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 met hods. The study has been carried out for two catalysts-a molecular com plex of a Zn2+ ion with two imidazole molecules and a formate ion, mod eling the active site of the enzyme, and the whole enzyme-and for two mechanisms involving one and two water molecules. In every case, the f irst 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 invo lving an ancillary water molecule (water-assisted process) is always f avored 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 a n electron reservoir. The slight differences between the reactions cat alyzed by the model complex and by the whole enzyme are explained on t he basis of small geometry distortions induced by the amino acids resi dues surrounding the active center.