Computation of the dipole moments of proteins

A simple and computationally feasible procedure for the calculation of net charges and dipole moments of proteins at arbitrary pH and salt conditions is described. The method is intended to provide data that may be compared to the results of transient electric dichroism experiments on protein solutions. The procedure consists of three major steps: (i) calculation of self energies and interaction energies for ionizable groups in the protein by using the finite-difference Poisson-Boltzmann method, (ii) determination of the position of the center of diffusion (to which the calculated dipole moment refers) and the extinction coefficient tensor for the protein, and (iii) generation of the equilibrium distribution of protonation states of the protein by a Monte Carlo procedure, from which mean and root-mean-square dipole moments and optical anisotropies are calculated. The procedure is applied to 12 proteins. It is shown that it gives hydrodynamic and electrical parameters for proteins in good agreement with experimental data.