Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Go model.

ABSTRACT: We study the folding thermodynamics and kinetics of the Pin1 WW domain, a three-stranded beta-sheet protein, by using all-atom (except nonpolar hydrogens) discontinuous molecular dynamics simulations at various temperatures with a Gō model. The protein exhibits a two-state folding kinetics near the folding transition temperature. A good agreement between our simulations and the experimental measurements by the Gruebele group has been found, and the simulation sheds new insights into the structure of transition state, which is hard to be straightforwardly captured in experiments. The simulation also reveals that the folding pathways at approximately the transition temperature and at low temperatures are much different, and an intermediate state at a low temperature is predicted. The transit

SUBMITTER: Luo Z 

PROVIDER: S-EPMC1959547 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature