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Published August 1998 | public
Journal Article

Pairwise calculation of protein solvent-accessible surface areas


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.

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.

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