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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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Madabeni A, Orian L. The Key Role of Chalcogenurane Intermediates in the Reduction Mechanism of Sulfoxides and Selenoxides by Thiols Explored In Silico. Int J Mol Sci 2023; 24:ijms24097754. [PMID: 37175462 PMCID: PMC10178455 DOI: 10.3390/ijms24097754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Sulfoxides and selenoxides oxidize thiols to disulfides while being reduced back to sulfides and selenides. While the reduction mechanism of sulfoxides to sulfides has been thoroughly explored experimentally as well as computationally, less attention has been devoted to the heavier selenoxides. In this work, we explore the reductive mechanism of dimethyl selenoxide, as an archetypal selenoxide and, for the sake of comparison, the reductive mechanism of dimethyl sulfoxide to gain insight into the role of the chalcogen on the reaction substrate. Particular attention is devoted to the key role of sulfurane and selenurane intermediates. Moreover, the capacity of these system to oxidize selenols rather than thiols, leading to the formation of selenyl sulfide bridges, is explored in silico. Notably, this analysis provides molecular insight into the role of selenocysteine in methionine sulfoxide reductase selenoenzyme. The activation strain model of chemical reactivity is employed in the studied reactions as an intuitive tool to bridge the computationally predicted effect of the chalcogen on the chalcogenoxide as well as on the chalcogenol.
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Affiliation(s)
- Andrea Madabeni
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
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Sakai N, Shimada R, Ogiwara Y. Indium‐Catalyzed Deoxygenation of Sulfoxides with Hydrosilanes. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Norio Sakai
- Department of Pure and Applied Chemistry Faculty of Science and Technology Tokyo University of Science (RIKADAI) Noda Chiba 278-8510 Japan
| | - Retsu Shimada
- Department of Pure and Applied Chemistry Faculty of Science and Technology Tokyo University of Science (RIKADAI) Noda Chiba 278-8510 Japan
| | - Yohei Ogiwara
- Department of Pure and Applied Chemistry Faculty of Science and Technology Tokyo University of Science (RIKADAI) Noda Chiba 278-8510 Japan
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Ramondo F, Leonzi I, Meloni G. Reducing Properties of Superalkalis on Pyridinic Graphene Surfaces: a Computational Study. Chemphyschem 2019; 20:3251-3258. [PMID: 31609060 DOI: 10.1002/cphc.201900789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/16/2019] [Indexed: 11/09/2022]
Abstract
The hyperlithiated species Li k + 1 F k (k=1, 2, 3, and 4) have been studied by quantum mechanical (QM) methods. Different structures have been localized for each molecule by the CBS-QB3 composite method: all the isomers show superalkali properties and strong tendency to donate an electron to carbon dioxide forming stable Li k + 1 F k · · · CO 2 complexes. With the aim to find molecular systems able to stabilize superalkalis, geometries of complexes between superalkalis and pyridine and superalkalis and graphene surfaces doped with a pyridinic vacancy were calculated. The pyridinic graphene sheets were modeled with two finite molecular systems C69 H21 N3 and C117 H27 N3 . The interaction with one pyridine molecule is quite weak and the superalkali maintains its structure and electron properties. The affinity for graphene sheets is instead stronger and the superalkalis tend to deform their geometry to better interact with the graphene surface. However, the superalkalis continue to show the tendency to transfer electrons to carbon dioxide reducing CO2 , as found in graphene absence.
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Affiliation(s)
- Fabio Ramondo
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67100, L'Aquila, Italy.,Department of Chemistry, University of Rome La Sapienza, P.le A. Moro 5, I-00185, Rome, Italy
| | - Ilenia Leonzi
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67100, L'Aquila, Italy
| | - Giovanni Meloni
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67100, L'Aquila, Italy.,Department of Chemistry, University of San Francisco, San Francisco, CA 94117, USA
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is perhaps the most widely used technology from the undergraduate teaching labs in organic chemistry to advanced research for the determination of three-dimensional structure as well as dynamics of biomolecular systems... The NMR spectrum of a molecule under a given experimental condition is unique, providing both quantitative and structural information. In particular, the quantitative nature of NMR spectroscopy offers the ability to follow a reaction pathway of the given molecule in a dynamic process under well-defined experimental conditions. To highlight the use of NMR when determining the molecular thermodynamic parameters, a review of three distinct applications developed from our laboratory is presented. These applications include the thermodynamic parameters of (a) molecular oxidation from time-dependent kinetics, (b) intramolecular rotation, and (c) intermolecular exchange. An experimental overview and the method of data analysis are provided so that these applications can be adopted in a range of molecular systems.
