Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies

Coarse-grained features of macromolecular assemblies are understood via a set of order parameters (OPs) constructed in terms of their all-atom configuration. OPs are shown to be slowly changing in time and capture the large-scale spatial features of macromolecular assemblies. The relationship of the...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2012-07, Vol.116 (29), p.8423-8434
Main Authors: Singharoy, Abhishek, Joshi, Harshad, Miao, Yinglong, Ortoleva, Peter J
Format: Article
Language:English
Subjects:
Assemblies
Broken symmetry
Bromovirus - chemistry
Capsid - chemistry
Dynamics
Environment
Macromolecular Substances - chemistry
Mathematical analysis
Molecular Dynamics Simulation
Order parameters
RNA, Viral - chemistry
Simulation
Tobacco mosaic satellite virus - chemistry
Warpage
Warping
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Summary:Coarse-grained features of macromolecular assemblies are understood via a set of order parameters (OPs) constructed in terms of their all-atom configuration. OPs are shown to be slowly changing in time and capture the large-scale spatial features of macromolecular assemblies. The relationship of these variables to the classic notion of OPs based on symmetry breaking phase transitions is discussed. OPs based on space warping transformations are analyzed in detail as they naturally provide a connection between overall structure of an assembly and all-atom configuration. These OPs serve as the basis of a multiscale analysis that yields Langevin equations for OP dynamics. In this context, the characteristics of OPs and PCA modes are compared. The OPs enable efficient all-atom multiscale simulations of the dynamics of macromolecular assemblies in response to changes in microenvironmental conditions, as demonstrated on the structural transitions of cowpea chlorotic mottle virus capsid (CCMV) and RNA of the satellite tobacco mosaic virus (STMV).
ISSN:1520-6106
1520-5207
DOI:10.1021/jp2119247