Long-range electrostatic contributions to protein-ligand binding estimated using protein charge ladders, affinity capillary electrophoresis, and continuum electrostatic theory

Affinity capillary electrophoresis and protein charge ladders are used together to measure the contributions of long-range electrostatic interactions to binding of substituted benzene sulfonamide inhibitors to derivatives of human carbonic anhydrase II. The results are analyzed by continuum electrostatic calculations, which afford a detailed analysis of interactions of individual members of a population from a charge ladder. A Monte Carlo simulation of the experimental data using calculated contributions of individual lysine side chains to inhibitor binding shows that a large number of different patterns of acetylation are consistent with the experimental results. The calculations predict significant differences in the contributions of some lysines to Delta G and simulations suggest that experimental resolution must be enhanced to be able to measure such differences.