye
Aggregate. The Journal of Physical Chemistry. A:
Molecules, Spectroscopy, Kinetics, Environment, & General
Theory, 118(6), 1012-1023. https://doi.org/10.1021/jp4112487
Ingólfsson,
H. I., Melo, M. N., van Eerden, F. J., Arnarez, C., Lopez, C.
A., Wassenaar, T. A., Periole, X., de Vries, A.
H., Tieleman, D. P., & Marrink, S. J.
(2014). Lipid organization of the plasma membrane.
Journal of the American Chemical Society,
136(41), 14554-14559. https://doi.org/10.1021/ja507832e
Solopova,
A., van Gestel, J., Weissing, F. J., Bachmann, H.,
Teusink, B., Kok, J., & Kuipers, O.
P. (2014). Bet-hedging during bacterial diauxic
shift. Proceedings of the National Academy of
Science of the United States of America,
111(20), 7427-7432. https://doi.org/10.1073/pnas.1320063111
C.
Abrantes, M., Kok, J., & de Fatima Silva Lopes, M.
(2014). Enterococcus faecalis zinc-responsive proteins
mediate bacterial defence against zinc overload, lysozyme and
oxidative stress. Microbiology,
160(12), 2755-2762. https://doi.org/10.1099/mic.0.080341-0
Visweswaran,
G. R. R., Leenhouts, K., van Roosmalen, M., Kok,
J., & Buist, G. (2014). Exploiting
the peptidoglycan-binding motif, LysM, for medical and industrial
applications. Applied Microbiology and
Biotechnology, 98(10), 4331-4345. https://doi.org/10.1007/s00253-014-5633-7
Kok,
J., Johansen, E., Kleerebezem, M., & Teusink, B. (2014).
Lactic Acid Bacteria: embarking on 30 more years of
research. Microbial Cell Factories,
13(Suppl 1), Article l1. https://doi.org/10.1186/1475-2859-13-S1-I1
Puri,
P., Eckhardt, T. H., Franken, L. E., Fusetti, F., Stuart, M.
C. A., Boekema, E. J., Kuipers, O. P.,
Kok, J., & Poolman, B. (2014).
Lactococcus lactis YfiA is necessary and sufficient for
ribosome dimerization. Molecular
Microbiology, 91(2), 394-407. https://doi.org/10.1111/mmi.12468
Ali,
H., Ries, M. I., Lankhorst, P. P., van der Hoeven, R. A. M.,
Schouten, O. L., Noga, M., Hankemeier, T., van Peij, N. N. M.
E., Bovenberg, R. A. L., Vreeken, R. J., &
Driessen, A. J. M. (2014). A Non-Canonical NRPS Is
Involved in the Synthesis of Fungisporin and Related Hydrophobic
Cyclic Tetrapeptides in Penicillium chrysogenum.
PLoS ONE, 9(6), Article e98212. https://doi.org/10.1371/journal.pone.0098212
Gorochowski,
T. E., van den Berg, E., Kerkman, R., Roubos, J. A., &
Bovenberg, R. A. L. (2014). Using Synthetic Biological
Parts and Microbioreactors to Explore the Protein Expression
Characteristics of Escherichia coli. ACS Synthetic
Biology, 3(3), 129-139. https://doi.org/10.1021/sb4001245
Jain,
S., Caforio, A., & Driessen, A. J. M. (2014).
Biosynthesis of archaeal membrane ether lipids.
Frontiers in Microbiology, 5,
Article 641. https://doi.org/10.3389/fmicb.2014.00641
Geng,
Y., Keyzer, J. D., Scheffers, D.-J., &
Driessen, A. J. M. (2014). Defining the Region of
Bacillus subtilis SpoIIIJ That Is Essential for Its
Sporulation-Specific Function. Journal of
Bacteriology, 196(7), 1318-1324. https://doi.org/10.1128/JB.01084-13
Yang,
N., & Driessen, A. J. M. (2014). Deletion of
cdvB paralogous genes of Sulfolobus acidocaldarius impairs cell
division. Extremophiles,
18(2), 331-339. https://doi.org/10.1007/s00792-013-0618-5
Daszczuk,
A., Dessalegne, Y., Drenth, I., Hendriks, E., Jo, E.,
van Lente, T., Oldebesten, A., Parrish, J., Poljakova, W.,
Purwanto, A. A., van Raaphorst, R., Boonstra,
M., van Heel, A., Herber, M., van der
Meulen, S., Siebring, J., Sorg, R. A., Heinemann,
M., Kuipers, O. P., & Veening, J.-W.
(2014). Bacillus subtilis Biosensor Engineered To Assess Meat
Spoilage. ACS Synthetic Biology,
3(12), 999-1002. https://doi.org/10.1021/sb5000252
Huberts,
D. H. E. W., Gonzalez Hernandez, J., Lee, S. S., Litsios, A.,
Hubmann, G., Wit, E. C., & Heinemann,
M. (2014). Calorie restriction does not elicit a
robust extension of replicative lifespan in Saccharomyces
cerevisiae. Proceedings of the National Academy of
Science of the United States of America,
111(32), 11727-11731. https://doi.org/10.1073/pnas.1410024111
Kotte,
O., Volkmer, B., Radzikowski, J. L., & Heinemann,
M. (2014). Phenotypic bistability in Escherichia
coli's central carbon metabolism. Molecular
Systems Biology, 10(7), Article 736. https://doi.org/10.15252/msb.20135022
Lee,
S. S., Dechant, R., Vizcarra, I. A., Huberts, D. H. E. W., Lee, L.
P., Heinemann, M., & Peter, M. (2014).
Single cell analysis of yeast aging using microfluidic
dissection. In 18th International Conference on
Miniaturized Systems for Chemistry and Life Sciences, MicroTAS
2014 (pp. 666-668). Chemical and Biological Microsystems
Society .
Opacic,
M., Giusti, F., Popot, J.-L., & Broos, J. (2014).
Isolation of Escherichia coli Mannitol Permease, EIImtl,
Trapped in Amphipol A8-35 and Fluorescein-Labeled A8-35.
Journal of membrane biology,
247(9-10), 1019-1030. https://doi.org/10.1007/s00232-014-9691-7
2013
Joosen,
R. V. L., Arends, D., Li, Y., Willems, L. A. J.,
Keurentjes, J. J. B., Ligterink, W., Jansen, R. C.,
& Hilhorst, H. W. M. (2013). Identifying
Genotype-by-Environment Interactions in the Metabolism of
Germinating Arabidopsis Seeds Using Generalized Genetical
Genomics. Plant Physiology,
162(2), 553-566. https://doi.org/10.1104/pp.113.216176
Westra,
H.-J., Peters, M. J., Esko, T., Yaghootkar, H., Schurmann,
C., Kettunen, J., Christiansen, M. W., Fairfax, B. P., Schramm, K.,
Powell, J. E., Zhernakova, A., Zhernakova, D.
V., Veldink, J. H., Van den Berg, L. H., Karjalainen,
J., Withoff, S., Uitterlinden, A. G., Hofman, A.,
Rivadeneira, F., ... Hoen, P. A. C. . (2013). Systematic
identification of trans eQTLs as putative drivers of known disease
associations. Nature Genetics,
45(10), 1238-1243. https://doi.org/10.1038/ng.2756
Snoek,
L. B., Van der Velde, K. J., Arends, D., Li,
Y., Beyer, A., Elvin, M., Fisher, J., Hajnal, A.,
Hengartner, M. O., Poulin, G. B., Rodriguez, M., Schmid, T.,
Schrimpf, S., Xue, F., Jansen, R. C., Kammenga, J.
E., & Swertz, M. A. (2013). WormQTL-public
archive and analysis web portal for natural variation data in
Caenorhabditis spp. Nucleic Acids
Research, 41(D1), D738-D743. https://doi.org/10.1093/nar/gks1124
Szymanski,
W., Wu, B., Poloni, C., Janssen, D. B.,
& Feringa, B. L. (2013). Azobenzene Photoswitches
for Staudinger-Bertozzi Ligation. Angewandte
Chemie-International Edition, 52(7),
2068-2072. https://doi.org/10.1002/anie.201208596
Schallmey,
M., Floor, R. J., Hauer, B., Breuer, M., Jekel, P. A., Wijma,
H. J., Dijkstra, B., & Janssen, D. B.
(2013). Biocatalytic and Structural Properties of a Highly
Engineered Halohydrin Dehalogenase.
ChemBioChem, 14(7), 870-881. https://doi.org/10.1002/cbic.201300005
Crismaru,
C. G., Wybenga, G. G., Szymanski, W., Wijma, H.
J., Wu, B., Bartsch, S., de Wildeman, S., Poelarends,
G. J., Feringa, B. L., Dijkstra, B.,
& Janssen, D. B. (2013). Biochemical Properties
and Crystal Structure of a β-Phenylalanine Aminotransferase
from Variovorax paradoxus. Applied and
environmental microbiology, 79(1), 185-195. https://doi.org/10.1128/AEM.02525-12
Wijma,
H. J., & Janssen, D. B. (2013).
Computational design gains momentum in enzyme catalysis
engineering. Febs Journal,
280(13), 2948-2960. https://doi.org/10.1111/febs.12324
Di
Toma, C., Sonke, T., Quaedflieg, P. J., Wagner, A. F. V.,
& Janssen, D. B. (2013). Corrigendum:
“Purification and use of Escherichia coli peptide deformylase
for peptide deprotection in chemoenzymatic peptide synthesis”
[Protein Expr. Purif. 89 (2013) 73–79].
Protein Expression and Purification,
90(2), 141. https://doi.org/10.1016/j.pep.2013.06.001
Schmidt,
E., Mandt, C., Janssen, D. B., Pieper, D. H., &
Reineke, W. (2013). Degradation of chloroaromatics: structure
and catalytic activities of wild-type chlorocatechol
2,3-dioxygenases and modified ones. Environmental
Microbiology, 15(1), 183-190. https://doi.org/10.1111/j.1462-2920.2012.02831.x
Raj,
H., Szymanski, W., Villiers, J. D., Puthan Veetil,
V., Quax, W. J., Shimamoto, K., Janssen, D.
B., Feringa, B. L., & Poelarends, G.
J. (2013). Kinetic Resolution and Stereoselective
Synthesis of 3-Substituted Aspartic Acids by Using Engineered
Methylaspartate Ammonia Lyases.
Chemistry, 19(34), 11148-11152. https://doi.org/10.1002/chem.201301832
Heberling,
M. M., Wu, B., Bartsch, S., & Janssen, D. B.
(2013). Priming ammonia lyases and aminomutases for
industrial and therapeutic applications. Current
Opinion in Chemical Biology, 17(2), 250-260.
https://doi.org/10.1016/j.cbpa.2013.02.013
Toplak,
A., Wu, B., Fusetti, F., Quaedflieg, P. J. L. M., &
Janssen, D. B. (2013). Proteolysin, a Novel Highly
Thermostable and Cosolvent-Compatible Protease from the
Thermophilic Bacterium Coprothermobacter proteolyticus.
Applied and environmental microbiology,
79(18), 5625-5632. https://doi.org/10.1128/AEM.01479-13
Di
Toma, C., Sonke, T., Quaedflieg, P. J., & Janssen, D.
B. (2013). Purification and use of E. coli peptide
deformylase for peptide deprotection in chemoenzymatic peptide
synthesis. Protein Expression and
Purification, 89(1), 73-79. https://doi.org/10.1016/j.pep.2013.01.004
Bartsch,
S., Wybenga, G. G., Jansen, M., Heberling, M. M., Wu, B., Dijkstra,
B. W., & Janssen, D. B. (2013). Redesign of
a Phenylalanine Aminomutase into a Phenylalanine Ammonia
Lyase. ChemCatChem, 5(7),
1797-1802. https://doi.org/10.1002/cctc.201200871
Bracco,
P., Janssen, D. B., & Schallmey, A. (2013).
Selective steroid oxyfunctionalisation by CYP154C5, a
bacterial cytochrome P450. Microbial Cell
Factories, 12, Article 95. https://doi.org/10.1186/1475-2859-12-95
Wijma,
H. J., Floor, R. J., & Janssen, D. B.
(2013). Structure- and sequence-analysis inspired engineering
of proteins for enhanced thermostability. Current
Opinion in Structural Biology, 23(4), 588-594.
https://doi.org/10.1016/j.sbi.2013.04.008
Kataria,
R., Xu, X., Fusetti, F., Keizer-Gunnink, I., Jin,
T., van Haastert, P. J. M., & Kortholt,
A. (2013). Dictyostelium Ric8 is a nonreceptor guanine
exchange factor for heterotrimeric G proteins and is important for
development and chemotaxis. Proceedings of the
National Academy of Sciences of the United States of
America, 110(16), 6424-6429. https://doi.org/10.1073/pnas.1301851110
Veltman,
D. M., & Van Haastert, P. J. M. (2013).
Extrachromosomal inducible expression.
Methods in Molecular Biology, 983,
269-281. https://doi.org/10.1007/978-1-62703-302-2_14
Plak,
K., Veltman, D., Fusetti, F., Beeksma, J., Rivero, F., Van
Haastert, P. J. M., & Kortholt, A. (2013).
GxcC connects Rap and Rac signaling during Dictyostelium
development. BMC Cell Biology,
14(1), 6-1-6-9. Article 6. https://doi.org/10.1186/1471-2121-14-6
Kortholt,
A., Keizer-Gunnink, I., Kataria, R.,
& Van Haastert, P. J. M. (2013). Ras activation
and symmetry breaking during Dictyostelium chemotaxis.
Journal of Cell Science, 126(19),
4502-4513. https://doi.org/10.1242/jcs.132340
Kataria,
R., van Haastert, P. J. M., & Kortholt,
A. (2013). Reply to Tall et al. Dictyostelium Ric8
does not have a chaperoning function during development and
chemotaxis. Proceedings of the National Academy of
Sciences of the United States of America,
110(34), E3149-E3149. https://doi.org/10.1073/pnas.1309837110
Koelsch,
V., Shen, Z., Lee, S., Plak, K., Lotfi, P., Chang, J., Charest, P.
G., Romero, J. L., Jeon, T. J., Kortholt, A., Briggs,
S. P., & Firtel, R. A. (2013). Daydreamer, a Ras effector
and GSK-3 substrate, is important for directional sensing and cell
motility. Molecular Biology of the
Cell, 24(2), 100-114. https://doi.org/10.1091/mbc.E12-04-0271
Mueller-Taubenberger,
A., Kortholt, A., & Eichinger, L. (2013).
Simple system - substantial share: The use of Dictyosrelium
in cell biology and molecular medicine. European
Journal of Cell Biology, 92(2), 45-53. https://doi.org/10.1016/j.ejcb.2012.10.003
Franceschini,
L., Soskine, M., Biesemans, A., & Maglia, G.
(2013). A nanopore machine promotes the vectorial transport
of DNA across membranes. Nature
Communications, 4, 1-8. Article 2415. https://doi.org/10.1038/ncomms3415
Soskine,
M., Biesemans, A., De Maeyer, M., & Maglia, G.
(2013). Tuning the size and properties of ClyA nanopores
assisted by directed evolution. Journal of the
American Chemical Society, 135(36),
13456-13463. https://doi.org/10.1021/ja4053398
Hänelt,
I., Wunnicke, D., Bordignon, E., Steinhoff, H.-J., &
Slotboom, D. J. (2013). Conformational heterogeneity
of the aspartate transporter Glt(Ph). Nature
Structural & Molecular Biology, 20(2),
210-214. https://doi.org/10.1038/nsmb.2471
Jensen,
S., Guskov, A., Rempel, S., Hänelt, I.,
& Slotboom, D. J. (2013). Crystal structure of a
substrate-free aspartate transporter. Nature
Structural & Molecular Biology, 20(10),
1224-1226. https://doi.org/10.1038/nsmb.2663
Slotboom,
D. J. (2013). Flipping the Sidedness of Disulfide Bond
Formation. Journal of Molecular
Biology, 425(18), 3265-3267. https://doi.org/10.1016/j.jmb.2013.07.005
Fulyani,
F., Schuurman-Wolters, G. K., Vujicic - Zagar,
A., Guskov, A., Slotboom, D.-J.,
& Poolman, B. (2013). Functional Diversity of
Tandem Substrate-Binding Domains in ABC Transporters from
Pathogenic Bacteria. Structure,
21(10), 1879-1888. https://doi.org/10.1016/j.str.2013.07.020
Kolbusz,
M. A., Slotboom, D. J., & Lolkema, J. S. (2013).
Genomic distribution of the small multidrug resistance
protein EmrE over 29 Escherichia coli strains reveals two forms of
the protein. Febs Journal,
280(1), 244-255. https://doi.org/10.1111/febs.12065
Ejby,
M., Fredslund, F., Vujicic - Zagar, A., Svensson, B.,
Slotboom, D. J., & Abou Hachem, M. (2013).
Structural basis for arabinoxylo-oligosaccharide capture by
the probiotic Bifidobacterium animalis subsp lactis Bl-04.
Molecular Microbiology, 90(5),
1100-1112. https://doi.org/10.1111/mmi.12419
Poolman,
B., & Slotboom, D.-J. (2013).
Substrate Capture by ABC Transporters. In G. C. K.
Roberts (Ed.), Encyclopedia of Biophysics (pp. 2503-2509).
Springer.
Majsnerowska,
M., Hänelt, I., Wunnicke, D., Schaefer, L. V., Steinhoff,
H.-J., & Slotboom, D. J. (2013).
Substrate-Induced Conformational Changes in the S-Component
ThiT from an Energy Coupling Factor Transporter.
Structure, 21(5), 861-867. https://doi.org/10.1016/j.str.2013.03.007
Erkens,
G. B., Hänelt, I., Goudsmits, J. M. H., Slotboom, D.
J., & van Oijen, A. M. (2013).
Unsynchronised subunit motion in single trimeric
sodium-coupled aspartate transporters.
Nature, 502(7469), 119-123. https://doi.org/10.1038/nature12538
El
Aidy, S., Derrien, M., Merrifield, C. A., Levenez, F.,
Doré, J., Boekschoten, M. V., Dekker, J., Holmes, E.,
Zoetendal, E. G., van Baarlen, P., Claus, S. P., & Kleerebezem,
M. (2013). Gut bacteria-host metabolic interplay during
conventionalisation of the mouse germfree colon.
The ISME journal, 7(4), 743-755. https://doi.org/10.1038/ismej.2012.142
El
Aidy, S., Van den Abbeele, P., Van de Wiele, T., Louis, P.,
& Kleerebezem, M. (2013). Intestinal colonization: how
key microbial players become established in this dynamic process:
microbial metabolic activities and the interplay between the host
and microbes. BioEssays,
35(10), 913-923. https://doi.org/10.1002/bies.201300073
El
Aidy, S., & Kleerebezem, M. (2013). Molecular
signatures for the dynamic process of establishing intestinal
host-microbial homeostasis: potential for disease
diagnostics? Current opinion in
gastroenterology, 29(6), 621-627. https://doi.org/10.1097/MOG.0b013e328365d365
Van
den Abbeele, P., Verstraete, W., El Aidy, S.,
Geirnaert, A., & Van de Wiele, T. (2013). Prebiotics,
faecal transplants and microbial network units to stimulate
biodiversity of the human gut microbiome.
Microbial Biotechnology, 6(4),
335-340. https://doi.org/10.1111/1751-7915.12049
El
Aidy, S., Hooiveld, G., Tremaroli, V., Bäckhed, F.,
& Kleerebezem, M. (2013). The gut microbiota and mucosal
homeostasis: colonized at birth or at adulthood, does it
matter? Gut Microbes, 4(2),
118-124. https://doi.org/10.4161/gmic.23362
El
Aidy, S., Merrifield, C. A., Derrien, M., van Baarlen, P.,
Hooiveld, G., Levenez, F., Dore, J., Dekker, J., Holmes, E., Claus,
S. P., Reijngoud, D.-J., & Kleerebezem, M. (2013).
The gut microbiota elicits a profound metabolic reorientation
in the mouse jejunal mucosa during conventionalisation.
Gut, 62(9), 1306-1314. https://doi.org/10.1136/gutjnl-2011-301955
Scheckhuber,
C. Q., Veenhuis, M., & van der Klei, I. J. (2013).
Improving penicillin biosynthesis in Penicillium chrysogenum
by glyoxalase overproduction. Metabolic
Engineering, 18, 36-43. https://doi.org/10.1016/j.ymben.2013.04.003
Kohlwein,
S. D., Veenhuis, M., & van der Klei, I. J. (2013).
Lipid Droplets and Peroxisomes: Key Players in Cellular Lipid
Homeostasis or A Matter of Fat-Store 'em Up or Burn 'em
Down. Genetics, 193(1), 1-50.
https://doi.org/10.1534/genetics.112.143362
Manivannan,
S., de Boer, R., Veenhuis, M., & van der
Klei, I. J. (2013). Lumenal peroxisomal protein
aggregates are removed by concerted fission and autophagy
events. Autophagy, 9(7),
1044-1056. https://doi.org/10.4161/auto.24543
Kawalek,
A., Lefevre, S. D., Veenhuis, M., & van der Klei, I.
J. (2013). Peroxisomal catalase deficiency modulates
yeast lifespan depending on growth conditions.
Aging-Us, 5(1), 67-83. https://doi.org/10.18632/aging.100519
Williams,
C., & van der Klei, I. J. (2013).
Pexophagy-linked degradation of the peroxisomal membrane
protein Pex3p involves the ubiquitin-proteasome system.
Biochemical and Biophysical Research
Communications, 438(2), 395-401. https://doi.org/10.1016/j.bbrc.2013.07.086
Lefevre,
S. D., van Roermund, C. W., Wanders, R. J. A., Veenhuis, M.,
& van der Klei, I. J. (2013). The significance of
peroxisome function in chronological aging of Saccharomyces
cerevisiae. Aging Cell,
12(5), 784-793. https://doi.org/10.1111/acel.12113
Klei,
I. J. V. D., & Veenhuis, M. (2013). The
Versatility of Peroxisome Function in Filamentous Fungi. In
L. A. D. Río (Ed.), Peroxisomes and their Key Role in
Cellular Signaling and Metabolism (69 ed., pp. 135-152).
(Subcellular Biochemistry; No. 69). Springer.
Lopez,
C. A., de Vries, A. H., & Marrink, S.
J. (2013). Computational microscopy of cyclodextrin
mediated cholesterol extraction from lipid model membranes.
Scientific Reports, 3, Article 2071.
https://doi.org/10.1038/srep02071
Haverkort,
F., Stradomska, A., de Vries, A. H., &
Knoester, J. (2013). Investigating the Structure of
Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics
Simulations. Journal of Physical Chemistry
B, 117(19), 5857-5867. https://doi.org/10.1021/jp4005696
Lopez,
C. A., Sovova, Z., van Eerden, F. J., de Vries, A.
H., & Marrink, S. J. (2013). Martini
Force Field Parameters for Glycolipids. Journal of
Chemical Theory and Computation, 9(3),
1694-1708. https://doi.org/10.1021/ct3009655
Gobbo,
C., Beurroies, I., de Ridder, D., Eelkema, R., Marrink, S.
J., De Feyter, S., van Esch, J. H., & de Vries, A.
H. (2013). MARTINI Model for Physisorption of Organic
Molecules on Graphite. Journal of Physical
Chemistry C, 117(30), 15623-15631. https://doi.org/10.1021/jp402615p
Visweswaran,
G. R. R., Steen, A., Leenhouts, K., Szeliga, M.,
Ruban, B., Hesseling-Meinders, A., Dijkstra, B. W., Kuipers,
O. P., Kok, J., & Buist, G.
(2013). AcmD, a homolog of the major autolysin AcmA of
Lactococcus lactis, binds to the cell wall and contributes to cell
separation and autolysis. PLoS ONE,
8(8), Article e72167. https://doi.org/10.1371/journal.pone.0072167
van
Heel, A. J., de Jong, A., Montalban-Lopez,
M., Kok, J., & Kuipers, O. P. (2013).
BAGEL3: automated identification of genes encoding
bacteriocins and (non-)bactericidal posttranslationally modified
peptides. Nucleic Acids Research,
41(W1), W448-W453. https://doi.org/10.1093/nar/gkt391
Overkamp,
W., Beilharz, K., Weme, R. D. O., Solopova, A., Karsens,
H., Kovacs, A. T., Kok, J., Kuipers, O.
P., & Veening, J.-W. (2013). Benchmarking Various
Green Fluorescent Protein Variants in Bacillus subtilis,
Streptococcus pneumoniae, and Lactococcus lactis for Live Cell
Imaging. Applied and environmental
microbiology, 79(20), 6481-6490. https://doi.org/10.1128/AEM.02033-13
Abrantes,
M. C., Kok, J., & Lopes, M. D. F. (2013).
EfaR Is a Major Regulator of Enterococcus faecalis Manganese
Transporters and Influences Processes Involved in Host Colonization
and Infection. Infection and Immunity,
81(3), 935-944. https://doi.org/10.1128/IAI.06377-11
Steele,
J., Broadbent, J., & Kok, J. (2013).
Perspectives on the contribution of lactic acid bacteria to
cheese flavor development. Current Opinion in
Biotechnology, 24(2), 135-141. https://doi.org/10.1016/j.copbio.2012.12.001
de
Jong, A., Hansen, M. E., Kuipers, O. P.,
Kilstrup, M., & Kok, J. (2013). The
Transcriptional and Gene Regulatory Network of Lactococcus lactis
MG1363 during Growth in Milk. PLoS
ONE, 8(1), Article e53085. https://doi.org/10.1371/journal.pone.0053085
Eckhardt,
T. H., Skotnicka, D., Kok, J., & Kuipers, O.
P. (2013). Transcriptional Regulation of Fatty Acid
Biosynthesis in Lactococcus lactis. Journal of
Bacteriology, 195(5), 1081-1089. https://doi.org/10.1128/JB.02043-12
Khusainov,
R., Moll, G. N., & Kuipers, O. P.
(2013). Identification of distinct nisin leader peptide
regions that determine interactions with the modification enzymes
NisB and NisC. FEBS Open Bio,
3, 237-242. https://doi.org/10.1016/j.fob.2013.05.001
Plat,
A., Kuipers, A., Rink, R., & Moll, G. N. (2013).
Mechanistic aspects of lanthipeptide leaders.
Current Protein and Peptide Science,
14(2), 85-96. https://doi.org/10.2174/1389203711314020001
Arnison,
P. G., Bibb, M. J., Bierbaum, G., Bowers, A. A., Bugni, T. S.,
Bulaj, G., Camarero, J. A., Campopiano, D. J., Challis, G. L.,
Clardy, J., Cotter, P. D., Craik, D. J., Dawson, M., Dittmann, E.,
Donadio, S., Dorrestein, P. C., Entian, K.-D., Fischbach, M. A.,
Garavelli, J. S., ... Süssmuth, R. D. (2013).
Ribosomally synthesized and post-translationally modified
peptide natural products: overview and recommendations for a
universal nomenclature. Natural product
reports, 30(1), 108-160. https://doi.org/10.1039/c2np20085f
Ali,
H., Ries, M. I., Nijland, J. G., Lankhorst, P. P.,
Hankemeier, T., Bovenberg, R. A. L., Vreeken, R.
J., & Driessen, A. J. M. (2013). A Branched
Biosynthetic Pathway Is Involved in Production of Roquefortine and
Related Compounds in Penicillium chrysogenum. PLoS
ONE, 8(6), Article e65328. https://doi.org/10.1371/journal.pone.0065328
Ries,
M. I., Ali, H., Lankhorst, P. P., Hankemeier, T., Bovenberg,
R. A. L., Driessen, A. J. M., & Vreeken, R.
J. (2013). Novel Key Metabolites Reveal Further Branching of
the Roquefortine/Meleagrin Biosynthetic Pathway.
J. Biol. Chem., 288(52),
37289-37295. https://doi.org/10.1074/jbc.M113.512665
Scheffers,
DJ. (2013). Bacterial Reproduction and Growth.
In eLS Wiley. https://doi.org/10.1002/9780470015902.a0001419.pub2
Trip,
E. N., Veening, J.-W., Stewart, E. J., Errington, J., &
Scheffers, D.-J. (2013). Balanced transcription of
cell division genes in Bacillus subtilis as revealed by single cell
analysis. Environmental Microbiology,
15(12), 3196-3209. https://doi.org/10.1111/1462-2920.12148
Boekema,
E. J., Scheffers, D.-J., van Bezouwen, L. S., Bolhuis,
H., & Folea, I. M. (2013). Focus on Membrane
Differentiation and Membrane Domains in the Prokaryotic
Cell. Journal of Molecular Microbiology and
Biotechnology, 23(4-5), 345-356. https://doi.org/10.1159/000351361
Król,
E., & Scheffers, D.-J. (2013). FtsZ
Polymerization Assays: Simple Protocols and Considerations.
Journal of Visualized Experiments, (81),
e50844-1-e50844-13. https://doi.org/10.3791/50844
Ballesteros-Plaza,
D., Holguera, I., Scheffers, D.-J., Salas, M., &
Munoz-Espin, D. (2013). Phage phi 29 protein p1 promotes
replication by associating with the FtsZ ring of the divisome in
Bacillus subtilis. Proceedings of the National
Academy of Sciences of the United States of America,
110(30), 12313-12318. https://doi.org/10.1073/pnas.1311524110
Lages,
M. C. A., Beilharz, K., Angeles, D. M., Veening, J.-W., &
Scheffers, D.-J. (2013). The localization of key
Bacillus subtilis penicillin binding proteins during cell growth is
determined by substrate availability.
Environmental Microbiology, 15(12),
3272-3281. https://doi.org/10.1111/1462-2920.12206
Huberts,
D. H. E. W., Sik Lee, S., Gonzáles, J., Janssens, G. E.,
Vizcarra, I. A., & Heinemann, M. (2013).
Construction and use of a microfluidic dissection platform
for long-term imaging of cellular processes in budding
yeast. Nature protocols,
8(6), 1019-1027. https://doi.org/10.1038/nprot.2013.060
Huberts,
D. H. E. W., Janssens, G. E., Lee, S. S., Vizcarra, I. A.,
& Heinemann, M. (2013). Continuous High-resolution
Microscopic Observation of Replicative Aging in Budding
Yeast. Journal of visualized experiments :
JoVE, (78), Article 50143. https://doi.org/10.3791/50143
Gerosa,
L., Kochanowski, K., Heinemann, M., & Sauer, U.
