title: Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar.
abstract: 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 (epsilon (p)) of 4; b), the dielectric boundary specified as the molecular (i.e., solvent-exclusion (SE)) surface along with epsilon (p) = 4; and c), "SE + epsilon (p) = 20." The "vdW + epsilon (p) = 4" and "SE + epsilon (p) = 20" protocols predicted an overall electrostatic stabilization whereas the "SE + epsilon (p) = 4" protocol predicted an overall electrostatic destabilization. The "vdW + epsilon (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 + epsilon (p) = 4" protocol predicted significantly larger coupling energies of charge pairs whereas the "SE + epsilon (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.
authors.affiliation: Department of Physics, Florida State University, Tallahassee, Florida 32306, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Dong
authors.forename: M
authors.initials: M
authors.lastname: Vijayakumar
authors.forename: Huan-Xiang
authors.initials: HX
authors.lastname: Zhou
mesh_terms: D001426:Bacterial Proteins; D001665:Binding Sites; D003198:Computer Simulation; D004563:Electrochemistry / Q000379:methods*; D004735:Energy Transfer; D004789:Enzyme Activation; D004795:Enzyme Stability; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D046911:Macromolecular Substances; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D021122:Protein Subunits; D011506:Proteins / Q000737:chemistry*; D012260:Ribonucleases / Q000737:chemistry*; D055672:Static Electricity; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D046911:Macromolecular Substances; D021122:Protein Subunits; D011506:Proteins; C057438:barstar protein, Bacillus amyloliquefaciens; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease