Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates.

ABSTRACT: A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce minor structural cooperativity are included in the interaction potential. In general, the cooperative folding routes have sharper interfaces between folded and unfolded regions of the folding nucleus and higher free energy barriers. The calculated free energy barriers are strongly correlated with native topology as characterized by contact order. Increasing the rigidity of the folding nucleus changes the local structure of the transition state ensemble nonuniformly across the set of proteins studied. Nevertheless, the calculated prefactors k(0) are foun

SUBMITTER: Qi X 

PROVIDER: S-EPMC1891811 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature