Modeling of peptide hydrolysis by thermolysin.: A semiempirical and QM/MM study

The hydrolysis by thermolysin of formamide, considered as a model of a peptide bond, has been studied with semiempirical and mixed QM/MM methods. The study has been carried out for two catalysts-a molecular complex of a Zn2+ ion with two imidazole molecules and a formate ion, modeling the active site of the enzyme, and the whole enzyme-and for two mechanisms involving one and two water molecules. In every case, the first step of the reaction is a nucleophilic attack of the carbon atom by the oxygen of a water molecule or a water dimer. The mechanism involving an ancillary water molecule (water-assisted process) is always favored compared to the process in which a single water molecule reacts. The fact is explained by a better nucleophilicity of the oxygen atom in the water dimer and a less constrained transition state. The zinc atom of the catalytic center acts as a Lewis acid and the ligands as an electron reservoir. The slight differences between the reactions catalyzed by the model complex and by the whole enzyme are explained on the basis of small geometry distortions induced by the amino acids residues surrounding the active center.