title: Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.
abstract: Advances in computing have enabled microsecond all-atom molecular dynamics trajectories of protein folding that can be used to compare with and test critical assumptions of theoretical models. We show that recent simulations by the Shaw group (10, 11, 14, 15) are consistent with a key assumption of an Ising-like theoretical model that native structure grows in only a few regions of the amino acid sequence as folding progresses. The distribution of mechanisms predicted by simulating the master equation of this native-centric model for the benchmark villin subdomain, with only two adjustable thermodynamic parameters and one temperature-dependent kinetic parameter, is remarkably similar to the distribution in the molecular dynamics trajectories.
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520.
authors.forename: Eric R
authors.initials: ER
authors.lastname: Henry
authors.forename: Robert B
authors.initials: RB
authors.lastname: Best
authors.forename: William A
authors.initials: WA
authors.lastname: Eaton
mesh_terms: D007700:Kinetics; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D017510:Protein Folding
keywords: Ising-like model; funneled energy landscape; statistical mechanics; stochastic kinetics