Calculations of Electrostatic Energies in Proteins Using Microscopic, Semimicroscopic and Macroscopic Models and Free-Energy Perturbation Approaches

Abstract

This chapter discusses computer models for evaluating electrostatic interactions in proteins, with emphasis on calculations of the free energies of electron-transfer states in photosynthetic bacterial reaction centers. We describe the microscopic Protein Dipoles Langevin Dipoles (PDLD) method, semimicroscopic approaches including the Poisson-Boltzmann, PDLD/S and Generalized Born models, a macroscopic model with a homogeneous dielectric medium, and microscopic free-energy-perturbation methods based on molecular dynamics simulations. We also describe the use of molecular dynamics simulations to obtain free energy surfaces of the reactant and product states as functions of the reaction coordinate for electron transfer.