The general aim of the proposed research is to improve our understanding of electrostatic effects in biological molecules.
The specific aims are to develop new theoretical methods of calculating these effects in the context of a macroscopic dielectric model, and to apply these and existing methods to proteins and small molecules. In the model to be used, the protein is treated as a low dielectric medium immersed in a high dielectric solvent, and the electric potential is determined by the Poisson or Poisson-Boltzmann equation. The equations will be solved by finite difference methods. Three new theoretical methodologies will be developed: inclusion of conformation variation (previous calculations of this type have assumed rigid structures); incorporation of counterion adsorption; and combination of the macroscopic dielectric method with molecular dynamics and quantum mechanical methods through calculations of reaction fields. Applications to problems of biological interest and test cases for the methodology include the light harvesting protein bacteriorhodopsin and a family of phosphatase proteins involved in cell regulation.
