Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulations.

ABSTRACT: Characterization of the folding transition-state ensemble and the denatured-state ensemble is an important step toward a full elucidation of protein folding mechanisms. We report herein an investigation of the free-energy landscape of FSD-1 protein by a total of four sets of folding and unfolding molecular dynamics simulations with explicit solvent. The transition-state ensemble was initially identified from unfolding simulations at 500 K and was verified by simulations at 300 K starting from the ensemble structures. The denatured-state ensemble and the early-stage folding were studied by a combination of unfolding simulations at 500 K and folding simulations at 300 K starting from the extended conformation. A common feature of the transition-state ensemble was the substantial formation of

SUBMITTER: Lei H 

PROVIDER: S-EPMC3382983 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature