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Ion BF, Aboelnga MM, Gauld JW. QM/MM investigation of the discriminatory pre-transfer editing mechanism operated by Lysyl-tRNA synthetase. J Biomol Struct Dyn 2024:1-9. [PMID: 38197420 DOI: 10.1080/07391102.2023.2301054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 01/11/2024]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that remarkable facilitate the aminoacylation process during translation. With a high fidelity, the mischarged tRNA is prevented through implementing pre- and post-transfer proofreading mechanisms. For instance, Lysine-tRNA synthetase charges the native substrate, lysine, to its cognate tRNA. In spite of the great structural similarity between lysine to the noncognate and toxic ornithine, with the side chain of lysine being only one methylene group longer, LysRS is able to achieve this discrimination with a high efficiency. In this work, the hybrid quantum mechanics/molecular mechanics (QM/MM) investigation was applied to probe the pre-transfer editing mechanism catalyzed by lysyl-tRNA synthetase to reject the noncognte aminoacyl, L-ornityl (Orn), compared to the cognate substrate, L-lysyl. Particularly, the self-cyclization pre-transfer editing mechanism was explored for the two substrates. The substrate-assisted self-cyclization editing of Orn-AMP, where its phosphate moiety acts as the catalytic base, is found to be the rate-determining step with an energy barrier of 101.2 kJ mol-1. Meanwhile, the corresponding rate-limiting pathway for the native Lys-AMP lies at 140.2 kJ mol-1. This observation clearly indicated the infeasibility of this catalytic scenario in the presence of the native substrate. Interestingly, a thermodynamically favorable cyclic product of -92.9 kJ mol-1 with respect to the aminoacyl reactant complex demonstrated evidence of a successful pre-transfer editing. This reaction resulted in the discharge of the on-cognate -ornithine derivative from LysU's active site. These valuable mechanistic insights are valuable to enrich our knowledge of this extremely efficient and specific catalytic machinery of LysRS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bogdan F Ion
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Mohamed M Aboelnga
- Chemistry Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
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2
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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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3
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Enzymatic N N bond formation: Mechanism for the N-nitroso synthesis catalyzed by non-heme iron SznF enzyme. J Catal 2021. [DOI: 10.1016/j.jcat.2021.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Jen FEC, Semchenko EA, Day CJ, Seib KL, Jennings MP. The Neisseria gonorrhoeae Methionine Sulfoxide Reductase (MsrA/B) Is a Surface Exposed, Immunogenic, Vaccine Candidate. Front Immunol 2019; 10:137. [PMID: 30787927 PMCID: PMC6372556 DOI: 10.3389/fimmu.2019.00137] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/16/2019] [Indexed: 12/13/2022] Open
Abstract
Control of the sexually transmitted infection gonorrhea is a major public health challenge, due to the recent emergence of multidrug resistant strains of Neisseria gonorrhoeae, and there is an urgent need for novel therapies or a vaccine to prevent gonococcal disease. In this study, we evaluated the methionine sulfoxide reductase (MsrA/B) of N. gonorrhoeae as a potential vaccine candidate, in terms of its expression, sequence conservation, localization, immunogenicity, and the functional activity of antibodies raised to it. Gonococcal MsrA/B has previously been shown to reduce methionine sulfoxide [Met(O)] to methionine (Met) in oxidized proteins and protect against oxidative stress. Here we have shown that the gene encoding MsrA/B is present, highly conserved, and expressed in all N. gonorrhoeae strains investigated, and we determined that MsrA/B is surface is exposed on N. gonorrhoeae. Recombinant MsrA/B is immunogenic, and mice immunized with MsrA/B and either aluminum hydroxide gel adjuvant or Freund's adjuvant generated a humoral immune response, with predominantly IgG1 antibodies. Higher titers of IgG2a, IgG2b, and IgG3 were detected in mice immunized with MsrA/B-Freund's adjuvant compared to MsrA/B-aluminum hydroxide adjuvant, while IgM titers were similar for both adjuvants. Antibodies generated by MsrA/B-Freund's in mice mediated bacterial killing via both serum bactericidal activity and opsonophagocytic activity. Anti-MsrA/B was also able to functionally block the activity of MsrA/B by inhibiting binding to its substrate, Met(O). We propose that recombinant MsrA/B is a promising vaccine antigen for N. gonorrhoeae.
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Affiliation(s)
- Freda E-C Jen
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Evgeny A Semchenko
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Christopher J Day
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
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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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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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Tarrago L, Gladyshev VN. Recharging oxidative protein repair: catalysis by methionine sulfoxide reductases towards their amino acid, protein, and model substrates. BIOCHEMISTRY (MOSCOW) 2013; 77:1097-107. [PMID: 23157290 DOI: 10.1134/s0006297912100021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The sulfur-containing amino acid methionine (Met) in its free and amino acid residue forms can be readily oxidized to the R and S diastereomers of methionine sulfoxide (MetO). Methionine sulfoxide reductases A (MSRA) and B (MSRB) reduce MetO back to Met in a stereospecific manner, acting on the S and R forms, respectively. A third MSR type, fRMSR, reduces the R form of free MetO. MSRA and MSRB are spread across the three domains of life, whereas fRMSR is restricted to bacteria and unicellular eukaryotes. These enzymes protect against abiotic and biotic stresses and regulate lifespan. MSRs are thiol oxidoreductases containing catalytic redox-active cysteine or selenocysteine residues, which become oxidized by the substrate, requiring regeneration for the next catalytic cycle. These enzymes can be classified according to the number of redox-active cysteines (selenocysteines) and the strategies to regenerate their active forms by thioredoxin and glutaredoxin systems. For each MSR type, we review catalytic parameters for the reduction of free MetO, low molecular weight MetO-containing compounds, and oxidized proteins. Analysis of these data reinforces the concept that MSRAs reduce various types of MetO-containing substrates with similar efficiency, whereas MSRBs are specialized for the reduction of MetO in proteins.
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Affiliation(s)
- L Tarrago
- Brigham and Women's Hospital and Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA 02115, USA
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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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Heverly-Coulson GS, Boyd RJ, Mó O, Yáñez M. Revealing Unexpected Mechanisms for Nucleophilic Attack on SS and SeSe Bridges. Chemistry 2013; 19:3629-38. [DOI: 10.1002/chem.201203328] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/28/2012] [Indexed: 01/01/2023]
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Robinet JJ, Dokainish HM, Paterson DJ, Gauld JW. Reply to the “Comment on 'A Sulfonium Cation Intermediate in the Mechanism of Methionine Sulfoxide Reductase B: A DFT Study’”. J Phys Chem B 2011. [DOI: 10.1021/jp2069418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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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