P versus Q: structural reaction coordinates capture protein folding on smooth landscapes.

ABSTRACT: Minding your p's and q's has become as important to protein-folding theorists as it is for those being instructed in the rules of etiquette. To assess the quality of structural reaction coordinates in predicting the transition-state ensemble (TSE) of protein folding, we benchmarked the accuracy of four structural reaction coordinates against the kinetic measure P(fold), whose value of 0.50 defines the stochastic separatrix for a two-state folding mechanism. For two proteins that fold by a simple two-state mechanism, c-src SH3 and CI-2, the Phi-values of the TSEs predicted by native topology-based reaction coordinates (including Q, the fraction of native contacts) are almost identical to those of the TSE based on P(fold), with correlation coefficients of >0.90. For proteins with complex fol

SUBMITTER: Cho SS 

PROVIDER: S-EPMC1334664 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature