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Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin

J. Chem. Phys. 128, 205104 (2008); doi:10.1063/1.2928634

Published 23 May 2008

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Swarnendu Tripathi and John J. Portman
Department of Physics, Kent State University, Kent, Ohio 44240, USA
The key to understand a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility, and function of the N-terminal calmodulin domain (nCaM). In this model, two energy basins corresponding to the “closed” apo conformation and “open” holo conformation of nCaM are coupled by a uniform interpolation parameter. The resulting detailed transition route from our model is largely consistent with the recently proposed EFbeta-scaffold mechanism in EF-hand family proteins. We find that the N-terminal parts of the calcium binding loops shows higher flexibility than the C-terminal parts which form this EFbeta-scaffold structure. The structural transition of binding loops I and II are compared in detail. Our model predicts that binding loop II, with higher flexibility and earlier structural change than binding loop I, dominates the open/closed conformational transition in nCaM. ©2008 American Institute of Physics
History: Received 7 January 2008; accepted 23 April 2008; published 23 May 2008
Permalink: http://link.aip.org/link/?JCPSA6/128/205104/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.hp
    Conformational changes of biomolecules
  • 87.14.E-
    Proteins
  • 36.20.Ey
    Macromolecular conformation (statistics and dynamics)
  • 87.15.B-
    Structure of biomolecules
  • 02.60.Ed
    Interpolation; curve fitting
  • YEAR: 2008

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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