Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges

Abstract

A boundary element formulation of continuum electrostatics is used to examine time-independent dielectric relaxation and screening in two proteins, and time-dependent relaxation in two simpler solutes. Cytochrome c oxidation is modeled by inserting partial charges on the heme, using one to three dielectric regions in the protein. It was suggested recently that for charge insertion on a protein-bound ligand, all or part of the ligand should be treated as a cavity within the protein medium. Here, the effect of an internal cavity surrounding the central heme atoms is examined, considering separately the static and relaxation (or reorganization) free energies. The former is the free energy to remove the redox electron while maintaining the rest of the structure and charge distribution fixed; the latter is the free energy associated with the relaxation into the product state after the corresponding constraints are released. The effect of the cavity is found to be small for the static free energy, while for the relaxation free energy it is large, as polarization of groups immediately around the heme dominates the relaxation. If the protein surface groups are treated as a distinct medium with a dielectric of 25 (as suggested by recent molecular dynamics simulations), the relaxation free energy decreases significantly (from −37.0 to −43.9 kcal/mol), compared to a model where the whole protein has a dielectric constant of two. Therefore, with this model, although polarization of groups immediately around the heme still dominates the relaxation, polar groups near the protein surface also contribute significantly, and solvent negligibly. The screening of an applied field within myoglobin is calculated, with the protein surrounded by either a low-dielectric or a high-dielectric glass. In the vicinity of the CO ligand, the screening is approximately isotropic with a low-dielectric glass. It is anisotropic with a high-dielectric glass, but the applied and local fields are still approximately parallel. This has implications for experiments that probe dielectric screening in proteins with the newly developed technique of vibrational Stark spectroscopy: with a high-dielectric glass, a single, rotationally averaged screening factor can be used, the local field being about 1.65 times the applied field. Finally, we calculate the time-dependent relaxation in response to instantaneous charge insertion within a spherical cavity in a Debye solvent, and to photoexcitation of a tryptophan solute, illustrating the extension of the boundary element formulation to time-dependent problems. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 290–305, 2001