Multipass membrane protein structure prediction using Rosetta.

ABSTRACT: We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures. The membrane environment is modeled by embedding the protein chain into a model membrane represented by parallel planes defining hydrophobic, interface, and polar membrane layers for each energy evaluation. The optimal embedding is determined by maximizing the exposure of surface hydrophobic residues within the membrane and minimizing hydrophobic exposure outside of the membrane. Protein conformations are built up using the Rosetta fragment assembly method and evaluated using a new membrane-specific version of the Rosetta low-resolution energy function in which residue-residue and residue-environment interactions are functions of the membrane layer in ad

SUBMITTER: Yarov-Yarovoy V 

PROVIDER: S-EPMC1479309 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature