Space warping order parameters and symmetry: Application to multiscale simulation of macromolecular assemblies

Abhishek Singharoy, Harshad Joshi, Yinglong Miao, Peter J. Ortoleva

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

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).

Original languageEnglish (US)
Pages (from-to)8423-8434
Number of pages12
JournalJournal of Physical Chemistry B
Volume116
Issue number29
DOIs
StatePublished - Jul 26 2012
Externally publishedYes

Fingerprint

Tobacco mosaic satellite virus
Bromovirus
Passive Cutaneous Anaphylaxis
Capsid
Phase Transition
assemblies
RNA
symmetry
Viruses
Atoms
Satellite RNAs
simulation
Tobacco
viruses
Phase transitions
Satellites
atoms
tobacco
configurations
broken symmetry

ASJC Scopus subject areas

  • Surfaces, Coatings and Films
  • Physical and Theoretical Chemistry
  • Materials Chemistry

Cite this

Space warping order parameters and symmetry : Application to multiscale simulation of macromolecular assemblies. / Singharoy, Abhishek; Joshi, Harshad; Miao, Yinglong; Ortoleva, Peter J.

In: Journal of Physical Chemistry B, Vol. 116, No. 29, 26.07.2012, p. 8423-8434.

Research output: Contribution to journalArticle

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