Identification of dynamic structural domains in proteins, analysis of local bond flexibility and application for interpretation of NMR experiments

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DOIResolve DOI: http://doi.org/10.1080/08927020903260843
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TypeArticle
Journal titleMolecular Simulation
ISSN0892-7022
Volume37
Issue8
Pages729732; # of pages: 4
SubjectCharacterisation; Coarse Graining; Covariance analysis; Drug Design; interpretation of NMR measurements; Langevin dynamics; Langevin equation; Local flexibility; Molecular dynamics trajectories; Multi-scale approaches; Multi-scale modelling; Prion protein; Projection Operator; Protein G; Stable region; Structural biology; Structural domains; Bioinformatics; Differential equations; Experiments; Mathematical operators; Molecular dynamics; Nuclear magnetic resonance spectroscopy; Proteins; Structural analysis
AbstractA novel theoretical methodology is described that allows the identification of dynamic structural domains and the analysis of local flexibility in proteins. The methodology employs a multiscale approach that combines definition of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates and analysis of the corresponding generalised Langevin equations. The domains are associated with relatively stable regions in the protein, whereas off-domain regions are relatively soft. The applications include the domain coarse-graining and characterisation of the local flexibility in protein G and prion proteins. The results are compared with published NMR experiments. The methodology is apt to provide rigorous dynamic scores and characterisation tools for structural biology, bioinformatics and rational drug design. © 2011 Taylor & Francis.
Publication date
LanguageEnglish
AffiliationNational Research Council Canada (NRC-CNRC); National Institute for Nanotechnology (NINT-INNT)
Peer reviewedYes
NPARC number21271562
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Record identifiera2448a89-4598-4432-97d7-aa1abbad93de
Record created2014-03-24
Record modified2016-05-09
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