Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

ABSTRACT: To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and

SUBMITTER: Zhou R 

PROVIDER: S-EPMC4280612 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature