COMPUTER-SIMULATION OF THE CO2/HCO3- INTERCONVERSION STEP IN HUMAN CARBONIC ANHYDRASE-I

The CO2/HCO3- interconversion step in human carbonic anhydrase I is simulated using the empirical valence bond (EVB) method in combination with free energy perturbation molecular dynamics calculations. The calculated free energy profile for the enzyme reaction is found to be in reasonable agreement with experimental kinetic data. The simulations show that the enzyme is able to reduce both the activation barrier as well as the exothermicity of the interconversion step (compared to the water reaction). The catalytic zinc ion appears to be important for both of these effects, its strong interaction with the reacting hydroxide ion being a key element of the catalytic effect. The predicted conformation of the HCO3- complex with the enzyme is similar to that observed experimentally for a mutant version of isozyme II. The geometry of the transition state generated by the EVB simulations is compared to ab initio studies of model systems and also to some relevant experimental inhibitor complexes. The simulated energetics of the uncatalyzed solution reaction is used to estimate the reaction free energy in vacuo, and the results are found to be in good agreement with high-level basis set ab initio calculations.