Sparsely populated folding intermediates of the Fyn SH3 domain: matching native-centric essential dynamics and experiment.

ABSTRACT: A complete description of how a protein folds requires the characterization of intermediate conformations traversed during the folding transition. We have calculated dynamics trajectories of a simplified model of the Fyn SH3 domain with a native-centric potential energy function. Analysis of the resulting site-resolved energy trajectory identifies an ensemble of intermediate conformations for folding and another for unfolding. The model's folding intermediate is structured in the three beta-strands that make up the protein's core and is strikingly similar to intermediates detected in a recent NMR study of Fyn SH3 folding and to folding transition states elucidated in mutagenesis studies of SH3 domains. The unfolding intermediate is formed by dissociation of the folded protein's two termina

SUBMITTER: Ollerenshaw JE 

PROVIDER: S-EPMC522025 | biostudies-literature | 2004 Oct

REPOSITORIES: biostudies-literature