On the electrostatic component of protein-protein binding free energy
1 Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
2 James Byrnes High School, Duncan, SC 29334, USA
3 South Carolina Governor School for Science and Mathematics, Hartsville, SC 29550, USA
4 Center for Bioinformatics, The University of Kansas, Lawrence, KS 66047, USA
PMC Biophysics 2008, 1:2 doi:10.1186/1757-5036-1-2Published: 5 November 2008
Calculations of electrostatic properties of protein-protein complexes are usually done within framework of a model with a certain set of parameters. In this paper we present a comprehensive statistical analysis of the sensitivity of the electrostatic component of binding free energy (ΔΔGel) with respect with different force fields (Charmm, Amber, and OPLS), different values of the internal dielectric constant, and different presentations of molecular surface (different values of the probe radius). The study was done using the largest so far set of entries comprising 260 hetero and 2148 homo protein-protein complexes extracted from a previously developed database of protein complexes (ProtCom). To test the sensitivity of the energy calculations with respect to the structural details, all structures were energy minimized with corresponding force field, and the energies were recalculated. The results indicate that the absolute value of the electrostatic component of the binding free energy (ΔΔGel) is very sensitive to the force field parameters, the minimization procedure, the values of the internal dielectric constant, and the probe radius. Nevertheless our results indicate that certain trends in ΔΔGel behavior are much less sensitive to the calculation parameters. For instance, the fraction of the homo-complexes, for which the electrostatics was found to oppose binding, is 80% regardless of the force fields and parameters used. For the hetero-complexes, however, the percentage of the cases for which electrostatics opposed binding varied from 43% to 85%, depending on the protocol and parameters employed. A significant correlation was found between the effects caused by raising the internal dielectric constant and decreasing the probe radius. Correlations were also found among the results obtained with different force fields. However, despite of the correlations found, the absolute ΔΔGel calculated with different force field parameters could differ more than tens of kcal/mol in some cases. Set of rules of obtaining confident predictions of absolute ΔΔGel and ΔΔGel sign are provided in the conclusion section.
PACS codes: 87.15.A-, 87.15. km