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Rahaman H, Herojit K, Singh LR, Haobam R, Fisher AB. Structural and Functional Diversity of the Peroxiredoxin 6 Enzyme Family. Antioxid Redox Signal 2024; 40:759-775. [PMID: 37463006 DOI: 10.1089/ars.2023.0287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Significance: Peroxiredoxins (Prdxs) with a single peroxidative cysteine (CP) in a conserved motif PXXX(T/S)XXCP within its thioredoxin fold, have been classified as the peroxiredoxin 6 (Prdx6 ) family. All Prdxs can reduce H2O2 and short chain hydroperoxides while Prdx6 in addition, can reduce phospholipid hydroperoxides (PLOOH) due to its ability to interact with peroxidized phospholipid substrate. The single CP of Prdx6 uses various external electron donors including glutathione thioredoxin, and ascorbic acid for resolution of its peroxidized state and, therefore, its peroxidase activity. Prdx6 proteins also exhibit Ca2+-independent phospholipase A2 (PLA2), lysophosphatidylcholine acyltransferase (LPCAT), and chaperone activities that depend on cellular localization and the oxidation and oligomerisation states of the protein. Thus, Prdx6 is a "moonlighting" enzyme. Recent Advance: Physiologically, Prdx6s have been reported to play an important role in protection against oxidative stress, repair of peroxidized cell membranes, mammalian lung surfactant turnover, activation of some NADPH oxidases, the regulation of seed germination in plants, as an indicator of cellular levels of reactive O2 species through Nrf-Klf9 activation, and possibly in male fertility, regulation of cell death through ferroptosis, cancer metastasis, and oxidative stress-related signalling pathways. Critical Issues: This review outlines Prdx6 enzyme unique structural features and explores its wide range of physiological functions. Yet, existing structural data falls short of fully revealing all of human Prdx6 multifunctional roles. Further endeavour is required to bridge this gap in its understanding. Although there are wide variations in both the structure and function of Prdx6 family members in various organisms, all Prdx6 proteins show the unique a long C-terminal extension that is also seen in Prdx1, but not in other Prdxs. Future Directions: As research data continues to accumulate, the potential for detailed insights into the role of C-terminal of Prdx6 in its oligomerisation and activities. There is a need for thorough exploration of structural characteristics of the various biological functions. Additionally, uncovering the interacting partners of Prdx6 and understanding its involvement in signalling pathways will significantly contribute to a more profound comprehension of its role.
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Affiliation(s)
- Hamidur Rahaman
- Department of Biotechnology, Manipur University, Imphal, India
| | - Khundrakpam Herojit
- Department of Biotechnology, Manipur University, Imphal, India
- Department of Biotechnology, Mangolnganbi College, Ningthoukhong, India
| | | | - Reena Haobam
- Department of Biotechnology, Manipur University, Imphal, India
| | - Aron B Fisher
- Institute for Environmental Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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2
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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3
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Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance. Antioxidants (Basel) 2022; 11:antiox11030561. [PMID: 35326211 PMCID: PMC8945050 DOI: 10.3390/antiox11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 12/10/2022] Open
Abstract
Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.
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Bioinformatic Analyses of Peroxiredoxins and RF-Prx: A Random Forest-Based Predictor and Classifier for Prxs. Methods Mol Biol 2022; 2499:155-176. [PMID: 35696080 PMCID: PMC9844236 DOI: 10.1007/978-1-0716-2317-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Peroxiredoxins (Prxs) are a protein superfamily, present in all organisms, that play a critical role in protecting cellular macromolecules from oxidative damage but also regulate intracellular and intercellular signaling processes involving redox-regulated proteins and pathways. Bioinformatic approaches using computational tools that focus on active site-proximal sequence fragments (known as active site signatures) and iterative clustering and searching methods (referred to as TuLIP and MISST) have recently enabled the recognition of over 38,000 peroxiredoxins, as well as their classification into six functionally relevant groups. With these data providing so many examples of Prxs in each class, machine learning approaches offer an opportunity to extract additional information about features characteristic of these protein groups.In this study, we developed a novel computational method named "RF-Prx" based on a random forest (RF) approach integrated with K-space amino acid pairs (KSAAP) to identify peroxiredoxins and classify them into one of six subgroups. Our process performed in a superior manner compared to other machine learning classifiers. Thus the RF approach integrated with K-space amino acid pairs enabled the detection of class-specific conserved sequences outside the known functional centers and with potential importance. For example, drugs designed to target Prx proteins would likely suffer from cross-reactivity among distinct Prxs if targeted to conserved active sites, but this may be avoidable if remote, class-specific regions could be targeted instead.
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5
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Bolduc J, Koruza K, Luo T, Malo Pueyo J, Vo TN, Ezeriņa D, Messens J. Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities. Redox Biol 2021; 42:101959. [PMID: 33895094 PMCID: PMC8113037 DOI: 10.1016/j.redox.2021.101959] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/07/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. Understanding the role of the multiple structural and post-translational modification (PTM) layers that tunes the peroxiredoxin specificities is still a challenge. In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. Armed with numerous cellular and atomic level experimental techniques, we look at the future and ask ourselves what is still needed to give us a clearer view on the cellular operating power of Prdxs in both stress and non-stress conditions.
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Affiliation(s)
- Jesalyn Bolduc
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Katarina Koruza
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Ting Luo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Julia Malo Pueyo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Trung Nghia Vo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Daria Ezeriņa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium.
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6
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Shivaiah KK, Upton B, Nikolau BJ. Kinetic, Structural, and Mutational Analysis of Acyl-CoA Carboxylase From Thermobifida fusca YX. Front Mol Biosci 2021; 7:615614. [PMID: 33511159 PMCID: PMC7835884 DOI: 10.3389/fmolb.2020.615614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
Acyl-CoA carboxylases (AcCCase) are biotin-dependent enzymes that are capable of carboxylating more than one short chain acyl-CoA substrate. We have conducted structural and kinetic analyses of such an AcCCase from Thermobifida fusca YX, which exhibits promiscuity in carboxylating acetyl-CoA, propionyl-CoA, and butyryl-CoA. The enzyme consists of two catalytic subunits (TfAcCCA and TfAcCCB) and a non-catalytic subunit, TfAcCCE, and is organized in quaternary structure with a A6B6E6 stoichiometry. Moreover, this holoenzyme structure appears to be primarily assembled from two A3 and a B6E6 subcomplexes. The role of the TfAcCCE subunit is to facilitate the assembly of the holoenzyme complex, and thereby activate catalysis. Based on prior studies of an AcCCase from Streptomyces coelicolor, we explored whether a conserved Asp residue in the TfAcCCB subunit may have a role in determining the substrate selectivity of these types of enzymes. Mutating this D427 residue resulted in alterations in the substrate specificity of the TfAcCCase, increasing proficiency for carboxylating acetyl-CoA, while decreasing carboxylation proficiency with propionyl-CoA and butyryl-CoA. Collectively these results suggest that residue D427 of AcCCB subunits is an important, but not sole determinant of the substrate specificity of AcCCase enzymes.
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Affiliation(s)
- Kiran-Kumar Shivaiah
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States.,Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States.,Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Bryon Upton
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States.,Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States.,Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Basil J Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States.,Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States.,Center for Metabolic Biology, Iowa State University, Ames, IA, United States
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7
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Klein F, Cáceres D, Carrasco MA, Tapia JC, Caballero J, Alzate-Morales J, Pantano S. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. J Chem Inf Model 2020; 60:3935-3943. [DOI: 10.1021/acs.jcim.0c00160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florencia Klein
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Daniela Cáceres
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Mónica A. Carrasco
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
| | - Juan Carlos Tapia
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
| | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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8
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Foglia NO, González Lebrero MC, Biekofsky RR, Estrin DA. Reaction Path Analysis from Potential Energy Contributions Using Forces: An Accessible Estimator of Reaction Coordinate Adequacy. J Chem Theory Comput 2020; 16:1618-1629. [PMID: 31999449 DOI: 10.1021/acs.jctc.9b01081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calculation of potential energy and free-energy profiles along complex chemical reactions or rare event processes is of great interest because of their importance for many areas in chemistry, molecular biology, and material science. One typical way to generate these profiles is to add a bias potential to modify the energy surface, which can act on a selected degree of freedom in the system. However, in these cases, the quality of the result is strongly dependent on the selection of the degree of freedom over which this bias potential acts. The present work introduces a simple method for the analysis of the degree of freedom selected to describe a chemical process. The proposed methodology is based on the decomposition of contributions to the potential energy profiles by the integration of forces along a reaction path, which allows evaluating the different contributions to the energy change. This could be useful for discriminating the contributions to the energy arising from different regions of the system, which is particularly useful in systems with complex environments that must be represented using hybrid quantum mechanics/molecular mechanics schemes. Furthermore, this methodology allows in generating a quick and simple analysis of the degree of freedom which is used to describe the potential energy profile associated with the reactive process. This is computationally more accessible than the corresponding free-energy profile and can therefore be used as a simple estimator of reaction coordinate adequacy.
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Affiliation(s)
- Nicolás O Foglia
- Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Mariano C González Lebrero
- Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Rodolfo R Biekofsky
- Moebius Research Ltd., Systems Biomedicine, 24 Chedworth House, West Green Rd, N15 5EH London, U.K
| | - Darío A Estrin
- Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
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9
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Himiyama T, Nakamura T. Disassembly of the ring-type decameric structure of peroxiredoxin from Aeropyrum pernix K1 by amino acid mutation. Protein Sci 2020; 29:1138-1147. [PMID: 32022337 DOI: 10.1002/pro.3837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/13/2022]
Abstract
The quaternary structure of peroxiredoxin from Aeropyrum pernix K1 (ApPrx) is a decamer, in which five homodimers are assembled in a pentagonal ring through hydrophobic interactions. In this study, we determined the amino acid (AA) residues of ApPrx crucial for forming the decamer using AA mutations. The ApPrx0Cys mutant, wherein all cysteine residues were mutated to serine, was prepared as a model protein to remove the influence of the redox states of the cysteines on its assembling behavior. The boundary between each homodimer of ApPrx0Cys contains characteristic aromatic AA residues forming hydrophobic interactions: F46, F80, W88, W210, and W211. We found that a single mutation of F46, F80, or W210 to alanine completely disassembled the ApPrx0Cys decamer to homodimers, which was clarified by gel-filtration chromatography and dynamic light scattering measurements. F46A, F80A, and W210A mutants lacked only one aromatic ring compared with ApPrx0Cys, indicating that the assembly is very sensitive to the surface structure of the protein. X-ray structures revealed two mechanisms of disassembly of the ApPrx decamer: loss of hydrophobicity between homodimers and flip of the arm domain. The AA residues targeted in this study are well conserved in ring-type Prx proteins, suggesting the importance of these residues in the assembly. This study demonstrates the sensitivity and modifiability of peroxiredoxin assembly by a simple AA mutation.
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Affiliation(s)
- Tomoki Himiyama
- National Institute of Advanced Industrial Science and Technology, Ikeda, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Japan
| | - Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology, Ikeda, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Japan
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10
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Semelak JA, Battistini F, Radi R, Trujillo M, Zeida A, Estrin DA. Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide. J Chem Inf Model 2019; 60:843-853. [PMID: 31718175 DOI: 10.1021/acs.jcim.9b00817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work, we employ a multiscale quantum-classical mechanics (QM/MM) scheme to investigate the chemical reactivity of sulfenic acids toward hydrogen peroxide, both in aqueous solution and in the protein environment of the peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE). The reaction of oxidation of cysteine with hydrogen peroxides, catalyzed by peroxiredoxins, is usually accelerated several orders of magnitude in comparison with the analogous reaction in solution. The resulting cysteine sulfenic acid is then reduced in other steps of the catalytic cycle, recovering the original thiol. However, under some conditions, the sulfenic acid can react with another equivalent of oxidant to form a sulfinic acid. This process is called overoxidation and has been associated with redox signaling. Herein, we employed a multiscale scheme based on density function theory calculations coupled to the classical AMBER force field, developed in our group, to establish the molecular basis of thiol overoxidation by hydrogen peroxide. Our results suggest that residues that play key catalytic roles in the oxidation of MtAhpE are not relevant in the overoxidation process. Indeed, the calculations propose that the process is unfavored by this particular enzyme microenvironment.
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Affiliation(s)
- J A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales , Ciudad Universitaria, Pab. 2 , CP 1428 , Buenos Aires , Argentina
| | - F Battistini
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , 08028 Barcelona , Spain
| | - R Radi
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - M Trujillo
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - A Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - D A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales , Ciudad Universitaria, Pab. 2 , CP 1428 , Buenos Aires , Argentina
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11
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Zeida A, Trujillo M, Ferrer-Sueta G, Denicola A, Estrin DA, Radi R. Catalysis of Peroxide Reduction by Fast Reacting Protein Thiols. Chem Rev 2019; 119:10829-10855. [PMID: 31498605 DOI: 10.1021/acs.chemrev.9b00371] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Life on Earth evolved in the presence of hydrogen peroxide, and other peroxides also emerged before and with the rise of aerobic metabolism. They were considered only as toxic byproducts for many years. Nowadays, peroxides are also regarded as metabolic products that play essential physiological cellular roles. Organisms have developed efficient mechanisms to metabolize peroxides, mostly based on two kinds of redox chemistry, catalases/peroxidases that depend on the heme prosthetic group to afford peroxide reduction and thiol-based peroxidases that support their redox activities on specialized fast reacting cysteine/selenocysteine (Cys/Sec) residues. Among the last group, glutathione peroxidases (GPxs) and peroxiredoxins (Prxs) are the most widespread and abundant families, and they are the leitmotif of this review. After presenting the properties and roles of different peroxides in biology, we discuss the chemical mechanisms of peroxide reduction by low molecular weight thiols, Prxs, GPxs, and other thiol-based peroxidases. Special attention is paid to the catalytic properties of Prxs and also to the importance and comparative outlook of the properties of Sec and its role in GPxs. To finish, we describe and discuss the current views on the activities of thiol-based peroxidases in peroxide-mediated redox signaling processes.
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Affiliation(s)
| | | | | | | | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 2160 Buenos Aires , Argentina
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12
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Cuevasanta E, Reyes AM, Zeida A, Mastrogiovanni M, De Armas MI, Radi R, Alvarez B, Trujillo M. Kinetics of formation and reactivity of the persulfide in the one-cysteine peroxiredoxin from Mycobacterium tuberculosis. J Biol Chem 2019; 294:13593-13605. [PMID: 31311857 DOI: 10.1074/jbc.ra119.008883] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/12/2019] [Indexed: 12/20/2022] Open
Abstract
Hydrogen sulfide (H2S) participates in prokaryotic metabolism and is associated with several physiological functions in mammals. H2S reacts with oxidized thiol derivatives (i.e. disulfides and sulfenic acids) and thereby forms persulfides, which are plausible transducers of the H2S-mediated signaling effects. The one-cysteine peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE-SH) reacts fast with hydroperoxides, forming a stable sulfenic acid (MtAhpE-SOH), which we chose here as a model to study the interactions between H2S and peroxiredoxins (Prx). MtAhpE-SOH reacted with H2S, forming a persulfide (MtAhpE-SSH) detectable by mass spectrometry. The rate constant for this reaction was (1.4 ± 0.2) × 103 m-1 s-1 (pH 7.4, 25 °C), six times higher than that reported for the reaction with the main low-molecular-weight thiol in M. tuberculosis, mycothiol. H2S was able to complete the catalytic cycle of MtAhpE and, according to kinetic considerations, it could represent an alternative substrate in M. tuberculosis. MtAhpE-SSH reacted 43 times faster than did MtAhpE-SH with the unspecific electrophile 4,4'-dithiodipyridine, a disulfide that exhibits no preferential reactivity with peroxidatic cysteines, but MtAhpE-SSH was less reactive toward specific Prx substrates such as hydrogen peroxide and peroxynitrite. According to molecular dynamics simulations, this loss of specific reactivity could be explained by alterations in the MtAhpE active site. MtAhpE-SSH could transfer its sulfane sulfur to a low-molecular-weight thiol, a process likely facilitated by the low pKa of the leaving thiol MtAhpE-SH, highlighting the possibility that Prx participates in transpersulfidation. The findings of our study contribute to the understanding of persulfide formation and reactivity.
