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Journal of Chemical Physics / Volume 118 / Issue 18 / ARTICLES / Polymers, Biopolymers, and Complex Systems

J. Chem. Phys. 118, 8500 (2003); http://dx.doi.org/10.1063/1.1565106 (13 pages)

Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach

Michael P. Eastwood1, Corey Hardin2, Zaida Luthey-Schulten2, and Peter G. Wolynes1

1Department of Chemistry and Biochemistry, University of California, La Jolla, California 92093-0371
2Department of Chemistry, University of Illinois, Urbana, Illinois 61801

(Received 16 December 2002; accepted 10 February 2003)

We investigate the use of a Mayer cluster expansion to quantify changes to the energy landscape of an ab initio protein structure prediction Hamiltonian as side-chain excluded volume radii are increased. The expansion is generalized so that the effect of other changes in the Hamiltonian, which would alone be best treated with a cumulant expansion, can be evaluated simultaneously. The effect of changing the excluded volume radii on various thermodynamic quantities, in particular the free energy and glass transition temperature, is calculated with the expansion and compared to results from simulation. The expansion is found to be sufficiently accurate at the second-order level to be useful for calculating values of the excluded volume radii that refine the energy landscape for structure prediction. This is explicitly checked by a free energy profile analysis and examining the quality of predictions before and after the optimization. A useful method to test whether equilibrium has been attained during molecular dynamics sampling is also described. © 2003 American Institute of Physics.

© 2003 American Institute of Physics

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KEYWORDS and PACS

Keywords

proteins, molecular biophysics, ab initio calculations, molecular configurations, thermodynamic properties, free energy, glass transition, statistical mechanics

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.1565106

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.
    M. P. Eastwood, C. Hardin, Z. Luthey-Schulten, and P. G. Wolynes, J. Chem. Phys. 117, 4602 (2002)JCPSA6000117000009004602000001.

    J. M. Deutsch and T. Kurosky, Phys. Rev. E 56, 4553 (1997).

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    W. G. McMillan and J. E. Mayer, J. Chem. Phys. 13, 276 (1945)JCPSA6000013000007000276000001.

    H. C. Andersen, J. D. Weeks, and D. Chandler, Phys. Rev. A 4, 1597 (1971).

    R. W. Zwanzig, J. Chem. Phys. 22, 1420 (1954)JCPSA6000022000008001420000001.

    A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).

    X. Kong and C. L. Brooks III, J. Chem. Phys. 105, 2414 (1996)JCPSA6000105000006002414000001.


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