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Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology

Lezon, TR and Bahar, I (2010) Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology. PLoS Computational Biology, 6 (6). 1 - 12. ISSN 1553-734X

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Abstract

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics. © 2010 Lezon, Bahar.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Lezon, TRlezon@pitt.eduLEZON
Bahar, Ibahar@pitt.eduBAHAR
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorDunbrack, Roland L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 1 June 2010
Date Type: Publication
Journal or Publication Title: PLoS Computational Biology
Volume: 6
Number: 6
Page Range: 1 - 12
DOI or Unique Handle: 10.1371/journal.pcbi.1000816
Schools and Programs: School of Medicine > Computational Biology
Refereed: Yes
ISSN: 1553-734X
MeSH Headings: Algorithms; Computational Biology--methods; Databases, Protein; Entropy; Hydrogen Bonding; Molecular Dynamics Simulation; Normal Distribution; Nuclear Magnetic Resonance, Biomolecular--methods; Protein Conformation; Proteins--chemistry; Proteins--metabolism
Other ID: NLM PMC2887458
PubMed Central ID: PMC2887458
PubMed ID: 20585542
Date Deposited: 03 Aug 2012 21:01
Last Modified: 02 Feb 2019 16:58
URI: http://d-scholarship.pitt.edu/id/eprint/13379

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