(2013). Dissecting specific and global transcriptional
regulation of bacterial gene expression. Molecular
Systems Biology, 9, Article 658. https://doi.org/10.1038/msb.2013.14
Kochanowski,
K., Volkmer, B., Gerosa, L., Haverkorn van Rijsewijk, B. R.,
Schmidt, A., & Heinemann, M. (2013).
Functioning of a metabolic flux sensor in Escherichia
coli. Proceedings of the National Academy of
Sciences of the United States of America,
110(3), 1130-1135. https://doi.org/10.1073/pnas.1202582110
Ibáñez,
A. J., Fagerer, S. R., Schmidt, A. M., Urban, P. L., Jefimovs, K.,
Geiger, P., Dechant, R., Heinemann, M., & Zenobi,
R. (2013). Mass spectrometry-based metabolomics of single
yeast cells. Proceedings of the National Academy
of Sciences of the United States of America,
110(22), 8790-8794. https://doi.org/10.1073/pnas.1209302110
Zampar,
G. G., Kümmel, A., Ewald, J., Jol, S., Niebel, B., Picotti,
P., Aebersold, R., Sauer, U., Zamboni, N., & Heinemann,
M. (2013). Temporal system-level organization of the
switch from glycolytic to gluconeogenic operation in yeast.
Molecular Systems Biology, 9,
651-1-651-13. Article 651. https://doi.org/10.1038/msb.2013.11
Broos,
J. (2014). Biosynthetic Incorporation of Tryptophan
Analogs in Proteins. Methods in Molecular
Biology, 1076, 359-370. https://doi.org/10.1007/978-1-62703-649-8_15
Petrovic,
D. M., Leenhouts, K., van Roosmalen, M. L., & Broos,
J. (2013). An expression system for the efficient
incorporation of an expanded set of tryptophan analogues.
Amino Acids, 44(5), 1329-1336. https://doi.org/10.1007/s00726-013-1467-3
Petrovic,
D. M., Hesp, B. H., & Broos, J. (2013).
Emitting State of 5‑Hydroxyindole,
5‑Hydroxytryptophan, and 5‑Hydroxytryptophan
Incorporated in Proteins. The Journal of Physical
Chemistry B, 117(37), 10792-10797. https://doi.org/10.1021/jp406676j
Xu,
J., Chen, B., Callis, P., Rozeboom, H., Broos,
J., & Knutson, J. (2013). Femtosecond Fluorescence
Dynamics of Tryptophan and 5-Fluorotryptophan in Monellin: Slow
Water Relaxation Unmasked. Biophysical
Journal, 104(2), 681a-681a. https://doi.org/10.1016/j.bpj.2012.11.3759
Rohman,
A., van Oosterwijk, N., Thunnissen, A.-M. W. H., &
Dijkstra, B. W. (2013). Crystal Structure and Site-directed
Mutagenesis of 3-Ketosteroid Δ1-Dehydrogenase from Rhodococcus
erythropolis SQ1 Explain Its Catalytic Mechanism.
The Journal of Biological Chemistry,
288(49), 35559-35568. https://doi.org/10.1074/jbc.M113.522771
2012
Durrant,
C., Swertz, M. A., Alberts, R., Arends, D., Moeller,
S., Mott, R., Prins, P., van der Velde, K.
J., Jansen, R. C., & Schughart, K. (2012).
Bioinformatics tools and database resources for systems
genetics analysis in mice-a short review and an evaluation of
future needs. Briefings in
Bioinformatics, 13(2), 135-142. https://doi.org/10.1093/bib/bbr026
Colomé
Tatché, M., Cortijo, S., Wardenaar, R.,
Monteiro Morgado, L., Lahouze, B., Sarazin, A., Etcheverry, M.,
Martin, A., Feng, S., Duvernois-Berthet, E., Labadie, K., Wincker,
P., Jacobsen, S. E., Jansen, R. C., Colot, V., &
Johannes, F. (2012). Features of the Arabidopsis
recombination landscape resulting from the combined loss of
sequence variation and DNA methylation.
Proceedings of the National Academy of Sciences of the
United States of America, 109(40),
16240-16245. https://doi.org/10.1073/pnas.1212955109
Prins,
P., Smant, G., & Jansen, R. C. (2012).
Genetical Genomics for Evolutionary Studies.
Methods in Molecular Biology, 856,
469-485. https://doi.org/10.1007/978-1-61779-585-5_19
Demirkan,
A., van Duijn, C. M., Ugocsai, P., Isaacs, A., Pramstaller, P. P.,
Liebisch, G., Wilson, J. F., Johansson, A., Rudan, I., Aulchenko,
Y. S., Kirichenko, A. V., Janssens, A. C. J. W., Jansen, R.
C., Gnewuch, C., Domingues, F. S., Pattaro, C., Wild, S. H.,
Jonasson, I., Polasek, O., ... EUROSPAN Consortium (2012).
Genome-Wide Association Study Identifies Novel Loci
Associated with Circulating Phospho- and Sphingolipid
Concentrations. PLoS genetics,
8(2), Article e1002490. https://doi.org/10.1371/journal.pgen.1002490
Lendvai,
Á., Johannes, F., Grimm, C., Eijsink, J. J.
H., Wardenaar, R., Volders, H. H., Klip, H.
G., Hollema, H., Jansen, R. C.,
Schuuring, E., Wisman, G. B. A., &
van der Zee, A. G. J. (2012). Genome-wide methylation
profiling identifies hypermethylated biomarkers in high-grade
cervical intraepithelial neoplasia.
Epigenetics, 7(11), 1268-1278. https://doi.org/10.4161/epi.22301
Diekstra,
F. P., Saris, C. G. J., van Rheenen, W., Franke,
L., Jansen, R. C., van Es, M. A., van Vught, P.
W. J., Blauw, H. M., Groen, E. J. N., Horvath, S., Estrada, K.,
Rivadeneira, F., Hofman, A., Uitterlinden, A. G., Robberecht, W.,
Andersen, P. M., Melki, J., Meininger, V., Hardiman, O., ... Brown
Jr., R. H. (2012). Mapping of Gene Expression Reveals CYP27A1
as a Susceptibility Gene for Sporadic ALS. PLoS
ONE, 7(4), Article e35333. https://doi.org/10.1371/journal.pone.0035333
Zych,
K., Arends, D., & Jansen, R. (2012).
Pheno2geno; generating genetic markers and maps from
molecular phenotypes. http://pheno2geno.nl
Neto,
E. C., Keller, M. P., Broman, A. F., Attie, A. D., Jansen, R.
C., Broman, K. W., & Yandell, B. S. (2012).
Quantile-Based Permutation Thresholds for Quantitative Trait
Loci Hotspots. Genetics,
191(4), 1355-1365. https://doi.org/10.1534/genetics.112.139451
Fu,
J., Wolfs, M. G. M., Deelen, P., Westra,
H. J., Fehrmann, R. S. N., te Meerman,
G., Buurman, W. A., Rensen, S. S. M., Groen,
H., Weersma, R. K., van den Berg, L. H.,
Veldink, J., Ophoff, R. A., Snieder, H., van Heel,
D., Jansen, R. C., Hofker, M. H., Wijmenga,
C., & Franke, L. (2012). Unraveling
the regulatory mechanisms underlying tissue-dependent genetic
variation of gene expression. PLoS
genetics, 8(1), Article e1002431. https://doi.org/10.1371/journal.pgen.1002431
Joosen,
R. V. L., Arends, D., Willems, L. A. J., Ligterink, W.,
Jansen, R. C., & Hilhorst, H. W. M. (2012).
Visualizing the Genetic Landscape of Arabidopsis Seed
Performance. Plant Physiology,
158(2), 570-589. https://doi.org/10.1104/pp.111.186676
Arends,
D., van der Velde, K. J., Prins, P.,
Broman, K. W., Moller, S., Jansen, R. C., &
Swertz, M. A. (2012). xQTL workbench: a scalable web
environment for multi-level QTL analysis.
Bioinformatics, 28(7), 1042-1044. https://doi.org/10.1093/bioinformatics/bts049
Hasan,
S. A., Wietzes, P., & Janssen, D. B. (2012).
Biodegradation kinetics of 4-fluorocinnamic acid by a
consortium of Arthrobacter and Ralstonia strains.
Biodegradation, 23(1), 117-125. https://doi.org/10.1007/s10532-011-9491-z
Raj,
H., Puthan Veetil, V., Szymanski, W., Dekker, F.
J., Quax, W. J., Feringa, B.
L., Janssen, D. B., & Poelarends, G.
J. (2012). Characterization of a thermostable
methylaspartate ammonia lyase from Carboxydothermus
hydrogenoformans. Applied Microbiology and
Biotechnology, 94(2), 385-397. https://doi.org/10.1007/s00253-011-3615-6
Wu,
B., Szymanski, W., Crismaru, G. C., Feringa,
B., & Janssen, D. (2012). C-N lyases
catalyzing addition of ammonia, amines and amides to C=C and C=O
bonds. In K. Drauz, H. Groeger, & O. May (Eds.),
Enzyme Catalysis in Organic Synthesis (3 ed., pp.
749-778). Wiley. https://doi.org/10.1002/9783527639861
van
Leeuwen, J. G. E., Wijma, H. J., Floor, R. J., van der
Laan, J.-M., & Janssen, D. B. (2012).
Directed Evolution Strategies for Enantiocomplementary
Haloalkane Dehalogenases: From Chemical Waste to Enantiopure
Building Blocks. ChemBioChem,
13(1), 137-148. https://doi.org/10.1002/cbic.201100579
Raj,
H., Szymanski, W., de Villiers, J., Rozeboom, H.
J., Puthan Veetil, V., Reis, C. R., Villiers, M. D.,
Dekker, F. J., Wildeman, S. D., Quax, W.
J., Thunnissen, A.-M. W. H., Feringa, B.
L., Janssen, D. B., & Poelarends, G.
J. (2012). Engineering methylaspartate ammonia lyase
for the asymmetric synthesis of unnatural amino acids.
Nature Chemistry, 4(6), 478-484. https://doi.org/10.1038/NCHEM.1338
Westerbeek,
A., van Leeuwen, J. G. E., Szymanski, W.,
Feringa, B. L., & Janssen, D. B. (2012).
Haloalkane dehalogenase catalysed desymmetrisation and tandem
kinetic resolution for the preparation of chiral
haloalcohols. Tetrahedron,
68(37), 7645-7650. https://doi.org/10.1016/j.tet.2012.06.059
Schallmey,
M., Floor, R. J., Szymanski, W., & Janssen,
D. B. (2012). Hydrolysis and Reverse Hydrolysis:
Halohydrin Dehalogenases. In E. M. Carreira, & H.
Yamamoto (Eds.), Synthetic Methods VI – Enzymatic and
Semi-Enzymatic (7 ed., pp. 143-155). (Comprehensive Chirality;
No. 7).
Duque,
A. F., Hasan, S. A., Bessa, V. S., Carvalho, M. F., Samin,
G., Janssen, D. B., & Castro, P. M. L. (2012).
Isolation and characterization of a Rhodococcus strain able
to degrade 2-fluorophenol. Applied Microbiology
and Biotechnology, 95(2), 511-520. https://doi.org/10.1007/s00253-011-3696-2
Wu,
B., Szymanski, W., Wybenga, G. G., Heberling, M. M.,
Bartsch, S., de Wildeman, S., Poelarends, G. J.,
Feringa, B. L., Dijkstra, B. W., & Janssen, D.
B. (2012). Mechanism-Inspired Engineering of
Phenylalanine Aminomutase for Enhanced β-Regioselective
Asymmetric Amination of Cinnamates. Angewandte
Chemie-International Edition, 51(2), 482-486.
https://doi.org/10.1002/anie.201106372
Arif,
M. I., Samin, G., van Leeuwen, J. G. E., Oppentocht,
J., & Janssen, D. B. (2012). Novel
Dehalogenase Mechanism for 2,3-Dichloro-1-Propanol Utilization in
Pseudomonas putida Strain MC4. Applied and
environmental microbiology, 78(17), 6128-6136.
https://doi.org/10.1128/AEM.00760-12
Wybenga,
G. G., Crismaru, C. G., Janssen, D. B., &
Dijkstra, B. W. (2012). Structural Determinants of the
beta-Selectivity of a Bacterial Aminotransferase.
The Journal of Biological Chemistry,
287(34), 28495-28502. https://doi.org/10.1074/jbc.M112.375238
Wu,
B., Szymanski, W., Feringa, B. L.,
& Janssen, D. B. (2012). Tandem Biocatalytic
Process for the Kinetic Resolution of β-Phenylalanine and its
Analogs. In P. W. Sutton, & J. Whittall (Eds.),
Practical Methods for Biocatalysis and Biotransformations
2 (2 ed., pp. 331-335). (Practical Methods for Biocatalysis
and Biotransformations; No. 2). s.n..
Samin,
G., & Janssen, D. B. (2012). Transformation
and biodegradation of 1,2,3-trichloropropane (TCP).
Environmental Science and Pollution Research,
19(8), 3067-3078. https://doi.org/10.1007/s11356-012-0859-3
Kortholt,
A., van Egmond, W. N., Plak, K., Bosgraaf,
L., Keizer-Gunnink, I., & van Haastert, P.
J. M. (2012). Multiple Regulatory Mechanisms for the
Dictyostelium Roco Protein GbpC. The Journal of
Biological Chemistry, 287(4), 2749-2758. https://doi.org/10.1074/jbc.M111.315739
Gilsbach,
B. K., Ho, F. Y., Vetter, I. R., van Haastert,
P. J. M., Wittinghofer, A., & Kortholt, A.
(2012). Roco kinase structures give insights into the
mechanism of Parkinson disease-related leucine-rich-repeat kinase 2
mutations. Proceedings of the National Academy of
Sciences of the United States of America,
109(26), 10322-10327. https://doi.org/10.1073/pnas.1203223109
Soskine,
M., Biesemans, A., Moeyaert, B., Cheley, S., Bayley, H.,
& Maglia, G. (2012). An engineered ClyA nanopore
detects folded target proteins by selective external association
and pore entry. Nano Letters,
12(9), 4895-4900. https://doi.org/10.1021/nl3024438
Fransceschini,
L., Mikhailova, E., Bayley, H., & Maglia, G.
(2012). Nucleobase recognition at alkaline pH and apparent
pK(a) of single DNA bases immobilised within a biological
nanopore. Chemical Communications,
48(10), 1520-1522. https://doi.org/10.1039/c1cc16124e
Erkens,
G. B., Dosz-Majsnerowska, M., ter Beek, J., & Slotboom,
D. J. (2012). Energy Coupling Factor-Type ABC
Transporters for Vitamin Uptake in Prokaryotes.
Biochemistry, 51(22), 4390-4396. https://doi.org/10.1021/bi300504v
Schlegel,
S., Lofblom, J., Lee, C., Hjelm, A., Klepsch, M., Strous, M., Drew,
D., Slotboom, D. J., & de Gier, J.-W. (2012).
Optimizing Membrane Protein Overexpression in the Escherichia
coli strain Lemo21(DE3). Journal of Molecular
Biology, 423(4), 648-659. https://doi.org/10.1016/j.jmb.2012.07.019
Kolbusz,
M. A., Slotboom, D. J., & Lolkema, J. S. (2012).
Role of Individual Positive Charges in the Membrane
Orientation and Activity of Transporters of the Small Multidrug
Resistance Family. Biochemistry,
51(44), 8867-8876. https://doi.org/10.1021/bi300854c
Berntsson,
R. P. .-A., ter Beek, J., Dosz-Majsnerowska, M., Duurkens, R. H.,
Puri, P., Poolman, B., & Slotboom,
D.-J. (2012). Structural divergence of paralogous S
components from ECF-type ABC transporters.
Proceedings of the National Academy of Sciences of the
United States of America, 109(35),
13990-13995. https://doi.org/10.1073/pnas.1203219109
Berntsson,
R. P. .-A., Schuurman-Wolters, G. K., Dunny, G.,
Slotboom, D.-J., & Poolman, B. (2012).
Structure and Mode of Peptide Binding of Pheromone Receptor
PrgZ. The Journal of Biological
Chemistry, 287(44), 37165-37170. https://doi.org/10.1074/jbc.M112.386334
El
Aidy, S., van Baarlen, P., Derrien, M.,
Lindenbergh-Kortleve, D. J., Hooiveld, G., Levenez, F., Dore, J.,
Dekker, J., Samsom, J. N., Nieuwenhuis, E. E. S., &
Kleerebezem, M. (2012). Temporal and spatial interplay of
microbiota and intestinal mucosa drive establishment of immune
homeostasis in conventionalized mice. Mucosal
immunology, 5(5), 567-579. https://doi.org/10.1038/mi.2012.32
El
Aidy, S., Kunze, W., Bienenstock, J., & Kleerebezem, M.
(2012). The microbiota and the gut-brain axis: insights from
the temporal and spatial mucosal alterations during colonisation of
the germfree mouse intestine. Beneficial
microbes, 3(4), 251-259. https://doi.org/10.3920/BM2012.0042
Opalinski,
L., Bartoszewska, M., Fekken, S., Liu, H., de Boer,
R., van der Klei, I., Veenhuis, M., &
Kiel, J. A. K. W. (2012). De Novo Peroxisome
Biogenesis in Penicillium Chrysogenum Is Not Dependent on the Pex11
Family Members or Pex16. PLoS ONE,
7(4), Article e35490. https://doi.org/10.1371/journal.pone.0035490
Kumar,
S., Lefevre, S. D., Veenhuis, M., & van der Klei, I.
J. (2012). Extension of Yeast Chronological Lifespan
by Methylamine. PLoS ONE,
7(11), Article e48982. https://doi.org/10.1371/journal.pone.0048982
et
al., Carra, S., Kampinga, H. H., Kiel, J. A. K.
W., & van der Klei, I. J. (2012).
Guidelines for the use and interpretation of assays for
monitoring autophagy. Autophagy,
8(4), 445-544. https://doi.org/10.4161/auto.19496
Veiga,
T., Gombert, A. K., Landes, N., Verhoeven, M. D., Kiel, J. A.
K. W., Krikken, A. M., Nijland, J.
G., Touw, H., Luttik, M. A. H., van der Toorn, J. C.,
Driessen, A. J. M., Bovenberg, R. A. L., van
den Berg, M. A., van der Klei, I. J., Pronk, J. T.,
& Daran, J.-M. (2012). Metabolic engineering of
beta-oxidation in Penicillium chrysogenum for improved
semi-synthetic cephalosporin biosynthesis.
Metabolic Engineering, 14(4),
437-448. https://doi.org/10.1016/j.ymben.2012.02.004
Zerbes,
R. M., van der Klei, I. J., Veenhuis, M., Pfanner, N.,
van der Laan, M., & Bohnert, M. (2012). Mitofilin
complexes: conserved organizers of mitochondrial membrane
architecture. Biological Chemistry,
393(11), 1247-1261. https://doi.org/10.1515/hsz-2012-0239
Saraya,
R., Krikken, A. M., Kiel, J. A. K. W.,
Baerends, R. J. S., Veenhuis, M., & van der Klei, I.
J. (2012). Novel genetic tools for Hansenula
polymorpha. Fems Yeast Research,
12(3), 271-278. https://doi.org/10.1111/j.1567-1364.2011.00772.x
Bartoszewska,
M., Williams, C., Kikhney, A., Opalinski, L., van Roermund, C. W.
T., de Boer, R., Veenhuis, M., & van der
Klei, I. J. (2012). Peroxisomal Proteostasis Involves
a Lon Family Protein That Functions as Protease and
Chaperone. The Journal of Biological
Chemistry, 287(33), 27380-27395. https://doi.org/10.1074/jbc.M112.381566
Otzen,
M., Rucktaeschel, R., Thoms, S., Ernmrich, K.,
Krikken, A. M., Erdmann, R., van der Klei, I.
J., Emmrich, K., & Krikken, A. M. (2012). Pex19p
Contributes to Peroxisome Inheritance in the Association of
Peroxisomes to Myo2p. Traffic,
13(7), 947-959. https://doi.org/10.1111/j.1600-0854.2012.01364.x
Zerbes,
R. M., Bohnert, M., Stroud, D. A., von der Malsburg, K.,
Kram, A., Oeljeklaus, S., Warscheid, B., Becker, T.,
Wiedemann, N., Veenhuis, M., van der Klei, I. J.,
Pfanner, N., & van der Laan, M. (2012). Role of MINOS in
Mitochondrial Membrane Architecture: Cristae Morphology and Outer
Membrane Interactions Differentially Depend on Mitofilin
Domains. Journal of Molecular Biology,
422(2), 183-191. https://doi.org/10.1016/j.jmb.2012.05.004
Bohnert,
M., Wenz, L.-S., Zerbes, R. M., Horvath, S. E., Stroud, D. A., von
der Malsburg, K., Mueller, J. M., Oeljeklaus, S., Perschil, I.,
Warscheid, B., Chacinska, A., Veenhuis, M., van der Klei, I.
J., Daum, G., Wiedemann, N., Becker, T., Pfanner, N., &
van der Laan, M. (2012). Role of mitochondrial inner membrane
organizing system in protein biogenesis of the mitochondrial outer
membrane. Molecular Biology of the
Cell, 23(20), 3948-3956. https://doi.org/10.1091/mbc.E12-04-0295
Manivannan,
S., Scheckhuber, C. Q., Veenhuis, M., & van der Klei, I.
J. (2012). The impact of peroxisomes on cellular aging
and death. Frontiers in Oncology,
2(7), 1-7. Article 50. https://doi.org/10.3389/fonc.2012.00050
Zerbes,
R. M., Bohnert, M., Malsburg, K. V. D., Warscheid, B., Klei,
I. J. V. D., Pfanner, N., & Laan, M. V. D. (2012).
The MINOS complex: Keeper of mitochondrial membrane
architecture. Biochimica et Biophysica
Acta, 1817(33), S74-S75. https://doi.org/10.1016/j.bbabio.2012.06.208
Williams,
C., Aksam, E. B., Gunkel, K., Veenhuis, M., & van der
Klei, I. J. (2012). The relevance of the non-canonical
PTS1 of peroxisomal catalase. Biochimica et
Biophysica Acta-Molecular Cell Research,
1823(7), 1133-1141. https://doi.org/10.1016/j.bbamcr.2012.04.006
Lopez,
C. A., de Vries, A. H., & Marrink, S.
J. (2012). Amylose folding under the influence of
lipids. Carbohydrate Research,
364, 1-7. https://doi.org/10.1016/j.carres.2012.10.007
Goga,
N., Rzepiela, A. J., de Vries, A. H.,
Marrink, S. J., & Berendsen, H. J. C. (2012).
Efficient Algorithms for Langevin and DPD Dynamics.
Journal of Chemical Theory and Computation,
8(10), 3637-3649. https://doi.org/10.1021/ct3000876
Goga,
N., Rzepiela, A., de Sousa Pereira Simoes de Melo, M.,
de Vries, A., Hadar, A., Markvoort, A. J., Nedea, S., &
Berendsen, H. (2012). Methods for multiscale modeling of
membranes. In A. Iglic (Ed.), Advances in Planar Lipid
Bilayers and Liposomes (Vol. 15, pp. 139-170). Academic Press.
https://doi.org/10.1016/B978-0-12-396533-2.00003-3
Visweswaran,
G. R. R., Dijkstra, B. W., & Kok, J. (2012).
A genetically engineered protein domain binding to bacterial
murein, archaeal pseudomurein, and fungal chitin cell wall
material. Applied Microbiology and
Biotechnology, 96(3), 729-737. https://doi.org/10.1007/s00253-012-3871-0
Solopova,
A., Bachmann, H., Teusink, B., Kok, J., Neves, A.
R., & Kuipers, O. P. (2012). A Specific
Mutation in the Promoter Region of the Silent cel Cluster Accounts
for the Appearance of Lactose-Utilizing Lactococcus lactis
MG1363. Applied and environmental
microbiology, 78(16), 5612-5621. https://doi.org/10.1128/AEM.00455-12
Price,
C. E., Zeyniyev, A., Kuipers, O. P., & Kok,
J. (2012). From meadows to milk to mucosa - adaptation
of Streptococcus and Lactococcus species to their nutritional
environments. FEMS Microbiology
Reviews, 36(5), 949-971. https://doi.org/10.1111/j.1574-6976.2011.00323.x
Tariq,
M., Bruijs, C., Kok, J., & Krom, B. P. (2012).
Link between Culture Zeta Potential Homogeneity and Ebp in
Enterococcus faecalis. Applied and environmental
microbiology, 78(7), 2282-2288. https://doi.org/10.1128/AEM.07618-11
de
Jong, A., Pietersma, H., Cordes, M., Kuipers, O.
P., & Kok, J. (2012). PePPER: a
webserver for prediction of prokaryote promoter elements and
regulons. BMC Genomics,
13(1), Article 299. https://doi.org/10.1186/1471-2164-13-299
Honda,
H., Nagaoka, S., Kawai, Y., Kemperman, R., Kok, J.,
Yamazaki, Y., Tateno, Y., Kitazawa, H., & Saito, T. (2012).
Purification and characterization of two
phospho-β-galactosidases, LacG1 and LacG2, from Lactobacillus
gasseri ATCC33323T. The Journal of General and
Applied Microbiology, 58(1), 11-17. https://doi.org/10.2323/jgam.58.11
Roces,
C., Pérez, V., Campelo, A. B., Blanco, D., Kok,
J., Kuipers, O. P., Rodríguez, A., &
Martínez, B. (2012). The putative lactococcal
extracytoplasmic function anti-sigma factor llmg2447 determines
resistance to the cell wall-active bacteriocin lcn972.
Antimicrobial Agents and Chemotherapy,
56(11), 5520-5527. https://doi.org/10.1128/AAC.01206-12
Puri,
P., Eckhardt, T., Franken, L., Fusetti, F., Stuart,
M., Boekema, E., Kok, J., Kuipers,
O., & Poolman, B. (2012). YfiA is
necessary and sufficient for dimerization and inactivation of
ribosomes in Lactococcus lactis. Molecular Biology
of the Cell, 23, 1695.
de
Vries, L., Nelemans, S. A., Rink, R., Roks, A. J. M., &
Moll, G. N. (2012). Novel angiotensin
type 2 (AT2) receptor agonists and uses thereof. (Patent No.
wo2012070936 (A1)). http://worldwide.espacenet.com/publicationDetails/biblio?DB=EPODOC&II=0&ND=3&adjacent=true&locale=nl_NL&FT=D&date=20120531&CC=WO&NR=2012070936A1&KC=A1
Durik,
M., Van Veghel, R., Kuipers, A., Rink, R., Haas Jimoh
Akanbi, M., Moll, G., Danser, A. H. J., & Roks, A.
J. M. (2012). The effect of the thioether-bridged, stabilized
angiotensin-(1-7) analogue cyclic Ang-(1-7) on cardiac remodeling
and endothelial function in rats with myocardial infarction.
International Journal of Hypertension,
2012, Article 536426. https://doi.org/10.1155/2012/536426
Takano,
E., Bovenberg, R. A. L., & Breitling, R. (2012).
A turning point for natural product discovery - ESF-EMBO
research conference: synthetic biology of antibiotic
production. Molecular Microbiology,
83(5), 884-893. https://doi.org/10.1111/j.1365-2958.2012.07984.x
Weber,
S. S., Bovenberg, R. A. L., & Driessen, A.
J. M. (2012). Biosynthetic concepts for the production
of beta-lactam antibiotics in Penicillium chrysogenum.
Biotechnology Journal, 7(2),
225-236. https://doi.org/10.1002/biot.201100065
Moser,
F., Broers, N. J., Hartmans, S., Tamsir, A., Kerkman, R., Roubos,
J. A., Bovenberg, R., & Voigt, C. A. (2012).
Genetic Circuit Performance under Conditions Relevant for
Industrial Bioreactors. ACS Synthetic
Biology, 1(11), 555-564. https://doi.org/10.1021/sb3000832
Veiga,
T., Nijland, J. G., Driessen, A. J.
M., Bovenberg, R. A. L., Touw, H., van den
Berg, M. A., Pronk, J. T., Daran, J.-M., & Veiga, T. (2012).
Impact of Velvet Complex on Transcriptome and Penicillin G
Production in Glucose-Limited Chemostat Cultures of a beta-Lactam
High-Producing Penicillium chrysogenum Strain.
OMICS: A Journal of Integrative Biology,
16(6), 320-333. https://doi.org/10.1089/omi.2011.0153
Weber,
S. S., Polli, F., Boer, R., Bovenberg, R. A. L.,
& Driessen, A. J. M. (2012). Increased Penicillin
Production in Penicillium chrysogenum Production Strains via
Balanced Overexpression of Isopenicillin N Acyltransferase.
Applied and environmental microbiology,
78(19), 7107-7113. https://doi.org/10.1128/AEM.01529-12
Weber,
S. S., Kovalchuk, A., Bovenberg, R. A. L., &
Driessen, A. J. M. (2012). The ABC transporter ABC40
encodes a phenylacetic acid export system in Penicillium
chrysogenum. Fungal Genetics and
Biology, 49(11), 915-921. https://doi.org/10.1016/j.fgb.2012.09.003
Krol,
E., van Kessel, S. P., van Bezouwen, L.
S., Kumar, N., Boekema, E. J., & Scheffers,
D.-J. (2012). Bacillus subtilis SepF Binds to the
C-Terminus of FtsZ. PLoS ONE,
7(8), Article e43293. https://doi.org/10.1371/journal.pone.0043293
Scheffers,
D.-J. (2012). Cell wall synthesis in Bacillus
subtilis. In P. Graumann (Ed.), Bacillus: Cellular and
Molecular Biology (pp. 285-318). Caister Academic Press.
Scheffers,
D.-J. (2012). The Cell Wall of Bacillus
subtilis. In P. Graumann (Ed.), Bacillus: Cellular and
Molecular Biology (2 ed.). Caister Academic Press.
Huberts,
D. H. E. W., Niebel, B., & Heinemann, M. (2012).
A flux-sensing mechanism could regulate the switch between
respiration and fermentation. Fems Yeast
Research, 12(2), 118-128. https://doi.org/10.1111/j.1567-1364.2011.00767.x
Schuetz,
R., Zamboni, N., Zampieri, M., Heinemann, M., &
Sauer, U. (2012). Multidimensional optimality of microbial
metabolism. Science,
336(6081), 601-604. https://doi.org/10.1126/science.1216882
Adadi,
R., Volkmer, B., Milo, R., Heinemann, M., &
Shlomi, T. (2012). Prediction of Microbial Growth Rate versus
Biomass Yield by a Metabolic Network with Kinetic
Parameters. PLoS Computational
Biology, 8(7), Article e1002575. https://doi.org/10.1371/journal.pcbi.1002575
Jol,
S. J., Kümmel, A., Terzer, M., Stelling, J., &
Heinemann, M. (2012). System-level insights into yeast
metabolism by thermodynamic analysis of elementary flux
modes. PLoS Computational Biology,
8(3), Article e1002415. https://doi.org/10.1371/journal.pcbi.1002415
Lee,
S. S., Avalos Vizcarra, I., Huberts, D. H. E. W., Lee, L. P.,
& Heinemann, M. (2012). Whole lifespan microscopic
observation of budding yeast aging through a microfluidic
dissection platform. Proceedings of the National
Academy of Sciences of the United States of America,
109(13), 4916-4920. https://doi.org/10.1073/pnas.1113505109
Broos,
J., Petrovic, D. M., Leenhouts, K., Roosmalen, M. L. V.,
Gonelli, M., & Strambini, G. B. (2012). Chloro- and
Bromo-Tryptophan Analogs as Phosphorescent Probes in
Proteins. Biophysical Journal,
102(3), 209a-209a. https://doi.org/10.1016/j.bpj.2011.11.1142
Petrovic,
D. M., Leenhouts, K., van Roosmalen, M. L., KleinJan, F.,
& Broos, J. (2012). Monitoring lysin motif-ligand
interactions via tryptophan analog fluorescence
spectroscopy. Analytical Biochemistry,
428(2), 111-118. https://doi.org/10.1016/j.ab.2012.06.009
Opacic,
M., Hesp, B. H., Fusetti, F., Dijkstra, B., & Broos,
J. (2012). Structural investigation of the
transmembrane C domain of the mannitol permease from Escherichia
coli using 5-FTrp fluorescence spectroscopy.
Biochimica et Biophysica Acta-Biomembranes,
1818(3), 861-868. https://doi.org/10.1016/j.bbamem.2011.11.001
Veetil,
V. P., Fibriansah, G., Raj, H., Thunnissen, A.-M. W.
H., & Poelarends, G. J. (2012).
Aspartase/Fumarase Superfamily: A Common Catalytic Strategy
Involving General Base-Catalyzed Formation of a Highly Stabilized
aci-Carboxylate Intermediate.
Biochemistry, 51(21), 4237-4243. https://doi.org/10.1021/bi300430j
Fibriansah,
G., Kovacs, A. T., Pool, T. J., Boonstra, M., Kuipers, O.
P., & Thunnissen, A.-M. W. H. (2012).
Crystal Structures of Two Transcriptional Regulators from
Bacillus cereus Define the Conserved Structural Features of a PadR
Subfamily. PLoS ONE, 7(11),
Article e48015. https://doi.org/10.1371/journal.pone.0048015
Fibriansah,
G., Gliubich, F. I., & Thunnissen, A.-M. W. H.
(2012). On the Mechanism of Peptidoglycan Binding and
Cleavage by the endo-Specific Lytic Transglycosylase MltE from
Escherichia coli. Biochemistry,
51(45), 9164-9177. https://doi.org/10.1021/bi300900t
2011
Trelles,
O., Prins, P., Snir, M., & Jansen, R.
C. (2011). Big data, but are we ready?
Nature Reviews Genetics, 12(3),
224-224. https://doi.org/10.1038/nrg2857-c1
Roux,
F., Colomé-Tatché, M., Edelist, C.,
Wardenaar, R., Guerche, P., Hospital, F., Colot, V.,
Jansen, R. C., & Johannes, F. (2011). Genome-Wide
Epigenetic Perturbation Jump-Starts Patterns of Heritable Variation
Found in Nature. Genetics,
188(4), 1015-1017. https://doi.org/10.1534/genetics.111.128744
Westra,
H.-J., Jansen, R. C., Fehrmann, R. S.
N., te Meerman, G. J., van Heel, D.,
Wijmenga, C., Franke, L., & te
Meerman, G. (2011). MixupMapper: correcting sample
mix-ups in genome-wide datasets increases power to detect small
genetic effects. Bioinformatics,
27(15), 2104-2111. https://doi.org/10.1093/bioinformatics/btr323
Scheltema,
R. A., Jankevics, A., Jansen, R. C., Swertz, M.
A., & Breitling, R. (2011). PeakML/mzMatch: A File
Format, Java Library, R Library, and Tool-Chain for Mass
Spectrometry Data Analysis. Analytical
Chemistry, 83(7), 2786-2793. https://doi.org/10.1021/ac2000994
Seinen,
E., Burgerhof, J. G., Jansen, R.
C., & Sibon, O. C. (2011).
RNAi-induced off-target effects in Drosophila melanogaster:
frequencies and solutions. Briefings in Functional
Genomics, 10(4), 206-214. https://doi.org/10.1093/bfgp/elr017
Fehrmann,
R. S. N., Jansen, R. C., Veldink, J. H.,
Westra, H. J., Arends, D., Bonder, M. J.,
Fu, J., Deelen, P., Groen, H.,
Smolonska, J., Weersma, R. K., Hofstra, R. M. W.,
Buurman, W. A., Rensen, S., Wolfs, M. G. M., Platteel,
M., Zhernakova, A., Elbers, C. C.,
Festen, E. A., ... Franke, L. (2011).
Trans-eQTLs reveal that independent genetic variants
associated with a complex phenotype converge on intermediate genes,
with a major role for the HLA. PLoS
genetics, 7(8), Article 1002197. https://doi.org/10.1371/journal.pgen.1002197
Koetsier,
M. J., Jekel, P. A., Wijma, H. J., Bovenberg, R.
A. L., & Janssen, D. B. (2011).
Aminoacyl-coenzyme A synthesis catalyzed by a CoA ligase from
Penicillium chrysogenum. FEBS Letters,
585(6), 893-898. https://doi.org/10.1016/j.febslet.2011.02.018
Wu,
B., Szymanski, W., Heberling, M. M., Feringa, B.
L., & Janssen, D. B. (2011).
Aminomutases: Mechanistic diversity, biotechnological
applications and future perspectives. Trends in
Biotechnology, 29(7), 352-362. https://doi.org/10.1016/j.tibtech.2011.02.005
Szymanski,
W., Westerbeek, A., Janssen, D. B., &
Feringa, B. L. (2011). A simple enantioconvergent and
chemoenzymatic synthesis of optically active α-substituted
amides. Angewandte Chemie - International
Edition, 50(45), 10712-10715. https://doi.org/10.1002/anie.201105164
Schallmey,
A., den Besten, G., Teune, I. G. P., Kembaren, R. F., &
Janssen, D. B. (2011). Characterization of cytochrome
P450 monooxygenase CYP154H1 from the thermophilic soil bacterium
Thermobifida fusca. Applied Microbiology and
Biotechnology, 89(5), 1475-1485. https://doi.org/10.1007/s00253-010-2965-9
Hasan,
S. A., Ferreira, M. I. M., Koetsier, M. J., Arif, M. I.,
& Janssen, D. B. (2011). Complete Biodegradation
of 4-Fluorocinnamic Acid by a Consortium Comprising Arthrobacter
sp. Strain G1 and Ralstonia sp. Strain H1. Applied
and environmental microbiology, 77(2),
572-579. https://doi.org/10.1128/AEM.00393-10
Westerbeek,
A., Szymanski, W., Feringa, B. L.,
& Janssen, D. B. (2011). Dynamic kinetic
resolution process employing haloalkane dehalogenase.
ACS Catalysis, 1(12), 1654-1660. https://doi.org/10.1021/cs2003565
Westerbeek,
A., Szymanski, W., Wijma, H. J.,
Marrink, S., Feringa, B. L., &
Janssen, D. B. (2011). Kinetic resolution of
α-bromoamides: Experimental and theoretical investigation of
highly enantioselective reactions catalyzed by haloalkane
dehalogenases. Advanced Synthesis &
Catalysis, 353(6), 931-944. https://doi.org/10.1002/adsc.201000726
Van
Haastert, P. J. M. (2011). Amoeboid Cells Use
Protrusions for Walking, Gliding and Swimming.
PLoS ONE, 6(11), Article e27532. https://doi.org/10.1371/journal.pone.0027532
Neilson,
M. P., Veltman, D. M., van Haastert, P. J. M., Webb,
S. D., Mackenzie, J. A., & Insall, R. H. (2011).
Chemotaxis: A Feedback-Based Computational Model Robustly
Predicts Multiple Aspects of Real Cell Behaviour.
PLOS BIOLOGY, 9(5), Article 1000618.
https://doi.org/10.1371/journal.pbio.1000618
Kortholt,
A., Kataria, R., Keizer-Gunnink, I., Van
Egmond, W. N., Khanna, A., & Van Haastert, P. J.
M. (2011). Dictyostelium chemotaxis: essential Ras
activation and accessory signalling pathways for
amplification. Embo Reports,
12(12), 1273-1279. https://doi.org/10.1038/embor.2011.210
Van
Haastert, P. J. M. (2011). How Cells Use Pseudopods
for Persistent Movement and Navigation. Science
signaling, 4(159), Article 6. https://doi.org/10.1126/scisignal.2001708
Rincon-Restrepo,
M., Milthallova, E., Bayley, H., & Maglia, G.
(2011). Controlled Translocation of Individual DNA Molecules
through Protein Nanopores with Engineered Molecular Brakes.
Nano Letters, 11(2), 746-750. https://doi.org/10.1021/nl1038874
Klepsch,
M. M., Kovermann, M., Löw, C., Balbach, J., Permentier,
H. P., Fusetti, F., de Gier, J. W., Gier, J.-W.
D., Slotboom, D. J., & Berntsson, R. P. .-A.
(2011). Escherichia coli Peptide Binding Protein
OppA Has a Preference for Positively Charged Peptides.
Journal of Molecular Biology,
414(1), 75-85. https://doi.org/10.1016/j.jmb.2011.09.043
Berntsson,
R. P.-A., Thunnissen, A.-M. W. H., Poolman,
B., & Slotboom, D.-J. (2011).
Importance of a Hydrophobic Pocket for Peptide Binding in
Lactococcal OppA. Journal of
Bacteriology, 193(16), 4254-4256. https://doi.org/10.1128/JB.00447-11
Steen,
A., Wiederhold, E., Gandhi, T., Breitling, R., &
Slotboom, D. J. (2011). Physiological Adaptation of
the Bacterium Lactococcus lactis in Response to the Production of
Human CFTR. Molecular & Cellular
Proteomics, 10(7),
MCP200–1-MCP200–16. https://doi.org/10.1074/mcp.M000052-MCP200
Beek,
J. T., Duurkens, R. H., Erkens, G. B., & Slotboom, D.
J. (2011). Quaternary Structure and Functional Unit of
Energy Coupling Factor (ECF)-type Transporters.
The Journal of Biological Chemistry,
286(7), 5471-5475. https://doi.org/10.1074/jbc.M110.199224
Van
den Abbeele, P., Gérard, P., Rabot, S., Bruneau, A., El
Aidy, S., Derrien, M., Kleerebezem, M., Zoetendal, E. G.,
Smidt, H., Verstraete, W., Van de Wiele, T., & Possemiers, S.
(2011). Arabinoxylans and inulin differentially modulate the
mucosal and luminal gut microbiota and mucin-degradation in
humanized rats. Environmental
Microbiology, 13(10), 2667-2680. https://doi.org/10.1111/j.1462-2920.2011.02533.x
Bartosweska,
M., Kiel, J. A. K. W., Bovenberg, R. A.
L., Veenhuis, M., & van der Klei, I. J.
(2011). Autophagy Deficiency Promotes β-Lactam
Production in Penicillium chrysogenum. Applied and
environmental microbiology, 77(4), 1413-1422.
https://doi.org/10.1128/aem.01531-10
Boender,
L. G. M., van Maris, A. J. A., de Hulster, E. A. F., Almering, M.
J. H., van der Klei, I. J., Veenhuis, M., de Winde, J.
H., Pronk, J. T., & Daran-Lapujade, P. (2011). Cellular
responses of Saccharomyces cerevisiae at near-zero growth rates:
transcriptome analysis of anaerobic retentostat cultures.
Fems Yeast Research, 11(8), 603-620.
https://doi.org/10.1111/j.1567-1364.2011.00750.x
Van
Der Klei, I., Veenhuis, M., Brul, S., Klis, F. M., De Groot,
P. W. J., Müller, W. H., van Driel, K. G. A., & Boekhout,
T. (2011). Cytology, cell walls and septa: A summary of yeast
cell biology from a phylogenetic perspective. In C. P.
Kurtzman, J. W. Fell, & T. Boekhout (Eds.), The Yeasts
(5 ed., Vol. 1, pp. 111-128). Elsevier. https://doi.org/10.1016/B978-0-444-52149-1.00008-2
van
Zutphen, T., Veenhuis, M., & van der Klei, I.
J. (2011). Damaged peroxisomes are subject to rapid
autophagic degradation in the yeast Hansenula polymorpha.
Autophagy, 7(8), 863-872. https://doi.org/10.4161/auto.7.8.15697
von
der Malsburg, K., Mueller, J. M., Bohnert, M., Oeljeklaus, S.,
Kwiatkowska, P., Becker, T., Loniewska-Lwowska, A., Wiese, S., Rao,
S., Milenkovic, D., Hutu, D. P., Zerbes, R. M., Schulze-Specking,
A., Meyer, H. E., Martinou, J.-C., Rospert, S., Rehling, P.,
Meisinger, C., Veenhuis, M., ... Müller, J. M. (2011).
Dual Role of Mitofilin in Mitochondrial Membrane Organization
and Protein Biogenesis. Developmental
Cell, 21(4), 694-707. https://doi.org/10.1016/j.devcel.2011.08.026
van
der Klei, I., Veenhuis, M., & Klompmaker, S. (2011).
Improved methods and host cells for the
production and use of D-amino acid oxidase (DAO). (Patent
No. 10158443.1-2403).
van
der Klei, I. J. (2011). Live by fusion, avoid fission:
Comment on: Scheckhuber CQ, et al. Cell Cycle 2011;
10:3105–10. Cell Cycle,
10(22), 3826. https://doi.org/10.4161/cc.10.22.18234
Opalinski,
L., Kiel, J. A. K. W., Williams, C., Veenhuis,
M., & van der Klei, I. J. (2011). Membrane
curvature during peroxisome fission requires Pex11.
EMBO Journal, 30(1), 5-16. https://doi.org/10.1038/emboj.2010.299
Krygowska,
M., Veenhuis, M., Klei, I. J. V. D., & Nagotu, S.
(2011). Peroxisome Fission is Associated with Reorganization
of Specific Membrane Proteins.
Traffic, 12(7), 925-937. https://doi.org/10.1111/j.1600-0854.2011.01198.x
Opalinski,
L., Veenhuis, M., & van der Klei, I. J. (2011).
Peroxisomes: Membrane events accompanying peroxisome
proliferation. International journal of
biochemistry & cell biology, 43(6),
847-851. https://doi.org/10.1016/j.biocel.2011.03.006
van
Zutphen, T., & van der Klei, I. J. (2011).
Quantitative analysis of organelle abundance, morphology and
dynamics. Current Opinion in
Biotechnology, 22(1), 127-132. https://doi.org/10.1016/j.copbio.2010.10.015
Bartoszewska,
M., Opalinski, L., Veenhuis, M., & van der Klei, I.
J. (2011). The significance of peroxisomes in
secondary metabolite biosynthesis in filamentous fungi.
Biotechnology Letters, 33(10),
1921-1931. https://doi.org/10.1007/s10529-011-0664-y
De
Jong, D. H., Schafer, L. V., De Vries, A. H.,
Marrink, S. J., Berendsen, H. J. C., & Grubmueller, H.
(2011). Determining Equilibrium Constants for Dimerization
Reactions from Molecular Dynamics Simulations.
Journal of Computational Chemistry,
32(9), 1919-1928. https://doi.org/10.1002/jcc.21776
Schaefer,
L. V., de Jong, D. H., Holt, A., Rzepiela, A. J., de Vries,
A. H., Poolman, B., Killian, J. A., &
Marrink, S. J. (2011). Lipid packing drives the
segregation of transmembrane helices into disordered lipid domains
in model membranes. Proceedings of the National
Academy of Sciences of the United States of America,
108(4), 1343-1348. https://doi.org/10.1073/pnas.1009362108
Lopez,
C. A., de Vries, A. H., & Marrink, S.
J. (2011). Molecular Mechanism of Cyclodextrin
Mediated Cholesterol Extraction. PLoS
Computational Biology, 7(3), Article e1002020.
https://doi.org/10.1371/journal.pcbi.1002020
Visweswaran,
G. R. R., Dijkstra, B. W., & Kok, J. (2011).
A minimum of three motifs is essential for optimal binding of
pseudomurein cell wall-binding domain of Methanothermobacter
thermautotrophicus. PLoS ONE,
6(6), Article 21582. https://doi.org/10.1371/journal.pone.0021582
de
Jong, A., Kok, J., & Kuipers,
O. (2011). Data resources and mining tools for
reconstructing gene networks in Lactococcus lactis.
Japanese Journal of Lactic Acid Bacteria,
22(1), 3-14.
Pinto,
J. P. C., Kuipers, O. P., Marreddy, R. K. R.,
Poolman, B., & Kok, J. (2011).
Efficient overproduction of membrane proteins in Lactococcus
lactis requires the cell envelope stress sensor/regulator couple
CesSR. PLoS ONE, 6(7),
Article 21873. https://doi.org/10.1371/journal.pone.0021873
Papadimitriou,
K., & Kok, J. (2011). Future Challenges in
Lactic Acid Bacteria Stress Physiology Research. In K.
Papadimitriou, & E. Tsakalidou (Eds.), Stress Responses of
Lactic Acid Bacteria (pp. 507-518). (Food Microbiology and
Food Safety). Springer. https://doi.org/10.1007/978-0-387-92771-9_21
Kabuki,
T., Kawai, Y., Uenishi, H., Seto, Y., Kok, J.,
Nakajima, H., & Saito, T. (2011). Gene cluster for
biosynthesis of thermophilin 1277-a lantibiotic produced by
Streptococcus thermophilus SBT1277, and heterologous expression of
TepI, a novel immunity peptide. Journal of Applied
Microbiology, 110(3), 641-649. https://doi.org/10.1111/j.1365-2672.2010.04914.x
Abrantes,
M. C., Lopes, M. D. F., & Kok, J. (2011).
Impact of manganese, copper and zinc ions on the
transcriptome of the nosocomial pathogen Enterococcus faecalis
V583. PLoS ONE, 6(10),
Article e26519. https://doi.org/10.1371/journal.pone.0026519
Rigottier-Gois,
L., Alberti, A., Houel, A., Taly, J.-F., Palcy, P., Manson, J.,
Pinto, D., Matos, R. C., Carrilero, L., Montero, N., Tariq,
M., Karsens, H., Repp, C., Kropec, A., Budin-Verneuil,
A., Benachour, A., Sauvageot, N., Bizzini, A., Gilmore, M. S., ...
Serror, P. (2011). Large-Scale Screening of a Targeted
Enterococcus faecalis Mutant Library Identifies Envelope Fitness
Factors. PLoS ONE, 6(12),
Article 29023. https://doi.org/10.1371/journal.pone.0029023
Visweswaran,
G. R. R., Dijkstra, B. W., & Kok, J. (2011).
Murein and pseudomurein cell wall binding domains of bacteria
and archaea-a comparative view. Applied
Microbiology and Biotechnology, 92(5),
921-928. https://doi.org/10.1007/s00253-011-3637-0
Pinto,
J. P. C., Zeyniyev, A., Karsens, H., Trip, H.,
Lolkema, J. S., Kuipers, O. P., & Kok,
J. (2011). pSEUDO, a Genetic Integration Standard for
Lactococcus lactis. Applied and environmental
microbiology, 77(18), 6687-6690. https://doi.org/10.1128/AEM.05196-11
Coelho
Pinto, J., Kuipers, O., & Kok, J.
(2011). Responses of lactic acid bacteria to cell envelop
stresses. In E. Tsakalidou, & K. Papadimitriou (Eds.),
Stress Responses of Lactic Acid Bacteria: Food Microbiology and
Food Safety (pp. 141-161). (Food Microbiology and Safety).
Springer. https://doi.org/10.1007/978-0-387-92771-8_8
Campelo,
A. B., Gaspar, P., Roces, C., Rodriguez, A., Kok,
J., Kuipers, O. P., Neves, A. R., &
Martinez, B. (2011). The Lcn972 Bacteriocin-Encoding Plasmid
pBL1 Impairs Cellobiose Metabolism in Lactococcus lactis.
Applied and environmental microbiology,
77(21), 7576-7585. https://doi.org/10.1128/AEM.06107-11
Hill,
C., Kleerebezem, M., & Kok, J. (2011). The
proceedings of the Tenth Symposium on Lactic Acid Bacteria.
Microbial Cell Factories, 10((Suppl.
1) : S1), S1-S1. https://doi.org/10.1186/1475-2859-10-S1-S1
Plat,
A., Kuipers, A., de Lange, J. G., Moll, G. N., &
Rink, R. (2011). Activity and export of engineered
nisin-(1-22) analogs. Polymers,
3(3), 1282-1296. https://doi.org/10.3390/polym3031282
Woesten-van
Asperen, R. M., Lutter, R., Specht, P. A., Moll, G.
N., van Woensel, J. B., van der Loos, C. M., van Goor,
H., Kamilic, J., Florquin, S., & Bos, A. P. (2011).
Acute respiratory distress syndrome leads to reduced ratio of
ACE/ACE2 activities and is prevented by angiotensin-(1-7) or an
angiotensin II receptor antagonist. The Journal of
Pathology, 225(4), 618-627. https://doi.org/10.1002/path.2987
Bosma,
T., Kuipers, A., Bulten, E., de Vries, L., Rink,
R., & Moll, G. N. (2011). Bacterial display
and screening of posttranslationally thioether-stabilized
peptides. Applied and environmental
microbiology, 77(19), 6794-6801. https://doi.org/10.1128/AEM.05550-11
Khusainov,
R., Heils, R., Lubelski, J., Moll, G. N., &
Kuipers, O. P. (2011). Determining sites of
interaction between prenisin and its modification enzymes NisB and
NisC. Molecular Microbiology,
82(3), 706-718. https://doi.org/10.1111/j.1365-2958.2011.07846.x
Plat,
A., Kluskens, L. D., Kuipers, A., Rink, R.,
& Moll, G. N. (2011). Requirements of the
engineered leader peptide of nisin for inducing modification,
export, and cleavage. Applied and environmental
microbiology, 77(2), 604-611. https://doi.org/10.1128/AEM.01503-10
Mavaro,
A., Abts, A., Bakkes, P. J., Moll, G. N.,
Driessen, A. J. M., Smits, S. H. J., & Schmitt, L.
(2011). Substrate Recognition and Specificity of the NisB
Protein, the Lantibiotic Dehydratase Involved in Nisin
Biosynthesis. The Journal of Biological
Chemistry, 286(35), 30552-30560. https://doi.org/10.1074/jbc.M111.263210
Kovalchuk,
A., Weber, S. S., Nijland, J. G., Bovenberg, R.
A. L., & Driessen, A. J. M. (2012).
Fungal ABC Transporter Deletion and Localization
Analysis. In Plant Fungal Pathogens: Methods and
Protocols (Vol. 835, pp. 1-16). Humana Press. https://doi.org/10.1007/978-1-61779-501-5_1
Douma,
R. D., Batista, J. M., Touw, K. M., Kiel, J. A. K. W.,
Zhao, Z., Veiga, T., Klaassen, P., Bovenberg, R. A.
L., Daran, J.-M., van Gulik, W. M., Heijnen, J. J.,
& Krikken, A. (2011). Degeneration of penicillin
production in ethanol-limited chemostat cultivations of Penicillium
chrysogenum: A systems biology approach. BMC
Systems Biology, 5, Article 132. https://doi.org/10.1186/1752-0509-5-132
Medema,
M. H., Breitling, R., Bovenberg, R., & Takano, E.
(2011). Exploiting plug-and-play synthetic biology for drug
discovery and production in microorganisms. Nature
Reviews Microbiology, 9(2), 131-137. https://doi.org/10.1038/nrmicro2478
Medema,
M. H., Alam, M. T., Heijne, W. H. M., Berg, M. A. V. D.,
Müller, U., Trefzer, A., Bovenberg, R. A. L.,
Breitling, R., & Takano, E. (2011). Genome-wide gene
expression changes in an industrial clavulanic acid overproduction
strain of Streptomyces clavuligerus. Microbial
Biotechnology, 4(2), 300-305. https://doi.org/10.1111/j.1751-7915.2010.00226.x
Yu,
Z., Bekker, M., Tramonti, A., Cook, G. M., van Ulsen, P.,
Scheffers, D.-J., de Mattos, J. T., De Biase, D., &
Luirink, J. (2011). Activators of the Glutamate-Dependent
Acid Resistance System Alleviate Deleterious Effects of YidC
Depletion in Escherichia coli. Journal of
Bacteriology, 193(6), 1308-1316. https://doi.org/10.1128/JB.01209-10
Guendogdu,
M. E., Kawai, Y., Pavlendova, N., Ogasawara, N., Errington,
J., Scheffers, D.-J., Hamoen, L. W., &
Gündoğdu, M. E. (2011). Large ring polymers align
FtsZ polymers for normal septum formation. EMBO
Journal, 30(3), 617-626. https://doi.org/10.1038/emboj.2010.345
Urban,
P. L., Schmidt, A. M., Fagerer, S. R., Amantonico, A., Ibañez,
A., Jefimovs, K., Heinemann, M., & Zenobi, R.
(2011). Carbon-13 labelling strategy for studying the ATP
metabolism in individual yeast cells by micro-arrays for mass
spectrometry. Molecular BioSystems,
7(10), 2837-2840. https://doi.org/10.1039/c1mb05248a
Costenoble,
R., Picotti, P., Reiter, L., Stallmach, R., Heinemann,
M., Sauer, U., & Aebersold, R. (2011).
Comprehensive quantitative analysis of central carbon and
amino-acid metabolism in Saccharomyces cerevisiae under multiple
conditions by targeted proteomics. Molecular
Systems Biology, 7(1), 464-1-464-13. Article
464. https://doi.org/10.1038/msb.2010.122
Volkmer,
B., & Heinemann, M. (2011).
Condition-dependent cell volume and concentration of
Escherichia coli to facilitate data conversion for systems biology
modeling. PLoS ONE, 6(7),
Article 23126. https://doi.org/10.1371/journal.pone.0023126
Heinemann,
M., & Sauer, U. (2011). From good old biochemical
analyses to high-throughput omics measurements and back.
Current Opinion in Biotechnology,
22(1), 1-2. https://doi.org/10.1016/j.copbio.2010.12.002
Bujara,
M., Schümperli, M., Pellaux, R., Heinemann, M.,
& Panke, S. (2011). Optimization of a blueprint for in
vitro glycolysis by metabolic real-time analysis.
Nature Chemical Biology, 7(5),
271-277. https://doi.org/10.1038/nchembio.541
Heinemann,
M., & Zenobi, R. (2011). Single cell
metabolomics. Current Opinion in
Biotechnology, 22(1), 26-31. https://doi.org/10.1016/j.copbio.2010.09.008
Sturm,
A., Heinemann, M., Arnoldini, M., Benecke, A.,
Ackermann, M., Benz, M., Dormann, J., & Hardt, W.-D. (2011).
The cost of virulence: retarded growth of Salmonella
Typhimurium cells expressing type III secretion system 1.
PLoS Pathogens, 7(7), Article
1002143. https://doi.org/10.1371/journal.ppat.1002143
Broos,
J. (2011). 5-Fluorotryptophan as Fluorescent Probe to
Characterize an Oligomeric Membrane Protein.
Biophysical Journal, 100(3),
609a-609a. https://doi.org/10.1016/j.bpj.2010.12.3509
Szperl,
A. M., Golachowska, M. R., Bruinenberg, M.,
Prekeris, R., Thunnissen, A.-M. W. H.,
Karrenbeld, A., Dijkstra, G., Hoekstra,
D., Mercer, D., Ksiazyk, J., Wijmenga, C.,
Wapenaar, M. C., Rings, E. H. H. M., & van IJzendoorn, S.
C. D. (2011). Functional characterization of mutations
in the myosin Vb gene associated with microvillus inclusion
disease. Journal of Pediatric Gastroenterology and
Nutrition, 52(3), 307-313. https://doi.org/10.1097/MPG.0b013e3181eea177
Fibriansah,
G., Veetil, V. P., Poelarends, G. J., &
Thunnissen, A.-M. W. H. (2011). Structural Basis for
the Catalytic Mechanism of Aspartate Ammonia Lyase.
Biochemistry, 50(27), 6053-6062. https://doi.org/10.1021/bi200497y
2010
Johannes,
F., Wardenaar, R., Colomé Tatché,
M., Mousson, F., de Graaf, P., Mokry, M.,
Guryev, V., Timmers, H. T. M., Cuppen, E., &
Jansen, R. C. (2010). Comparing genome-wide chromatin
profiles using ChIP-chip or ChIP-seq.
Bioinformatics, 26(8), 1000-1006. https://doi.org/10.1093/bioinformatics/btq087
Li,
Y., Tesson, B. M., Churchill, G. A., & Jansen, R.
C. (2010). Critical reasoning on causal inference in
genome-wide linkage and association studies.
