Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulation |
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Authors: | Yinglong Miao Peter J Ortoleva |
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Institution: | Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405 |
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Abstract: | 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. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 61–73, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com |
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Keywords: | structural transition mechanisms all‐atom multiscale molecular dynamics/order parameter extrapolation (MD/OPX) cowpea chlorotic mottle virus (CCMV) symmetry‐breaking local initiation front propagation |
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