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Journal of Chemical Physics / Volume 135 / Issue 23 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 135, 235105 (2011); http://dx.doi.org/10.1063/1.3670106 (10 pages)

Transition network based on equilibrium sampling: A new method for extracting kinetic information from Monte Carlo simulations of protein folding

Konstantin V. Klenin1 and Wolfgang Wenzel2

1Steinbuch Center for Computing, Karlsruhe Institute of Technology, P.O. Box 3640, D-76021 Karlsruhe, Germany
2Institute of Nanotechnology, Karlsruhe Institute of Technology, P.O. Box 3640, D-76021 Karlsruhe, Germany

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(Received 29 June 2011; accepted 28 November 2011; published online 21 December 2011)

We propose a new type of transition network for modeling of protein dynamics. The nodes of the network correspond to the conformations taken from random sampling of equilibrium ensemble available, e.g., by Monte Carlo simulations. Although this approach does not provide absolute values of folding/unfolding rates, it allows identification of reaction pathways, transition state ensemble, and, eventually, intermediates. The new method is verified by a comparison with direct molecular dynamic simulations performed for a coarse-grained Gō-like model of proteins. As an illustrative example, we analyze kinetics of formation of a small β-hairpin (Trp zipper 1) in the all-atom representation.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. METHODS
    1. Transition network based on random sampling of an equilibrium ensemble
    2. Molecular dynamics simulations
    3. Monte Carlo simulations
  3. RESULTS
    1. Verification for a one-dimensional system
    2. Simple multidimensional model system
    3. Comparison with molecular dynamics simulations
    4. Example of a non-two-state system
    5. Application to a β-hairpin
  4. DISCUSSION
  5. CONCLUSIONS

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KEYWORDS and PACS

Keywords

biochemistry, molecular biophysics, molecular configurations, molecular dynamics method, Monte Carlo methods, phase transformations, proteins, reaction kinetics theory

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3670106

PUBLICATION DATA

ISSN

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

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
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    F. Noé, I. Horenko, C. Schütte, and J. C. Smith, J. Chem. Phys. 126, 155102 (2007)JCPSA6000126000015155102000001.

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    K. V. Klenin and J. Langowski, J. Chem. Phys. 121, 4951 (2004)JCPSA6000121000010004951000001.

    J. W. Pitera, I. Haque, and W. C. Swope, J. Chem. Phys. 124, 141102 (2006)JCPSA6000124000014141102000001.


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