Trends in Genetics, 26(12), 493-498.
https://doi.org/10.1016/j.tig.2010.09.002
Tesson,
B. M., Breitling, R., & Jansen, R. C. (2010).
DiffCoEx: a simple and sensitive method to find
differentially coexpressed gene modules. Bmc
Bioinformatics, 11(1), 497-1-497-9. Article
497. https://doi.org/10.1186/1471-2105-11-497
Li,
Y., Breitling, R., Snoek, L. B., van der Velde, K.
J., Swertz, M. A., Riksen, J., Jansen, R.
C., & Kammenga, J. E. (2010). Global Genetic
Robustness of the Alternative Splicing Machinery in Caenorhabditis
elegans. Genetics, 186(1),
405-U620. https://doi.org/10.1534/genetics.110.119677
Seinen,
E., Burgerhof, J. G. M., Jansen, R.
C., & Sibon, O. C. M. (2010). RNAi
Experiments in D. melanogaster: Solutions to the Overlooked Problem
of Off-Targets Shared by Independent dsRNAs. PLoS
ONE, 5(10), Article 13119. https://doi.org/10.1371/journal.pone.0013119
Arends,
D., Prins, P., Jansen, R. C., &
Broman, K. W. (2010). R/qtl: high-throughput multiple QTL
mapping. Bioinformatics,
26(23), 2990-2992. https://doi.org/10.1093/bioinformatics/btq565
Nieselt,
K., Battke, F., Herbig, A., Bruheim, P., Wentzel, A., Jakobsen, O.
M., Sletta, H., Alam, M. T., Merlo, M. E., Moore, J.,
Omara, W. A. M., Morrissey, E. R., Juarez-Hermosillo, M. A.,
Rodriguez-Garcia, A., Nentwich, M., Thomas, L., Iqbal, M., Legaie,
R., Gaze, W. H., ... Morrisey, E. R. (2010). The dynamic
architecture of the metabolic switch in Streptomyces
coelicolor. BMC Genomics, 11,
Article 10. https://doi.org/10.1186/1471-2164-11-10
Swertz,
M. A., Dijkstra, M., Adamusiak, T., van der Velde, J.
K., Kanterakis, A., Roos, E. T., Lops, J., Thorisson, G. A.,
Arends, D., Byelas, G., Muilu, J., Brookes, A. J., de Brock,
E. O., Jansen, R. C., & Parkinson, H.
(2010). The MOLGENIS toolkit: rapid prototyping of
biosoftware at the push of a button. Bmc
Bioinformatics, 11 suppl 12 (S12),
S12-1-S12-9. Article 12. https://doi.org/10.1186/1471-2105-11-S12-S12
Swertz,
M. A., van der Velde, K. J., Tesson, B. M.,
Scheltema, R. A., Arends, D., Vera, G., Alberts, R., Dijkstra, M.,
Schofield, P., Schughart, K., Hancock, J. M., Smedley, D.,
Wolstencroft, K., Goble, C., de Brock, E. O., Jones,
A. R., Parkinson, H. E., & Jansen, R. C. (2010).
XGAP: A uniform and extensible data model and software
platform for genotype and phenotype experiments.
Genome Biology, 11(3), Article 27.
https://doi.org/10.1186/gb-2010-11-3-r27
Szymanski,
W., Postema, C., Tarabiono, C., Berthiol, F.,
Campbell-Verduyn, L., de Wildeman, S., de Vries, J. G.,
Feringa, B. L., & Janssen, D. B. (2010).
Combining designer cells and click chemistry for a one-pot
four-step preparation of enantiopure beta-hydroxytriazoles.
Advanced Synthesis & Catalysis,
352(13), 2111-2115. https://doi.org/10.1002/adsc.201000502
Van
Haastert, P. J. M. (2010). A Model for a Correlated
Random Walk Based on the Ordered Extension of Pseudopodia.
PLoS Computational Biology, 6(8),
Article e1000874. https://doi.org/10.1371/journal.pcbi.1000874
Kortholt,
A., Bolourani, P., Rehmann, H., Keizer-Gunnink,
I., Weeks, G., Wittinghofer, A., & Van Haastert,
P. J. M. (2010). A Rap/Phosphatidylinositol 3-Kinase
Pathway ControlsPseudopod Formation. Molecular
Biology of the Cell, 21(6), 936-945. https://doi.org/10.1091/mbc.E09-03-0177
Van
Haastert, P. J. M. (2010). A Stochastic Model for
Chemotaxis Based on the Ordered Extension of Pseudopods.
Biophysical Journal, 99(10),
3345-3354. https://doi.org/10.1016/j.bpj.2010.09.042
van
Egmond, W. N., & van Haastert, P. J. M.
(2010). Characterization of the Roco Protein Family in
Dictyostelium discoideum. Eukaryotic
Cell, 9(5), 751-761. https://doi.org/10.1128/EC.00366-09
Van
Haastert, P. J. M. (2010). Chemotaxis: insights from
the extending pseudopod. Journal of Cell
Science, 123(18), 3031-3037. https://doi.org/10.1242/jcs.071118
Araki,
T., van Egmond, W. N., van Haastert, P. J.
M., & Williams, J. G. (2010). Dual regulation of a
Dictyostelium STAT by cGMP and Ca2+ signalling.
Journal of Cell Science, 123(6),
837-841. https://doi.org/10.1242/jcs.064436
Bosgraaf,
L., & Van Haastert, P. J. M. (2010). Quimp3,
an automated pseudopod-tracking algorithm. Cell
Adhesion & Migration, 4(1), 46-55. https://doi.org/10.4161/cam.4.1.9953
Maglia,
G., Heron, AJ., Stoddart, D., Japrung, D., & Bayley, H.
(2010). ANALYSIS OF SINGLE NUCLEIC ACID MOLECULES WITH
PROTEIN NANOPORES. Methods in
Enzymology, 475, 591-623.
Wallace,
E. VB., Stoddart, D., Heron, A., Mikhailova, E., Maglia,
G., Donohoe, T. J., & Bayley, H. (2010).
Identification of epigenetic DNA modifications with a protein
nanopore. Chemical Communications,
46(43), 8195-8197.
Stoddart,
D., Heron, A. J., Maglia, G., & Bayley, J. H. P.
(2010). Method for sequencing heteropolymeric
target nucleic acid sequence. (Patent No.
WO2010109197).
Maglia,
G., & Bayley, J. H. P. (2010). Methods of enhancing translocation of charged
analytes through transmembrane protein pores. (Patent No.
WO2010055307).
Stoddart,
D., Maglia, G., Mikhailova, E., Heron, A., &
Bayley, H. (2010). Multiple Base-Recognition Sites in a
Biological Nanopore: Two Heads are Better than One.
Angewandte Chemie - International Edition,
49(3), 556-559.
Stoddart,
D., Heron, A., Klingelhoefer, J., Mikhailova, E., Maglia,
G., & Bayley, H. (2010). Nucleobase Recognition in
ssDNA at the Central Constriction of the alpha-Hemolysin
Pore. Nano Letters, 10(9),
3633-3637.
Japrung,
D., Henricus, M., Li, QH., Maglia, G., & Bayley,
H. (2010). Urea Facilitates the Translocation of
Single-Stranded DNA and RNA Through the alpha-Hemolysin
Nanopore. Biophysical Journal,
98(9), 1856-1863.
Booijink,
C. C. G. M., El-Aidy, S.,
Rajilić-Stojanović, M., Heilig, H. G. H. J., Troost, F.
J., Smidt, H., Kleerebezem, M., De Vos, W. M., & Zoetendal, E.
G. (2010). High temporal and inter-individual variation
detected in the human ileal microbiota.
Environmental Microbiology, 12(12),
3213-3227. https://doi.org/10.1111/j.1462-2920.2010.02294.x
Van
den Abbeele, P., Grootaert, C., Marzorati, M., Possemiers, S.,
Verstraete, W., Gerard, P., Rabot, S., Bruneau, A., El Aidy,
S., Derrien, M., Zoetendal, E., Kleerebezem, M., Smidt, H.,
& Van de Wiele, T. (2010). Microbial Community
Development in a Dynamic Gut Model Is Reproducible, Colon Region
Specific, and Selective for Bacteroidetes and Clostridium Cluster
IX. Applied and environmental
microbiology, 76(15), 5237-5246. https://doi.org/10.1128/AEM.00759-10
Saraya,
R., Cepinska, M. N., Kiel, J. A. K. W., Veenhuis,
M., van der Klei, I. J., & Cepińska, M. N.
(2010). A conserved function for Inp2 in peroxisome
inheritance. Biochimica et Biophysica
Acta-Molecular Cell Research, 1803(5), 617 -
622. https://doi.org/10.1016/j.bbamcr.2010.02.001
Klompmaker,
S. H., Kilic, A., Baerends, R. J., Veenhuis, M., & van
der Klei, I. J. (2010). Activation of a peroxisomal
Pichia pastoris d-amino acid oxidase, which uses d-alanine as a
preferred substrate, depends on pyruvate carboxylase.
Fems Yeast Research, 10(6), 708-716.
https://doi.org/10.1111/j.1567-1364.2010.00647.x
van
Zutphen, T., Baerends, R. J. S., Susanna,
K., de Jong, A., Kuipers, O. P.,
Veenhuis, M., & van der Klei, I. J. (2010).
Adaptation of Hansenula polymorpha to methanol: A
transcriptome analysis. BMC Genomics,
11(1). https://doi.org/10.1186/1471-2164-11-1
van
den Berg, M. A., Gidijala, L., Kiel, J. A. K.
W., Bovenberg, R. A. L., & van der
Klei, I. J. (2010). Biosynthesis of active
pharmaceuticals: β-lactam biosynthesis in filamentous
fungi. Biotechnol Genet Eng Rev,
27(1), 1-31.
Nagotu,
S., Veenhuis, M., & van der Klei, I. J. (2010).
Divide et impera: The dictum of peroxisomes.
Traffic, 11(2), 175-184. https://doi.org/10.1111/j.1600-0854.2009.01019.x
Huberts,
D., & van der Klei, I. J. (2010).
Moonlighting proteins: An intriguing mode of
multitasking. Biochimica et Biophysica
Acta-Molecular Cell Research, 1803(4),
520-525. https://doi.org/10.1016/j.bbamcr.2010.01.022
Opalinski,
L., Kiel, J. A. K. W., Homan, T. G., Veenhuis,
M., van der Klei, I. J., & Opaliński, Ł.
(2010). Penicillium chrysogenum Pex14/17p – a novel
component of the peroxisomal membrane that is important for
penicillin production. Febs Journal,
277(15), 3203-3218. https://doi.org/10.1111/j.1742-4658.2010.07726.x
Meijer,
W. H., Gidijala, L., Fekken, S., Kiel, J. A. K. W.,
van den Berg, M. A., Lascaris, R., Bovenberg, R. A.
L., & van der Klei, I. J. (2010).
Peroxisomes are required for efficient penicillin
biosynthesis in Penicillium chrysogenum. Applied
and environmental microbiology, 76(17),
5702-5709. https://doi.org/10.1128/AEM.02327-09
Saraya,
R., Veenhuis, M., & van der Klei, I. J. (2010).
Peroxisomes as dynamic organelles: peroxisome abundance in
yeast. Febs Journal, 277(16),
3279-3288. https://doi.org/10.1111/j.1742-4658.2010.07740.x
van
der Klei, I. J. (2010). Peroxisomes as dynamic
organelles. Febs Journal,
277(16), 3267. https://doi.org/10.1111/j.1742-4658.2010.07738.x
Huberts,
D. H. E. W., Venselaar, H., Vriend, G., Veenhuis, M., &
van der Klei, I. J. (2010). The moonlighting function
of pyruvate carboxylase resides in the non-catalytic end of the TIM
barrel. Biochimica et Biophysica Acta-Molecular
Cell Research, 1803(9), 1038-1042. https://doi.org/10.1016/j.bbamcr.2010.03.018
Koetsier,
M. J., Gombert, A. K., Fekken, S., Bovenberg, R. A.
L., Van den Berg, M. A., Kiel, J. A. K. W.,
Jekel, P. A., Janssen, D. B., Pronk, J. T., Van
der Klei, I. J., & Daran, J.-M. (2010). The
Penicillium chrysogenum aclA gene encodes a
broad-substrate-specificity acyl-coenzyme A ligase involved in
activation of adipic acid, a side-chain precursor for cephem
antibiotics. Fungal Genetics and
Biology, 47(1), 33-42. https://doi.org/10.1016/j.fgb.2009.10.003
Marrink,
S. J., Periole, X., Tieleman, D. P., & de Vries,
A. H. (2010). Comment on "On using a too large
integration time step in molecular dynamics simulations of
coarse-grained molecular models'' by M. Winger, D. Trzesniak, R.
Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11,
1934. Physical Chemistry Chemical
Physics, 12(9), 2254-2256. https://doi.org/10.1039/b915293h
Fuhrmans,
M., Sanders, B. P., Marrink, S.-J., & de
Vries, A. H. (2010). Effects of bundling on the
properties of the SPC water model. Theoretical
Chemistry Accounts, 125(3-6), 335-344. https://doi.org/10.1007/s00214-009-0590-4
Horta,
B. A. C., de Vries, A. H., & Hunenberger, P. H.
(2010). Simulating the Transition between Gel and
Liquid-Crystal Phases of Lipid Bilayers: Dependence of the
Transition Temperature on the Hydration Level.
Journal of Chemical Theory and Computation,
6(8), 2488-2500. https://doi.org/10.1021/ct100200w
Rzepiela,
A. J., Schafer, L. V., Goga, N., Risselada, H.
J., De Vries, A. H., & Marrink, S. J.
(2010). Software News and Update Reconstruction of Atomistic
Details from Coarse-Grained Structures. Journal of
Computational Chemistry, 31(6), 1333-1343. https://doi.org/10.1002/jcc.21415
de
Jong, A., van Heel, A. J., Kok,
J., & Kuipers, O. P. (2010). BAGEL2:
Mining for bacteriocins in genomic data. Nucleic
Acids Research, 38, W647-W651. https://doi.org/10.1093/nar/gkq365
Linares,
D. M., Kok, J., & Poolman, B. (2010).
Genome Sequences of Lactococcus lactis MG1363 (Revised) and
NZ9000 and Comparative Physiological Studies.
Journal of Bacteriology, 192(21),
5806 - 5812. https://doi.org/10.1128/JB.00533-10
Chikindas,
M., Emond, E., Haandrikman, A. J., Kok, J., Leenhouts,
K., Pandian, S., Venema, G., & Venema, K. (2010).
Heterologous Processing and Export of the Bacteriocins
Pediocin PA-1 and Lactococcin A in Lactococcus Lactis: A Study with
Leader Exchange. Probiotics and Antimicrobial
Proteins, 2(2), 66-76. https://doi.org/10.1007/s12602-009-9023-x
Neves,
A. R., Pool, W., Solopova, A., Kok, J., Santos,
H., & Kuipers, O. P. (2010). Towards
Enhanced Galactose Utilization by Lactococcus lactis.
Applied and environmental microbiology,
76(21), 7048 - 7060. https://doi.org/10.1128/AEM.01195-10
Visweswaran,
G. R. R., Dijkstra, B. W., & Kok, J. (2010).
Two Major Archaeal Pseudomurein Endoisopeptidases: PeiW and
PeiP. Archaea-An international microbiological
journal, 2010(3), 1-4. Article 480492. https://doi.org/10.1155/2010/480492
Moll,
G. N., Kuipers, A., & Rink, R. (2010).
Microbial engineering of dehydro-amino acids and lanthionines
in non-lantibiotic peptides. Antonie van
Leeuwenhoek, International Journal of General and Molecular
Microbiology, 97(4), 319-333. https://doi.org/10.1007/s10482-010-9418-4
de
Vries, L., Reitzema-Klein, C. E., Meter-Arkema, A.,
van Dam, A., Rink, R., Moll, G. N., & Akanbi, M.
H. J. (2010). Oral and pulmonary delivery of
thioether-bridged angiotensin-(1-7).
Peptides, 31(5), 893-898. https://doi.org/10.1016/j.peptides.2010.02.015
Majchrzykiewicz,
J. A., Lubelski, J., Moll, G. N., Kuipers,
A., Bijlsma, J. J. E., Kuipers, O. P., &
Rink, R. (2010). Production of a Class II Two-Component
Lantibiotic of Streptococcus pneumoniae Using the Class I Nisin
Synthetic Machinery and Leader Sequence.
Antimicrobial Agents and Chemotherapy,
54(4), 1498-1505. https://doi.org/10.1128/AAC.00883-09
Rink,
R., Arkema-Meter, A., Baudoin, I.,
Post, E., Kuipers, A., Nelemans, S. A., Akanbi,
M. H. J., & Moll, G. N. (2010). To protect
peptide pharmaceuticals against peptidases.
Journal of Pharmacological and Toxicological
Methods, 61(2), 210-218. https://doi.org/10.1016/j.vascn.2010.02.010
Nijland,
J. G., Ebbendorf, B., Woszczynska, M., Boer, R.,
Bovenberg, R. A. L., & Driessen, A. J. M.
(2010). Nonlinear Biosynthetic Gene Cluster Dose Effect on
Penicillin Production by Penicillium chrysogenum.
Applied and environmental microbiology,
76(21), 7109-7115. https://doi.org/10.1128/AEM.01702-10
Medema,
M. H., Trefzer, A., Kovalchuk, A., van den Berg, M., Muller, U.,
Heijne, W., Wu, L., Alam, M. T., Ronning, C. M., Nierman, W.
C., Bovenberg, R. A. L., Breitling, R., & Takano,
E. (2010). The Sequence of a 1.8-Mb Bacterial Linear Plasmid
Reveals a Rich Evolutionary Reservoir of Secondary Metabolic
Pathways. Genome Biology and
Evolution, 2, 212-224. https://doi.org/10.1093/gbe/evq013
Fernandes
de Oliveira, I. F., Sousa Borges, A. D., Kooij, V.,
Bartosiak-Jentys, J., Luirink, J., & Scheffers,
D.-J. (2010). Characterization of ftsZ Mutations that
Render Bacillus subtilis Resistant to MinC. PLoS
ONE, 5(8), Article e12048. https://doi.org/10.1371/journal.pone.0012048
Ribeiro,
J. P., Palczewska, M., André, S., Cañada, F. J., Gabius,
H.-J., Jiménez-Barbero, J., Mellström, B., Naranjo, J.
R., Scheffers, D.-J., & Groves, P. (2010).
Diffusion nuclear magnetic resonance spectroscopy detects
substoichiometric concentrations of small molecules in protein
samples. Analytical Biochemistry,
396(1), 117-123. https://doi.org/10.1016/j.ab.2009.09.001
Kotte,
O., Zaugg, J. B., & Heinemann, M. (2010).
Bacterial adaptation through distributed sensing of metabolic
fluxes. Molecular Systems Biology,
82(9), 1492-1493. Article 355. https://doi.org/10.1038/msb.2010.10
Kummel,
A., Ewald, J. C., Fendt, S.-M., Jol, S. J., Picotti, P., Aebersold,
R., Sauer, U., Zamboni, N., & Heinemann, M.
(2010). Differential glucose repression in common yeast
strains in response to HXK2 deletion. Fems Yeast
Research, 10(3), 322-332. https://doi.org/10.1111/j.1567-1364.2010.00609.x
Bujara,
M., Schümperli, M., Billerbeck, S.,
Heinemann, M., & Panke, S. (2010). Exploiting
Cell-Free Systems: Implementation and Debugging of a System of
Biotransformations. Biotechnology and
Bioengineering, 106(3), 376-389. https://doi.org/10.1002/bit.22666
Heinemann,
M., & Sauer, U. (2010). Systems biology of
microbial metabolism. Current Opinion in
Microbiology, 13(3), 337-343. https://doi.org/10.1016/j.mib.2010.02.005
Jol,
S. J., Kümmel, A., Hatzimanikatis, V., Beard, D. A.,
& Heinemann, M. (2010). Thermodynamic calculations
for biochemical transport and reaction processes in metabolic
networks. Biophysical Journal,
99(10), 3139-3144. https://doi.org/10.1016/j.bpj.2010.09.043
Kleijn,
R., Fendt, S.-M., Schuetz, R., Heinemann, M., Zamboni,
N., & Sauer, U. (2010). Transcriptional control of
metabolic fluxes and computational identification of the governing
principles. Febs Journal,
277, 27-27.
Opacic,
M., Vos, E. P. P., Hesp, B. H., & Broos, J.
(2010). Localization of the substrate binding site in the
homodimeric mannitol transporter, EIImtl, of Escherichia
coli. The Journal of Biological
Chemistry, 285(33), 25324-25331. https://doi.org/10.1074/jbc.M110.122523
Kale,
A., Pijning, T., Sonke, T., Dijkstra, B. W.,
& Thunnissen, A.-M. W. H. (2010). Crystal
Structure of the Leucine Aminopeptidase from Pseudomonas putida
Reveals the Molecular Basis for its Enantioselectivity and Broad
Substrate Specificity. Journal of Molecular
Biology, 398(5), 703-714. https://doi.org/10.1016/j.jmb.2010.03.042
Wolters,
J. C., Berntsson, R. P.-A., Gul, N., Karasawa, A.,
Thunnissen, A.-M. W. H., Slotboom, D.-J.,
& Poolman, B. (2010). Ligand Binding and Crystal
Structures of the Substrate-Binding Domain of the ABC Transporter
OpuA. PLoS ONE, 5(4), Article
10361. https://doi.org/10.1371/journal.pone.0010361
Madoori,
P. K., & Thunnissen, A.-M. W. H. (2010).
Purification, crystallization and preliminary X-ray
diffraction analysis of the lytic transglycosylase MltF from
Escherichia coli. Acta Crystallographica Section
F: Structural Biology and Crystallization
Communications, 66(5), 534-538. https://doi.org/10.1107/S1744309110010596
Wasiel,
A. A., Rozeboom, H. J., Hauke, D., Baas, B.-J.,
Zandvoort, E., Quax, W. J., Thunnissen, A.-M. W.
H., & Poelarends, G. J. (2010).
Structural and Functional Characterization of a Macrophage
Migration Inhibitory Factor Homologue from the Marine
Cyanobacterium Prochlorococcus marinus.
Biochemistry, 49(35), 7572-7581. https://doi.org/10.1021/bi1008276
2009
Heap,
G. A., Trynka, G., Jansen, R. C., Bruinenberg,
M., Swertz, M. A., Dinesen, L. C., Hunt, K.
A., Wijmenga, C., vanHeel, D. A., Franke,
L., & Heel, D. A. V. (2009). Complex nature of SNP
genotype effects on gene expression in primary human
leucocytes. BMC Medical Genomics,
2(1), Article 1. https://doi.org/10.1186/1755-8794-2-1
Jansen,
R. C., Tesson, B. M., Fu, J., Yang, Y.,
McIntyre, L. M., & McInttyre, L. M. (2009). Defining gene
and QTL networks. Current Opinion in Plant
Biology, 12(2), 241-246. https://doi.org/10.1016/j.pbi.2009.01.003
Li,
Y., Swertz, M. A., Vera, G., Fu,
J., Breitling, R., & Jansen, R. C. (2009).
designGG: an R-package and web tool for the optimal design of
genetical genomics experiments. Bmc
Bioinformatics, 10(188), Article 188. https://doi.org/10.1186/1471-2105-10-188
Franke,
L., & Jansen, R. C. (2009). eQTL
Analysis in Humans. In K. DiPetrillo (Ed.),
Cardiovascular Genomics: Methods and Protocols (Vol. 573,
pp. 311-328). (Methods in Molecular Biology; No. 573). Springer. https://doi.org/10.1007/978-1-60761-247-6_17
Franke,
L. H., & Jansen, R. C. (2009). eQTL
Analysis in Humans in Methods in Molecular Biology. In
Dipetrello (Ed.), Cardiovascular Genomics
Tesson,
B. M., & Jansen, R. C. (2009). eQTL Analysis
in Mice and Rats. In K. DiPetrillo (Ed.), Cardiovascular
Genomics: Methods and Protocols (573 ed., pp. 285-309).
(Methods in Molecular Biology; No. 573). Springer. https://doi.org/10.1007/978-1-60761-247-6_16
Tesson,
B. M., & Jansen, R. C. (2009). eQTL Analysis
in mice and rats Methods in Molecular Biology. In Dipetrello
K. (Ed.), Cardiovascular Genetics
Gerrits,
A., Li, Y., Tesson, B. M., Bystrykh, L.
V., Weersing, E., Ausema, A.,
Dontje, B., Wang, X., Breitling, R., Jansen, R.
C., de Haan, G., & Dethmers-Ausema, B.
(2009). Expression Quantitative Trait Loci Are Highly
Sensitive to Cellular Differentiation State. PLoS
genetics, 5(10), Article 1000692. https://doi.org/10.1371/journal.pgen.1000692
Dijkstra,
M., & Jansen, R. C. (2009). Optimal analysis
of complex protein mass spectra.
Proteomics, 9(15), 3869-3876. https://doi.org/10.1002/pmic.200701064
Scheltema,
R. A., Decuypere, S., Dujardin, J. C., Watson, D. G., Jansen,
R. C., & Breitling, R. (2009). Simple
data-reduction method for high-resolution LC-MS data in
metabolomics. Bioanalysis,
1(9), 1551-1557. https://doi.org/10.4155/BIO.09.146
Fu,
J., Keurentjes, J. J. B., Bouwmeester, H., America, T.,
Verstappen, F. W. A., Ward, J. L., Beale, M. H., de Vos, R. C. H.,
Dijkstra, M., Scheltema, R. A., Johannes, F., Koornneef, M.,
Vreugdenhil, D., Breitling, R., & Jansen, R. C.
(2009). System-wide molecular evidence for phenotypic
buffering in Arabidopsis. Nature
Genetics, 41(2), 166-167. https://doi.org/10.1038/ng.308
Bosgraaf,
L., van Haastert, P. J. M., & Bretschneider, T.
(2009). Analysis of Cell Movement by Simultaneous
Quantification of Local Membrane Displacement and Fluorescent
Intensities Using Quimp2. Cell Motility and the
Cytoskeleton, 66(3), 156-165. https://doi.org/10.1002/cm.20338
Veltman,
D. M., Akar, G., Bosgraaf, L., & Van Haastert, P. J.
M. (2009). A new set of small, extrachromosomal
expression vectors for Dictyostelium discoideum.
Plasmid, 61(2), 110-118. https://doi.org/10.1016/j.plasmid.2008.11.003
Veltman,
D. M., Keizer-Gunnink, I., & Van Haastert,
P. J. M. (2009). An extrachromosomal, inducible
expression system for Dictyostelium discoideum.
Plasmid, 61(2), 119-125. https://doi.org/10.1016/j.plasmid.2008.11.002
Van
Haastert, P. J. M., & Bosgraaf, L. (2009). Food
Searching Strategy of Amoeboid Cells by Starvation Induced Run
Length Extension. PLoS ONE,
4(8), Article 6814. https://doi.org/10.1371/journal.pone.0006814
Bosgraaf,
L., & Van Haastert, P. J. M. (2009).
Navigation of Chemotactic Cells by Parallel Signaling to
Pseudopod Persistence and Orientation. PLoS
ONE, 4(8), Article 6842. https://doi.org/10.1371/journal.pone.0006842
Sato,
M. J., Kuwayama, H., van Egmond, W. N., Takayama, A.
L. K., Takagi, H., van Haastert, P. J. M., Yanagida,
T., & Ueda, M. (2009). Switching direction in
electric-signal-induced cell migration by cyclic guanosine
monophosphate and phosphatidylinositol signaling.
Proceedings of the National Academy of Sciences of the
United States of America, 106(16), 6667-6672.
https://doi.org/10.1073/pnas.0809974106
Van
Haastert, P. J. M., & Bosgraaf, L. (2009). The
local cell curvature guides pseudopodia towards
chemoattractants. HFSP Journal,
3(4), 282-286. https://doi.org/10.2976/1.3185725
Bosgraaf,
L., & Van Haastert, P. J. M. (2009). The
Ordered Extension of Pseudopodia by Amoeboid Cells in the Absence
of External Cues. PLoS ONE,
4(4), Article 5253. https://doi.org/10.1371/journal.pone.0005253
Kortholt,
A. (2009). Chemotaxis: a complex netwerk of
interconnecting signalling pathways and amplification
loops. [S.n.].
Salomons,
H. M., Mulder, G. A., Zande, L. V. D.,
Haussmann, M. F., Linskens, M. H. K., &
Verhulst, S. (2009). Telomere shortening and survival
in free-living corvids. Proceedings of the Royal
Society B, 276(1670), 3157-3165. https://doi.org/10.1098/rspb.2009.0517
Maglia,
G., Henricus, M., Wyss, R., Li, QH., Cheley, S., &
Bayley, H. (2009). DNA Strands from Denatured Duplexes are
Translocated through Engineered Protein Nanopores at Alkaline
pH. Nano Letters, 9(11),
3831-3836.
Maglia,
G., Heron, AJ., Hwang, WL., Holden, MA., Mikhailova, E., Li,
QH., Cheley, S., & Bayley, H. (2009). Droplet networks
with incorporated protein diodes show collective properties.
Nature Nanotechnology, 4(7),
437-440.
Bayley,
J. H. P., Wu, H., Maglia, G., & Astier, Y. (2009).
Molecular adaptors. (Patent No.
WO2009044170).
Stoddart,
D., Heron, AJ., Mikhailova, E., Maglia, G., &
Bayley, H. (2009). Single-nucleotide discrimination in
immobilized DNA oligonucleotides with a biological nanopore.
Proceedings of the National Academy of Science of the
United States of America, 106(19),
7702-7707.
Gidijala,
L., Kiel, J. A. K. W., Douma, R. D., Seifar, R. M.,
van Gulik, W. M., Bovenberg, R. A. L., Veenhuis,
M., & van der Klei, I. J. (2009). An
Engineered Yeast Efficiently Secreting Penicillin.
PLoS ONE, 4(12), Article 8317. https://doi.org/10.1371/journal.pone.0008317
Todde,
V., Veenhuis, M., & van der Klei, I. J. (2009).
Autophagy: Principles and significance in health and
disease. Biochimica et biophysica acta-Molecular
basis of disease, 1792(1), 3-13. https://doi.org/10.1016/j.bbadis.2008.10.016
Krikken,
A. M., Veenhuis, M., & van der Klei, I. J.
(2009). Hansenula polymorpha pex11 cells are affected in
peroxisome retention. Febs Journal,
276(5), 1429-1439. https://doi.org/10.1111/j.1742-4658.2009.06883.x
Kiel,
J. A. K. W., van den Berg, M. A., Fusetti, F.,
Poolman, B., Bovenberg, R. A. L., Veenhuis,
M., & van der Klei, I. J. (2009). Matching
the proteome to the genome: the microbody of penicillin-producing
Penicillium chrysogenum cells. FUNCTIONAL &
INTEGRATIVE GENOMICS, 9(2), 167-184. https://doi.org/10.1007/s10142-009-0110-6
Kurbatova,
E., Otzen, M., & van der Klei, I. J.
(2009). p24 proteins play a role in peroxisome proliferation
in yeast. FEBS Letters,
583(19), 3175-3180. https://doi.org/10.1016/j.febslet.2009.08.040
Sagt,
C. M. J., Haaft, P. J. T., Minneboo, I. M., Hartog, M. P., Damveld,
R. A., Laan, J. M. V. D., Akeroyd, M., Wenzel, T. J., Luesken, F.
A., Veenhuis, M., Klei, I. V. D., & Winde, J. H.
D. (2009). Peroxicretion: a novel secretion pathway in the
eukaryotic cell. BMC Biotechnology,
9(1), Article 48. https://doi.org/10.1186/1472-6750-9-48
Aksam,
E. B., de Vries, B., van der Klei, I.
J., & Kiel, J. A. K. W. (2009).
Preserving organelle vitality: peroxisomal quality control
mechanisms in yeast. Fems Yeast
Research, 9(6), 808-820. https://doi.org/10.1111/j.1567-1364.2009.00534.x
Kiel,
J. A. K. W., & van der Klei, I. J. (2009).
Proteins involved in microbody biogenesis and degradation in
Aspergillus nidulans. Fungal Genetics and
Biology, 46(1), S62-S71. https://doi.org/10.1016/j.fgb.2008.07.009
Lee,
H., de Vries, A. H., Marrink, S.-J.,
& Pastor, R. W. (2009). A Coarse-Grained Model for
Polyethylene Oxide and Polyethylene Glycol: Conformation and
Hydrodynamics. Journal of Physical Chemistry
B, 113(40), 13186-13194. https://doi.org/10.1021/jp9058966
Siwko,
M. E., de Vries, A. H., Mark, A. E., Kozubek,
A., & Marrink, S. J. (2009). Disturb or
Stabilize? A Molecular Dynamics Study of the Effects of
Resorcinolic Lipids on Phospholipid Bilayers.
Biophysical Journal, 96(8),
3140-3153. https://doi.org/10.1016/j.bpj.2009.01.040
Winger,
M., de Vries, A. H., & van Gunsteren, W. F.
(2009). Force-field dependence of the conformational
properties of ,-dimethoxypolyethylene glycol.
Molecular Physics, 107(13),
1313-1321. Article 911054506. https://doi.org/10.1080/00268970902794826
Marrink,
S. J., de Vries, A. H., & Tieleman, D. P.
(2009). Lipids on the move: Simulations of membrane pores,
domains, stalks and curves. Biochimica et
Biophysica Acta-Biomembranes, 1788(1),
149-168. https://doi.org/10.1016/j.bbamem.2008.10.006
Hinner,
M. J., Marrink, S.-J., & de Vries, A.
H. (2009). Location, Tilt, and Binding: A Molecular
Dynamics Study of Voltage-Sensitive Dyes in Biomembranes.
Journal of Physical Chemistry B,
113(48), 15807-15819. https://doi.org/10.1021/jp907981y
Lopez,
C. A., Rzepiela, A. J., de Vries, A. H.,
Dijkhuizen, L., Huenenberger, P. H., & Marrink, S.
J. (2009). Martini Coarse-Grained Force Field:
Extension to Carbohydrates. Journal of Chemical
Theory and Computation, 5(12), 3195-3210. https://doi.org/10.1021/ct900313w
Castro,
R., Neves, A. R., Fonseca, L. L., Pool, W. A., Kok,
J., Kuipers, O. P., & Santos, H. (2009).
Characterization of the individual glucose uptake systems of
Lactococcus lactis: mannose-PTS, cellobiose-PTS and the novel GlcU
permease. Molecular Microbiology,
71(3), 795-806. https://doi.org/10.1111/j.1365-2958.2008.06564.x
Kawai,
Y., Kusnadi, J., Kemperman, R., Kok, J., Ito, Y.,
Endo, M., Arakawa, K., Uchida, H., Nishimura, J., Kitazawa, H.,
& Saito, T. (2009). DNA Sequencing and Homologous
Expression of a Small Peptide Conferring Immunity to Gassericin A,
a Circular Bacteriocin Produced by Lactobacillus gasseri
LA39. Applied Environmental
Microbiology, 75(5), 1324-1330. https://doi.org/10.1128/AEM.02485-08
Moll,
G. N., Kuipers, A., De Vries, L., Bosma, T.,
& Rink, R. (2009). A biological stabilization technology
for peptide drugs: Enzymatic introduction of
thioether-bridges. Drug Discovery Today:
Technologies, 6(1-4), e13-e18. https://doi.org/10.1016/j.ddtec.2009.03.001
Kluskens,
L. D., Nelemans, S. A., Rink, R., de Vries, L.,
Meter-Arkema, A., Wang, Y., Walther, T., Kuipers,
A., Moll, G. N., & Haas, M. (2009).
Angiotensin-(1-7) with Thioether Bridge: An
Angiotensin-Converting Enzyme-Resistant, Potent Angiotensin-(1-7)
Analog. Journal of Pharmacology and Experimental
Therapeutics, 328(3), 849-854. https://doi.org/10.1124/jpet.108.146431
Kuipers,
A., Rink, R., & Moll, G. N. (2009).
Translocation of a thioether-bridged azurin peptide fragment
via the Sec pathway in Lactococcus lactis. Applied
and environmental microbiology, 75(11),
3800-3802. https://doi.org/10.1128/AEM.00341-09
Koetsier,
M. J., Jekel, P. A., van den Berg, M. A., Bovenberg, R. A.
L., & Janssen, D. B. (2009).
Characterization of a phenylacetate-CoA ligase from
Penicillium chrysogenum. Biochemical
Journal, 417, 467-476. https://doi.org/10.1042/BJ20081257
Pop,
O. I., Soprova, Z., Koningstein, G., Scheffers, D.-J.,
Ulsen, P. V., Wickström, D., Gier, J.-W. D., & Luirink, J.
(2009). YidC is required for the assembly of the MscL
homopentameric pore. The FEBS Journal,
276(17), 4891-4899. https://doi.org/10.1111/j.1742-4658.2009.07188.x
Kotte,
O., & Heinemann, M. (2009). A
divide-and-conquer approach to analyze underdetermined biochemical
models. Bioinformatics,
25(4), 519-525. https://doi.org/10.1093/bioinformatics/btp004
Lee,
S. S., Vizcarra, I. A., Lee, L. P., & Heinemann,
M. (2009). Long-term monitoring of yeast cell division
via elastic micro-pad. In Proceedings of Conference,
MicroTAS 2009 - The 13th International Conference on Miniaturized
Systems for Chemistry and Life Sciences (pp. 478-480).
Chemical and Biological Microsystems Society .
Graaf,
A. A. D., Freidig, A. P., Roos, B. D., Jamshidi, N.,
Heinemann, M., Rullmann, J. A. C., Hall, K. D., Adiels, M.,
& Ommen, B. V. (2009). Nutritional Systems Biology
Modeling: From Molecular Mechanisms to Physiology.
PLoS Computational Biology, 5(11),
Article e1000554. https://doi.org/10.1371/journal.pcbi.1000554
Cook,
G. M., Berney, M., Gebhard, S., Heinemann, M., Cox, R.
A., Danilchanka, O., & Niederweis, M. (2009). Physiology
of mycobacteria. Advances in microbial
physiology, 55, 81-182. https://doi.org/10.1016/S0065-2911(09)05502-7
Heinemann,
M., & Panke, S. (2009). Synthetic Biology: Putting
Engineering into Bioengineering. In P. Fu, & S. Panke
(Eds.), Systems Biology and Synthetic Biology (pp.
387-409). Wiley. https://doi.org/10.1002/9780470437988.ch11
Visser,
N. V., Westphal, A. H., Nabuurs, S. M., van Hoek, A., Mierlo, C. P.
M. V., Visser, A. J. W. G., Broos, J., & van
Amerongen, H. (2009). 5-Fluorotryptophan as dual probe for
ground-state heterogeneity and excited-state dynamics in
apoflavodoxin. FEBS Letters,
583(17), 2785-2788. https://doi.org/10.1016/j.febslet.2009.07.022
Vos,
E. P. P., ter Horst, R., Poolman, B., &
Broos, J. (2009). Domain complementation studies
reveal residues critical for the activity of the mannitol permease
from Escherichia coli. Biochimica et Biophysica
Acta-Biomembranes, 1788(2), 581-586. https://doi.org/10.1016/j.bbamem.2008.10.008
Broos,
J., Tveen Jensen, K., Strambini, G. B., Gonelli, M., &
Jackson, B. (2009). Mutations In Transhydrogenase Change The
Fluorescence Emission State Of Trp72 From 1La To 1Lb. In
EPRINTS-BOOK-TITLE University of Groningen, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB).
Opacic,
M., Hesp, B. H., & Broos, J. (2009).
Structural and Mechanistic Characterization of the Mannitol
Transporter from E. coli using 5-fluorotryptophan as a
Spectroscopic Probe. Biophysical
Journal, 46a.
Vos,
E. P. P., Bokhove, M., Hesp, B. H., & Broos, J.
(2009). Structure of the Cytoplasmic Loop between Putative
Helices II and III of the Mannitol Permease of Escherichia coli: A
Tryptophan and 5-Fluorotryptophan Spectroscopy Study.
Biochemistry, 48(23), 5284-5290. https://doi.org/10.1021/bi8020668
Golachowska,
M. R., Szperl, A., Bruineberg, M., Prekeris, R.,
Thunnissen, A.-M. W. H., Hoekstra, D., Wijmenga,
C., Ksiazyk, J., Rings, E. H., Wapenaar, M. C., Ijzendoorn,
S. C., & van Ijzendoorn, S. (2009). Apical
Recycling Endosome-Associated Myosin Vb Is Mutated in Microvillus
Inclusion Disease and Is Involved in Intestinal Brush Border
Development. Gastroenterology,
136(5), A66-A66.
Golachowska,
M. R., Szperl, A., Bruineberg, M., Prekeris, R.,
Thunnissen, A.-M. W. H., Hoekstra, D., Wijmenga,
C., Ksiazyk, J., Rings, E. H., Wapenaar, M. C., &
IJzendoorn, S. C. (2009). Apical Recycling
Endosome-Associated Myosin Vb Is Mutated in Microvillus Inclusion
Disease and Is Involved in Intestinal Brush Border
Development.
Berntsson,
R. P. .-A., Oktaviani, N. A., Fusetti, F., Thunnissen, A.-M.
W. H., Poolman, B., & Slotboom,
D.-J. (2009). Selenomethionine incorporation in
proteins expressed in Lactococcus lactis. Protein
Science, 18(5), 1121-1127. https://doi.org/10.1002/pro.97
Madoori,
P. K., Agustiandari, H., Driessen, A. J. M.,
& Thunnissen, A.-M. W. H. (2009). Structure of the
transcriptional regulator LmrR and its mechanism of multidrug
recognition. EMBO Journal,
28(2), 156-166. https://doi.org/10.1038/emboj.2008.263
Berntsson,
R. P.-A., Doeven, M. K., Fusetti, F., Duurkens, R. H., Sengupta,
D., Marrink, S.-J., Thunnissen, A.-M. W.
H., Poolman, B., & Slotboom,
D.-J. (2009). The structural basis for peptide
selection by the transport receptor OppA. EMBO
Journal, 28(9), 1332-1340. https://doi.org/10.1038/emboj.2009.65
2008
Alberts,
R., Vera, G., & Jansen, R. C. (2008).
affyGG: computational protocols for genetical genomics with
Affymetrix arrays. Bioinformatics,
24(3), 433-434. https://doi.org/10.1093/bioinformatics/btm614
Johannes,
F., Colot, V., & Jansen, R. C. (2008).
Epigenome dynamics: a quantitative genetics
perspective. Nature Reviews Genetics,
9, 883 - 890. http://www.rug.nl/biologie/onderzoek/onderzoekGroepen/bioinformatics/pdfPapers/nrg2467johannes.pdf
Li,
Y., Breitling, R., & Jansen, R. C. (2008).
Generalizing genetical genomics: getting added value from
environmental perturbation. Trends in
Genetics, 24(10), 518-524. https://doi.org/10.1016/j.tig.2008.08.001
Breitling,
R., Li, Y., Tesson, B. M., Fu, J., Wu,
C., Wiltshire, T., Gerrits, A., Bystrykh, L. V.,
de Haan, G., Su, A. I., & Jansen, R. C.
(2008). Genetical Genomics: Spotlight on QTL Hotspots.
PLoS genetics, 4(10), Article
e1000232. https://doi.org/10.1371/journal.pgen.1000232
Scheltema,
R. A., Kamleh, A., Wildridge, D., Ebikeme, C., Watson, D. G.,
Barrett, M. R., Jansen, R. C., Breitling, R., &
Barrett, M. P. (2008). Increasing the mass accuracy of
high-resolution LC-MS data using background ions - a case study on
the LTQ-Orbitrap. Proteomics,
8(22), 4647-4656. https://doi.org/10.1002/pmic.200800314
Johannes,
F., Colot, V., & Jansen, R. C. (2008).
OPINION Epigenome dynamics: a quantitative genetics
perspective. Nature Reviews Genetics,
9(11), 883-890. https://doi.org/10.1038/nrg2467
Lam,
A. C., Fu, J., Jansen, R. C., Haley, C.
S., & de Koning, D.-J. (2008). Optimal Design of Genetic
Studies of Gene Expression With Two-Color Microarrays in Outbred
Crosses. Genetics, 180(3),
1691-1698. https://doi.org/10.1534/genetics.108.090308
Vera,
G., Jansen, R. C., & Suppi, R. L. (2008).
R/parallel - speeding up bioinformatics analysis with
R. Bmc Bioinformatics, 22(9),
390. Article 390. https://doi.org/10.1186/1471-2105-9-390
Swertz,
M. A., Smedley, D., Wolstencroft, K., Alberts, R.,
Zouberakis, M., Aidinis, V., Schughart, K., Schofield, P. N.,
& Jansen, R. C. (2008). Towards dynamic database
infrastructures for mouse genetics. In 8th IEEE
International Conference on BioInformatics and BioEngineering,
2008. BIBE 2008 University of Groningen, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB).
Veltman,
D. M., Keizer-Gunnink, I., & Van Haastert,
P. J. M. (2008). Four key signaling pathways mediating
chemotaxis in Dictyostelium discoideum. Journal of
Cell Biology, 180(4), 747-753. https://doi.org/10.1083/jcb.200709180
Kortholt,
A., & van Haastert, P. J. M. (2008).
Highlighting the role of Ras and Rap during Dictyostelium
chemotaxis. Cellular Signalling,
20(8), 1415-1422. https://doi.org/10.1016/j.cellsig.2008.02.006
Egmond,
W. N. V., Kortholt, A., Plak, K., Bosgraaf, L.,
Bosgraaf, S., Keizer-Gunnink, I., &
Haastert, P. J. M. V. (2008). Intramolecular
Activation Mechanism of the Dictyostelium LRRK2 Homolog Roco
Protein GbpC. The Journal of Biological
Chemistry, 283(44). https://doi.org/10.1074/jbc.M804265200
Bosgraaf,
L., Keizer-Gunnink, I., & van Haastert, P.
J. M. (2008). PI3-kinase signaling contributes to
orientation in shallow gradients and enhances speed in steep
chemoattractant gradients. Journal of Cell
Science, 121(21), 3589-3597. https://doi.org/10.1242/jcs.031781
Gotthardt,
K., Weyand, M., Kortholt, A., Van Haastert, P.
J. M., & Wittinghofer, A. (2008). Structure of the
Roc-COR domain tandem of C-tepidum, a prokaryotic homologue of the
human LRRK2 Parkinson kinase. EMBO
Journal, 27(16), 2239-2249. https://doi.org/10.1038/emboj.2008.150
Marin,
I., van Egmond, W. N., & van Haastert, P. J.
M. (2008). The Roco protein family: a functional
perspective. The FASEB Journal,
22(9), 3103-3110. https://doi.org/10.1096/fj.08-111310
Veltman,
D. M., & van Haastert, P. J. M. (2008). The
role of cGMP and the rear of the cell in Dictyostelium chemotaxis
and cell streaming. Journal of Cell
Science, 121(1), 120-127. https://doi.org/10.1242/jcs.015602
Marrink,
S. J., de Vries, A. H., Harroun, T. A.,
Katsaras, J., & Wassall, S. R. (2008). Cholesterol shows
preference for the interior of polyunsaturated lipid.
Journal of the American Chemical Society,
130(1), 10 - 11. https://doi.org/10.1021/ja076641c
Kramer,
N. E., Hasper, H. E., van den Bogaard, P. T. C., Morath, S., de
Kruijff, B., Hartung, T., Smid, E. J., Breukink, E., Kok,
J., & Kuipers, O. P. (2008).
Increased D-alanylation of lipoteichoic acid and a thickened
septum are main determinants in the nisin resistance mechanism of
Lactococcus lactis. Microbiology-Sgm,
154(6), 1755-1762. https://doi.org/10.1099/mic.0.2007/015412-0
Buist,
G., Steen, A., Kok, J.,
& Kuipers, O. P. (2008). LysM, a widely
distributed protein motif for binding to (peptido)glycans.
Molecular Microbiology, 68(4),
838-847. https://doi.org/10.1111/j.1365-2958.2008.06211.x
Steen,
A., Buist, G., Kramer, N. E., Jalving, R.,
Benus, G. F. J. D., Venema, G., Kuipers, O. P.,
& Kok, J. (2008). Reduced lysis upon growth of
Lactococcus lactis on galactose is a consequence of decreased
binding of the autolysin AcmA. Applied
Environmental Microbiology, 74(15), 4671-4679.
https://doi.org/10.1128/AEM.00103-08
van
Hijum, S. A. F. T., Baerends, R. J. S., Zomer, A. L.,
Karsens, H. A., Martin-Requena, V., Trelles, O., Kok,
J., & Kuipers, O. P. (2008).
Supervised Lowess normalization of comparative genome
hybridization data - application to lactococcal strain
comparisons. Bmc Bioinformatics,
9(93), Article 93. https://doi.org/10.1186/1471-2105-9-93
Larsen,
R., van Hijum, S. A. F. T., Martinussen, J., Kuipers, O.
P., & Kok, J. (2008). Transcriptome
analysis of the Lactococcus lactis ArgR and AhrC Regulons.
Applied and environmental microbiology,
74(15), 4768-4771. https://doi.org/10.1128/AEM.00117-08
Lubelski,
J., Rink, R., Khusainov, R., Moll, G. N., &
Kuipers, O. P. (2008). Biosynthesis, immunity,
regulation, mode of action and engineering of the model lantibiotic
nisin. Cellular and molecular life
sciences, 65(3), 455-476. https://doi.org/10.1007/s00018-007-7171-2
Haas,
M., Kluskens, L. D., Kuipers, A., Rink, R., Nelemans, S. A.,
& Moll, G. (2008). Cyclic
angiotensin analogs. (Patent No.
WO2008018792).
van
Saparoea, H. B. V. D. B., Bakkes, P. J., Moll, G.
N., & Driessen, A. J. M. (2008).
Distinct contributions of the nisin biosynthesis enzymes NisB
and NisC and transporter NisT to prenisin production by Lactococcus
lactis. Applied and environmental
microbiology, 74(17), 5541-5548. https://doi.org/10.1128/AEM.00342-08
Lubelski,
J., Overkamp, W., Kluskens, L. D., Moll, G. N.,
& Kuipers, O. P. (2008). Influence of shifting
positions of Ser, Thr, and Cys residues in prenisin on the
efficiency of modification reactions and on the antimicrobial
activities of the modified prepeptides. Applied
and environmental microbiology, 74(15),
4680-4685. https://doi.org/10.1128/AEM.00112-08
Kuipers,
A., Meijer-Wierenga, J., Rink, R., Kluskens, L. D.,
& Moll, G. N. (2008). Mechanistic dissection of
the enzyme complexes involved in biosynthesis of lacticin 3147 and
nisin. Applied and environmental
microbiology, 74(21), 6591-6597. https://doi.org/10.1128/AEM.01334-08
Nijland,
J. G., Kovalchuk, A., van den Berg, M. A., Bovenberg,
R. A. L., & Driessen, A. J. M. (2008).
Expression of the transporter encoded by the cefT gene of
Acremonium chrysogenum increases cephalosporin production in
Penicillium chrysogenum. Fungal Genetics and
Biology, 45(10), 1415-1421. https://doi.org/10.1016/j.fgb.2008.07.008
van
den Berg, M. A., Albang, R., Albermann, K., Badger, J. H., Daran,
J.-M., Driessen, A. J. M., Garcia-Estrada, C.,
Fedorova, N. D., Harris, D. M., Heijne, W. H. M., Joardar,
V., Kiel, J. A. K. W., Kovalchuk, A., Martin, J. F.,
Nierman, W. C., Nijland, J. G., Pronk, J. T., Roubos,
J. A., van der Klei, I. J., ... Bovenberg, R. A.
L. (2008). Genome sequencing and analysis of the
filamentous fungus Penicillium chrysogenum. Nature
Biotechnology, 26(10), 1161-1168. https://doi.org/10.1038/nbt.1498
Gidijala,
L., Bovenberg, R. A. L., Klaassen, P., van der
Klei, I. J., Veenhuis, M., & Kiel, J. A. K.
W. (2008). Production of functionally active
Penicillium chrysogenum isopenicillin N synthase in the yeast
Hansenula polymorpha. BMC
Biotechnology, 8(1), Article 29. https://doi.org/10.1186/1472-6750-8-29
Formstone,
A., Carballido-López, R., Noirot, P., Errington, J.,
& Scheffers, D.-J. (2008). Localization and
Interactions of Teichoic Acid Synthetic Enzymes in Bacillus
subtilis. Journal of Bacteriology,
190(5), 1812-1821. https://doi.org/10.1128/JB.01394-07
Scheffers,
D.-J. (2008). The effect of MinC on FtsZ
polymerization is pH dependent and can be counteracted by
ZapA. FEBS Letters, 582(17),
2601-2608. https://doi.org/10.1016/j.febslet.2008.06.038
Herrgård,
M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas,
M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann,
M., Hucka, M., Novère, N. L., Li, P., Liebermeister,
W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S.,
Simeonidis, E., ... Kell, D. B. (2008). A consensus yeast
metabolic network reconstruction obtained from a community approach
to systems biology. Nature
Biotechnology, 26(10), 1155-1160. https://doi.org/10.1038/nbt1492
Zamboni,
N., Kümmel, A., & Heinemann, M. (2008).
anNET: a tool for network-embedded thermodynamic analysis of
quantitative metabolome data. Bmc
Bioinformatics, 9(199), Article 199. https://doi.org/10.1186/1471-2105-9-199
Amantonico,
A., Oh, J. Y., Sobek, J., Heinemann, M., & Zenobi,
R. (2008). Mass Spectrometric Method for Analyzing
Metabolites in Yeast with Single Cell Sensitivity.
Angewandte Chemie International Edition,
47(29), 5382-5385. https://doi.org/10.1002/anie.200705923
Vos,
E. P., ter Horst, R., & Broos, J. (2008).
Domain complementation studies reveal residues critical for
the activity of the mannitol permease from Escherichia coli.
Biochimica et Biophysica Acta.
El
Khattabi, M., van Roosmalen, M. L., Jager, D., Metselaar, H.,
Permentier, H., Leenhouts, K., & Broos, J.
(2008). Lactococcus lactis as expression host for the
biosynthetic incorporation of tryptophan analogues into recombinant
proteins. Biochemical Journal,
409(1), 193-198. https://doi.org/10.1042/BJ20070909
Jensen,
K. T., Strambini, G., Gonnelli, M., Broos, J., &
Jackson, J. B. (2008). Mutations in transhydrogenase change
the fluorescence emission state of TRP72 from L-1(a) to
L-1(b). Biophysical Journal,
95(7), 3419-3428. https://doi.org/10.1529/biophysj.108.134650
2007
Nolte,
I. M., Vries, A. R. D., Spijker, G. T., Jansen, R.
C., Brinza, D., Zelikovsky, A., & Meerman, G. J.
T. (2007). Association testing by haplotype-sharing
methods applicable to whole-genome analysis. BMC
Proceedings, 1 Suppl 1, S129. https://doi.org/10.1186/1753-6561-1-s1-s129
Alberts,
R., Terpstra, P., Hardonk, M., Bystrykh, L. V.,
de Haan, G., Breitling, R., Nap, J.-P., & Jansen,
R. C. (2007). A verification protocol for the probe
sequences of Affymetrix genome arrays reveals high probe accuracy
for studies in mouse, human and rat. Bmc
Bioinformatics, 8(1), Article 132. https://doi.org/10.1186/1471-2105-8-132
Swertz,
M. A., & Jansen, R. C. (2007). Beyond
standardization: dynamic software infrastructures for systems
biology. Nature Reviews Genetics,
8(3), 235-243. https://doi.org/10.1038/nrg2048
Fu,
J., Swertz, M. A., Keurentjes, J. J. B.,
& Jansen, R. C. (2007). MetaNetwork: A
computational protocol for the genetic study of metabolic
networks. Nature protocols,
2(3), 685-694. https://doi.org/10.1038/nprot.2007.96
Nyangoma,
S. O., van Kampen, A. A. H. C., Reijmers, T. H., Govorukhina,
N. I., van der Zee, A. G. J., Billingham, L.
J., Bischoff, R., & Jansen, R. C.
(2007). Multiple testing issues in discriminating
compound-related peaks and chromatograms from high frequency noise,
spikes and solvent-based noise in LC-MS data sets.
Statistical applications in genetics and molecular
biology, 6(1), Article 23.
Nyangoma,
S. O., Van Kampen, A. A., Reijmers, T. H., Govorukhina, N.
I., van der Zee, A. G., Billingham, I.
J., Bischoff, R., & Jansen, R. C.
(2007). Multiple testing issues in discriminating
compound-related peaks and chromatograms from high frequency noise,
spikes and solvent-based nois in LC-MS data sets.
Statistical applications in genetics and molecular
biology, 6(article 23). http://www.ncbi.nlm.nih.gov/pubmed/17910529?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
Keurentjes,
J. J. B., Fu, J., Terpstra, I. R., Garcia, J. M.,
Ackerveken, G. V. D., Snoek, L. B., Peeters, A. J. M., Vreugdenhil,
D., Koornneef, M., & Jansen, R. C. (2007).
Regulatory network construction in Arabidopsis by using
genome-wide gene expression quantitative trait loci.
Proceedings of the National Academy of Sciences of the
United States of America, 104(5), 1708-1713.
https://doi.org/10.1073/pnas.0610429104
Keurentjes,
J. J. B., Fu, J. J., Terpstra, I. R., Garcia, J. M.,
van den Ackerveken, G., Snoek, L. B., Peeters, A. J. M.,
Vreugdenhil, D., Koornreef, M., & Jansen, R. C.
(2007). Regulatory Network Construction in Arabidopsis using
genome-wide gene expression QTLs.
PNAS, 104, 1708 - 1713. http://www.pnas.org/cgi/reprint/104/5/1708
Dijkstra,
M., Vonk, R., & Jansen, R. C. (2007).
SELDI-TOF mass spectra: A view on sources of
variation. Journal of Chromatography
B, 847(1), 12-23. https://doi.org/10.1016/j.jchromb.2006.11.004
Alberts,
R., Terpstra, P., Li, Y., Breitling, R., Nap,
J., & Jansen, R. C. (2007). Sequence
Polymorphisms Cause Many False cis eQTLs. PLoS
ONE, 2(7), 132 - 136. Article 622. https://doi.org/10.1371/journal.pone.0000622
van
Haastert, P. J. M., & Postma, M. (2007). Biased
random walk by Stochastic fluctuations of chemoattractant-receptor
interactions at the lower limit of detection.
Biophysical Journal, 93(5),
1787-1796. https://doi.org/10.1529/biophysj.107.104356
Keizer-Gunnink,
I., Kortholt, A., & Van Haastert, P.
J. M. (2007). Chemoattractants and chemorepellents act
by inducing opposite polarity in phospholipase C and PI3-kinase
signaling. Journal of Cell Biology,
177(4), 579-585. https://doi.org/10.1083/jcb.200611046
Kae,
H., Kortholt, A., Rehmann, H., Insall, R., Van
Haastert, P. J. M., Spiegelman, G. B., & Weeks, G.
(2007). Cyclic AMP signalling in Dictyostelium: G-proteins
activate separate Ras pathways using specific RasGEFs.
Embo Reports, 8(5), 477-482. https://doi.org/10.1038/sj.embor.7400936
van
Haastert, P. J. M., Keizer-Gunnink, I.,
& Kortholt, A. (2007). Essential role of
PI3-kinase and phospholipase A2 in Dictyostelium discoideum
chemotaxis. Journal of Cell Biology,
177(5), 809-816. https://doi.org/10.1083/jcb.200701134
Kortholt,
A., King, J. S., Keizer-Gunnink, I., Harwood,
A. J., & Van Haastert, P. J. M. (2007).
Phospholipase C regulation of phosphatidylinositol
3,4,5-trisphosphate-mediated chemotaxis. Molecular
Biology of the Cell, 18(12), 4772-4779. https://doi.org/10.1091/mbc.E07-05-0407
Loovers,
H. M., Kortholt, A., de Groote, H., Whitty, L.,
Nussbaum, R. L., & van Haastert, P. J. M. (2007).
Regulation of phagocytosis in Dictyostelium by the inositol
5-phosphatase OCRL homolog Dd5P4.
Traffic, 8(5), 618 - 628. https://doi.org/10.1111/j.1600-0854.2007.00546.x
Bader,
S., Kortholt, A., & van Haastert, P. J.
