Role of second coordination sphere amino acid residues on the proton transfer mechanism of human carbonic anhydrase II (HCA II)

Abstract

The barrier for the proton transfer in human carbonic anhydrase II (HCA II) has been studied by including the important second coordination sphere residues to the minimalistic model of the active site using B3LYP/6-31+G** level of calculation. Specifically, proton transfer from a zinc-bound water molecule to a histidine residue (His64) mediated by a water bridge (consists of two and three water molecules) has been investigated. The new model contains three functional groups of second coordination sphere residues such as Gln92, Glu117, and Asn244. These residues interact with His94, His119, and His96, respectively. We have calculated the barrier for the proton transfer using the total energies of reactants, transition states, and products. The calculated barrier height for the models with two water and three water molecules are 8.94 and 8.67 kcal/mol, respectively, which are in close agreement with the experimental value of 7.8 kcal/mol obtained from the kinetic experiments and to the range 8−10 kcal/mol predicted from the pK_a considerations (Silverman, D. N. Biochim. Biophys. Acta 2000, 1458, 88−103.). In addition, our own N-layered integrated molecular orbital + molecular mechanics (ONIOM) calculations have also been carried out on various model systems to understand the effect of complete environment. It is possible to note from the results that the confinement of water molecules by the protein milieu appreciably decreases the O•••O distance between water molecules in the water bridge when compared to the free water dimer which enables the proton transfer from one water to the other and finally to the His64 residue.