Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

ABSTRACT: It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We f

SUBMITTER: Kukic P 

PROVIDER: S-EPMC4624779 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature