Anhydride formation is not a valid mechanism for peptide cleavage by carboxypeptidase-A: A semiempirical reaction pathway study

Alexandra Vardi-Kilshtain, Gil Shoham, Amiram Goldblum*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

The mechanism of action of zinc metalloproteinases has been studied by following the direct nucleophilic pathway, which has been frequently suggested but not yet examined by computational methods, and comparing it to other pathways. We computed the reaction enthalpies for the direct nucleophilic attack by Glu270 in the active site model of carboxypeptidase-A on a model substrate's peptide carbonyl and followed this pathway through mixed anhydride formation and subsequent anhydride cleavage by water. The starting molecular coordinates originate in our own high-resolution crystal structure and the computations have been conducted with the minimal neglect of differential overlap (MNDO) Hamiltonian, modified to include the d-orbitals of zinc and the effects of multiple hydrogen bonding, thus labelled MNDO/d/H. Compared to our recent results for two other candidate pathways for this mechanism, both of the General-Acid-General-Base type, we conclude that the direct nucleophilic or 'anhydride' pathway has a much higher energy barrier at the rate determining step, which is a proton transfer, than previously calculated paths. We argue that the 'anhydride' pathway is thus not a valid one for the cleavage of peptides by carboxypeptidase-A.

Original languageAmerican English
Pages (from-to)2715-2724
Number of pages10
JournalMolecular Physics
Volume101
Issue number17
DOIs
StatePublished - 10 Sep 2003

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