Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations.

ABSTRACT: Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 micros) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding

SUBMITTER: Lei H 

PROVIDER: S-EPMC2671663 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature