Simultaneous prediction of protein folding and docking at high resolution.

ABSTRACT: Interleaved dimers and higher order symmetric oligomers are ubiquitous in biology but present a challenge to de novo structure prediction methodology: The structure adopted by a monomer can be stabilized largely by interactions with other monomers and hence not the lowest energy state of a single chain. Building on the Rosetta framework, we present a general method to simultaneously model the folding and docking of multiple-chain interleaved homo-oligomers. For more than a third of the cases in a benchmark set of interleaved homo-oligomers, the method generates near-native models of large alpha-helical bundles, interlocking beta sandwiches, and interleaved alpha/beta motifs with an accuracy high enough for molecular replacement based phasing. With the incorporation of NMR chemical shift in

SUBMITTER: Das R 

PROVIDER: S-EPMC2770007 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature