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Backbone and side-chain ordering in a small protein

J. Chem. Phys. 128, 025105 (2008); doi:10.1063/1.2819679

Published 14 January 2008

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Yanjie Wei
Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA

Walter Nadler and Ulrich H. E. Hansmann
Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA and John-von-Neumann Institute for Computing, Forschungszentrum Jülich, D-52425 Jülich, Germany
We investigate the relation between backbone and side-chain ordering in a small protein. For this purpose, we have performed multicanonical simulations of the villin headpiece subdomain HP-36, an often used toy model in protein studies. Concepts of circular statistics are introduced to analyze side-chain fluctuations. In contrast to earlier studies on homopolypeptides [Wei et al., J. Phys. Chem. B 111, 4244 (2007)], we do not find collective effects leading to a separate transition. Rather, side-chain ordering is spread over a wide temperature range. Our results indicate a thermal hierarchy of ordering events, with side-chain ordering appearing at temperatures below the helix-coil transition but above the folding transition. We conjecture that this thermal hierarchy reflects an underlying temporal order, and that side-chain ordering facilitates the search for the correct backbone topology. ©2008 American Institute of Physics
History: Received 24 September 2007; accepted 7 November 2007; published 14 January 2008
Permalink: http://link.aip.org/link/?JCPSA6/128/025105/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.Cc
    Folding of biomolecules: thermodynamics, statistical mechanics, models and pathways
  • 87.15.Ya
    Fluctuations (molecular biophysics)
  • 87.15.B-
    Structure of biomolecules
  • YEAR: 2008

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PUBLICATION DATA

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