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

被引：77

作者：

Henry, Eric R. ^{[1
]}

Best, Robert B. ^{[1
]}

Eaton, William A. ^{[1
]}

机构：

[1] NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2013年 / 110卷 / 44期

基金：

美国国家卫生研究院;

关键词：

stochastic kinetics; funneled energy landscape; Ising-like model; statistical mechanics; TRANSITION PATH TIMES; ENERGY LANDSCAPE; MICROSCOPIC THEORY; KINETICS; RATES; MECHANISMS; PHYSICS; HELIX; THERMODYNAMICS; COOPERATIVITY;

D O I：

10.1073/pnas.1317105110

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：17880 / 17885

页数：6

共 64 条

[1] Analyses of simulations of three-dimensional lattice proteins in comparison with a simplified statistical mechanical model of protein folding [J].