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 A2 favoring hydrophobic burial and 100 cal/mol A2 opposing polar burial.


CONCLUSIONS
An accurate pairwise approximation to calculate exposed and buried protein solvent-accessible surface area is achieved.
Street
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AG
Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena 91125, USA.
Mayo
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SL
D000465:Algorithms; D016208:Databases, Factual; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013499:Surface Properties
D011506:Proteins; D012997:Solvents