Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

ABSTRACT: Characterizing the equilibrium ensemble of folding pathways, including their relative probability, is one of the major challenges in protein folding theory today. Although this information is in principle accessible via all-atom molecular dynamics simulations, it is difficult to compute in practice because protein folding is a rare event and the affordable simulation length is typically not sufficient to observe an appreciable number of folding events, unless very simplified protein models are used. Here we present an approach that allows for the reconstruction of the full ensemble of folding pathways from simulations that are much shorter than the folding time. This approach can be applied to all-atom protein simulations in explicit solvent. It does not use a predefined reaction coordinat

SUBMITTER: Noe F 

PROVIDER: S-EPMC2772816 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature