Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

ABSTRACT: We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent using the Amberff99SB force field. Replica-exchange molecular dynamics simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states at two densities. The obtained ensembles are shown to reach equilibrium in the 1 mus/replica timescale. The total simulation time used in the calculations exceeds 100 mus. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, DeltaG(P, T), over the whole region of t

SUBMITTER: Day R 

PROVIDER: S-EPMC3534748 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature