On the water-promoted mechanism of peptide cleavage by carboxypeptidase A. A theoretical study
作者:
Silvia Alvarez-Santos,
Angels González-Lafont,
José M. Lluch,
Baldomero Oliva,
Francesc X. Avilés,
期刊:
Canadian Journal of Chemistry
(NRC Available online 1994)
卷期:
Volume 72,
issue 10
页码: 2077-2083
ISSN:0008-4042
年代: 1994
DOI:10.1139/v94-264
出版商: NRC Research Press
数据来源: NRC
摘要:
The water-promoted pathway of peptide cleavage by carboxypeptidase A has been studied by semiempirical (AM1) quantum mechanical calculations. A relatively large model for the CPA-active site elements plus substrate has been designed, using two imidazoles and one acetate as the Zn2+ligands, acetate as the proton acceptor (simulating Glu-270), andN-ethylacetamide as the peptide-like substrate. This model, although simpler than the natural one, is one of the largest used for theoretical calculations on CPA catalytic mechanisms. To ensure that this model is able to mimic the natural system, it has been compared with the structure of the (Gly)3-L-Tyr + water + CPA complex resulting from several molecular dynamics/energy minimization simulations. Among the different steps involved in the water-promoted pathway proposed by Lipscomb's group, the attack of the oxygen atom that comes from the activated water molecule to the carbon atom of the peptide bond of the substrate has been found to be the rate-determining step, with a high enthalpy barrier of 37.9 kcal/mol. However, this enthalpy barrier is dramatically decreased when a positive charge, simulating Arg-127, is included near the scissile carbonyl. The reported results seem to favour the occurrence of the mechanism studied and indicate the limitations of using simple elements for the theoretical analysis of enzyme-catalyzed reactions.
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