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6
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Park H, Meloni G. Activation of Dinitrogen with a Superalkali Species, Li3
F2. Chemphyschem 2018; 19:256-260. [DOI: 10.1002/cphc.201701232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Heejune Park
- Department of Chemistry; University of San Francisco; 2130 Fulton St San Francisco CA 94117 USA
| | - Giovanni Meloni
- Department of Chemistry; University of San Francisco; 2130 Fulton St San Francisco CA 94117 USA
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7
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Baldus M, Klie R, De X, Methner FJ. Effect of l-Cysteine and Transition Metal Ions on Dimethyl Sulfide Oxidation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:2180-2188. [PMID: 28215084 DOI: 10.1021/acs.jafc.6b05472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
During malt kilning, significant amounts of dimethyl sulfide (DMS) oxidize leading to the formation of dimethyl sulfoxide (DMSO), a precursor of DMS during fermentation. Yet, knowledge regarding reaction mechanisms of DMSO formation during malt production is limited. The role of thiols in sulfide oxidation is unclear as they possess sulfoxide reducing ability as well as pro- and antioxidative properties. This study investigated the effects of the thiol l-cysteine (Cys), molecular oxygen, transition metal ions, and EDTA on DMS oxidation in aqueous model solutions. Highest oxidative DMS consumption was observed when Cys was combined with iron(II) (∼12%) and copper(II) (∼40%). Response surface modeling (RSM) revealed that Cys together with copper(II) had a strictly prooxidative effect and no antioxidative behavior was found. Hydrogen peroxide, as generated via autoxidation of Cys-Cu(I)-Cys complexes, was supposed to be the primary DMS oxidant in this work. Based on redox kinetics, potential reaction mechanisms, and their impact on oxidative processes in thermal food processing, such as malt and beer production, are discussed.
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Affiliation(s)
- Matthias Baldus
- Department of Food Technology and Food Chemistry, Chair of Brewing Science, Technische Universität Berlin , Seestrasse 13, 13353 Berlin, Germany
| | - Rüdiger Klie
- Department of Food Technology and Food Chemistry, Chair of Brewing Science, Technische Universität Berlin , Seestrasse 13, 13353 Berlin, Germany
| | - Xi De
- Department of Food Technology and Food Chemistry, Chair of Brewing Science, Technische Universität Berlin , Seestrasse 13, 13353 Berlin, Germany
| | - Frank-Jürgen Methner
- Department of Food Technology and Food Chemistry, Chair of Brewing Science, Technische Universität Berlin , Seestrasse 13, 13353 Berlin, Germany
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8
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Dougherty RJ, Singh J, Krishnan V. Kinetics and thermodynamics of oxidation mediated reaction in l-cysteine and its methyl and ethyl esters in dimethyl sulfoxide-d6 by NMR spectroscopy. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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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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10
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Lindquist BA, Woon DE, Dunning TH. Effects of Ligand Electronegativity on Recoupled Pair Bonds with Application to Sulfurane Precursors. J Phys Chem A 2014; 118:5709-19. [DOI: 10.1021/jp503982e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Beth A. Lindquist
- Department of Chemistry, University of Illinois at Urbana−Champaign, 601 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - David E. Woon
- Department of Chemistry, University of Illinois at Urbana−Champaign, 601 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Thom H. Dunning
- Department of Chemistry, University of Illinois at Urbana−Champaign, 601 South Mathews Avenue, Urbana, Illinois 61801, United States
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11
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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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12
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A specific and rapid colorimetric method to monitor the activity of methionine sulfoxide reductase A. Enzyme Microb Technol 2013; 53:391-7. [DOI: 10.1016/j.enzmictec.2013.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/17/2013] [Accepted: 08/25/2013] [Indexed: 12/16/2022]
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13
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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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14
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15
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Chee GL, Bhattarai B, Daniel Gietz R, Alrushaid S, Nitiss JL, Hasinoff BB. Chemical reactivity and microbicidal action of bethoxazin. Bioorg Med Chem 2012; 20:1494-501. [DOI: 10.1016/j.bmc.2011.12.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 01/03/2023]
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16
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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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18
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Methionine sulfoxide reductase A is a stereospecific methionine oxidase. Proc Natl Acad Sci U S A 2011; 108:10472-7. [PMID: 21670260 DOI: 10.1073/pnas.1101275108] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methionine sulfoxide reductase A (MsrA) catalyzes the reduction of methionine sulfoxide to methionine and is specific for the S epimer of methionine sulfoxide. The enzyme participates in defense against oxidative stresses by reducing methionine sulfoxide residues in proteins back to methionine. Because oxidation of methionine residues is reversible, this covalent modification could also function as a mechanism for cellular regulation, provided there exists a stereospecific methionine oxidase. We show that MsrA itself is a stereospecific methionine oxidase, producing S-methionine sulfoxide as its product. MsrA catalyzes its own autooxidation as well as oxidation of free methionine and methionine residues in peptides and proteins. When functioning as a reductase, MsrA fully reverses the oxidations which it catalyzes.
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19
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Korang J, Grither WR, McCulla RD. Comparison of Experimental and Computationally Predicted Sulfoxide Bond Dissociation Enthalpies. J Phys Chem A 2011; 115:2859-65. [DOI: 10.1021/jp1109465] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James Korang
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri 63103, United States
| | - Whitney R. Grither
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri 63103, United States
| | - Ryan D. McCulla
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri 63103, United States
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20
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Thiriot E, Monard G, Boschi-Muller S, Branlant G, Ruiz-López MF. Reduction mechanism in class A methionine sulfoxide reductases: a theoretical chemistry investigation. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0901-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Aversa MC, Barattucci A, Bonaccorsi P, Contini A. Addition of sulfenic acids to monosubstituted acetylenes: a theoretical and experimental study. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1557] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Patil MP, Sunoj RB. On the relative preference of enamine/iminium pathways in an organocatalytic Michael addition reaction. Chem Asian J 2009; 4:714-24. [PMID: 19353592 DOI: 10.1002/asia.200800351] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism of the organocatalyzed Michael addition between propanal and methyl vinyl ketone is investigated using the density functional and ab intio methods. Different modes of substrate activation offered by a secondary amine (pyrrolidine) organocatalyst are reported. The electrophilic activation of enone (P-I) through the formation of an iminium ion, and nucleophilic activation of propanal (P-II) in the form of enamine have been examined by identifying the corresponding transition states. The kinetic preference for the formation of key intermediates is established in an effort to identify the competing pathways associated with the title reaction. A comparison of barriers associated with different pathways as well as intermediate formation allows us to provide a suitable mechanistic rationale for Michael addition reactions catalyzed by a secondary amine. The overall barriers for the C-C bond formation pathways involving enol or iminium intermediates are identified as higher than the enamine pathway. Additionally, the generation of iminium is found to be less favored as compared to enamine formation. The effect of co-catalyst/protic solvent on the energetics of the overall reaction is also studied using the cluster continuum approach. Significant reduction in the activation energies for each step of the reaction is predicted for the solvent-assisted models. The co-catalyst assisted addition of propanal-enamine to methyl vinyl ketone is identified as the most preferred pathway (P-IV) for the Michael addition reaction. The results are in concurrence with the available experimental reports on the rate acceleration by the use of a co-catalyst in this reaction.
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Affiliation(s)
- Mahendra P Patil
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Kano N, Itoh Y, Watanabe Y, Kusaka S, Kawashima T. Structure and Properties of a Sulfur(IV)Sulfur(II)-Bond Compound: Reversible Conversion of a Sulfur-Substituted Organosulfurane into a Thiol. Angew Chem Int Ed Engl 2008; 47:9430-3. [DOI: 10.1002/anie.200803945] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kano N, Itoh Y, Watanabe Y, Kusaka S, Kawashima T. Structure and Properties of a Sulfur(IV)Sulfur(II)-Bond Compound: Reversible Conversion of a Sulfur-Substituted Organosulfurane into a Thiol. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Patil M, Sunoj R. The Role of Noninnocent Solvent Molecules in Organocatalyzed Asymmetric Michael Addition Reactions. Chemistry 2008; 14:10472-85. [DOI: 10.1002/chem.200800877] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Boschi-Muller S, Gand A, Branlant G. The methionine sulfoxide reductases: Catalysis and substrate specificities. Arch Biochem Biophys 2008; 474:266-73. [PMID: 18302927 DOI: 10.1016/j.abb.2008.02.007] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 02/05/2008] [Accepted: 02/05/2008] [Indexed: 02/01/2023]
Abstract
Oxidation of Met residues in proteins leads to the formation of methionine sulfoxides (MetSO). Methionine sulfoxide reductases (Msr) are ubiquitous enzymes, which catalyze the reduction of the sulfoxide function of the oxidized methionine residues. In vivo, the role of Msrs is described as essential in protecting cells against oxidative damages and to play a role in infection of cells by pathogenic bacteria. There exist two structurally-unrelated classes of Msrs, called MsrA and MsrB, with opposite stereoselectivity towards the S and R isomers of the sulfoxide function, respectively. Both Msrs present a similar three-step catalytic mechanism. The first step, called the reductase step, leads to the formation of a sulfenic acid on the catalytic Cys with the concomitant release of Met. In recent years, significant efforts have been made to characterize structural and molecular factors involved in the catalysis, in particular of the reductase step, and in structural specificities.
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Affiliation(s)
- Sandrine Boschi-Muller
- UMR 7567 CNRS-UHP--Maturation des ARN et Enzymologie Moléculaire, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy, France.
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Ranaivoson FM, Antoine M, Kauffmann B, Boschi-Muller S, Aubry A, Branlant G, Favier F. A structural analysis of the catalytic mechanism of methionine sulfoxide reductase A from Neisseria meningitidis. J Mol Biol 2008; 377:268-80. [PMID: 18255097 DOI: 10.1016/j.jmb.2008.01.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 12/21/2007] [Accepted: 01/02/2008] [Indexed: 01/30/2023]
Abstract
The methionine sulfoxide reductases (Msrs) are thioredoxin-dependent oxidoreductases that catalyse the reduction of the sulfoxide function of the oxidized methionine residues. These enzymes have been shown to regulate the life span of a wide range of microbial and animal species and to play the role of physiological virulence determinant of some bacterial pathogens. Two structurally unrelated classes of Msrs exist, MsrA and MsrB, with opposite stereoselectivity towards the R and S isomers of the sulfoxide function, respectively. Both Msrs share a similar three-step chemical mechanism including (1) the formation of a sulfenic acid intermediate on the catalytic Cys with the concomitant release of the product-methionine, (2) the formation of an intramonomeric disulfide bridge between the catalytic and the regenerating Cys and (3) the reduction of the disulfide bridge by thioredoxin or its homologues. In this study, four structures of the MsrA domain of the PilB protein from Neisseria meningitidis, representative of four catalytic intermediates of the MsrA catalytic cycle, were determined by X-ray crystallography: the free reduced form, the Michaelis-like complex, the sulfenic acid intermediate and the disulfide oxidized forms. They reveal a conserved overall structure up to the formation of the sulfenic acid intermediate, while a large conformational switch is observed in the oxidized form. The results are discussed in relation to those proposed from enzymatic, NMR and theoretical chemistry studies. In particular, the substrate specificity and binding, the catalytic scenario of the reductase step and the relevance and role of the large conformational change observed in the oxidized form are discussed.
