The energy landscape, folding pathways and the kinetics of a knotted protein.

ABSTRACT: The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N or C terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N terminus portion of the knot and a rate-determining step where the C terminus is incorporated. The low-lying minima with the N termi

SUBMITTER: Prentiss MC 

PROVIDER: S-EPMC2895632 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature