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Sastre S, Manta B, Semelak JA, Estrin D, Trujillo M, Radi R, Zeida A. Catalytic Mechanism of Mycobacterium tuberculosis Methionine Sulfoxide Reductase A. Biochemistry 2024; 63:533-544. [PMID: 38286790 DOI: 10.1021/acs.biochem.3c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The oxidation of Met to methionine sulfoxide (MetSO) by oxidants such as hydrogen peroxide, hypochlorite, or peroxynitrite has profound effects on protein function. This modification can be reversed by methionine sulfoxide reductases (msr). In the context of pathogen infection, the reduction of oxidized proteins gains significance due to microbial oxidative damage generated by the immune system. For example, Mycobacterium tuberculosis (Mt) utilizes msrs (MtmsrA and MtmsrB) as part of the repair response to the host-induced oxidative stress. The absence of these enzymes makes Mycobacteria prone to increased susceptibility to cell death, pointing them out as potential therapeutic targets. This study provides a detailed characterization of the catalytic mechanism of MtmsrA using a comprehensive approach, including experimental techniques and theoretical methodologies. Confirming a ping-pong type enzymatic mechanism, we elucidate the catalytic parameters for sulfoxide and thioredoxin substrates (kcat/KM = 2656 ± 525 M-1 s-1 and 1.7 ± 0.8 × 106 M-1 s-1, respectively). Notably, the entropic nature of the activation process thermodynamics, representing ∼85% of the activation free energy at room temperature, is underscored. Furthermore, the current study questions the plausibility of a sulfurane intermediate, which may be a transition-state-like structure, suggesting the involvement of a conserved histidine residue as an acid-base catalyst in the MetSO reduction mechanism. This mechanistic insight not only advances our understanding of Mt antioxidant enzymes but also holds implications for future drug discovery and biotechnological applications.
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Affiliation(s)
- Santiago Sastre
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Departamento de Biofísica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Programa de Doctorado en Química, Facultad de Química, Universidad de la República, Gral Flores 2124, CP 11800 Montevideo, Uruguay
| | - Bruno Manta
- Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Cátedra de Fisiopatología, Facultad de Odontología, Universidad de la República, Gral Las Heras 1925, CP 11600 Montevideo, Uruguay
| | - Jonathan A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Ciudad Universitaria, Intendente Güiraldes 2160, CP C1428EGA Buenos Aires, Argentina
| | - Dario Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Ciudad Universitaria, Intendente Güiraldes 2160, CP C1428EGA Buenos Aires, Argentina
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Gral Flores 2125, CP 11800 Montevideo, Uruguay
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Wu J, Chen X, Peng LY, Cui G, Xia SH. Excited-State Deactivation Mechanism of 3,5-bis(2-hydroxyphenyl)-1 H-1,2,4-triazole: Electronic Structure Calculations and Nonadiabatic Dynamics Simulations. J Phys Chem A 2022; 126:4002-4012. [PMID: 35730538 DOI: 10.1021/acs.jpca.2c02080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
3,5-bis(2-Hydroxyphenyl)-1H-1,2,4-triazole (bis-HPTA) has attracted wide attention due to the important application in the detection of microorganisms and insecticidal activity. However, the mechanisms of excited-state intramolecular proton transfer (ESIPT) process and decay pathways are still a matter of debate. In this work, we have comprehensively investigated the photodynamics of bis-HPTA by executing combined electronic structure calculations and nonadiabatic surface-hopping dynamics simulations. Based on the computed electronic structure and dynamics information, we propose two nonadiabatic deactivation channels that efficiently populate the ground state from the Franck-Condon region. In the first one, after being excited to the bright S1 state, bis-HPTA molecule undergoes an ultrafast and barrierless ESIPT-1 process. Then, the system encounters with an energetically accessible S1/S0 conical intersection (CI), which funnels the system to the ground state speedily. Afterward, the keto species either arrives at the keto product or return to its enol species via a ground-state proton transfer in the S0 state. In the other excited-state decay channel, the S1 system hops to the ground state through a different CI, which involves the ESIPT-2 process. In our dynamics simulations, about 79.6% of the trajectories decay to the S0 state via the first CI, while the remaining ones employ the second conical intersection. The results of dynamics simulations also demonstrated that the lifetime of the S1 state is estimated as 315 fs. The present work will give elaborating mechanistic information of similar compounds in various environments.
