title: Effect of interprotein polarization on protein-protein binding energy.
abstract: Molecular dynamics simulation in explicit water for the binding of the benchmark barnase-barstar complex was carried out to investigate the effect polarization of interprotein hydrogen bonds on its binding free energy. Our study is based on the AMBER force field but with polarized atomic charges derived from fragment quantum mechanical calculation for the protein complex. The quantum-derived atomic charges include the effect of polarization of interprotein hydrogen bonds, which was absent in the standard force fields that were used in previous theoretical calculations of barnase-barstar binding energy. This study shows that this polarization effect impacts both the static (electronic) and dynamic interprotein electrostatic interactions and significantly lowers the free energy of the barnase-barstar complex.
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.
authors.forename: Chang G
authors.initials: CG
authors.lastname: Ji
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
mesh_terms: D001407:Bacillus / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011789:Quantum Theory; D012260:Ribonucleases / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D014867:Water; C057438:barstar protein, Bacillus amyloliquefaciens; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease