Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations

Abstract

The static and frequency dependent dielectric properties of trypsin inhibitor and hen egg white lysozyme have been calculated from the fluctuations in the total dipole moment of the two proteins. Total dipole moment fluctuations were obtained from long molecular dynamics simulations of both proteins in an explicit solvent environment. Despite differences in the total charge, volume, shape and secondary structure composition of the two proteins, consistent values for the dielectric constant were obtained. The static dielectric constant of trypsin inhibitor was calculated to be 36, compared with a value of 30 for hen egg white lysozyme. Convergence in the calculations required 1 ns of simulation. The calculated frequency dependent dielectric constant was also consistent with known experimental dielectric dispersion curves for proteins in aqueous solution. The implications for free energy calculations involving significant charge redistribution are also discussed.