Computer simulation of the initial proton transfer step in human carbonic anhydrase I.

The initial water proteolysis step in the proton transfer "half-reaction" of human carbonic anhydrase I is simulated using the empirical valence bond method in combination with free energy perturbation molecular dynamics calculations. A free energy profile for the enzyme catalysed reaction and the corresponding pKa associated with ionization of the zinc-bound water is calculated. The obtained pKa value of 7 to 8 appears to be in good agreement with experimental observations and the calculated rate constant for this step is also compatible with kinetic data. The simulations clearly emphasize the important electrostatic effect associated with the catalytic zinc ion.