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Pairwise calculation of protein solvent-accessible surface areas

Street, Arthur G. and Mayo, Stephen L. (1998) Pairwise calculation of protein solvent-accessible surface areas. Folding and Design, 3 (4). pp. 253-258. ISSN 1359-0278. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160423998

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Abstract

Background: The tractability of many algorithms for determining the energy state of a system depends on the pairwise nature of an energy expression. Some energy terms, such as the standard implementation of the van der Waals potential, satisfy this criterion whereas others do not. One class of important potentials that are not pairwise involves benefits and penalties for burying hydrophobic and/or polar surface areas. It has been found previously that, in some cases, a pairwise approximation to these surface areas correlates with the true surface areas. We set out to generalize the applicability of this approximation. Results: We develop a pairwise expression with one scalable parameter that closely reproduces both the true buried and the true exposed solvent- accessible surface areas. We then refit our previously published coiled-coil stability data to give solvation parameters of 26 cal/mol Å^2 favoring hydrophobic burial and 100 cal/mol Å^2 opposing polar burial. Conclusions: An accurate pairwise approximation to calculate exposed and buried protein solvent-accessible surface area is achieved.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1016/S1359-0278(98)00036-4 DOIUNSPECIFIED
http://www.sciencedirect.com/science/article/pii/S1359027898000364PublisherUNSPECIFIED
Additional Information:© 1998 Current Biology Ltd. Received: 12 January 1998; Revisions requested: 16 February 1998; Revisions received: 16 March 1998; Accepted: 23 March 1998; Published: 03 June 1998. Available online 2 July 2005. We thank D.B. Gordon and B.I. Dahiyat for helpful discussions and assistance. This work was supported by the Rita Allen Foundation, the David and Lucile Packard Foundation and the Searle Scholars Program/The Chicago Community Trust. A.G.S. is partially supported by the Eleanor Sophia Wood Travelling Scholarship from the University of Sydney, Australia.
Funders:
Funding AgencyGrant Number
Rita Allen FoundationUNSPECIFIED
David and Lucile Packard FoundationUNSPECIFIED
Searle Scholars Program/Chicago Community TrustUNSPECIFIED
Eleanor Sophia Wood Traveling Scholarship from University of Sydney, AustraliaUNSPECIFIED
Subject Keywords:Surface Properties; Databases: Factual; Algorithms; Solvents; Proteins; dead-end elimination; hydrophobic burial; pairwise surface area; protein design; solvent-accessible surface area
Record Number:CaltechAUTHORS:20110620-160423998
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20110620-160423998
Official Citation:Arthur G. Street, Stephen L. Mayo, Pairwise calculation of protein solvent-accessible surface areas, Folding and Design, Volume 3, Issue 4, August 1998, Pages 253-258, ISSN 1359-0278, 10.1016/S1359-0278(98)00036-4.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:24079
Collection:CaltechAUTHORS
Deposited By: Marie Ary
Deposited On:03 Oct 2011 22:32
Last Modified:03 Oct 2011 22:32

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