Point charge distributions and electrostatic steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases

Abstract

The electrostatic steering mechanism of bovine erythrocyte Cu/Zn superoxide dismutase (SOD) was investigated through the use of Brownian dynamics. Simulations of enzyme/substrate encounter were carried out on 14 different SOD models defined by simple changes in the enzyme's point charge distribution. The magnitude and ionic strength dependence of reaction rates, rates for collision anywhere on the enzyme surface, and collision efficiency factors were analyzed to elucidate both the general and specific roles for point charges associated with amino acid residues. Collision rates for the general enzyme surface appear to be solely determined by the net charge on the enzyme. At physiological ionic strength this effect is negligible, with only 6% variation in collision rates observed as the net charge ranges from +2e to -10e. With the exception of a few charged residues in the active-site channel of SOD, point charge modifications had modest effects on reaction rates. For a large region within and surrounding the channel, reaction rates increased or decreased by only 10-15% with the addition or subtraction of a protonic unit of charge, respectively. This effect simply disappeared with increasing distance from the active site. More dramatic effects were seen at only three residues: arginine-141, glutamate-131, and lysine-134. Implications for rate enhancement through site-directed mutagenesis are discussed.