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Affiliation(s)
- Fanomezana M Ranaivoson
- LCM3B, Equipe Biocristallographie, UMR 7036 CNRS-UHP, Faculté des Sciences et Techniques, Nancy Université, BP 239, 54506 Vandoeuvre-les-Nancy, France
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Patil MP, Sunoj RB. Insights on co-catalyst-promoted enamine formation between dimethylamine and propanal through ab initio and density functional theory study. J Org Chem 2007; 72:8202-15. [PMID: 17900139 DOI: 10.1021/jo071004q] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mechanistic details on enamine formation between dimethylamine and propanal are unraveled using the ab initio and density functional theory methods. The addition of secondary amine to the electrophile and simultaneous proton transfer results in a carbinolamine intermediate, which subsequently undergoes dehydration to form enamine. The direct addition of amine as well as the dehydration of the resulting carbinolamine intermediate is predicted to possess fairly high activation barrier implying that a unimolecular process is unlikely to be responsible for enamine formation. Different models are therefore proposed which could explain the relative ease of enamine formation under neat condition as well as under the influence of methanol as the co-catalyst. The explicit inclusion of either the reagent or the co-catalyst is considered in the transition states as stabilizing agents. The participation of the reagent or the co-catalyst as a monofunctional ancillary species is found to stabilize the transition states relative to the unassisted or the direct addition/dehydration pathways. The reduction in enthalpy of activation is found to be much more dramatic when two co-catalysts participate in an active bifunctional mode in the rate-determining dehydration step. The transition structures exhibited characteristic features of a relay proton transfer mechanism. The free energy of activation associated with the two methanol-assisted pathway is found to be 16.7 kcal/mol lower than that of the unassisted pathway. The results are found to be in concurrence with the available reports on the rate acceleration by co-catalysts in the Michael reaction between enamine and methyl vinyl ketone under neat conditions.
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Affiliation(s)
- Mahendra P Patil
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Gand A, Antoine M, Boschi-Muller S, Branlant G. Characterization of the Amino Acids Involved in Substrate Specificity of Methionine Sulfoxide Reductase A. J Biol Chem 2007; 282:20484-91. [PMID: 17500063 DOI: 10.1074/jbc.m702350200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methionine sulfoxide reductases (Msrs) are ubiquitous enzymes that catalyze the thioredoxin-dependent reduction of methionine sulfoxide (MetSO) back to methionine. In vivo, Msrs are essential in protecting cells against oxidative damages on proteins and in the virulence of some bacteria. There exists two structurally unrelated classes of Msrs. MsrAs are stereo-specific toward the S epimer on the sulfur of the sulfoxide, whereas MsrBs are specific toward the R isomer. Both classes of Msrs display a similar catalytic mechanism of sulfoxide reduction by thiols via the sulfenic acid chemistry and a better affinity for protein-bound MetSO than for free MetSO. Recently, the role of the amino acids implicated in the catalysis of the reductase step of Neisseria meningitidis MsrA was determined. In the present study, the invariant amino acids potentially involved in substrate binding, i.e. Phe-52, Trp-53, Asp-129, His-186, Tyr-189, and Tyr-197, were substituted. The catalytic parameters under steady-state conditions and of the reductase step of the mutated MsrAs were determined and compared with those of the wild type. Altogether, the results support the presence of at least two binding subsites. The first one, whose contribution is major in the efficiency of the reductase step and in which the epsilon-methyl group of MetSO binds, is the hydrophobic pocket formed by Phe-52 and Trp-53, the position of the indole ring being stabilized by interactions with His-186 and Tyr-189. The second subsite composed of Asp-129 and Tyr-197 contributes to the binding of the main chain of the substrate but to a lesser extent.