M. (2007). Seven Dictyostelium discoideum
phosphodiesterases degrade three pools of cAMP and cGMP.
Biochemical Journal, 402(1), 153 -
161. https://doi.org/10.1042/BJ20061153
Baron,
R., Trzesniak, D., de Vries, A. H., Elsener, A.,
Marrink, S. J., & van Gunsteren, W. F. (2007).
Comparison of thermodynamic properties of coarse-grained and
atomic-level simulation models.
Chemphyschem, 8(3), 452 - 461. https://doi.org/10.1002/cphc.200600658
van
den Bogaart, G., Hermans, N., Krasnikov,
V., de Vries, A. H., & Poolman,
B. (2007). On the decrease in lateral mobility of
phospholipids by sugars. Biophysical
Journal, 92(5), 1598-1605. https://doi.org/10.1529/biophysj.106.096461
Marrink,
S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P.,
& de Vries, A. H. (2007). The MARTINI force field:
Coarse grained model for biomolecular simulations.
Journal of Physical Chemistry B,
111(27), 7812-7824. https://doi.org/10.1021/jp071097f
Martinez,
B., Zomer, A. L., Rodriguez, A., Kok, J., &
Kuipers, O. P. (2007). Cell envelope stress induced by
the bacteriocin Lcn972 is sensed by the lactococcal two-component
system CesSR. Molecular Microbiology,
64(2), 473-486. https://doi.org/10.1111/j.1365-2958.2007.05668.x
Ventura,
M., Zomer, A., Canchaya, C., O'Connell-Motherway, M.,
Kuipers, O., Turroni, F., Ribbera, A., Foroni, E.,
Buist, G., Wegmann, U., Shearman, C., Gasson, M. J.,
Fitzgerald, G. F., Kok, J., van Sinderen, D., &
O’Connell-Motherway, M. (2007). Comparative analyses of
prophage-like elements present in two Lactococcus lactis
strains. Applied Environmental
Microbiology, 73(23), 7771-7780. https://doi.org/10.1128/AEM.01273-07
Wegmann,
U., O'Connell-Motherwy, M., Zomer, A., Buist, G.,
Shearman, C., Canchaya, C., Ventura, M., Goesmann, A., Gasson, M.
J., Kuipers, O. P., van Sinderen, D., & Kok,
J. (2007). Complete genome sequence of the prototype
lactic acid bacterium Lactococcus lactis subsp cremoris
MG1363. Journal of Bacteriology,
189(8), 3256-3270. https://doi.org/10.1128/JB.01768-06
Reviriego,
C., Fernandez, L., Kuipers, O. P., Kok,
J., & Rodriguez, J. M. (2007). Enhanced production
of pediocin PA-1 in wild nisin- and non-nisin-producing Lactococcus
lactis strains of dairy origin. International
Dairy Journal, 17(5), 574-577. https://doi.org/10.1016/j.idairyj.2006.05.013
Steen,
A., van Schalkwijk, S., Buist, G., Twigt, M.,
Szeliga, M., Meijer, W., Kuipers, O. P., Kok,
J., & Hugenholtz, J. (2007). Lytr, a phage-derived
amidase is most effective in induced lysis of Lactococcus lactis
compared with other lactococcal amidases and
glucosaminidases. International Dairy
Journal, 17(8), 926-936. https://doi.org/10.1016/j.idairyj.2006.12.007
Veiga,
P., Bulbarela-Sampieri, C., Furlan, S., Maisons, A.,
Chapot-Chartier, M.-P., Erkelenz, M., Mervelet, P., Noirot, P.,
Frees, D., Kuipers, O. P., Kok, J.,
Gruss, A., Buist, G., & Kulakauskas, S. (2007).
SpxB regulates O-acetylation-dependent resistance of
Lactococcus lactis peptidoglycan to hydrolysis.
The Journal of Biological Chemistry,
282(27), 19342-19354. https://doi.org/10.1074/jbc.M611308200
Zomer,
A. L., Buist, G., Larsen, R., Kok,
J., & Kuipers, O. P. (2007).
Time-resolved determination of the CcpA regulon of
Lactococcus lactis subsp cremoris MG1363. Journal
of Bacteriology, 189(4), 1366-1381. https://doi.org/10.1128/JB.01013-06
Lulko,
A. T., Buist, G., Kok, J., &
Kuipers, O. P. (2007). Transcriptome analysis of
temporal regulation of carbon metabolism by CcpA in Bacillus
subtilis reveals additional target genes. Journal
of Molecular Microbiology and Biotechnology,
12(1-2), 82-95. https://doi.org/10.1159/000096463
Rink,
R., Wierenga, J., Kuipers, A., Kluskens, L. D.,
Driessen, A. J. M., Kuipers, O. P., &
Moll, G. N. (2007). Dissection and modulation of the
four distinct activities of nisin by mutagenesis of rings A and B
and by C-terminal truncation. Applied
Environmental Microbiology, 73(18), 5809-5816.
https://doi.org/10.1128/AEM.01104-07
Rink,
R., Kluskens, L. D., Kuipers, A., Driessen, A.
J. M., Kuipers, O. P., & Moll, G.
N. (2007). NisC, the cyclase of the lantibiotic nisin,
can catalyze Cyclization of designed nonlantibiotic
peptides. Biochemistry,
46(45), 13179-13189. https://doi.org/10.1021/bi700106z
Rink,
R., Wierenga, J., Kuipers, A., Kluskens, L. D.,
Driessen, A. J. M., Kuipers, O. P., &
Moll, G. (2007). Production of dehydroamino
acid-containing peptides by Lactococcus lactis.
Applied Environmental Microbiology,
73(6), 1792 - 1796. https://doi.org/10.1128/AEM.02350-06
Scheffers,
D.-J. (2007). Cell wall growth during elongation and
division: one ring to bind them? Molecular
Microbiology, 64(4), 877-880. https://doi.org/10.1111/j.1365-2958.2007.05731.x
Scheffers,
D.-J., Robichon, C., Haan, G. J., Blaauwen, T. D.,
Koningstein, G., Bloois, E. V., Beckwith, J., &
Luirink, J. (2007). Contribution of the FtsQ Transmembrane
Segment to Localization to the Cell Division Site.
Journal of Bacteriology, 189(20),
7273-7280. https://doi.org/10.1128/JB.00723-07
Makart,
S., Heinemann, M., & Panke, S. (2007).
Characterization of the AlkS/P-alkB-expression system as an
efficient tool for the production of recombinant proteins in
Escherichia coli fed-batch fermentations.
Biotechnology and Bioengineering,
96(2), 326-336. https://doi.org/10.1002/bit.21117
Sauer,
U., Heinemann, M., & Zamboni, N. (2007).
Genetics - Getting closer to the whole picture.
Science, 316(5824), 550-551. https://doi.org/10.1126/science.1142502
Hübscher,
J., Jansen, A., Kotte, O., Schäfer, J., Majcherczyk, P. A.,
Harris, L. G., Bierbaum, G., Heinemann, M., &
Berger-Bächi, B. (2007). Living with an imperfect cell
wall: compensation of femAB inactivation in Staphylococcus
aureus. BMC Genomics, 8,
Article 307. https://doi.org/10.1186/1471-2164-8-307
de
Groot, M., Broos, J., & Buma, W. J. (2007).
Tagging multiphoton ionization events by two-dimensional
photoelectron spectroscopy. Journal of Chemical
Physics, 126(20), 204312 - 204312. Article
204312. https://doi.org/10.1063/1.2738465
Broos,
J., Tveen-Jensen, K., de Waal, E., Hesp, B. H., Jackson, J.
B., Canters, G. W., & Callis, P. R. (2007). The emitting
state of tryptophan in proteins with highly blue-shifted
fluorescence. Angewandte Chemie-International
Edition, 46(27), 5137-5139. https://doi.org/10.1002/anie.200700839
Jong,
R. M. D., Bazzacco, P., Poelarends, G. J., Johnson,
J., Kim, Y. J., Burks, E. A., Serrano, H., Thunnissen, A.-M.
W. H., Whitman, C. P., Dijkstra, B. W., & Johnson, W. H.
(2007). Crystal Structures of Native and Inactivated
cis-3-Chloroacrylic Acid Dehalogenase. Structural Basis for
Substrate Specificity and Inactivation by
(R)-Oxirane-2-Carboxylate. The Journal of
Biological Chemistry, 282(4), 2440 - 2449. https://doi.org/10.1074/jbc.M608134200
van
Straaten, K. E., Barends, T. R. M., Dijkstra, B. W., &
Thunnissen, A.-M. W. H. (2007). Structure of
Escherichia coli lytic transglycosylase MltA with bound
chitohexaose - Implications for peptidoglycan binding and
cleavage. The Journal of Biological
Chemistry, 282(29), 21197-21205. https://doi.org/10.1074/jbc.M701818200
2006
Govorukhina,
N. I., Reijmers, T. H., Nyangoma, S. O., van der Zee,
A. GJ., Jansen, R. C., & Bischoff,
R. (2006). Analysis of human serum by liquid
chromatography-mass spectrometry: Improved sample preparation and
data analysis: Improved sample preparation and data
analysis. Journal of Chromatography A,
1120(1-2), 142 - 150. https://doi.org/10.1016/j.chroma.2006.02.088
Nyangoma,
S. O., Fung, W.-K., & Jansen, R. C. (2006).
Identifying influential multinomial observations by
perturbation. Computational Statistics %26 Data
Analysis, 50(10), 2799 - 2821. https://doi.org/10.1016/j.csda.2005.04.023
Li,
Y., Gutteling, E. W., Tijsterman, M., Fu, J.,
Riksen, J. A. G., Hazendonk, E., Prins, P., Plasterk,
R. H. A., Jansen, R. C., Breitling, R., Kammenga, J.
E., & Álvarez, O. A. (2006). Mapping determinants of
gene expression plasticity by genetical genomics in
C-elegans. PLoS genetics,
2(12), 2155 - 2161. Article 222. https://doi.org/10.1371/journal.pgen.0020222
Fu,
J., & Jansen, R. C. (2006). Optimal
Design and Analysis of Genetic Studies on Gene Expression.
Genetics, 172(3), 1993-1999. https://doi.org/10.1534/genetics.105.047001
Dijkstra,
M., Roelofsen, H., Vonk, R. J., & Jansen, R.
C. (2006). Peak quantification in surface-enhanced
laser desorption/ionization by using mixture models.
Proteomics, 6(19), 5106 - 5116. https://doi.org/10.1002/pmic.200600181
Albers,
C. J., Jansen, R. C., Kok,
J., Kuipers, O. P., & Hijum, S. A. F. T. V.
(2006). SIMAGE: simulation of DNA-microarray gene expression
data. Bmc Bioinformatics,
7(205), Article 205. https://doi.org/10.1186/1471-2105-7-205
Keurentjes,
J. J. B., Fu, J., Vos, C. H. R. D., Lommen, A., Hall,
R. D., Bino, R. J., Plas, L. H. W. V. D., Jansen, R.
C., Vreugdenhil, D., Koornneef, M., Hall, RD., Bino, RJ.,
& van der Plas, LHW. (2006). The genetics of plant
metabolism. Nature Genetics,
38(7), 842 - 849. https://doi.org/10.1038/ng1815
van
Haastert, P. J. M. (2006). Analysis of Signal
Transduction: Formation of cAMP, cGMP, and Ins(1,4,5)P3 In Vivo and
In Vitro. In L. Eichinger, & F. Rivero (Eds.),
Dictyostelium discoideum Protocols (pp. 369 - 392).
(Methods in Molecular Biology; No. IV). Springer.
Kortholt,
A., Rehmann, H., Kae, H., Bosgraaf, L.,
Keizer-Gunnink, I., Weeks, G., Wittinghofer, A., &
Haastert, P. J. M. V. (2006). Characterization of the
GbpD-activated Rap1 Pathway Regulating Adhesion and Cell Polarity
in Dictyostelium discoideum. The Journal of
Biological Chemistry, 281(33), 23367 - 23376.
https://doi.org/10.1074/jbc.M600804200
Bader,
S., Kortholt, A., Snippe, H., & van
Haastert, P. J. M. (2006). DdPDE4, a novel
cAMP-specific phosphodiesterase at the surface of dictyostelium
cells. The Journal of Biological
Chemistry, 281(29), 20018 - 20026. https://doi.org/10.1074/jbc.M600040200
Loovers,
H., Postma, M., Keizer-Gunnink, I., Huang, Y. E.,
Devreotes, P. N., & Haastert, P. J. M. V. (2006).
Distinct Roles of PI(3,4,5)P3 during Chemoattractant
Signaling in Dictyostelium: A Quantitative In Vivo Analysis by
Inhibition of PI3-Kinase. Molecular Biology of the
Cell, 17(4), 1503-1513. https://doi.org/10.1091/mbc.E05-09-0825
Veltman,
D. M., & van Haastert, P. J. M. (2006).
Guanylyl cyclase protein and cGMP product independently
control front and back of chemotaxing Dictyostelium cells.
Molecular Biology of the Cell,
17(9), 3921 - 3929. https://doi.org/10.1091/mbc.E06-05-0381
Goldberg,
J. M., Wolpin, E. S., Bosgraaf, L., Clarkson, B. K., van
Haastert, P. J. M., & Smith, J. L. (2006). Myosin
light chain kinase A is activated by cGMP-dependent and
cGMP-independent pathways. FEBS
Letters, 580(8), 2059 - 2064. https://doi.org/10.1016/j.febslet.2006.03.008
Engel,
R., van Haastert, P. J. M., & Visser, A. J. W. G.
(2006). Spectral characterization of Dictyostelium
autofluorescence. Microscopy Research and
Technique, 69(3), 168-174. https://doi.org/10.1002/jemt.20282
Bosgraaf,
L., & van Haastert, P. J. M. (2006). The
regulation of myosin II in Dictyostelium. European
Journal of Cell Biology, 85(9-10), 969 - 979.
https://doi.org/10.1016/j.ejcb.2006.04.004
Waarde-Verhagen,
M. A. W. H. V., Kampinga, H. H., &
Linskens, M. H. K. (2006). Continuous growth of
telomerase-immortalised fibroblasts: How long do cells remain
normal? Mechanisms of Ageing and
Development, 127(1), 85 - 87. https://doi.org/10.1016/j.mad.2005.08.008
Wright,
L. S., Prowse, K. R., Wallace, K., Linskens, M. H. K.,
& Svendsen, C. N. (2006). Human progenitor cells isolated
from the developing cortex undergo decreased neurogenesis and
eventual senescence following expansion in vitro.
Experimental Cell Research, 312(11),
2107 - 2120. https://doi.org/10.1016/j.yexcr.2006.03.012
Siwko,
M. E., Marrink, S. J., de Vries, A. H.,
Arkadiusz, K., Schoot Uiterkamp, A. J. M., & Mark,
A. E. (2007). Does isoprene protect plant membranes for
thermal shock? A molecular dynamics study.
Biochimica et Biophysica Acta-Biomembranes,
1768(2), 198-206. https://doi.org/10.1016/j.bbamem.2006.09.023
Baron,
R., de Vries, A. H., Hunenberger, PH., & van
Gunsteren, W. F. (2006). Comparison of atomic-level and
coarse-grained models for liquid hydrocarbons from molecular
dynamics configurational entropy estimates.
Journal of Physical Chemistry B,
110(16), 8464-8473. https://doi.org/10.1021/jp055888y
Baron,
R., de Vries, A. H., Huenenberger, P. H., & van
Gunsteren, W. F. (2006). Configurational entropies of lipids
in pure and mixed bilayers from atomic-level and coarse-grained
molecular dynamics simulations. Journal of
Physical Chemistry B, 110(31), 15602-15614. https://doi.org/10.1021/jp061627s
Hozoi,
L., de Vries, A. H., Broer, R., de
Graaf, C., & Bagus, P. S. (2006). Ni 3s-hole
states in NiO by non-orthogonal configuration interaction.
Chemical Physics, 331(1), 178-185.
https://doi.org/10.1016/j.chemphys.2006.10.015
de
Jong, A., van Hijum, S. A. F. T., Bijlsma, J. J. E.,
Kok, J., & Kuipers, O. P. (2006).
BAGEL: a web-based bacteriocin genome mining tool.
Nucleic Acids Research, 34,
W273-W279. https://doi.org/10.1093/nar/gkl237
Kenny,
JG., Leach, S., de la Hoz, AB., Venema, G., Kok, J.,
Fitzgerald, GF., Nauta, A., Alonso, JC., van Sinderen, D., Kenny,
J. G., Hoz, A. B. D. L., Fitzgerald, G. F., & Alonso, J. C.
(2006). Characterization of the lytic-lysogenic switch of the
lactococcal bacteriophage Tuc2009.
Virology, 347(2), 434-446. https://doi.org/10.1016/j.virol.2005.11.041
Buist,
G., Ridder, A. N. J. A., Kok, J., &
Kuipers, O. P. (2006). Different subcellular locations
of secretome components of Gram-positive bacteria.
Microbiology-Sgm, 152(10),
2867-2874. https://doi.org/10.1099/mic.0.29113-0
Larsen,
R., Kloosterman, TG., Kok, J., & Kuipers,
OP. (2006). GlnR-mediated regulation of nitrogen
metabolism in Lactococcus lactis. Journal of
Bacteriology, 188(13), 4978-4982. https://doi.org/10.1128/JB.00025-06
Gutierrez,
J., Larsen, R., Cintas, L. M., Kok, J., &
Hernandez, P. E. (2006). High-level heterologous production
and functional expression of the sec-dependent enterocin P from
Enterococcus faecium P13 in Lactococcus lactis.
Applied Microbiology and Biotechnology,
72(1), 41-51. https://doi.org/10.1007/s00253-005-0233-1
den
Hengst, CD., Groeneveld, M., Kuipers, OP., Kok,
J., & Hengst, C. D. D. (2006). Identification and
functional characterization of the Lactococcus lactis
CodY-regulated branched-chain amino acid permease BcaP
(CtrA). Journal of Bacteriology,
188(9), 3280-3289. https://doi.org/10.1128/JB.188.9.3280-3289.2006
Kuipers,
A., Wierenga, J., Rink, R., Kluskens, L. D., Driessen,
A. J. M., Kuipers, O. P., & Moll, G.
N. (2006). Sec-Mediated Transport of
Posttranslationally Dehydrated Peptides in Lactococcus
lactis. Applied and environmental
microbiology, 72(12), 7626 - 7633. https://doi.org/10.1128/AEM.01802-06
Li,
B., Yu, J. P. J., Brunzelle, J. S., Moll, G. N., Van
Der Donk, W. A., & Nair, S. K. (2006). Structure and
mechanism of the lantibiotic cyclase involved in nisin
biosynthesis. Science,
311(5766), 1464-1467. https://doi.org/10.1126/science.1121422
Seggewib,
J., Becker, K., Kotte, O., Eisenacher, M., Khoschkhoi Yazdi, M. R.,
Fischer, A., McNamara, P., Proctor, R. A., Peters, G.,
Heinemann, M., & von Eiff, C. (2006). Detailed
survey of genome-wide expression differences between a
Staphylococcus aureus mutant displaying the small colony variant
phenotype and its parental strain. International
journal of medical microbiology, 296,
132-133.
Bechtold,
M., Makart, S., Heinemann, M., & Panke, S. (2006).
Integrated operation of continuous chromatography and
biotransformations for the generic high yield production of fine
chemicals. Journal of Biotechnology,
124(1), 146-162. https://doi.org/10.1016/j.jbiotec.2006.01.019
Kümmel,
A., Panke, S., & Heinemann, M. (2006).
Putative regulatory sites unraveled by network-embedded
thermodynamic analysis of metabolome data.
Molecular Systems Biology, 2,
2006.0034. https://doi.org/10.1038/msb4100074
Seggewiß,
J., Becker, K., Kotte, O., Eisenacher, M., Khoschkhoi Yazdi, M. R.,
Fischer, A., McNamara, P., Laham, N. A., Proctor, R., Peters,
G., Heinemann, M., & Eiff, C. V. (2006).
Reporter Metabolite Analysis of Transcriptional Profiles of a
Staphylococcus aureus Strain with Normal Phenotype and Its Isogenic
hemB Mutant Displaying the Small-Colony-Variant Phenotype.
Journal of Bacteriology, 188(22),
7765-7777. https://doi.org/10.1128/JB.00774-06
Davidescu,
F. P., Madsen, H., Schümperli, M., Heinemann, M.,
Panke, S., & Jørgensen, S. B. (2006). Stochastic
grey box modeling of the enzymatic biochemical reaction network of
E. coli mutants. In Proceedings of the 16th European
Symposium on Computer Aided Process Engineering and 9th
International Symposium on Process Systems Engineering (21
ed., pp. 161-166). Elsevier.
Bechtold,
M., Heinemann, M., & Panke, S. (2006).
Suitability of teicoplanin-aglycone bonded stationary phase
for simulated moving bed enantio separation of racemic amino acids
employing composition-constrained eluents. Journal
of Chromatography A, 1113(1-2), 167-176. https://doi.org/10.1016/j.chroma.2006.02.007
Heinemann,
M., & Panke, S. (2006). Synthetic biology--putting
engineering into biology.
Bioinformatics, 22(22), 2790-2799.
https://doi.org/10.1093/bioinformatics/btl469
Kümmel,
A., Panke, S., & Heinemann, M. (2006).
Systematic assignment of thermodynamic constraints in
metabolic network models. Bmc
Bioinformatics, 7(512). https://doi.org/10.1186/1471-2105-7-512,
https://doi.org/10.1186/1471-2105-5-133
Jensen,
K. T., Jackson, J. B., Broos, J., & Strambini, G.
B. (2006). Intra-domain and inter-domain motions in
proton-translocating transhydrogenase. Biochimica
et Biophysica Acta-Bioenergetics, 244 - 244.
Hamiaux,
C., Eerde, A. V., Parsot, C., Broos, J., &
Dijkstra, B. W. (2006). Structural mimicry for vinculin
activation by IpaA, a virulence factor of Shigella flexneri.
Embo Reports, 62(11), 794-799. https://doi.org/10.1038/sj.embor.7400753
Veldhuis,
G., Hink, M., Krasnikov, V., Van Den Bogaart,
G., Hoeboer, J., Visser, A. J. W. G., Broos,
J., & Poolman, B. (2006). The
oligomeric state and stability of the mannitol transporter,
EnzymeII(mtl), from Escherichia coli: A fluorescence correlation
spectroscopy study. Protein Science,
15(8), 1977-1986. https://doi.org/10.1110/ps.062113906
Susanna,
K., Fusetti, F., Thunnissen, A. M. W. H.,
Hamoen, L. W., & Kuipers, O. P. (2006).
Functional analysis of the competence transcription factor
ComK of Bacillus subtilis by characterization of truncation
variants. Microbiology-Sgm,
152(2), 473-483. https://doi.org/10.1099/mic.0.28357-0
2005
Alberts,
R., Terpstra, P., Bystrykh, L. V., Haan, G.
D., & Jansen, R. C. (2005). A
statistical multiprobe model for analyzing cis and trans genes in
genetical genomics experiments with short-oligonucleotide
arrays. Genetics, 171(3),
1437 - 1439. https://doi.org/10.1534/genetics.105.045930
Horvatovich,
P., Govorukhina, N. I., Reijmers, T. H.,
Nyangoma, S., Jansen, R. C., & Bischoff,
R. (2005). Biomarker discovery for the early diagnosis
of cervical cancer. Febs Journal,
272, 494 - 495.
Alberts,
R., Fu, J., Swertz, M. A., Lubbers, L.
A., Albers, C. J., & Jansen, R. C.
(2005). Combining microarrays and genetic analysis.
Briefings in Bioinformatics, 6(2),
135-145. https://doi.org/10.1093/bib/6.2.135
de
Haan, G., Bystrykh, L. V., Weersing, E.,
Sutton, S., Manly, K., Chesler, E., Jansen, R.
C., Vellenga, E., Williams, R. W., & Cooke,
M. P. (2005). Genetical genomics to identify gene networks in
hematopoietic stem cells. Experimental
Hematology, 33(7), 60 - 60.
Spijker,
G. T., Nolte, I. M., Jansen, R. C.,
& te Meerman, G. J. (2005). Genetic association
studies in complex disease: Disentangling additional predisposing
loci from associated neutral loci using a constrained - permutation
approach. Annals of Human Genetics,
69(1), 90 - 101. https://doi.org/10.1046/j.1529-8817.2004.00129.x
Fu,
J. J., & Jansen, R. C. (2005).
Optimal Design and Analysis of Genetic Studies on Gene
Expression. Genetics, 172,
1993 - 1999.
Bystrykh,
L., Weersing, E., Dontje, B., Sutton, S.,
Pletcher, M. T., Wiltshire, T., Su, A. I., Vellenga,
E., Wang, J., Manly, K. F., Lu, L., Chesler, E. J., Alberts,
R., Jansen, R. C., Williams, R. W., Cooke, M.,
Pletcher, MT., de Haan, G., Su, AI., ... Williams, O.
(2005). Uncovering regulatory pathways that effect
hematopoietic stem cell function using 'genetical genomics'.
Nature Genetics, 37(3), 225 - 232.
https://doi.org/10.1038/ng1497
Veltman,
D. M., Roelofs, J., Engel, R., Visser, A. J. W. G., &
Haastert, P. J. M. V. (2005). Activation of soluble
guanylyl cyclase at the leading edge during Dictyostelium
chemotaxis. Molecular Biology of the
Cell, 16(2), 976 - 983. https://doi.org/10.1091/mbc.E04-08-0701
Bukharova,
T., Weijer, G., Bosgraaf, L., Dormann, D., van Haastert, P.
J., & Weijer, C. J. (2005). Paxillin is required
for cell-substrate adhesion, cell sorting and slug migration during
Dictyostelium development (vol 118, pg 4295, 2005).
Journal of Cell Science, 118(18),
4295 - 4310. https://doi.org/10.1242/jcs.02557
Bosgraaf,
L., Waijer, A., Engel, R., Visser, A. J. W. G., Wessels, D., Soll,
D., & van Haastert, P. J. M. (2005).
RasGEF-containing proteins GbpC and GbpD have differential
effects on cell polarity and chemotaxis in Dictyostelium.
Journal of Cell Science, 118(9),
1899-1910. https://doi.org/10.1242/jcs.02317
Knol,
J., Engel, R., Blaauw, M., Visser, A. J. W. G., &
Haastert, P. J. M. V. (2005). The Phosducin-Like
Protein PhLP1 Is Essential for Gβγ Dimer Formation in
Dictyostelium discoideum. Molecular and Cellular
Biology, 25(18), 8393-8400. https://doi.org/10.1128/MCB.25.18.8393-8400.2005
de
Vries, A. H., Chandrasekhar, I., van Gunsteren, W. F., &
Hunenberger, P. H. (2005). Molecular Dynamics Simulations of
Phospholipid Bilayers: Influence of Artificial Periodicity, System
Size, and Simulation Time. Journal of Physical
Chemistry B, 109(23), 11643-11652. https://doi.org/10.1021/jp0507952
de
Vries, AH., Yefimov, S., Mark, AE., & Marrink,
SJ. (2005). Molecular structure of the lecithin ripple
phase. Proceedings of the National Academy of
Sciences of the United States of America,
102(15), 5392-5396. https://doi.org/10.1073/pnas.0408249102
Rink,
R., Kuipers, A., de Boef, E., Leenhouts, KJ.,
Driessen, AJM., Moll, GN., Kuipers,
OP., & Leenhouts, K. J. (2005). Lantibiotic
structures as guidelines for the design of peptides that can be
modified by lantibiotic enzymes.
Biochemistry, 44(24), 8873-8882. https://doi.org/10.1021/bi050081h
Kluskens,
LD., Kuipers, A., Rink, R., de Boef, E., Fekken, S.,
Driessen, AJM., Kuipers, OP., & Moll,
GN. (2005). Post-translational modification of
therapeutic peptides by NisB, the dehydratase of the lantibiotic
nisin. Biochemistry, 44(38),
12827-12834. https://doi.org/10.1021/bi050805p
Kiel,
J. A. K. W., van der Klei, I. J., van den Berg,
M. A., Bovenberg, R. A. L., & Veenhuis, M. (2005).
Overproduction of a single protein, Pc-Pex 11p, results in
2-fold enhanced penicillin production by Penicillium
chrysogenum. Fungal Genetics and
Biology, 42(2), 154 - 164. https://doi.org/10.1016/j.fgb.2004.10.010
Lutz,
M. V., Bovenberg, R. A. L., Klei, I. J. V.
D., & Veenhuis, M. (2005). Synthesis of
Penicillium chrysogenum acetyl-CoA: Isopenicillin N acyltransferase
in Hansenula polymorpha: First step towards the introduction of a
new metabolic pathway. Fems Yeast
Research, 5(11), 1063-1067. https://doi.org/10.1016/j.femsyr.2005.07.002
Scheffers,
D.-J., & Pinho, M. G. (2005). Bacterial Cell Wall
Synthesis: New Insights from Localization Studies.
Microbiology and Molecular Biology Reviews,
69(4), 585-607. https://doi.org/10.1128/MMBR.69.4.585-607.2005
Scheffers,
D.-J. (2005). Dynamic localization of
penicillin-binding proteins during spore development in Bacillus
subtilis. Microbiology,
151(3), 999-1012. https://doi.org/10.1099/mic.0.27692-0
Schumperli,
M., Heinemann, M., Gomolka, S., Kummel, A., &
Panke, S. (2005). A new approach for the production of DHAP:
The system of biotransformations. Journal of
Biotechnology, 118, S90-S90.
Kummel,
A., Schumperli, M., & Heinemann, M. (2005).
Design of a system of biotransformations by means of
stoichiometric network analysis. Journal of
Biotechnology, 118, S105-S105.
Heinemann,
M., Kümmel, A., Ruinatscha, R., & Panke, S. (2005).
In Silico Genome-Scale Reconstruction and Validation of the
Staphylococcus aureus Metabolic Network.
Biotechnology and Bioengineering,
92(7), 850-864.
Heinemann,
M., Meinberg, H., Büchs, J., Koß, H.-J., &
Ansorge-Schumacher, M. B. (2005). Method for Quantitative
Determination of Spatial Polymer Distribution in Alginate Beads
Using Raman Spectroscopy. Applied
Spectroscopy, 59(3), 280-285. https://doi.org/10.1366/0003702053585363
Kluge,
J., Kummel, A., Panke, S., & Heinemann, M. (2005).
Model-based identification of regulation patterns controlling
metabolic redundancy in central carbon metabolism.
Journal of Biotechnology, 118,
S3-S3.
Trivedi,
A., Heinemann, M., Spiess, A. C., Daussmann, T., &
Büchs, J. (2005). Optimization of Adsorptive
Immobilization of Alcohol Dehydrogenases. Journal
of Bioscience and Bioengineering, 99(4),
340-347. https://doi.org/10.1263/jbb.99.340
Liu,
TQ., Callis, PR., Hesp, BH., de Groot, M., Buma, WJ., Broos,
J., Liu, T., Callis, P. R., & Buma, W. J. (2005).
Ionization potentials of fluoroindoles and the origin of
nonexponential tryptophan fluorescence decay in proteins.
Journal of the American Chemical Society,
127(11), 4104-4113. https://doi.org/10.1021/ja043154d
Panella,
L., Broos, J., Jin, J., Fraaije, M.
W., Janssen, D. B., Jeronimus-Stratingh,
C., Feringa, B. L., Minnaard, A. J.,
& Vries, J. G. D. (2005). Merging homogeneous catalysis
with biocatalysis: papain as hydrogenation catalyst.
Chemical Communications, 103(45),
5656-5658. https://doi.org/10.1039/b512138h
Veldhuis,
G., Broos, J., Poolman, B., & Scheek,
R. M. (2005). Stoichiometry and Substrate Affinity of the
Mannitol Transporter, EnzymeIImtl, from Escherichia coli.
Biophysical Journal, 89(1), 201 -
210. https://doi.org/10.1529/biophysj.105.062877
Veldhuis,
G., Gabellieri, E., Poolman, B., Strambini, G.
B., & Broos, J. (2005). Substrate-induced
Conformational Changes in the Membrane-embedded IICmtl-domain of
the Mannitol Permease from Escherichia coli, EnzymeIImtl, Probed by
Tryptophan Phosphorescence Spectroscopy. The
Journal of Biological Chemistry, 280(42),
35148 - 35156. https://doi.org/10.1074/jbc.M507061200
Vervoort,
E. B., Bultema, J. B., Schuurman-Wolters, G. K., Geertsma, E.
R., Broos, J., & Poolman, B. (2005).
The first cytoplasmic loop of the mannitol permease from
Escherichia coli is accessible for sulfhydryl reagents from the
periplasmic side of the membrane. Journal of
Molecular Biology, 346(3), 733 - 743. https://doi.org/10.1016/j.jmb.2004.12.011
van
Straaten, K. E., Dijkstra, B. W., Vollmer, W., &
Thunnissen, A. M. W. H. (2005). Crystal structure of
MltA from Escherichia coli reveals a unique lytic transglycosylase
fold. Journal of Molecular Biology,
352(5), 1068 - 1080. https://doi.org/10.1016/j.jmb.2005.07.067
Barends,
T. R. M., de Jong, R. M., van Straaten, K. E., Thunnissen, A.
M. W. H., & Dijkstra, B. W. (2005). Escherichia
coli MltA: MAD phasing and refinement of a tetartohedrally twinned
protein crystal structure. Acta Crystallographica
Section D: Biological Crystallography, 61,
613-621. https://doi.org/10.1107/S0907444905005743
Barends,
T. R. M., Jong, R. M. D., Straaten, K. E. V., Thunnissen,
A.-M. W. H., & Dijkstra, B. W. (2005). Escherichia
coli MltA: MAD phasing and refinement of a tetartohedrally twinned
protein crystal structure (vol D61, pg 613, 2005).
Acta Crystallographica Section D: Biological
Crystallography, 61(8), 1172. https://doi.org/10.1107/S0907444905013533
2004
Swertz,
M. A., Brock, E. O. D., Hijum, S. A. F. T. V.,
Jong, A. D., Buist, G., Baerends, R. J. S., Kok,
J., Kuipers, O. P., & Jansen, R.
C. (2004). Molecular Genetics Information System
(MOLGENIS): alternatives in developing local experimental genomics
databases. Bioinformatics,
20(13), 2075 - 2083. https://doi.org/10.1093/bioinformatics/bth206
Jansen,
R. C., & Nap, J.-P. (2004). Regulating gene
expression: surprises still in store. Trends in
Genetics, 20(5), 223 - 225. https://doi.org/10.1016/j.tig.2004.03.002
Churchill,
G. A., Jansen, R. C., Airey, D. C., Allayee, H.,
Angel, J. M., Attie, A. D., Beatty, J., Beavis, W. D., Belknap, J.
K., Bennett, B., Berrettini, W., Bleich, A., Bogue, M., Broman, K.
W., Buck, K. J., Buckler, E., Burmeister, M., Chesler, E. J.,
Cheverud, J. M., ... Complex Trait Consortium (2004). The
Collaborative Cross, a community resource for the genetic analysis
of complex traits. Nature Genetics,
36(11), 1133-1137. https://doi.org/10.1038/ng1104-1133
Haastert,
P. J. M. V., & Devreotes, P. N. (2004).
Chemotaxis: signalling modules join hands at front and
tail. Nature Reviews Molecular Cell
Biology, 5(8), 626 - 634. https://doi.org/10.1038/sj.embor.7400051
Lu,
Y. H., Knol, J. C., Linskens, M. H. K., Friehs,
K., van Haastert, P. J. M., & Flaschel, E. (2004).
Cultivation of immobilized Dictyostelium discoideum for the
production of soluble human Fas ligand. Applied
Microbiology and Biotechnology, 65(5), 547 -
552. https://doi.org/10.1007/s00253-004-1620-8
Verheijden,
G. F. M., Metz, B., van Ravestein, A. A. M., Bos, E. S., van de
Wetering, R., Westerveld, A., Kouwijzer, M., Hanssen, R. G. J. M.,
van Peij, N. V., van Haastert, P. J. M.,
Linskens, M. H. K., & van Peij, NN. (2004). Human
gonadotropins expressed in dictyostelium discoideum.
Biology of Reproduction, 177 - 177.
Engel,
R., Hink, M. A., Bosgraaf, L., Haastert, P. J. M. V.,
& Visser, A. J. W. G. (2004). Pleckstrin Homology Domain
Diffusion in Dictyostelium Cytoplasm Studied Using Fluorescence
Correlation Spectroscopy. The Journal of
Biological Chemistry, 279(11), 10013-10019. https://doi.org/10.1074/jbc.M310039200
Lu,
Y. H., Knol, J. C., Linskens, M. H. K., Friehs,
K., van Haastert, P. J. M., & Flaschel, E. (2004).
Production of the soluble human Fas ligand by Dictyostelium
discoideum cultivated on a synthetic medium.
Journal of Biotechnology, 108(3),
243-251. https://doi.org/10.1016/j.jbiotec.2003.12.006
Postma,
M., Roelofs, J., Goedhart, J., Loovers, H. M., Visser, A. J. W.
G., & van Haastert, P. J. M. (2004).
Sensitization of Dictyostelium chemotaxis by
phosphoinositide-3-kinase-mediated self-organizing signalling
patches. Journal of Cell Science,
117(14), 2925-2935. https://doi.org/10.1242/jcs.01143
Veltman,
D. M., Bosgraaf, L., & van Haastert, P. J. M.
(2004). Unusual guanylyl cyclases and cGMP signaling in
Dictyostelium discoideum. Vitamins and Hormones -
Advances in Research and Applications, 69,
95-115.
Vischer,
H. F., Marques, R. B., Granneman, J. C. M., Linskens, M. H.
K., Schulz, R. W., & Bogerd, J. (2004).
Receptor-selective determinants in catfish gonadotropin
seat-belt loops. Molecular and Cellular
Endocrinology, 224(1-2), 55 - 63. https://doi.org/10.1016/j.mce.2004.06.011
Kampinga,
H. H., Waarde-Verhagen, M. A. W. H. V.,
Assen-Bolt, A. J. V., Rodemann, H. P., Prowse, K. R., &
Linskens, M. H. K. (2004). Reconstitution of active
telomerase in primary human foreskin fibroblasts: effects on
proliferative characteristics and response to ionizing
radiation. International Journal of Radiation
Biology, 80(5), 377 - 388. https://doi.org/10.1080/09553000410001692735
Marrink,
SJ., de Vries, AH., & Mark, AE. (2004).
Coarse grained model for semiquantitative lipid
simulations. Journal of Physical Chemistry
B, 108(2), 750-760. https://doi.org/10.1021/jp036508g
Folgering,
J. H. A., Kuiper, J. M., Vries, A. H. D., Engberts, J.
B. F. N., & Poolman, B. (2004).
Lipid-Mediated Light Activation of a Mechanosensitive Channel
of Large Conductance. Langmuir,
20(17), 6985 - 6987. https://doi.org/10.1021/la048942v
de
Vries, AH., Mark, AE., & Marrink, SJ.
(2004). Molecular dynamics simulation of the spontaneous
formation of a small DPPC vesicle in water in atomistic
detail. Journal of the American Chemical
Society, 126(14), 4488-4489. https://doi.org/10.1021/ja0398417
de
Vries, AH., Mark, AE., & Marrink, SJ.
(2004). The binary mixing behavior of phospholipids in a
bilayer: A molecular dynamics study. Journal of
Physical Chemistry B, 108(7), 2454-2463. https://doi.org/10.1021/jp0366926
Kuipers,
A., Boef, E. D., Rink, R., Fekken, S., Kluskens, L.
D., Driessen, A. J. M., Leenhouts, K., Kuipers,
O. P., & Moll, G. N. (2004). NisT,
the Transporter of the Lantibiotic Nisin, Can Transport Fully
Modified, Dehydrated, and Unmodified Prenisin and Fusions of the
Leader Peptide with Non-lantibiotic Peptides. The
Journal of Biological Chemistry, 279(21),
22176 - 22182. https://doi.org/10.1074/jbc.M312789200
Evers,
M. E., Trip, H., van den Berg, M. A., Bovenberg, R. A.
L., & Driessen, A. J. M. (2004).
Compartmentalization and transport in beta-lactam antibiotics
biosynthesis. In A. A. Brakhage (Ed.), Molecular
Biotechnolgy of Fungal beta-Lactam Antibiotics and Related Peptide
Synthetases (Vol. 88, pp. 111 - 135). Springer. https://doi.org/10.1007/b99259
Kiel,
J. A. K. W., Berg, M. V. D., Bovenberg, R. A.
L., Klei, I. J. V. D., & Veenhuis, M.
(2004). Penicillium chrysogenum Pex5p mediates differential
sorting of PTS1 proteins to microbodies of the methylotrophic yeast
Hansenula polymorpha. Fungal Genetics and
Biology, 41(7), 708 - 720. https://doi.org/10.1016/j.fgb.2004.02.006
Scheffers,
D.-J., & Errington, J. (2004). PBP1 Is a Component
of the Bacillus subtilis Cell Division Machinery.
Journal of Bacteriology, 186(15),
5153-5156. https://doi.org/10.1128/JB.186.15.5153-5156.2004
Koppelman,
CM., Aarsman, MEG., Postmus, J., Pas, E., Muijsers, AO.,
Scheffers, DJ., Nanninga, N., & den Blaauwen, T. (2004).
R174 of Escherichia coli FtsZ is involved in membrane
interaction and protofilament bundling, and is essential for cell
division. Molecular Microbiology,
51(3), 645-657. https://doi.org/10.1046/j.1365-2958.2003.03876.x
Scheffers,
D.-J., Jones, L. J. F., & Errington, J. (2004).
Several distinct localization patterns for penicillin-binding
proteins in Bacillus subtilis. Molecular
Microbiology, 51(3), 749-764.
Veldhuis,
G., Broos, J., Poolman, B., & Scheek,
RM. (2004). Evaluation of the flow-dialysis technique for
analysis of protein-ligand interactions: An experimental and a
Monte Carlo study. Biophysical
Journal, 86(4), 1959-1968. https://doi.org/10.1016/S0006-3495(04)74259-9
Broos,
J., Maddalena, F., & Hesp, BH. (2004). In vivo
synthesized proteins with monoexponential fluorescence decay
kinetics. Journal of the American Chemical
Society, 126(1), 22-23. https://doi.org/10.1021/ja0385585
van
Straaten, K. E., Dijkstra, B. W., & Thunnissen, A.-M. W.
H. (2004). Purification, crystallization and
preliminary X-ray analysis of the lytic transglycosylase MltA from
Escherichia coli. Acta Crystallographica Section
D: Biological Crystallography, 60(4), 758-760.
https://doi.org/10.1107/S0907444904002574
2003
Jansen,
R. C. (2003). Levensecht puzzelen.
s.n.
Jansen,
R. C., Jannink, J.-L., & Beavis, W. D. (2003).
Mapping quantitative trait loci in plant breeding
populations: Use of parental haplotype sharing.
Crop Science, 43(3), 829-834. https://doi.org/10.2135/cropsci2003.0829
Jansen,
R. C. (2003). Studying complex biological systems
using multifactorial perturbation. Nature Reviews
Genetics, 4(2), 145-151. https://doi.org/10.1038/nrg996
Abiola,
O., Angel, JM., Avner, P., Bachmanov, AA., Belknap, JK., Bennett,
B., Blankenhorn, EP., Blizard, DA., Bolivar, N. V., Brockmann, GA.,
Buck, KJ., Bureau, JF., Casley, WL., Chesler, EJ., Cheverud, JM.,
Churchill, GA., Cook, M., Crabbe, JC., Crusio, WE., ... Complex
Trait Consortium (2003). The nature and identification of
quantitative trait loci: a community's view.
Nature Reviews Genetics, 4(11),
911-916. https://doi.org/10.1038/nrg1206
Loovers,
HM., Veenstra, K., Snippe, H., Pesesse, N. V., Erneux, C.,
van Haastert, PJM., Loovers, H. M., & Pesesse, X.
(2003). A diverse family of inositol 5-phosphatases playing a
role in growth and development in Dictyostelium discoideum.
The Journal of Biological Chemistry,
278(8), 5652-5658. https://doi.org/10.1074/jbc.M208396200
Roelofs,
J., Smith, J. L., & Haastert, P. J. M. V. (2003).
cGMP signalling: different ways to create a pathway.
Trends in Genetics, 19(3), 132-134.
https://doi.org/10.1016/S0168-9525(02)00044-6
Veltman,
DM., De Boer, JS., Van Haastert, PJM., & Boer, J.
S. D. (2003). Chemoattractant-stimulated calcium influx in
Dictyostelium discoideum does not depend on cGMP.
Biochimica et Biophysica Acta-General
Subjects, 1623(2-3), 129-134. https://doi.org/10.1016/j.bbagen.2003.08.006
Blaauw,
M., Knol, JC., Kortholt, A., Roelofs, J., (Engel), R.,
Postma, M., Visser, AJWG., Van Haastert, PJM., Knol,
J. C., & Visser, A. J. W. G. (2003). Phosducin-like
proteins in Dictyostelium discoideum: implications for the
phosducin family of proteins. EMBO
Journal, 22(19), 5047-5057. https://doi.org/10.1093/emboj/cdg508
Veltman,
D., & Van Haastert, PJM. (2003). Regulation
of Dictyostelium guanylyl cyclases.
Protist, 154(1), 33-42. https://doi.org/10.1078/143446103764928477
Bosgraaf,
L., & Haastert, P. J. M. V. (2003). Roc, a
Ras/GTPase domain in complex proteins. Biochimica
et Biophysica Acta (BBA) - Molecular Cell Research,
1643(1), 5 - 10. https://doi.org/10.1016/j.bbamcr.2003.08.008
Postma,
M., Roelofs, J., Goedhart, J., Gadella, TWJ., Visser, AJWG.,
Van Haastert, PJM., Gadella, T. W. J., & Visser, A. J.
W. G. (2003). Uniform cAMP stimulation of Dictyostelium cells
induces localized patches of signal transduction and
pseudopodia. Molecular Biology of the
Cell, 14(12), 5019-5027. https://doi.org/10.1091/mbc.E03-08-0566
Vischer,
HF., Granneman, JCM., Linskens, MHK., Schulz, RW.,
& Bogerd, J. (2003). Both recombinant African catfish LH
and FSH are able to activate the African catfish FSH
receptor. Journal of Molecular
Endocrinology, 31(1), 133-140. https://doi.org/10.1677/jme.0.0310133
Anezo,
C., de Vries, AH., Holtje, HD., Tieleman, DP.,
& Marrink, SJ. (2003). Methodological issues in
lipid bilayer simulations. Journal of Physical
Chemistry B, 107(35), 9424-9433. https://doi.org/10.1021/jp0348981
de
Vries, AH., Hozoi, L., & Broer, R. (2003).
Origin of the chemical shift in X-ray absorption near-edge
spectroscopy at the Mn K-Edge in manganese oxide compounds.
International Journal of Quantum Chemistry,
91(1), 57-61. https://doi.org/10.1002/qua.10370
Moll,
G. N., Leenhouts, C. J., Kuipers, O. P.,
& Driessen, A. J. M. (2003). Export
and modification of (poly)peptides in the lantibiotic way.
(Patent No. WO03099862).
Errington,
J., Daniel, R. A., & Scheffers, D.-J. (2003).
Cytokinesis in Bacteria. Microbiology and
Molecular Biology Reviews, 67(1), 52-65. https://doi.org/10.1128/MMBR.67.1.52-65.2003
Broos,
J., Gabellieri, E., Biemans-Oldehinkel, E., & Strambini,
G. B. (2003). Efficient biosynthetic incorporation of
tryptophan and indole analogs in an integral membrane
protein. Protein Science,
12(9), 1991-2000. https://doi.org/10.1110/ps.03142003
Broos,
J., Gabellieri, E., van Boxel, GI., Jackson, JB., Strambini,
GB., & Strambini, G. B. (2003). Tryptophan
phosphorescence spectroscopy reveals that a domain in the
NAD(H)-binding component (dI) of transhydrogenase from
Rhodospirillum rubrum has an extremely rigid and conformationally
homogeneous protein core. The Journal of
Biological Chemistry, 278(48), 47578-47584. https://doi.org/10.1074/jbc.M309287200
Verdon,
G., Albers, S. V., Dijkstra, B. W., Driessen, A. J.
M., & Thunnissen, A. M. W. H. (2003).
Crystal structures of the ATPase subunit of the glucose ABC
transporter from Sulfolobus solfataricus: Nucleotide-free and
nucleotide-bound conformations. Journal of
Molecular Biology, 330(2), 343-358. https://doi.org/10.1016/S0022-2836(03)00575-8
Verdon,
G., Albers, SV., van Oosterwijk, N., Dijkstra, BW., Driessen,
AJM., Thunnissen, AMWH., & Dijkstra, B. W.
(2003). Formation of the productive ATP-Mg2+-bound dimer of
GlcV, an ABC-ATPase from Sulfolobus solfataricus.
Journal of Molecular Biology,
334(2), 255-267. https://doi.org/10.1016/j.jmb.2003.08.065
2002
Boer,
M. P., Braak, C. J. F. T., & Jansen, R. C. (2002).
A penalized likelihood method for mapping epistatic
quantitative trait loci with one-dimensional genome
searches. Genetics, 162(2),
951-960. http://keur.eldoc.ub.rug.nl/wetenschappers/9//FILES/wetenschappers/9/62/62.pdf
Mlynárová,
L., Loonen, A., Mietkiewska, E., Jansen, R. C., &
Nap, J.-P. (2002). Assembly of Two Transgenes in an
Artificial Chromatin Domain Gives Highly Coordinated Expression in
Tobacco. Genetics, 160,
727-740.
Balding,
DJ., Carothers, AD., Marchini, JL., Cardon, LR., Vetta, A.,
Griffiths, B., Weir, BS., Hill, WG., Goldstein, D., Strimmer, K.,
Myers, S., Beaumont, MA., Glasbey, CA., Mayer, CD., Richardson, S.,
Marshall, C., Durrett, R., Nielsen, R., Visscher, PM., ...
Gabrielson, E. (2002). Discussion on the meeting on
'Statistical modelling and analysis of genetic data'.
Journal of the Royal Statistical Society. Series B:
Statistical Methodology, 64, 737-775. https://doi.org/10.1111/1467-9868.00359
Jansen,
R. C., Nap, J.-P., & Mlynárová, L. (2002).
Errors in genomics and proteomics. Nature
Biotechnology, 20(19). https://doi.org/10.1038/nbt0102-19b
van
Ooien, J. W., Boer, M. P., Jansen, R. C., &
Maliepaard, C. (2002). MapQTL 4.0: Software For The
Calculation Of QTL Positions On Genetic Maps. Plant
Research International.
Bosgraaf,
L., & Haastert, P. J. M. V. (2002). A model
for cGMP signal transduction in Dictyostelium in perspective of 25
years of cGMP research. Journal of muscle research
and cell motility, 23(7-8), 781-791.
Bosgraaf,
L., Russcher, H., Smith, J. L., Wessels, D., Soll, D. R.,
& Haastert, P. J. M. V. (2002). A novel cGMP
signalling pathway mediating myosin phosphorylation and chemotaxis
in Dictyostelium. The EMBO Journal,
21(17), 4560-4570. https://doi.org/10.1093/emboj/cdf438
Roelofs,
J., & Haastert, P. J. M. V. (2002).
Characterization of two unusual guanylyl cyclases from
Dictyostelium. The Journal of Biological
Chemistry, 277(11), 9167-9174. https://doi.org/10.1074/jbc.M111437200
Roelofs,
J., & Haastert, P. J. M. V. (2002). Deducing
the origin of soluble adenylyl cyclase, a gene lost in multiple
lineages. Molecular Biology and
Evolution, 19(12), 2239-2246. https://doi.org/10.1093/oxfordjournals.molbev.a004047
Bosgraaf,
L., Russcher, H., Snippe, H., Bader, S., Wind, J., & Van
Haastert, PJM. (2002). Identification and
characterization of two unusual cGMP-stimulated phoshodiesterases
in Dictyostelium. Molecular Biology of the
Cell, 13(11), 3878-3889. https://doi.org/10.1091/mbc.E02-05-0302
Goldberg,
JM., Bosgraaf, L., Van Haastert, PJM., & Smith,
JL. (2002). Identification of four candidate cGMP targets in
Dictylostelium. Proceedings of the National
Academy of Sciences of the United States of America,
99(10), 6749-6754. https://doi.org/10.1073/pnas.102167299
de
Vries, A. H., Hozoi, L., Broer, R., &
Bagus, P. S. (2002). Importance of interatomic hole screening
in core-level spectroscopy of transition metal oxides: Mn 3s hole
states in MnO. Physical Review B,
66(3), Article 035108. https://doi.org/10.1103/PhysRevB.66.035108
van
Duijnen, P. T., de Vries, A. H., Swart,
M., & Grozema, F. C. (2002). Polarizabilities in
the condensed phase and the local fields problem: A direct reaction
field formulation. Journal of Chemical
Physics, 117(18), 8442 - 8453. https://doi.org/10.1063/1.1512278
Hozoi,
L., de Vries, A. H., van Oosten, A. B.,
Broer-Braam, H. B., Cabrero, J., & Graaf, de,
C. (2002). Theoretical characterization of the ground
and optically excited states of alpha '-NaV2O5.
Physical Review Letters, 89(7),
Article 076407. https://doi.org/10.1103/physrevlett.89.076407
van
der Lende, T. R., de Kamp, M., den Berg, M. V., Sjollema, K.,
Bovenberg, R. A. L., Veenhuis, M., Konings, W. N.,
& Driessen, A. J. M. (2002).
delta-(L-alpha-Aminoadipyl)-L-cysteinyl-D-valine synthetase,
that mediates the first committed step in penicillin biosynthesis,
is a cytosolic enzyme. Fungal Genetics and
Biology, 37(1), 49-55. Article PII
S1087-1845(02)00036-1.
Lende,
T. R. V. D., Kamp, M. V. D., Berg, M. V. D., Sjollema,
K., Bovenberg, R. A. L., Veenhuis, M., Konings,
W. N., & Driessen, A. J. M. (2002).
δ-(L-α-Aminoadipyl)-L-cysteinyl-D-valine
synthetase, that mediates the first committed step in penicillin
biosynthesis, is a cytosolic enzyme. Fungal
Genetics and Biology, 37(1). https://doi.org/10.1016/S1087-1845(02)00036-1
Scheffers,
D.-J., de Wit, J. G., Blaauwen, T. D., & Driessen,
A. J. M. (2002). GTP hydrolysis of cell division
protein FtsZ: Evidence that the active site is formed by the
association of monomers: Evidence that the Active Site Is Formed by
the Association of Monomers.
Biochemistry, 41(2), 521 - 529. https://doi.org/10.1021/bi011370i
Scheffers,
D.-J., & Driessen, A. J. M. (2002).
Immediate GTP hydrolysis upon FtsZ polymerization.
Molecular Microbiology, 43(6), 1517
- 1521. https://doi.org/10.1046/j.1365-2958.2002.02828.x
Broos,
J. (2002). Impact of the enzyme flexibility on the
enzyme enantio- selectivity in organic media towards specific and
non-specific substrates. Biocatalysis and
Biotransformation, 20(4), 291 - 295. https://doi.org/10.1080/10242420290004938
Broos,
J., Pas, H. H., & Robillard, G. T. (2002).
The smallest resonance energy transfer acceptor for
tryptophan. Biophysical Journal,
82(1), 2088.
Broos,
J., Pas, HH., & Robillard, GT. (2002).
The smallest resonance energy transfer acceptor for
tryptophan. Journal of the American Chemical
Society, 124(24), 6812-6813. https://doi.org/10.1021/ja017812v
Broos,
J., Pas, H. H., & Robillard, G. T. (2002).
The Smallest Resonance Energy Transfer Acceptor for
Tryptophan. Biophysical Journal.
Verdon,
G., Albers, S. V., Dijkstra, B. W., Driessen, A. J.
M., & Thunnissen, A. .-M. W. H. (2002).
Purification, crystallization and preliminary X-ray
diffraction analysis of an archaeal ABC-ATPase.
Acta Crystallographica Section D: Biological
Crystallography, 58, 362 - 365. https://doi.org/10.1107/S0907444901020765
2001
Postma,
M., & Van Haastert, PJM. (2001). A
diffusion-translocation model for gradient sensing by chemotactic
cells. Biophysical Journal,
81(3), 1314-1323. https://doi.org/10.1016/S0006-3495(01)75788-8
Roelofs,
J., & Van Haastert, PJM. (2001). Genomics:
Genes lost during evolution. Nature,
411(6841), 1013-1014. https://doi.org/10.1038/35082627
Roelofs,
J., Loovers, H., & Van Haastert, PJM. (2001).
GTPγS Regulation of a 12-Transmembrane Guanylyl Cyclase
Is Retained after Mutation to an Adenylyl Cyclase.
The Journal of Biological Chemistry,
276(44), 40740-40745. https://doi.org/10.1074/jbc.M105154200
Roelofs,
J., Snippe, H., Kleineidam, RG., & Van Haastert,
PJM. (2001). Guanylate cyclase in Dictyostelium
discoideum with the topology of mammalian adenylate cyclase.
Biochemical Journal, 354(3),
697-706. https://doi.org/10.1042/0264-6021:3540697
Kuwayama,
H., Snippe, H., Derks, M., Roelofs, J., & van Haastert,
PJM. (2001). Identification and characterization of
DdPDE3, a cGMP-selective phosphodiesterase from
Dictyostelium. Biochemical Journal,
353(3), 635-644. https://doi.org/10.1042/0264-6021:3530635
Dijken,
P. V., & Haastert, P. J. M. V. (2001).
Phospholipase Cδ regulates germination of Dictyostelium
spores. BMC Cell Biology, 2,
Article 25. https://doi.org/10.1186/1471-2121-2-25
Potma,
E. O., Boeij, W. P. D., Haastert, P. J. M. V., &
Wiersma, D. A. (2001). Real-time visualization of
intracellular hydrodynamics in single living cells.
Proceedings of the National Academy of
Sciences, 98(4), 1577 - 1582. https://doi.org/10.1073/pnas.98.4.1577
Potma,
E. O., de Boeij, W. P., Bosgraaf, L., Roelofs, J., van
Haastert, P. J. M., & Wiersma, D. A. (2001).
Reduced protein diffusion rate by cytoskeleton in vegetative
and polarized Dictyostelium cells. Biophysical
Journal, 81(4), 2010 - 2019. https://doi.org/10.1016/S0006-3495(01)75851-1
Roelofs,
J., Meima, M., Schaap, P., & Van Haastert, PJM.
(2001). The Dictyostelium homologue of mammalian soluble
adenylyl cyclase encodes a guanylyl cyclase. EMBO
Journal, 20(16), 4341-4348. https://doi.org/10.1093/emboj/20.16.4341
Chen,
QM., Prowse, KR., Tu, VC., Purdom, S., Linskens, MHK.,
Chen, Q. M., Prowse, K. R., & Tu, V. C. (2001).
Uncoupling the senescent phenotype from telomere shortening
in hydrogen peroxide-treated fibroblasts.
Experimental Cell Research, 265(2),
294-303. https://doi.org/10.1006/excr.2001.5182
Hozoi,
L., de Vries, A. H., & Broer-Braam, H.
B. (2001). X-ray spectroscopy at the MnK edge in
LaMnO3: An ab initio study. Physical Review
B, 64(16), Article 165104. https://doi.org/10.1103/PhysRevB.64.165104
Herrandez,
C., Cintas, L. M., Hernandez, P. E., Moll, G.
N., Driessen, A. J. M., & Herranz, C.
(2001). Enterocin P causes potassium ion efflux from
Enterococcus faecium T136 cells. Antimicrobial
Agents and Chemotherapy, 45(3), 901-904. https://doi.org/10.1128/AAC.45.3.901-904.2001
Scheffers,
D.-J. (2001). Polymerization of the bacterial cell
division protein FtsZ. s.n.
