The MemGen structural classification of secondary transporters. A membrane topology screening approach

PhD ceremony: Mr. R. ter Horst, 12.45 uur, Academiegebouw, Broerstraat 5, Groningen

Dissertation: The MemGen structural classification of secondary transporters. A membrane topology screening approach

Promotor(s): prof. A.J.M. Driessen

Faculty: Mathematics and Natural Sciences

Notwithstanding their great variety and number, α-helical membrane proteins share a common architecture: one or more bundles of membrane spanning hydrophobic regions connected by hydrophilic loops. The alternation of regions of high and low hydrophobicity give rise to a hydropathy profile characteristic to the membrane protein, and provides a fingerprint of the structure of the protein. In the MemGen classification system, similarities between (seemingly non-related) proteins or protein families are identified by comparison of hydropathy profiles. Each familie of membrane proteins is grouped in one of the structural classes, ST[1], ST[2], ST[3] and ST[4]. All members of a structural class share a global fold characteristic for that class. Although the MemGen classification system is not a membrane topology prediction method in itself, knowing the topology of one protein in a structural class infers knowing them all [33].

The objective of this research was to develop an experimental method that allows discrimination between topology models derived from different predictors. The method was subsequently used to experimentally evaluate the structural classification by MemGen. The TopScreen approach provided a large amount of data that was in full agreement with MemGen predictions, providing strong support for the typical fold of ST[3] transporter families. Based on the studies reported in this thesis, it was suggested that the ‘core’ structure identified in the [st324]GltS and [st326]2HCT families is also valid for the seemingly unrelated IT superfamily transporters and other families in class ST[3].