Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction.

ABSTRACT: The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the "simple" case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently capt

SUBMITTER: Das P 

PROVIDER: S-EPMC1502548 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature