Effective Computational Method for Evaluation of Dynamic Elecrostatic Effects of Explicit Solvent and Membrane Molecules from Molecular Dynamics Simulations

Abstract

Knowledge of the electronic structures of local functional sites of proteins sheds light into their fundamental mechanisms of enzymatic reaction and processes related to electronic state. Although the dynamic effects due to solvent or membrane molecules surrounding the protein are indispensable for an accurate analysis, in current methods they have been approximated by a continuum model with polarized material, where a phenomenological and unreliable parameter, the dielectric constant, is always required. We have developed a new algorithm to reproduce an average field due to the solvent and membrane molecules, which are calculated from the long trajectory of a classical molecular dynamics simulation for a membrane protein-solvent system, by several thousands of pseudo-charges and dipoles on a closed surface surrounding a target quantum mechanical (QM) region. Since the dynamic effects are represented only by "static" pseudo-charges and dipoles, the QM calculation is necessarily done only once. We applied this algorithm to the photosynthetic reaction center of Rhodobacter sphaeroides with explicit all-atomic models of the solvent and membrane molecules. It is possible that the electronic structures of its ground state and excited state can be calculated with those microscopic "reaction field" effects.