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Journal of Chemical Physics / Volume 132 / Issue 24 / ARTICLES / Theoretical Methods and Algorithms

J. Chem. Phys. 132, 244101 (2010); http://dx.doi.org/10.1063/1.3435332 (16 pages)

Enhanced sampling and applications in protein folding in explicit solvent

Cheng Zhang1 and Jianpeng Ma1,2

1Department of Bioengineering and Applied Physics Program, Rice University Houston, Texas 77005, USA
2Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125 Houston, Texas 77030, USA

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(Received 1 March 2010; accepted 5 May 2010; published online 22 June 2010)

We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous temperature-space random walk. We first validated the method in a two-dimensional Ising model and a Lennard-Jones liquid system. It was then applied to folding of three small proteins, trpzip2, trp-cage, and villin headpiece in explicit solvent. Within 0.5 ∼ 1 microsecond, all three systems were reversibly folded into atomic accuracy: the alpha carbon root mean square deviations of the best folded conformations from the native states were 0.2, 0.4, and 0.4 Å, for trpzip2, trp-cage, and villin headpiece, respectively.

© 2010 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. METHOD
    1. Brief outline of implementation
    2. Generalized ensemble with a continuous temperature
    3. Unbiased estimate of a partition function
    4. Estimators based on integral identities
    5. Adaptive averaging
  3. NUMERICAL RESULTS
    1. Ising model
    2. Lennard-Jones system
  4. APPLICATIONS IN FOLDING SMALL PROTEINS
    1. Trpzip-2
    2. Trp-cage
    3. Villin headpiece
  5. CONCLUDING DISCUSSIONS

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KEYWORDS and PACS

Keywords

biochemistry, molecular biophysics, molecular configurations, proteins

PACS

  • 87.15.Cc

    Folding: thermodynamics, statistical mechanics, models, and pathways

  • 87.15.kr

    Protein-solvent interactions

  • 87.15.B-

    Structure of biomolecules

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3435332

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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