Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex.

ABSTRACT: We present a novel multi-level methodology to explore and characterize the low energy landscape and the thermodynamics of proteins. Traditional conformational search methods typically explore only a small portion of the conformational space of proteins and are hard to apply to large proteins due to the large amount of calculations required. In our multi-scale approach, we first provide an initial characterization of the equilibrium state ensemble of a protein using an efficient computational conformational sampling method. We then enrich the obtained ensemble by performing short Molecular Dynamics (MD) simulations on selected conformations from the ensembles as starting points. To facilitate the analysis of the results, we project the resulting conformations on a low-dimensional landscape

SUBMITTER: Haspel N 

PROVIDER: S-EPMC2827694 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature