Prediction of transmembrane helix orientation in polytopic membrane proteins.

ABSTRACT:

Background

Membrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental difficulties. Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins.

Results

We present a method for prediction of the TM helix orientation, which is an essential step in ab initio modeling of membrane proteins. Our method is based on a canonical model of the heptad repeat originally developed for coiled coils. We identify the helical surface patches that interface with lipid molecules at an accuracy of about 88% from the sequence information alone, using an empirical scoring function LIPS (LIPid-facing Surface), which combine

SUBMITTER: Adamian L 

PROVIDER: S-EPMC1540425 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature