Conservative Electrostatic Potential Patterns at Enzyme Active Sites: The Anion−Cation−Anion Triad

Abstract

Electrostatic potentials at enzyme active sites with the (− + −) charge distribution were calculated using the linearized Poisson−Boltzmann equation. It was found for all cases studied (five serine proteases, lipase, acetylcholinesterase, lysozyme, and d-xylose isomerase) that the protein and substrate electrostatic potential patterns on the van der Waals envelope of the latter complement each other. This calls attention to a convergent evolution of the active-site potential in the cases of serine proteases, providing similar patterns for enzymes with very different primary structures. Enzyme activities, as characterized by log kcat/kM for the same substrate (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide) of α-chymotrypsin, β-trypsin, α-lytic protease, subtilisin Novo, and subtilisin Carlsberg, respectively, correlate well with the calculated electrostatic interaction energies between the protein environment and the active site. To achieve a better fit between the calculated and experimental quantities, the geometry of the enzyme−substrate complexes had to be optimized by a technique based on molecular dynamics. For the same enzymes, it was found that a quantitative measure of the electrostatic complementarity between the active site and protein environment correlates with the electrostatic interaction energies, as well as the activities. On the basis of this observations we propose the use of electrostatic complementarity between the active site and surrounding protein for the characterization of enzyme catalytic power.