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MO‐Studies of enzyme reaction mechanisms. I. Model molecular orbital study of the cleavage of peptides by carboxypeptidase A
Author(s) -
Alex Alexander,
Clark Timothy
Publication year - 1992
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540130605
Subject(s) - chemistry , active site , formamide , ab initio , amide , moiety , bond cleavage , carboxypeptidase a , reaction coordinate , stereochemistry , computational chemistry , carboxypeptidase , catalysis , organic chemistry , enzyme
Ab initio and semiempiridal (AM1) molecular orbital theory has been used to model the cleavage of formamide at the active site of carboxypeptidase A. The model active site consists of a zinc dication coordinated to two imidazoles, an acetate, a water with a hydrogen‐bonded formate, and a formamide molecule as model substrate. AM1 has been compared with ab initio theory for the coordination of water and formamide to Zn ++ and found to give excellent energetic results. The course of the amide cleavage was therefore calculated with AM1. The first step of the reaction is the dissociation of the zinc‐coordinated water to give an active ZnOH + species. The remote formate acts as proton acceptor. This process has an activation energy of only 4.6 kcal mol −1 . The next and rate‐determining step is the concerted addition of the ZnOH + moiety to the formamide CO bond. The ZnO distance in the transition state is more than 3 Å. In four further steps, the amide nitrogen is protonated and the CN bond cleaved. The net activation energy for the entire process is 15.5 kcal mol −1 relative to the active site model and 19.6 kcal mol −1 relative to the most stable point on the calculated reaction profile.