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Affiliation(s)
- Adeline Gand
- Maturation des ARN et Enzymologie Moléculaire, Unité Mixte de Recherche CNRS-UHP 7567, Nancy Université, Faculté des Sciences et Techniques, Bld. des Aiguillettes, BP 239, 54506 Vandoeuvre-les-Nancy, France
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Coudevylle N, Antoine M, Bouguet-Bonnet S, Mutzenhardt P, Boschi-Muller S, Branlant G, Cung MT. Solution Structure and Backbone Dynamics of the Reduced Form and an Oxidized Form of E. coli Methionine Sulfoxide Reductase A (MsrA): Structural Insight of the MsrA Catalytic Cycle. J Mol Biol 2007; 366:193-206. [PMID: 17157315 DOI: 10.1016/j.jmb.2006.11.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 11/08/2006] [Accepted: 11/09/2006] [Indexed: 11/16/2022]
Abstract
Methionine sulfoxide reductases (Msr) reduce methionine sulfoxide (MetSO)-containing proteins, back to methionine (Met). MsrAs are stereospecific for the S epimer whereas MsrBs reduce the R epimer of MetSO. Although structurally unrelated, the Msrs characterized so far display a similar catalytic mechanism with formation of a sulfenic intermediate on the catalytic cysteine and a concomitant release of Met, followed by formation of at least one intramolecular disulfide bond (between the catalytic and a recycling cysteine), which is then reduced by thioredoxin. In the case of the MsrA from Escherichia coli, two disulfide bonds are formed, i.e. first between the catalytic Cys51 and the recycling Cys198 and then between Cys198 and the second recycling Cys206. Three crystal structures including E. coli and Mycobacterium tuberculosis MsrAs, which, for the latter, possesses only the unique recycling Cys198, have been solved so far. In these structures, the distances between the cysteine residues involved in the catalytic mechanism are too large to allow formation of the intramolecular disulfide bonds. Here structural and dynamical NMR studies of the reduced wild-type and the oxidized (Cys51-Cys198) forms of C86S/C206S MsrA from E. coli have been carried out. The mapping of MetSO substrate-bound C51A MsrA has also been performed. The data support (1) a conformational switch occurring subsequently to sulfenic acid formation and/or Met release that would be a prerequisite to form the Cys51-Cys198 bond and, (2) a high mobility of the C-terminal part of the Cys51-Cys198 oxidized form that would favor formation of the second Cys198-Cys206 disulfide bond.
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Affiliation(s)
- Nicolas Coudevylle
- Laboratoire de Chimie Physique Macromoléculaire UMR 7568 CNRS-INPL, Nancy Universités, 1 rue Grandville, B.P. 20451, 54001 Nancy cedex, France
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Antoine M, Gand A, Boschi-Muller S, Branlant G. Characterization of the Amino Acids from Neisseria meningitidis MsrA Involved in the Chemical Catalysis of the Methionine Sulfoxide Reduction Step. J Biol Chem 2006; 281:39062-70. [PMID: 17062561 DOI: 10.1074/jbc.m608844200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methionine sulfoxide reductases (Msrs) are ubiquitous enzymes that reduce protein-bound methionine sulfoxide back to Met in the presence of thioredoxin. In vivo, the role of the Msrs is described as essential in protecting cells against oxidative damages and as playing a role in infection of cells by pathogenic bacteria. There exist two structurally unrelated classes of Msrs, called MsrA and MsrB, specific for the S and the R epimer of the sulfoxide function of methionine sulfoxide, respectively. Both Msrs present a similar catalytic mechanism, which implies, as a first step, a reductase step that leads to the formation of a sulfenic acid on the catalytic cysteine and a concomitant release of a mole of Met. The reductase step has been previously shown to be efficient and not rate-limiting. In the present study, the amino acids involved in the catalysis of the reductase step of the Neisseria meningitidis MsrA have been characterized. The invariant Glu-94 and to a lesser extent Tyr-82 and Tyr-134 are shown to play a major role in the stabilization of the sulfurane transition state and indirectly in the decrease of the pK(app) of the catalytic Cys-51. A scenario of the reductase step is proposed in which the substrate binds to the active site with its sulfoxide function largely polarized via interactions with Glu-94, Tyr-82, and Tyr-134 and participates via the positive or partially positive charge borne by the sulfur of the sulfoxide in the stabilization of the catalytic Cys.
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Affiliation(s)
- Mathias Antoine
- Maturation des ARN et Enzymologie Moléculaire, Unite Mixte de Recherche, CNRS-UHP 7567, Nancy Université, Faculté des Sciences et Techniques, Bld des Aiguillettes, BP 239, 54506 Vandoeuvre-les-Nancy, France
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