Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins.

ABSTRACT: Although the structures of many beta-barrel membrane proteins are available, our knowledge of the principles that govern their energetics and oligomerization states is incomplete. Here we describe a computational method to study the transmembrane (TM) domains of beta-barrel membrane proteins. Our method is based on a physical interaction model, a simplified conformational space for efficient enumeration, and an empirical potential function from a detailed combinatorial analysis. Using this method, we can identify weakly stable regions in the TM domain, which are found to be important structural determinants for beta-barrel membrane proteins. By calculating the melting temperatures of the TM strands, our method can also assess the stability of beta-barrel membrane proteins. Predictions on m

SUBMITTER: Naveed H 

PROVIDER: S-EPMC2722334 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature