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Molecular simulation of the reversible mechanical unfolding of proteins

J. Chem. Phys. 120, 5781 (2004); doi:10.1063/1.1649314

Issue Date: 22 March 2004

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Nitin Rathore, Qiliang Yan, and Juan J. de Pablo
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706
In this work we have combined a Wang–Landau sampling scheme [F. Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformation of proteins. Comparisons are made with analytical results for simple model systems such as harmonic springs and Rouse chains. The method is then illustrated on a model 15-residue alanine molecule in an implicit solvent. Results for mechanical unfolding of this oligopeptide are compared to those of steered molecular dynamics calculations. ©2004 American Institute of Physics.
History: Received 25 November 2003; accepted 23 December 2003
Permalink: http://link.aip.org/link/?JCPSA6/120/5781/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.La
    Mechanical properties of biomolecules
  • 31.15.Qg
    Molecular dynamics and other numerical methods (atoms and molecules)
  • 36.20.Fz
    Macromolecular constitution (chains and sequences)
  • 36.20.Ey
    Macromolecular conformation (statistics and dynamics)
  • 82.37.Rs
    Single molecule manipulation of proteins and other biological molecules (chemical kinetics)
  • 87.14.Ee
    Proteins
  • 87.15.Aa
    Theory and modeling in molecular biophysics; computer simulation
  • 87.15.Cc
    Folding and sequence analysis of biomolecules
  • 87.15.He
    Biomolecular dynamics and conformational changes
  • 34.20.Gj
    Intermolecular and atom–molecule potentials and forces
  • YEAR: 2004

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PUBLICATION DATA

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