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Affiliation(s)
- Jiahui Wu
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xiaohang Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ling-Ya Peng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Shu-Hua Xia
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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Boschi-Muller S. Molecular Mechanisms of the Methionine Sulfoxide Reductase System from Neisseria meningitidis. Antioxidants (Basel) 2018; 7:antiox7100131. [PMID: 30275362 PMCID: PMC6210582 DOI: 10.3390/antiox7100131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 11/16/2022] Open
Abstract
Neisseria meningitidis, an obligate pathogenic bacterium in humans, has acquired different defense mechanisms to detect and fight the oxidative stress generated by the host’s defense during infection. A notable example of such a mechanism is the PilB reducing system, which repairs oxidatively-damaged methionine residues. This review will focus on the catalytic mechanism of the two methionine sulfoxide reductase (MSR) domains of PilB, which represent model enzymes for catalysis of the reduction of a sulfoxide function by thiols through sulfenic acid chemistry. The mechanism of recycling of these MSR domains by various “Trx-like” disulfide oxidoreductases will also be discussed.
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Affiliation(s)
- Sandrine Boschi-Muller
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Bâtiment Biopole, Faculté de Médecine, 54506 Vandoeuvre-lès-Nancy, France.
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Sahu S, Das M, Bharti AK, Krishnamoorthy G. Proton transfer triggered proton transfer: a self-assisted twin excited state intramolecular proton transfer. Phys Chem Chem Phys 2018; 20:27131-27139. [DOI: 10.1039/c8cp03835j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The double excited state intramolecular proton transfer (ESIPT) of 3,5-bis(2-hydroxyphenyl)-1H-1,2,4-triazole (bis-HPTA) has been investigated and found to undergo a new type of proton transfer.
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Affiliation(s)
- Saugata Sahu
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati
- India
| | - Minati Das
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati
- India
| | | | - G. Krishnamoorthy
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati
- India
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Boschi-Muller S, Branlant G. Methionine sulfoxide reductase: chemistry, substrate binding, recycling process and oxidase activity. Bioorg Chem 2014; 57:222-230. [PMID: 25108804 DOI: 10.1016/j.bioorg.2014.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 07/14/2014] [Accepted: 07/14/2014] [Indexed: 01/16/2023]
Abstract
Three classes of methionine sulfoxide reductases are known: MsrA and MsrB which are implicated stereo-selectively in the repair of protein oxidized on their methionine residues; and fRMsr, discovered more recently, which binds and reduces selectively free L-Met-R-O. It is now well established that the chemical mechanism of the reductase step passes through formation of a sulfenic acid intermediate. The oxidized catalytic cysteine can then be recycled by either Trx when a recycling cysteine is operative or a reductant like glutathione in the absence of recycling cysteine which is the case for 30% of the MsrBs. Recently, it was shown that a subclass of MsrAs with two recycling cysteines displays an oxidase activity. This reverse activity needs the accumulation of the sulfenic acid intermediate. The present review focuses on recent insights into the catalytic mechanism of action of the Msrs based on kinetic studies, theoretical chemistry investigations and new structural data. Major attention is placed on how the sulfenic acid intermediate can be formed and the oxidized catalytic cysteine returns back to its reduced form.
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Affiliation(s)
- Sandrine Boschi-Muller
- UMR 7365 CNRS, Université de Lorraine, IMoPA, Enzymologie Moléculaire et Structurale, Biopôle, CS 50184, 54505 Vandoeuvre-les-Nancy, France
| | - Guy Branlant
- UMR 7365 CNRS, Université de Lorraine, IMoPA, Enzymologie Moléculaire et Structurale, Biopôle, CS 50184, 54505 Vandoeuvre-les-Nancy, France.
