Catalytic Reaction Mechanism of Glyoxalase II : A Quantum Mechanics/Molecular Mechanics Study
Shirazi, Javad ; Jafari, Sonia ; Ryde, Ulf LU
and Irani, Mehdi
LU
(2023)
In Journal of Physical Chemistry B
127(20).
p.4480-4495
- Abstract
Methylglyoxal (MG) is a reactive and toxic compound produced in carbohydrate, lipid, and amino acid metabolism. The glyoxalase system is the main detoxifying route for MG and consists of two enzymes, glyoxalase I (GlxI) and glyoxalase II (GlxII). GlxI catalyzes the formation of S-d-lactoylglutathione from hemithioacetal, and GlxII converts this intermediate to d-lactate. A relationship between the glyoxalase system and some diseases like diabetes has been shown, and inhibiting enzymes of this system may be an effective means of controlling certain diseases. A detailed understanding of the reaction mechanism of an enzyme is essential to the rational design of competitive inhibitors. In this work, we use quantum mechanics/molecular... (More)
Methylglyoxal (MG) is a reactive and toxic compound produced in carbohydrate, lipid, and amino acid metabolism. The glyoxalase system is the main detoxifying route for MG and consists of two enzymes, glyoxalase I (GlxI) and glyoxalase II (GlxII). GlxI catalyzes the formation of S-d-lactoylglutathione from hemithioacetal, and GlxII converts this intermediate to d-lactate. A relationship between the glyoxalase system and some diseases like diabetes has been shown, and inhibiting enzymes of this system may be an effective means of controlling certain diseases. A detailed understanding of the reaction mechanism of an enzyme is essential to the rational design of competitive inhibitors. In this work, we use quantum mechanics/molecular mechanics (QM/MM) calculations and energy refinement utilizing the big-QM and QM/MM thermodynamic cycle perturbation methods to propose a mechanism for the GlxII reaction that starts with a nucleophilic attack of the bridging OH- group on the substrate. The coordination of the substrate to the Zn ions places its electrophilic center close to the hydroxide group, enabling the reaction to proceed. Our estimated reaction energies are in excellent agreement with experimental data, thus demonstrating the reliability of our approach and the proposed mechanism. Additionally, we examined alternative protonation states of Asp-29, Asp-58, Asp-134, and the bridging hydroxide ion in the catalytic process. However, these give less favorable reactions, a poorer reproduction of the crystal structure geometry of the active site, and higher root-mean-squared deviations of the active site residues in molecular dynamics simulations.
(Less)
- author
- Shirazi, Javad
; Jafari, Sonia
; Ryde, Ulf
LU
and Irani, Mehdi
LU
- organization
- publishing date
- 2023-05-25
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Physical Chemistry B
- volume
- 127
- issue
- 20
- pages
- 16 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- pmid:37191640
- scopus:85160204775
- ISSN
- 1520-6106
- DOI
- 10.1021/acs.jpcb.3c01495
- language
- English
- LU publication?
- yes
- id
- 8a441d4d-e5f7-449e-a1de-19271c389780
- date added to LUP
- 2023-09-14 12:09:52
- date last changed
- 2024-04-30 02:46:31
@article{8a441d4d-e5f7-449e-a1de-19271c389780,
abstract = {{<p>Methylglyoxal (MG) is a reactive and toxic compound produced in carbohydrate, lipid, and amino acid metabolism. The glyoxalase system is the main detoxifying route for MG and consists of two enzymes, glyoxalase I (GlxI) and glyoxalase II (GlxII). GlxI catalyzes the formation of S-d-lactoylglutathione from hemithioacetal, and GlxII converts this intermediate to d-lactate. A relationship between the glyoxalase system and some diseases like diabetes has been shown, and inhibiting enzymes of this system may be an effective means of controlling certain diseases. A detailed understanding of the reaction mechanism of an enzyme is essential to the rational design of competitive inhibitors. In this work, we use quantum mechanics/molecular mechanics (QM/MM) calculations and energy refinement utilizing the big-QM and QM/MM thermodynamic cycle perturbation methods to propose a mechanism for the GlxII reaction that starts with a nucleophilic attack of the bridging OH- group on the substrate. The coordination of the substrate to the Zn ions places its electrophilic center close to the hydroxide group, enabling the reaction to proceed. Our estimated reaction energies are in excellent agreement with experimental data, thus demonstrating the reliability of our approach and the proposed mechanism. Additionally, we examined alternative protonation states of Asp-29, Asp-58, Asp-134, and the bridging hydroxide ion in the catalytic process. However, these give less favorable reactions, a poorer reproduction of the crystal structure geometry of the active site, and higher root-mean-squared deviations of the active site residues in molecular dynamics simulations.</p>}},
author = {{Shirazi, Javad and Jafari, Sonia and Ryde, Ulf and Irani, Mehdi}},
issn = {{1520-6106}},
language = {{eng}},
month = {{05}},
number = {{20}},
pages = {{4480--4495}},
publisher = {{The American Chemical Society (ACS)}},
series = {{Journal of Physical Chemistry B}},
title = {{Catalytic Reaction Mechanism of Glyoxalase II : A Quantum Mechanics/Molecular Mechanics Study}},
url = {{http://dx.doi.org/10.1021/acs.jpcb.3c01495}},
doi = {{10.1021/acs.jpcb.3c01495}},
volume = {{127}},
year = {{2023}},
}