A state-of-the-art accurate quantum chemistry computational approach is proposed to investigate the mechanism of H2O2 reduction at the active site of GPx. In the model we consider explicitly six amino acids surrounding the catalytic SEC or CYS residue. The geometries of the plausible intermediate species and transition states as well as the energetics are carefully predicted. The computational protocol, rooted in advanced Density Functional Theory methodologies, is employed to explore possible mechanistic paths involving different initial active species (Se-; SeH; S- ; SH) and stability of protonated surrounding amino acids, in particular Gln (O), Gly (N) and Trp (N). The data so far acquired have demonstrated the following: i) the chosen amino acids forming the catalytic “cage” are fully optimized and their minimum energy conformation is perfectly superimposed to the initial crystal structure (see Fig. 1) and no difference has been observed when the active site contains either Se or S; ii) the proton of selenol or thiol has been dislocated in all of the available surrounding amino acids and it has been optimized in most of the tested locations leading to the conclusion that it is displaced in the positively charged catalytic pocket rather than exclusively bound to selenium or sulphur, iii) hydrogen peroxide is extremely instable in the active site and selenenic/sulphenic acid and water are formed instantaneously. This transition is the minimum energy path of the system and account for the non saturation kinetics of GPx where there is no evidence for the formation of a stable enzyme substrate complex. This set of data strongly suggests that for the catalysis of H2O2 reduction the active site of GPx is crucial, while the redox residue can be either SEC or CYS.

Novel insights on the mechanistic aspects of GPx-catalyzed H2O2 reduction: a DFT computational study

ORIAN, LAURA;POLIMENO, ANTONINO;MAIORINO, MATILDE;URSINI, FULVIO;TOPPO, STEFANO
2010

Abstract

A state-of-the-art accurate quantum chemistry computational approach is proposed to investigate the mechanism of H2O2 reduction at the active site of GPx. In the model we consider explicitly six amino acids surrounding the catalytic SEC or CYS residue. The geometries of the plausible intermediate species and transition states as well as the energetics are carefully predicted. The computational protocol, rooted in advanced Density Functional Theory methodologies, is employed to explore possible mechanistic paths involving different initial active species (Se-; SeH; S- ; SH) and stability of protonated surrounding amino acids, in particular Gln (O), Gly (N) and Trp (N). The data so far acquired have demonstrated the following: i) the chosen amino acids forming the catalytic “cage” are fully optimized and their minimum energy conformation is perfectly superimposed to the initial crystal structure (see Fig. 1) and no difference has been observed when the active site contains either Se or S; ii) the proton of selenol or thiol has been dislocated in all of the available surrounding amino acids and it has been optimized in most of the tested locations leading to the conclusion that it is displaced in the positively charged catalytic pocket rather than exclusively bound to selenium or sulphur, iii) hydrogen peroxide is extremely instable in the active site and selenenic/sulphenic acid and water are formed instantaneously. This transition is the minimum energy path of the system and account for the non saturation kinetics of GPx where there is no evidence for the formation of a stable enzyme substrate complex. This set of data strongly suggests that for the catalysis of H2O2 reduction the active site of GPx is crucial, while the redox residue can be either SEC or CYS.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11577/2490269
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