Towards coarse-grained modeling of proteins

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DOIResolve DOI: http://doi.org/10.5488/CMP.10.3.441
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TypeArticle
Journal titleCondensed Matter Physics
ISSN1607-324X
Volume10
Issue3(51)
Pages441457; # of pages: 17
Subjectprotein dynamics; conformational changes; theory and modelling; projection operator; principal component analysis
AbstractThis paper introduces a basic theoretical background to the description of conformational dynamics of proteins through a system of interacting domains. The essential collective degrees of freedom derived by principal component analysis of a molecular dynamics trajectory are used as dynamic variables defining the projection operator technique that underlies the formalism suggested. The explicit form of the corresponding projection operator is obtained, and the projection method is employed to derive systems of coupled generalized Langevin equations for both individual atomic degrees of freedom and essential collective degrees of freedom in a protein. A definition of correlated domains in proteins is introduced based on the analysis of the essential dynamics. Examples of identification of such domains are presented. A system of coupled generalized Langevin equations is derived representing the protein through a few interacting domains embedded into a dissipative medium. Further developments and potential applications of the formalism are outlined.
Publication date
LanguageEnglish
AffiliationNRC National Institute for Nanotechnology; National Research Council Canada
Peer reviewedYes
NRC number481
NPARC number8926185
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Record identifier3c54bcf4-ca86-481a-abb4-a720f408b790
Record created2009-04-23
Record modified2016-05-09
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