SOLVENT DIFFUSION OUTSIDE MACROMOLECULAR SURFACES

The effect of the inhomogeneous environment upon solvent molecules clo se to a macromolecular surface is evaluated from a molecular-dynamics simulation of a protein, myoglobin, in water solution. The simulation is analyzed in terms of a mean-field potential from the protein upon t he water molecules and spatially varying translational diffusion coeff icients for solvent molecules in directions parallel and perpendicular to the protein surface. The diffusion coefficients can be obtained fr om the slope of the average-square displacements vs time, as well as f rom the integral of the velocity autocorrelation functions. It is show n that the former procedure gives a lot of ambiguities due to the vari ation of the slope of the curve with time. The latter, however, after analytic correction for the contribution from algebraic long-time tail s, furnish a much more reliable alternative.