期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 110, 期 44, 页码 17880-17885出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1317105110
关键词
stochastic kinetics; funneled energy landscape; Ising-like model; statistical mechanics
资金
- Intramural Research Program of the National Institutes of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health
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.
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