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Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17880-5. doi: 10.1073/pnas.1317105110. Epub 2013 Oct 15.

Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.

Author information

1
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520.

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.

KEYWORDS:

Ising-like model; funneled energy landscape; statistical mechanics; stochastic kinetics

PMID:
24128764
PMCID:
PMC3816406
DOI:
10.1073/pnas.1317105110
[Indexed for MEDLINE]
Free PMC Article
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