Microscopic theory of the dielectric properties of proteins

This paper investigates the microscopic mechanisms of charge screening in proteins. The screening of an arbitrary perturbing charge density by a protein and its surrounding solution is characterized by a generalized susceptibility, which is approximately given by the mean dipole-dipole correlation matrix of the system. This susceptibility is a microscopic quantity; the sum of its matrix elements gives the macroscopic susceptibility of continuum electrostatics. When screening of a single perturbing point charge is considered, this susceptibility reduces to a scalar quantity, dependent on position within the protein. The contribution of the positional degrees of freedom of the protein atoms can be estimated from molecular dynamics simulations. This contribution gives rise to large spatial variations of the susceptibility, whose significance for protein function is discussed. The model is applied to the small alpha helix deca-alanine, and to the electron-transfer protein cytochrome c. The results agree qualitatively with previous normal mode calculations. The importance, and the large spatial variations, of charge screening by deca-alanine suggest that dielectric screening may play a role in the binding of charged ligands by helices. In cytochrome c, the dielectric susceptibility in response to a point charge is at a minimum in the central heme region, resulting in a lowering of the reorganization free energy for charge transfer to and from the heme.