Toward high-resolution prediction and design of transmembrane helical protein structures.

ABSTRACT: The prediction and design at the atomic level of membrane protein structures and interactions is a critical but unsolved challenge. To address this problem, we have developed an all-atom physical model that describes intraprotein and protein-solvent interactions in the membrane environment. We evaluated the ability of the model to recapitulate the energetics and structural specificities of polytopic membrane proteins by using a battery of in silico prediction and design tests. First, in side-chain packing and design tests, the model successfully predicts the side-chain conformations at 73% of nonexposed positions and the native amino acid identities at 34% of positions in naturally occurring membrane proteins. Second, the model predicts significant energy gaps between native and nonnative

SUBMITTER: Barth P 

PROVIDER: S-EPMC2000396 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature