Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method.
Implicit solvent methods have become popular tools in the field of protein dynamics simulations, yet evaluation of their validity has been primarily limited to comparisons with experimental and theoretical data for small molecules. In this paper, we use a recently developed hybrid explicit/implicit solvent methodology to evaluate the accuracy of several Poisson-based implicit solvent models. Specifically, we focus on the calculation of electrostatic solvation free energies of various fixed conformations for two proteins. We show that, among various dielectric boundary definitions, the Lee-Richards molecular surface has the best agreement with hybrid solvent results. Furthermore, certain modifications of the molecular surface Poisson protocol provide varied results. For instance, simple modifications of atomic radii on charged residues generally improve absolute errors but do not significantly reduce relative errors among conformations. On the other hand, using a water-probe radius of 1.0 A, as opposed to the standard value of 1.4 A, to generate the molecular surface, moderately improves both absolute and relative results.
Lee
Michael S
MS
Department of Cell Biology and Biochemistry, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, Maryland 21702, USA. michael.lee@amedd.army.mil
Olson
Mark A
MA
D002138:Calibration; D008956:Models, Chemical; D016012:Poisson Distribution; D011487:Protein Conformation; D012995:Solubility; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity
D012997:Solvents