Atomic solvation parameters in the analysis of protein-protein docking results.
Several sets of amino acid surface areas and transfer free energies were used to derive a total of nine sets of atomic solvation parameters (ASPs). We tested the accuracy of each of these sets of parameters in predicting the experimentally determined transfer free energies of the amino acid derivatives from which the parameters were derived. In all cases, the calculated and experimental values correlated well. We then chose three parameter sets and examined the effect of adding an energetic correction for desolvation based on these three parameter sets to the simple potential function used in our multiple start Monte Carlo docking method. A variety of protein-protein interactions and docking results were examined. In the docking simulations studied, the desolvation correction was only applied during the final energy calculation of each simulation. For most of the docking results we analyzed, the use of an octanol-water-based ASP set marginally improved the energetic ranking of the low-energy dockings, whereas the other ASP sets we tested disturbed the ranking of the low-energy dockings in many of the same systems. We also examined the correlation between the experimental free energies of association and our calculated interaction energies for a series of proteinase-inhibitor complexes. Again, the octanol-water-based ASP set was compatible with our standard potential function, whereas ASP sets derived from other solvent systems were not.
Cummings
M D
MD
Department of Biochemistry, University of Alberta, Edmonton, Canada.
Hart
T N
TN
Read
R J
RJ
D000596:Amino Acids; D000818:Animals; D003198:Computer Simulation; D010450:Endopeptidases / Q000737:chemistry*; D010059:Ovomucin / Q000737:chemistry* / Q000378:metabolism; D011480:Protease Inhibitors / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D012044:Regression Analysis; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000378:metabolism; D013305:Streptomyces griseus / Q000201:enzymology; D013499:Surface Properties; D013816:Thermodynamics; D014422:Turkeys; D029701:Saccharomyces cerevisiae Proteins
D000596:Amino Acids; D010450:Endopeptidases; D010059:Ovomucin; D011480:Protease Inhibitors; D011506:Proteins; D012697:Serine Endopeptidases; C023302:yeast proteinase B; D029701:Saccharomyces cerevisiae Proteins