Article

Role of the metal ion in formyl-peptide bond hydrolysis by a peptide deformylase active site model.

Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende, Italy.
The Journal of Physical Chemistry B (impact factor: 3.7). 02/2006; 110(2):1063-72. DOI:10.1021/jp054923y pp.1063-72
Source: PubMed

ABSTRACT The catalytic mechanism of peptide deformylase enzymes containing zinc, iron, cobalt, and nickel dications was explored in the gas phase and in the protein environment. The study was performed at the density functional level using three model systems to simulate the active site. The work had the aim to evaluate the effect of metal substitution on the hydrolytic properties and the possible different performances of the various catalysts. Results indicated that all of the metallic forms are active to hydrolyze the formyl-peptide bond and that the reaction pathways do not show significant peculiarities on going from a particular metal ion to another. No significant modification of the reaction paths occurs in solvent.

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Keywords

catalytic mechanism
 
cobalt
 
density functional level
 
formyl-peptide bond
 
gas phase
 
metal substitution
 
metallic forms
 
particular metal ion
 
peptide deformylase enzymes
 
possible different performances
 
protein environment
 
reaction paths
 
significant modification
 
significant peculiarities
 
various catalysts
 
zinc