Scheffers,
D.-J., de Wit, J. G., Blaauwen, T. D., & Driessen,
A. J. M. (2001). Substitution of a conserved aspartate
allows cation-induced polymerization of FtsZ. FEBS
Letters, 494(1-2), 34 - 37. https://doi.org/10.1016/S0014-5793(01)02310-9
Scheffers,
D.-J., & Driessen, A. J. M. (2001).
The polymerization mechanism of the bacterial cell division
protein FtsZ. FEBS Letters,
506(1), 6 - 10. https://doi.org/10.1016/S0014-5793(01)02855-1
van
Montfort, B. A., Schuurman-Wolters, G. K., Wind, J., Broos,
J., Robillard, G. T., & Poolman, B. (2001).
Mapping of the dimer interface of the Escherichia coli
mannitol permease by cysteine cross-linking. The
Journal of Biological Chemistry, 277(17),
14717 - 14723. https://doi.org/10.1074/jbc.M201533200
Broos,
J., Strambini, G. B., Gonnelli, M., Wolters, G. S.,
Robillard, G. T., & Gonelli, M. (2001). Studying membrane
transport protein dynamics with tryptophan phosphorescence
specroscopy. Biophysical Journal,
80(1), 1050.
Broos,
J., Strambini, G. B., Gonelli, M., Schuurman-Wolters, G.,
& Robillard, G. T. (2001). Studying Membrane
Transport Protein Dynamics with Tryptophan Phosphorescence
Spectroscopy.
2000
Blaauw,
M., Linskens, MHK., & van Haastert,
PJM. (2000). Efficient control of gene expression by a
tetracycline-dependent transactivator in single Dictyostelium
discoideum cells. Gene,
252(1-2), 71-82. https://doi.org/10.1016/S0378-1119(00)00227-4
Vervoort,
E. B., Ravestein, A. V., Peij , van, N., Heikoop, J. C.,
Haastert, van, P. J. M., Verheijden, G. F., &
Linskens, M. H. K. (2000). Optimizing heterologous
expression in Dictyostelium: importance of 5 ' codon
adaptation. Nucleic Acids Research,
28(10), 2069-2074. https://doi.org/10.1093/nar/28.10.2069
Ostenfeld,
T., Caldwell, MA., Prowse, KR., Linskens, MH.,
Jauniaux, E., Svendsen, CN., Prowse, K. R., & Svendsen, C. N.
(2000). Human neural precursor cells express low levels of
telomerase in vitro and show diminishing cell proliferation with
extensive axonal outgrowth following transplantation.
Experimental Neurology, 164(1),
215-226. https://doi.org/10.1006/exnr.2000.7427
Moll,
G. N., Brul, S., Konings, W. N., & Driessen, A. J.
M. (2000). Comparison of the membrane interaction and
permeabilization by the designed peptide Ac-MB21-NH2 and truncated
dermaseptin S3. Biochemistry,
39(39), 11907 - 11912. https://doi.org/10.1021/bi000917a
Kiel,
JAKW., Hilbrands, RE., Bovenberg,
RAL., & Veenhuis, M. (2000). Isolation of
Penicillium chrysogenum PEX1 and PEX6 encoding AAA proteins
involved in peroxisome biogenesis. Applied
Microbiology and Biotechnology, 54(2),
238-242. https://doi.org/10.1007/s002530000378
Scheffers,
D. J., den Blaauwen, T., & Driessen, A. J.
(2000). Non-hydrolysable GTP-gamma-S stabilizes the FtsZ
polymer in a GDP-bound state. Molecular
Microbiology, 35(5), 1211-1219. https://doi.org/10.1046/j.1365-2958.2000.01791.x
Broos,
J., ter Veld, F., & Robillard, G. T. (2000).
Membrane protein-ligand interactions in E-coli vesicles and
living cells monitored via a biosynthetically incorporated
tryptophan analog. Biophysical
Journal, 78(1), 949Pos.
Broos,
J., Strambini, G. B., Gonnelli, M., Vos, E. P. P., Koolhof,
M., & Robillard, G. T. (2000). Sensitive monitoring of
the dynamics of a membrane-bound transport protein by tryptophan
phosphorescence spectroscopy.
Biochemistry, 39(35), 10877 - 10883.
https://doi.org/10.1021/bi000803z
Meijer,
L., Thunnissen, A.-MWH., White, A. W., Garnier, M.,
Tsai, L.-H., Cleverley, K. E., Salinas, P. C., Wu, Y.-Z., Biernat,
J., Mandelkow, E.-M., Pettit, G. R., & Nikolic, M. (2000).
Inhibition of cyclin-dependent kinases, GSK-3β and CK1
by hymenialdisine, a marine sponge constituent.
Chemistry %26 Biology, 7(1). https://doi.org/10.1016/S1074-5521(00)00063-6
Verdon,
G., Albers, S. V., Dijkstra, B. W., Driessen, A. J.
M., & Thunnissen, A.-MWH. (2000).
Over-production, purification and preliminary X-ray
crystallographic analysis of GlcV, the ATP-binding cassette of the
glucose ABC transport system from Sulfolobus solfataricus.
Acta Crystallographica Section A,
56(suppl.), S266.
Gliubich,
F. I., Thunnissen, A. M. W. H., & Dijkstra, B. W.
(2000). The 22kDa endo-specific membrane-bound lytic
transglycosylase EmtA. Acta Crystallographica
Section A, 56(suppl.), s267.
1999
Vaes,
BLT., Vader, LW., Prowse, KR., & Linskens, MHK.
(1999). Expression of reporter constructs in human diploid
fibroblasts. In VA. Bohr, BFC. Clark, & T. Stevnsner
(Eds.), MOLECULAR BIOLOGY OF AGING (pp. 91-103). (ALFRED
BENZON SYMPOSIUM SERIES; Vol. 44). MUNKSGAARD.
Linskens,
M. H. K., Grootenhuis, P. D. J., Blaauw, M., Huisman-de
Winkel, B., Ravestein, A. V., Haastert, P. J. M. V.,
& Heikoop, J. C. (1999). Random mutagenesis and screening
of complex glycoproteins: expression of human gonadotropins in
Dictyostelium discoideum. European Journal of
Biochemistry, 256(6), 639-645.
Kipling,
D., Wynford-Thomas, D., Jones, CJ., Akbar, A., Aspinall, R.,
Bacchetti, S., Blasco, MA., Broccoli, D., DePinho, RA., Edwards,
DR., Effros, RB., Harley, CB., Lansdorp, PM.,
Linskens, MHK., Prowse, KR., Newbold, RF., Olovnikov, AM.,
Parkinson, EK., Pawelec, G., ... Faragher, RGA. (1999).
Telomere-dependent senescence. Nature
Biotechnology, 17(4), 313-313.
Kipling,
D., Wynford-Thomas, D., Jones, C. J., Akbar, A., Aspinall, R.,
Bacchetti, S., Blasco, M. A., Broccoli, D., DePinho, R. A.,
Edwards, D. R., Effros, R. B., Harley, C. B., Lansdorp, P.
M., Linskens, M. H. K., Prowse, K. R., Newbold,
R. F., Olovnikov, A. M., Parkinson, E. K., Pawelec, G., ...
Faragher, R. G. A. (1999). Telomere-dependent
senescence. Nature Biotechnology,
17, 313.
de
Vries, A. H., Sherwood, P., Collins, S. J., Rigby, A. M.,
Rigutto, M., & Kramer, G. J. (1999). Zeolite structure
and reactivity by combined quantum-chemical- classical
calculations. Journal of Physical Chemistry
B, 103(29), 6133 - 6141. https://doi.org/10.1021/jp9913012
Moll,
G. N., Konings, W. N., & Driessen, A. J. M.
(1999). Bacteriocins: mechanism of membrane insertion and
pore formation. Antonie Van Leeuwenhoek:
International Journal of General and Molecular
Microbiology, 76(1), 185-198.
Moll,
G. N., Akker, E. V. D., Hauge, H. H., Nissen-Meyer, J., Nes,
I. F., Konings, W. N., & Driessen, A. J. M.
(1999). Complementary and Overlapping Selectivity of the
Two-Peptide Bacteriocins Plantaricin EF and JK.
Journal of Bacteriology, 181(16),
4848 - 4852.
Broos,
J., Duurkens, R. H. T., & Robillard, G. T. (1999).
A mechanism to alter reversibly the oligomeric state of a
membrane bound protein. Biophysical
Journal, 76(1), A126 - A126.
Broos,
J., ter Veld, F., & Robillard, G. T. (1999).
Membrane protein-ligand interactions in Escherichia coli
vesicles and living cells monitored via a biosynthetically
incorporated tryptophan analogue.
Biochemistry, 38(31), 9798 - 9803.
https://doi.org/10.1021/bi991157a
Robillard,
G. T., & Broos, J. (1999).
Structure/function studies on the bacterial carbohydrate
transporters, enzymes II, of the phosphoenolpyruvate-dependent
phosphotransferase system. Biochimica et
Biophysica Acta-Reviews on Biomembranes,
1422(2), 73 - 104. https://doi.org/10.1016/S0304-4157(99)00002-7
Asselt,
E. J. V., Thunnissen, A.-M. W. H., & Dijkstra, B.
W. (1999). High resolution crystal structures of the
Escherichia coli lytic transglycosylase Slt70 and its complex with
a peptidoglycan fragment. Journal of Molecular
Biology, 291(4), 877-898. https://doi.org/10.1006/jmbi.1999.3013
1998
Heikoop,
JC., Grootenhuis, PDJ., Blaauw, M., Veldema, JS., Van
Haastert', PJM., Linskens, MHK., Heikoop, J.
C., & Veldema, J. S. (1998). Expression of a bioactive,
single-chain choriogonadotropin in Dictyostelium discoideum.
European Journal of Biochemistry,
256(2), 359-363. https://doi.org/10.1046/j.1432-1327.1998.2560359.x
Chambers,
K. J., Tonkin, L. A., Chang, E., Shelton, D. N., Linskens, M.
H., & Funk, W. D. (1998). Identification and
cloning of a sequence homologue of dopamine
β-hydroxylase. Gene,
218(1). https://doi.org/10.1016/S0378-1119(98)00344-8
Sinclair,
P. E., De Vries, A., Sherwood, P., Catlow, C. R. A.,
& Van Santen, R. A. (1998). Quantum-chemical studies of
alkene chemisorption in chabazite: A comparison of cluster and
embedded-cluster models. Journal of the Chemical
Society - Faraday Transactions, 94(22),
3401-3408. https://doi.org/10.1039/a805616a
Moll,
G. N., Hildeng-Hauge, H., Nissen-Meyer, J., Nes, I. F.,
Konings, W. N., & Driessen, A. J. M. (1998).
Mechanistic properties of the two-component bacteriocin
Lactococcin G. Journal of
Bacteriology, 180(1), 96 - 99.
Moll,
G., Hildeng-Hauge, H., Nissen-Meyer, J., Nes, I. F.,
Konings, W. N., & Driessen, A. J. M. (1998).
Mechanistic Properties of the Two-Component Bacteriocin
Lactococcin G. Biochemistry,
37(46).
Hildeng-Hauge,
H., Mantzilas, D., Moll, G. N., Konings, W. N.,
Driessen, A. J. M., Eijsink, V. G. H., & Nissen-Meyer,
J. (1998). Plantaricin A is an amphiphilic alpha-helical
bacteriocin-like pheromone which exerts antimicrobial and pheromone
activities through different mechanisms.
Biochemistry, 37(46), 16026 - 16032.
https://doi.org/10.1021/bi981532j
Moll,
G. N., Konings, W. N., & Driessen, A. J. M.
(1998). The lantibiotic nisin induces transmembrane movement
of a flourescent phospholipid. Journal of
Bacteriology, 180, 96 - 99.
Moll,
G. N., Konings, W. N., & Driessen, A. J. M.
(1998). The Lantibiotic Nisin Induces Transmembrane Movement
of a Fluorescent Phospholipid. Journal of
Bacteriology, 180(24), 6565 - 6570.
Broos,
J., ten Hoeve Duurkens, R. H., & Robillard, G. T.
(1998). A mechanism to alter reversibly the oligomeric state
of a membrane-bound protein demonstrated with E. coli EII mtl in
solution. The Journal of Biological
Chemistry, 273(7), 3865 - 3870. https://doi.org/10.1074/jbc.273.7.3865
Gray,
N. S., Wodicka, L., Thunnissen, A.-M. W. H., Norman,
T. C., Kwon, S., Espinoza, F. H., Morgan, D. O., Barnes, G.,
LeClerc, S., Meijer, L., Kim, S.-H., Lockhart, D. J., &
Schultz, P. G. (1998). Exploiting Chemical Libraries,
Structure, and Genomics in the Search for Kinase Inhibitors.
Science, 281(5376). https://doi.org/10.1126/science.281.5376.533
1997
Sherwood,
P., De Vries, A. H., Collins, S. J., Greatbanks, S.
P., Burton, N. A., Vincent, M. A., & Hillier, I. H. (1997).
Computer simulation of zeolite structure and reactivity using
embedded cluster methods. Faraday
Discussions, 106, 79-92. https://doi.org/10.1039/a701790a
deVries,
AH., vanDuijnen, PT., Zijlstra, RWJ., & Swart,
M. (1997). Thole's interacting polarizability model in
computational chemistry practice. Journal of
Electron Spectroscopy and Related Phenomena,
86(1-3), 49-55.
Moll,
G. N., Clark, J., Chan, W. C., Bycroft, B. W., Roberts, G.
C. K., Konings, W. N., & Driessen, A. J. M.
(1997). Role of transmembrane pH gradient and membrane
binding in nisin pore formation. Journal of
Bacteriology, 179(1), 135-140.
Aharonowitz,
Y., Van Der Voort, L. H. M., Cohen, G.,
Bovenberg, R. A. L., Schreiber, R., Argaman, A., Av-Gay, Y.,
Nan, H. M., Kattevilder, A., & Lissa, H. P. (1997). Oxido reductase enzyme system obtainable from P.
chrysogenum, the set of genes encoding the same and the use of
oxido reductase enzyme systems or genes encoding the same for
increasing antibiotic production. https://www.google.com/patents/US5652132
Swaving
Dijkstra, D., Broos, J., Visser, A. J. W. G., van
Hoek, A., & Robillard, G. (1997). Dynamic fluorescence
spectroscopy on single tryptophan mutants of EIImtl in detergent
micelles: Effects of substrate binding and phosphorylation on the
fluorescence and anisotropy decay.
Biochemistry, 36(16), 4860-4866. https://doi.org/10.1021/bi9629081
1996
West,
M. D., Shay, J. W., Wright, W. E., & Linskens, M. H.
K. (1996). Altered Expression of Plasminogen Activator
and Plasminogen Activator Inhibitor during Cellular
Senescence. Experimental Gerontology,
31(1). https://doi.org/10.1016/0531-5565(95)02013-6
Duijnen
, van, P. T., & de Vries, A. H. (1996).
Direct reaction field force field: A consistent way to
connect and combine quantum-chemical and classical descriptions of
molecules. International Journal of Quantum
Chemistry, 60(6), 1111-1132.
Zijlstra,
R. W. J., van Duijnen, P. T., & de Vries, A.
(1996). Polarization of the excited states of twisted
ethylene in a non-symmetrical environment.
Chemical Physics, 204(2-3),
439-446.
De
Vries, A. H., & Van Duijnen, P. T. (1996).
Solvatochromism of the π* ← n transition of
acetone by combined quantum mechanical—classical mechanical
calculations. International Journal of Quantum
Chemistry, 57(6), 1067-1076. https://doi.org/10.1002/(sici)1097-461x(1996)57:6<1067::aid-qua5>3.0.co;2-r
Moll,
G., Ubbink-Kok, T., Hildeng-Hauge, H., Nissen-Meyer, J.,
Nes, I. F., Konings, W. N., & Driessen, A. J. M.
(1996). Lactococcin G Is a Potassium Ion-Conducting,
Two-Component Bacteriocin. Journal of
Bacteriology, 178(3), 600 - 605.
Moll,
G., Konings, W. N., & Driessen, A. J. M.
(1996). Mechanism of lantibiotic-induced pore
formation. In S. G. Pandalai (Ed.), Recent research
developments in antimicrobial agents and chemotherapy (Vol. 1,
pp. 363 - 370). Scientific Information Guild.
Moll,
G. N., Roberts, G. C. K., Konings, W. N., &
Driessen, A. J. M. (1996). Mechanism of
lantibiotic-induced pore-formation. Antonie Van
Leeuwenhoek: International Journal of General and Molecular
Microbiology, 69(2), 370. https://doi.org/10.1007/BF00399423
Dijkstra,
D., Broos, J., Lolkema, J. S., Enequist, H., Minke,
W., & Robillard, G. T. (1996). A fluorescence study of
single tryptophan-containing mutants of enzyme IImtl of the
Escherichia coli phosphoenolpyruvate-dependent mannitol transport
system. Biochemistry, 35(21),
6628-6634. https://doi.org/10.1021/bi952222t
Robillard,
G., Boer, H., HARIS, PI., Meijberg, W., Swaving-Dijkstra, D.,
Schuurman-Wolters, G. K., Hoeve-Duurkens, R. T., CHAPMAN, D.,
& Broos, J. (1996). Domain and subunit
interactions and their role in the function of the E. Coli mannitol
transporter, EIIMTL. In W. N. Konings, H. R. Kaback, &
J. S. Lolkema (Eds.), Handbook of Biological Physics: Transport
processes in Eukaryotic and Prokaryotic organisms (Vol. 2, pp.
549-572). Elsevier.
Engbersen,
J. F. J., Broos, J., Verboom, W., & Reinhoudt, D.
N. (1996). Effects of crown ethers and small amounts of
cosolvent on the activity and enantioselectivity of
α-chymotrypsin in organic solvents. Pure and
Applied Chemistry, 68(11). https://doi.org/10.1351/pac199668112171
Broos,
J., Arends, R., van Dijk, G. B., Verboom, W., Engbersen, J.
F. J., & Reinhoudt, D. N. (1996). Enhancement of
tyrosinase activity by macrocycles in the oxidation of p-cresol in
organic solvents. Journal of the Chemical Society,
Perkin Transactions 1, 20(12), 1415-1417. https://doi.org/10.1039/p19960001415
Dijkstra,
D., Broos, J., & Robillard, G. T. (1996).
Membrane proteins and impure detergents: Procedures to purify
membrane proteins to a degree suitable for tryptophan fluorescence
spectroscopy. Analytical Biochemistry,
240(1), 142-147. https://doi.org/10.1006/abio.1996.0341
Robillard,
G. T., Swaving-Dijkstra, D., & Broos, J. (1996).
Tryptophan Fluorescence Spectroscopy, Fluorescent
Impurities & Membrane-Bound Proteins.
Broos,
J., Dijkstra, D., & Robillard, G. T. (1996).
Tryptophan fluorescence spectroscopy on the membrane-embedded
mannitol transport enzyme (ELL(mtl)) of E-coli.
Biophysical Journal, 70(2),
MP327-MP327.
Thunnissen,
A.-M. W. H., & Dijkstra, B. W. (1996). Cure for a
crisis? Nature Structural & Molecular
Biology, 3(3), 218-221. https://doi.org/10.1038/nsb0396-218
Dijkstra,
B. W., Thunnissen, A.-M. W. H., & Asselt, E. V.
(1996). Structure and mechanism of SLT70, a bacterial
muramidase. Acta Crystallographica Section
A, 52, C-95-C-95. https://doi.org/10.1107/S0108767396095281
1995
Dimri,
G. P., Lee, X., Basile, G., Acosta, M., Scott, G., Roskelley, C.,
Medrano, E. E., Linskens, M., Rubelj, I.,
Pereira-Smith, O., Peacocke, M., & Campisi, J. (1995). A
biomarker that identifies senescent human cells in culture and in
aging skin in vivo. Proceedings of the National
Academy of Sciences, 92(20). https://doi.org/10.1073/pnas.92.20.9363
Linskens,
M. H. K., Feng, J., Andrews, W. H., Enlow, B. E., Saati, S.
M., Tonkin, L. A., Funk, W. D., & Villeponteau, B. (1995).
Cataloging altered gene expression in young and senescent
cells using enhanced differential display. Nucleic
Acids Research, 23(16). https://doi.org/10.1093/nar/23.16.3244
Yaglom,
J., Linskens, M. H. K., Sadis, S., Rubin, D. M.,
Futcher, B., & Finley, D. (1995). p34Cdc28-Mediated
Control of Cln3 Cyclin Degradation. Molecular and
Cellular Biology, 15(2), 731-741. https://doi.org/10.1128/MCB.15.2.731
Linskens,
M. H. K., Harley, C. B., West, M. D., Campisi, J., &
Hayflick, L. (1995). Replicative Senescence and Cell
Death. Science, 267,
17.
De
Vries, A. H., Van Duijnen, P. T., Juffer, A. H., Rullmann,
J. A. C., Dijkman, J. P., Merenga, H., & Thole, B. T. (1995).
Erratum: Implementation of reaction field methods in quantum
chemistry computer codes (Vol 16, Pg 37, 1995).
Journal of Computational Chemistry,
16(11), 1445-1446. https://doi.org/10.1002/jcc.540161113
De
Vries, A. H., Van Duijnen, P. T., Juffer, A. H., Rullmann,
J. A. C., Dijkman, J. P., MERENGA, H., & Thole, B. T. (1995).
Implementation of reaction field methods in quantum chemistry
computer codes. Journal of Computational
Chemistry, 16(1), 37-55. https://doi.org/10.1002/jcc.540160105
de
Vries, A. H. (1995). Modelling condensed-phase
systems: from quantum chemistry to molecular models.
[Thesis fully internal (DIV), University of Groningen]. s.n.
Van
Duijnen, P. T., & De Vries, A. H. (1995).
Utopia dielectrica. International Journal of
Quantum Chemistry, 56(S29), 523-531. https://doi.org/10.1002/qua.560560855
Broos,
J., Engbersen, J. F. J., Sakodinskaya, I. K., Verboom, W.,
& Reinhoudt, D. N. (1995). Activity and
enantioselectivity of serine proteases in transesterification
reactions in organic media. Journal of the
Chemical Society%2C Perkin Transactions 1,
117(22). https://doi.org/10.1039/p19950002899
Broos,
J., Visser, A. J. W. G., Engbersen, J. F. J., Verboom, W.,
Hoek, A. V., & Reinhoudt, D. N. (1995). Flexibility of
Enzymes Suspended in Organic Solvents Probed by Time-Resolved
Fluorescence Anisotropy. Evidence That Enzyme Activity and
Enantioselectivity Are Directly Related to Enzyme
Flexibility. Journal of the American Chemical
Society, 117(51). https://doi.org/10.1021/ja00156a001
Broos,
J., ENGBERSEN, JFJ., VERBOOM, W., & Reinhoudt, D. N.
(1995). Inversion of enantioselectivity of serine
proteases. Recueil des Travaux Chimiques des
Pays-Bas, 114, 255-257.
Broos,
J., Sakodinskaya, I. K., Engbersen, J. F. J., Verboom, W.,
& Reinhoudt, D. N. (1995). Large Activation of Serine
Proteases by Pretreatment with Crown Ethers.
Journal of the Chemical Society%2C Chemical
Communications, 68(2). https://doi.org/10.1039/c39950000255
THUNNISSEN,
AMWH., ROZEBOOM, HJ., KALK, KH., &
DIJKSTRA, BW. (1995). STRUCTURE OF THE 70-KDA SOLUBLE LYTIC
TRANSGLYCOSYLASE COMPLEXED WITH BULGECIN-A - IMPLICATIONS FOR THE
ENZYMATIC MECHANISM. Biochemistry,
34(39), 12729-12737. https://doi.org/10.1021/bi00039a032
Thunnissen,
A.-M. W. H., Isaacs, N. W., & Dijkstra, B. W. (1995).
THE CATALYTIC DOMAIN OF A BACTERIAL LYTIC TRANSGLYCOSYLASE
DEFINES A NOVEL CLASS OF LYSOZYMES.
Proteins-Structure Function and
Bioinformatics, 22(3), 245-258. https://doi.org/10.1002/prot.340220305
Thunnissen,
A.-M. W. H. (1995). The hole story. Structure and
function of the 70 kDa soluble lytic transglycosylase from
escherichia coli. s.n.
1994
Thunnissen,
A.-M. W. H., Dijkstra, A. J., Kalk, K. H., Rozeboom,
H. J., Engel, H., Keck, W., & Dijkstra, B. W. (1994).
Doughnut-shaped structure of a bacterial muramidase revealed
by X-ray crystallography. Nature,
367(6465), 750-754. https://doi.org/10.1038/367750a0
Dijkstra,
B. W., & Thunnissen, A.-M. W. H. (1994).
'Holy' proteins II: the soluble lytic
transglycosylase. Current Opinion in Structural
Biology, 4(6), 810-813. https://doi.org/10.1016/0959-440X(94)90261-5
1993
Linskens,
M., Tyers, M., & Futcher, B. (1993). CLN3
Functions in Both Daughter and Mother Cells of S.
cerevisiae. Cell, 72(4). https://doi.org/10.1016/0092-8674(93)90067-Z
DEVRIES,
AH., VANDUIJNEN, PT., & JUFFER, AH. (1993).
SUCCESS AND PITFALLS OF THE DIELECTRIC CONTINUUM MODEL IN
QUANTUM-CHEMICAL CALCULATIONS. International
Journal of Quantum Chemistry, 451-466.
Thunnissen,
A.-M., Dijkstra, A., Rozeboom, H., Kalk, K. H.,
Keck, W., & Dijkstra, B. W. (1993). Crystal Structure of
a Bacterial Muramidase: The Soluble Lytic Transglycosylase from E.
Coli. Acta Crystallographica Section
A, 49(suppl.).
1992
de
Vries, A. H., & van Duijnen, P. T. (1992).
Theoretical calculation of tautomer equilibria of
4-substituted imidazoles in the gas phase and in solution.
Biophysical Chemistry, 43(2),
139-147. https://doi.org/10.1016/0301-4622(92)80028-4
Broos,
J., Verboom, W., Engbersen, J. F. J., & Reinhoudt, D. N.
(1992). Crown ethers can enhance enzyme activity in organic
solvents. In Progress in Biotechnology: Biocatalysis in
non-conventional media (Vol. 8, pp. 691-695)
1991
Tyers,
M., Fitch, I., Tokiwa, G., Dahmann, C., Nash, R., Linskens,
M., & Futcher, B. (1991). Characterization of
G1 and mitotic cyclins of budding yeast.
Cold spring harbor symposia on quantitative
biology, 56, 21-32. https://doi.org/10.1101/SQB.1991.056.01.005
Broos,
J., Martin, M., Rouwenhorst, I., Verboom, W., &
Reinhoudt, D. N. (1991). Acceleration of enzyme-catalyzed
reactions in organic solvents by crown ethers.
Recueil des Travaux Chimiques des Pays-Bas,
110, 222-225.
Noble,
M. E. M., Wierenga, R. K., Lambeir, A.-M., Opperdoes, F. R.,
Thunnissen, A.-M. W. H., Kalk, K., Groendijk, H., & Hol,
W. (1991). The Adaptability of the Active Site of
Trypanosomal Triosephosphate Isomerase as Observed in the Crystal
Structures of Three Different Complexes.
Proteins, 10(1), 50-69. https://doi.org/10.1002/prot.340100106
1990
Linskens,
M. H. K., & Huberman, J. A. (1990). Ambiguities in
results obtained with 2D gel replicon mapping techniques.
Nucleic Acids Research, 18(3). https://doi.org/10.1093/nar/18.3.647
Linskens,
M. H. K., & Huberman, J. A. (1990). The Two Faces
of Higher Eukaryotic DNA Replication Origins.
Cell, 62(5). https://doi.org/10.1016/0092-8674(90)90258-G
Broos,
J., & Kellogg, R. M. (1990). Modification of
papain with a NAD(P)H analogue. Reactivity towards charged
substrates and enhanced stability towards acid catalyzed
hydration. Recueil des Travaux Chimiques des
Pays-Bas-Journal of the Royal Netherlands Chemical
Society, 109(4), 299-301. https://doi.org/10.1002/recl.19901090406
1989
Darling,
D., Tavassdoli, M., Linskens, M. H. K., &
Farzaneh, F. (1989). DMSO induced modulation of c-myc
steady-state RNA levels in a variety of different cell
lines. Oncogene, 4(2),
175-179.
Darling,
D. C., Linskens, M. H. K., & Farzaneh, F. (1989).
HL-R5 and HL-D4: Two Differentiation Resistant HL-60
Variants. Leukemia Research,
13(5). https://doi.org/10.1016/0145-2126(89)90081-7
Umek,
R. M., Linskens, M. H. K., Kowalski, D., &
Huberman, J. A. (1989). New beginnings in studies of
eukaryotic DNA replication origins. Biochimica et
Biophysica Acta %28BBA%29 - Gene Structure and
Expression, 1007(1). https://doi.org/10.1016/0167-4781(89)90123-1
1988
Linskens,
M. H. K., & Huberman, J. A. (1988). Organization
of Replication of Ribosomal DNA in Saccharomyces cerevisiae.
Molecular and Cellular Biology,
8(11), 4927-4935. https://doi.org/10.1128/MCB.8.11.4927
1987
Linskens,
M. H. K., Eijsermans, A., & Dijkwel, P. A. (1987).
Comparative analysis of DNA loop length in nontransformed and
transformed hamster cells. Mutation
Research%2FFundamental and Molecular Mechanisms of
Mutagenesis, 178(2). https://doi.org/10.1016/0027-5107(87)90275-2
Schip,
F. D. V. H., Samallo, J., Broos, J., Ophuis, J.,
Mojet, M., Gruber, M., & AB, G. (1987). Nucleotide
Sequence of a Chicken Vitellogenin Gene and Derived Amino Acid
Sequence of the Encoded Yolk Precursor Protein.
Journal of Molecular Biology,
196(2), 245-260. https://doi.org/10.1016/0022-2836(87)90688-7
1985
Beintema,
J., Broos, J., Meulenberg, J., & Schüller, C.
(1985). The amino acid sequence of snapping turtle (Chelydra
serpentina) ribonuclease. European Journal of
Biochemistry, 153(2), 305-312. https://doi.org/10.1111/j.1432-1033.1985.tb09301.x
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