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6
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Kinetic evidence that methionine sulfoxide reductase A can reveal its oxidase activity in the presence of thioredoxin. Arch Biochem Biophys 2014; 548:54-9. [PMID: 24632144 DOI: 10.1016/j.abb.2014.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 02/26/2014] [Accepted: 03/03/2014] [Indexed: 01/18/2023]
Abstract
The mouse methionine sulfoxide reductase A (MsrA) belongs to the subclass of MsrAs with one catalytic and two recycling Cys corresponding to Cys51, Cys198 and Cys206 in Escherichia coli MsrA, respectively. It was previously shown that in the absence of thioredoxin, the mouse and the E. coli MsrAs, which reduce two mol of methionine-O substrate per mol of enzyme, displays an in vitro S-stereospecific methionine oxidase activity. In the present study carried out with E. coli MsrA, kinetic evidence are presented which show that formation of the second mol of Ac-L-Met-NHMe is rate-limiting in the absence of thioredoxin. In the presence of thioredoxin, the overall rate-limiting step is associated with the thioredoxin-recycling process. Kinetic arguments are presented which support the accumulation of the E. coli MsrA under Cys51 sulfenic acid state in the presence of Trx. Thus, the methionine oxidase activity could be operative in vivo without the action of a regulatory protein in order to block the action of Trx as previously proposed.
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Multi-scale computational enzymology: enhancing our understanding of enzymatic catalysis. Int J Mol Sci 2013; 15:401-22. [PMID: 24384841 PMCID: PMC3907816 DOI: 10.3390/ijms15010401] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 12/05/2013] [Accepted: 12/24/2013] [Indexed: 01/23/2023] Open
Abstract
Elucidating the origin of enzymatic catalysis stands as one the great challenges of contemporary biochemistry and biophysics. The recent emergence of computational enzymology has enhanced our atomistic-level description of biocatalysis as well the kinetic and thermodynamic properties of their mechanisms. There exists a diversity of computational methods allowing the investigation of specific enzymatic properties. Small or large density functional theory models allow the comparison of a plethora of mechanistic reactive species and divergent catalytic pathways. Molecular docking can model different substrate conformations embedded within enzyme active sites and determine those with optimal binding affinities. Molecular dynamics simulations provide insights into the dynamics and roles of active site components as well as the interactions between substrate and enzymes. Hybrid quantum mechanical/molecular mechanical (QM/MM) can model reactions in active sites while considering steric and electrostatic contributions provided by the surrounding environment. Using previous studies done within our group, on OvoA, EgtB, ThrRS, LuxS and MsrA enzymatic systems, we will review how these methods can be used either independently or cooperatively to get insights into enzymatic catalysis.
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Dokainish HM, Gauld JW. A Molecular Dynamics and Quantum Mechanics/Molecular Mechanics Study of the Catalytic Reductase Mechanism of Methionine Sulfoxide Reductase A: Formation and Reduction of a Sulfenic Acid. Biochemistry 2013; 52:1814-27. [DOI: 10.1021/bi301168p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Hisham M. Dokainish
- Department of Chemistry
and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department of Chemistry
and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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Neiers F, Boschi-Muller S, Branlant G. Comment on “A Sulfonium Cation Intermediate in the Mechanism of Methionine Sulfoxide Reductase B: A DFT Study”. J Phys Chem B 2011; 115:10775; discussion 10776-7. [DOI: 10.1021/jp2064744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabrice Neiers
- AREMS, UMR CNRS-UHP 7214, Nancy Université, Bâtiment Biopôle, Faculté de Médecine, BP 184, 9 avenue de la Forêt de Haye, 54506 Vandoeuvre-les-Nancy, France
| | - Sandrine Boschi-Muller
- AREMS, UMR CNRS-UHP 7214, Nancy Université, Bâtiment Biopôle, Faculté de Médecine, BP 184, 9 avenue de la Forêt de Haye, 54506 Vandoeuvre-les-Nancy, France
| | - Guy Branlant
- AREMS, UMR CNRS-UHP 7214, Nancy Université, Bâtiment Biopôle, Faculté de Médecine, BP 184, 9 avenue de la Forêt de Haye, 54506 Vandoeuvre-les-Nancy, France
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Robinet JJ, Dokainish HM, Paterson DJ, Gauld JW. A Sulfonium Cation Intermediate in the Mechanism of Methionine Sulfoxide Reductase B: A DFT Study. J Phys Chem B 2011; 115:9202-12. [DOI: 10.1021/jp111681e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jesse J. Robinet
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Hisham. M. Dokainish
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - David J. Paterson
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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