Numerical Calculations of Reaction Fields of Protein-Solvent Systems

Abstract

A reaction field in a protein molecule due to aqueous solvent, which is polarized by charges of the protein, has been calculated numerically. First, a Poisson equation for a macroscopic dielectric model of a protein in vacuo was solved by the self-consistent boundary method. Next, Poisson and Poisson-Boltzmann equations for the model of a protein in aqueous solvent were solved in the same manner. The reaction field was then obtained by taking the difference between the potentials of these two systems. The results agreed well with those calculated analytically for simple model cases. Applications of the present method of the particle-particle/particle-mesh algorithm were discussed for actual protein-solvent systems.