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Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306; and Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104
Correspondence: Address reprint requests to Huan-Xiang Zhou, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306. Tel.: 850-644-7052; Fax: 850-644-0098; E-mail: hxzhou{at}csit.fsu.edu.
The contributions of electrostatic interactions to the binding stability of barnase and barstar were studied by the Poisson-Boltzmann model with three different protocols: a), the dielectric boundary specified as the van der Waals (vdW) surface of the protein along with a protein dielectric constant (
p) of 4; b), the dielectric boundary specified as the molecular (i.e., solvent-exclusion (SE)) surface along with p = 4; and c), "SE + p = 20." The "vdW + p = 4" and "SE + p = 20" protocols predicted an overall electrostatic stabilization whereas the "SE + p = 4" protocol predicted an overall electrostatic destabilization. The "vdW + p = 4" protocol was most consistent with experiment. It quantitatively reproduced the observed effects of 17 mutations neutralizing charged residues lining the binding interface and the measured coupling energies of six charge pairs across the interface and reasonably rationalized the experimental ionic strength and pH dependences of the binding constant. In contrast, the "SE + p = 4" protocol predicted significantly larger coupling energies of charge pairs whereas the "SE + p = 20" protocol did not predict any pH dependence. This study calls for further scrutiny of the different Poisson-Boltzmann protocols and demonstrates potential danger in drawing conclusions on electrostatic contributions based on a particular calculation protocol.
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