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Published online before print March 9, 2004, 10.1110/ps.03486104
Protein Science (2004), 13:925-936. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Energy functions for protein design I: Efficient and accurate continuum electrostatics and solvation

Navin Pokala and Tracy M. Handel

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-3206, USA

(RECEIVED October 21, 2003; FINAL REVISION January 3, 2004; ACCEPTED January 9, 2004)



Abstract

Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition. Because these energies are difficult to compute quickly and accurately, they are often ignored or modeled very crudely in computational protein design. To address this problem, we have developed a simple, fast, and accurate approximation for calculating Born radii in the context of protein design calculations. When these approximate Born radii are used with the generalized Born continuum dielectric model, energies calculated by the 106-fold slower finite difference Poisson-Boltzmann model are faithfully reproduced. A similar approach can be used for estimating solvent-accessible surface areas (SASAs). As an independent test, we show that these approximations can be used to accurately predict the experimentally determined pKas of >200 ionizable groups from 15 proteins.

Keywords: protein design; electrostatics; solvation; pKa; generalized Born; solvent-accessible surface area calculation; EGAD

Abbreviations: FDPB, finite-difference Poisson-Boltzmann • MTK, modified Tanford-Kirkwood • GB, generalized Born • SASA, solvent-accessible surface area

Reprint requests to: Navin Pokala or Tracy M. Handel, Department of Molecular and Cell Biology, University of California, Berkeley, 237 Hilde-brand Hall, Berkeley, CA 94720-3206, USA; e-mail: navin{at}annapurna.berkeley.edu or handel{at}annapurna.berkeley.edu; fax: (510) 643-9321.

Supplemental material: see www.proteinscience.org

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03486104.


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