QM/MM study on the mechanism of peptide hydrolysis by carboxypeptidase A

Density functional theory-based QM/MM calculations (B3LYP/CHARMM27) are reported on a reaction path for the initial, rate-limiting, step in amide hydrolysis by Carboxypeptidase A. Obtaining a smooth energy profile with the QM/MM method for this system is difficult, and great care is needed in selecting the initial geometry and the method for optimising the reaction path. The calculations show the importance of the enzyme in stabilizing the tetrahedral intermediate, and suggest that the key step involves simultaneous deprotonation of the nucleophilic water, attack on the substrate carbonyl group, and protonation of the substrate amide nitrogen. (C) 2008 Elsevier B.V. All rights reserved.