Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation

被引:15
|
作者
Miao, Yinglong [1 ]
Ortoleva, Peter J. [1 ]
机构
[1] Indiana Univ, Dept Chem, Ctr Cell & Virus Theory, Bloomington, IN 47405 USA
关键词
structural transition mechanisms; all-atom multiscale; molecular dynamics/order parameter extrapolation (MD/OPX); cowpea chlorotic mottle virus (CCMV); symmetry-breaking; local initiation; front propagation; FOKKER-PLANCK EQUATION; CHLOROTIC MOTTLE VIRUS; BROWNIAN PARTICLES; PROTEIN DYNAMICS; CELL ENTRY; MATURATION; POLIOVIRUS; FRICTION; FLEXIBILITY; SCATTERING;
D O I
10.1002/bip.21299
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
On the basis of an all-atom multiscale analysis theory of nanosystem dynamics, a multiscale molecular dynamics/order parameter extrapolation (MD/OPX) approach has recently been developed. It accelerates MD for long-time simulation of large bionanosystems and addresses rapid atomistic fluctuations and slowly varying coherent dynamics simultaneously. In this study, MD/OPX is optimized and implemented to simulate viral capsid structural transitions. Specifically, 200 ns MD/OPX simulation of the swollen state of cowpea chlorotic mottle virus capsid reveals that it undergoes significant energy-driven shrinkage in vacuum, which is a symmetry-breaking process involving local initiation and front propagation. (C) 2009 Wiley Periodicals, Inc. Biopolymers 93:61-73, 2010.
引用
收藏
页码:61 / 73
页数:13
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