title: Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations.
abstract: Generalized Born (GB) implicit solvent models are widely used in molecular dynamics simulations to evaluate the interactions of biomolecular complexes. The continuum treatment of the solvent results in significant computational savings in comparison to an explicit solvent representation. It is, however, not clear how accurately the GB approach reproduces the absolute free energies of biomolecular binding. On the basis of induced dissociation by means of umbrella sampling simulations, the absolute binding free energies of small proline-rich peptide ligands and a protein receptor were calculated. Comparative simulations according to the same protocol were performed by employing an explicit solvent model and various GB-type implicit solvent models in combination with a nonpolar surface tension term. The peptide ligands differed in a key residue at the peptide-protein interface, including either a nonpolar, a neutral polar, a positively charged, or a negatively charged group. For the peptides with a neutral polar or nonpolar interface residue, very good agreement between the explicit solvent and GB implicit solvent results was found. Deviations in the main separation free energy contributions are smaller than 1 kcal/mol. In contrast, for peptides with a charged interface residue, significant deviations of 2-4 kcal/mol were observed. The results indicate that recent GB models can compete with explicit solvent representations in total binding free energy calculations as long as no charged residues are present at the binding interface.
authors.affiliation: Physik-Department T38, Technische Universität München , James-Franck-Str. 1, Garching 85748, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Zeller
authors.affiliation: Physik-Department T38, Technische Universität München , James-Franck-Str. 1, Garching 85748, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias