CALCULATION OF THE DIELECTRIC-PROPERTIES OF A PROTEIN AND ITS SOLVENT- THEORY AND A CASE-STUDY

This paper presents a rigorous derivation of a theory for the calculat ion of the frequency-dependent dielectric properties of each component of the system protein/water/ions with the aim of enabling comparison to experimentally determined dielectric properties. We apply this theo ry to a very long (13.1 ns) molecular dynamics simulation of an HIV1 z inc finger peptide, its co-ordinated zinc ion, and two chloride ions i n a box of SPC/E water molecules. We find the dielectric relaxation of the water molecules restricted compared to pure water, giving rise to a static dielectric constant for the water-component of only 47. The peptide is found to have a complicated dielectric relaxation behaviour , with a static dielectric constant of 15. We also calculate the frequ ency-dependent conductivity of the ions in this system. We analyze all contributions to the calculation of these dielectric properties and f ind that the coupling between the dielectric relaxation of the peptide and that of the water-component is particularly important for correct ly describing the dielectric constant of the peptide. (C) 1997 Academi c Press Limited.