Solvation energy density occlusion approximation for evaluation of desolvation penalties in biomolecular interactions.
In calculations involving many displacements of an interacting pair of biomolecules, such as brownian dynamics, the docking of a substrate/ligand to an enzyme/receptor, or the screening of a large number of ligands as prospective inhibitors for a particular receptor site, there is a need for rapid evaluation of the desolvation penalties of the interacting pair. Although continuum electrostatic treatments with distinct dielectric constants for solute and solvent provide an account of the electrostatics of solvation and desolvation, it is necessary to re-solve the Poisson equation, at considerable computational cost, for each displacement of the interacting pair. We present a new method that uses a formulation of continuum electrostatic solvation in terms of the solvation energy density and approximates desolvation in terms of the occlusion of this density. We call it the SEDO approximation. It avoids the need to re-solve the Poisson equation, as desolvation is now estimated by an integral over the occluded volume. Test calculations are presented for some simple model systems and for some real systems that have previously been studied using the Poisson equation approach: MHC class I protein-peptide complexes and a congeneric series of human immunodeficiency virus type 1 (HIV-1) protease--ligand complexes. For most of the systems considered, the trends and magnitudes of the desolvation component of interaction energies obtained using the SEDO approximation are in reasonable correlation with those obtained by re-solving the Poisson equation. In most cases, the error introduced by the SEDO approximation is much less than that of the often-used test-charge approximation for the charge-charge components of intermolecular interactions. Proteins 2001;43:12-27.
Arora
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N
Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA.
Bashford
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D
D003198:Computer Simulation; D005805:Genes, MHC Class I / Q000502:physiology*; D016333:HIV Protease / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D008962:Models, Theoretical; D009842:Oligopeptides / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D016012:Poisson Distribution; D011485:Protein Binding; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics
D008024:Ligands; D009842:Oligopeptides; D010446:Peptide Fragments; D012997:Solvents; D016333:HIV Protease