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Full-Text Articles in Physics
Optimization Of Electrostatic Interactions In Protein-Protein Complexes, Kelly Brock, Kemper Talley, Kacey Coley, Petras Kundrotas, Emil Alexov
Optimization Of Electrostatic Interactions In Protein-Protein Complexes, Kelly Brock, Kemper Talley, Kacey Coley, Petras Kundrotas, Emil Alexov
Publications
In this article, we present a statistical analysis of the electrostatic properties of 298 protein-protein complexes and 356 domain-domain structures extracted from the previously developed database of protein complexes (ProtCom, http://www.ces.clemson.edu/compbio/protcom). For each structure in the dataset we calculated the total electrostatic energy of the binding and its two components, Coulombic and reaction field energy. It was found that in a vast majority of the cases (>90%), the total electrostatic component of the binding energy was unfavorable. At the same time, the Coulombic component of the binding energy was found to favor the complex formation while …
Poisson-Boltzmann Calculations Of Nonspecific Salt Effects On Protein-Protein Binding Free Energies, Claudia Bertonati, Barry Honig, Emil Alexov
Poisson-Boltzmann Calculations Of Nonspecific Salt Effects On Protein-Protein Binding Free Energies, Claudia Bertonati, Barry Honig, Emil Alexov
Publications
The salt dependence of the binding free energy of five protein-protein hetero-dimers and two homo-dimers/tetramers was calculated from numerical solutions to the Poisson-Boltzmann equation. Overall, the agreement with experimental values is very good. In all cases except one involving the highly charged lactoglobulin homo-dimer, increasing the salt concentration is found both experimentally and theoretically to decrease the binding affinity. To clarify the source of salt effects, the salt-dependent free energy of binding is partitioned into screening terms and to self-energy terms that involve the interaction of the charge distribution of a monomer with its own ion atmosphere. In six of …