PAIRWISE CALCULATION OF PROTEIN SOLVENT-ACCESSIBLE SURFACE-AREAS

Background: The tractability of many algorithms for determining the en ergy state of a system depends on the pairwise nature of an energy exp ression. 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 ben efits and penalties for burying hydrophobic and/or polar surface areas , it has been found previously that, in some cases, a pairwise approxi mation to these surface areas correlates with the true surface areas. We set out to generalize the applicability of this approximation. Resu lts: 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 coile d-coil stability data to give solvation parameters of 26 cal/mol Angst rom(2) favoring hydrophobic burial and 100 cal/mol Angstrom(2) opposin g polar burial. Conclusions: An accurate pairwise approximation to cal culate exposed and buried protein solvent-accessible surface area is a chieved.