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Affiliation(s)
- Ernesto Cuevasanta
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay .,Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Aníbal M Reyes
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay .,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - María Inés De Armas
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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13
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Himiyama T, Oshima M, Uegaki K, Nakamura T. Distinct molecular assembly of homologous peroxiredoxins from Pyrococcus horikoshii and Thermococcus kodakaraensis. J Biochem 2019; 166:89-95. [DOI: 10.1093/jb/mvz013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Peroxiredoxins from Pyrococcus horikoshii (PhPrx) and Thermococcus kodakaraensis (TkPrx) are highly homologous proteins sharing 196 of the 216 residues. We previously reported a pentagonal ring-type decameric structure of PhPrx. Here, we present the crystal structure of TkPrx. Despite their homology, unlike PhPrx, the quaternary structure of TkPrx was found to be a dodecamer comprised of six homodimers arranged in a hexagonal ring-type assembly. The possibility of the redox-dependent conversion of the molecular assembly, which had been observed in PhPrx, was excluded for TkPrx based on the crystal structure of a mutant in which all of the cysteine residues were substituted with serine. The monomer structures of the dodecameric TkPrx and decameric PhPrx coincided well, but there was a slight difference in the relative orientation of the two domains. Molecular assembly of PhPrx and TkPrx in solution evaluated by gel-filtration chromatography was consistent with the crystallographic results. For both PhPrx and TkPrx, the gel-filtration elution volume slightly increased with a decrease in the protein concentration, suggesting the existence of an equilibrium state between the decameric/dodecameric ring and lower-order assembly. This structural assembly difference between highly homologous Prxs suggests a significant influence of quaternary structure on function, worthy of further exploration.
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Affiliation(s)
- Tomoki Himiyama
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
| | - Maki Oshima
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
| | - Koichi Uegaki
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Nara, Japan
| | - Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
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14
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15
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Structural and mechanistic insights into Mycothiol Disulphide Reductase and the Mycoredoxin-1-alkylhydroperoxide reductase E assembly of Mycobacterium tuberculosis. Biochim Biophys Acta Gen Subj 2017; 1861:2354-2366. [DOI: 10.1016/j.bbagen.2017.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 11/21/2022]
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16
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Lee S, Jeong H, Lee JH, Chung JM, Kim R, Yun HJ, Won J, Jung HS. Characterisation of conformational and functional features of alkyl hydroperoxide reductase E-like protein. Biochem Biophys Res Commun 2017; 489:217-222. [PMID: 28551405 DOI: 10.1016/j.bbrc.2017.05.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 11/25/2022]
Abstract
Alkyl hydroperoxide reductase E (AhpE) is a member of the peroxidase family of enzymes that catalyse the reduction of peroxides, however its structural and functional roles are still unclear in details. In this study, we used the Thermococcus kodakarensis AhpE-like protein as a model to investigate structure-function relationships including the molecular properties of DNA binding activity. Multiple sequence alignment, structural comparison and biochemical analyses revealed that TkAhpE includes conserved peroxidase residues in the active site, and exhibits peroxidase activity with structure-dependent holdase chaperone function. Following electrophoretic mobility shift assays and electron microscopy analysis demonstrated distinctive binding features of TkAhpE to the DNA showing that their dimeric conformer can bind to the double-stranded DNA, but not to the single-stranded DNA, indicating its striking molecular features to double-stranded DNA-specific interactions. Based on our results, we provided that TkAhpE is a multifunctional peroxidase displaying structure-dependent molecular chaperone and DNA binding activities.
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Affiliation(s)
- Sangmin Lee
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea.
| | - Hyeongseop Jeong
- Center for Electron Microscopy Research, Korea Basic Science Institute 161, Yeongudanji-ro, Ochang-eup, Chengwon-gu, Chengju-si, Chungchengbuk-do, 28119, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jeong Min Chung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Rumi Kim
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Hyung Joong Yun
- Advanced Nano Surface Research Group, Korea Basic Science Institute, 169-148 Gwahak-ro, Daejeon, 34133, Republic of Korea
| | - Jonghan Won
- Advanced Nano Surface Research Group, Korea Basic Science Institute, 169-148 Gwahak-ro, Daejeon, 34133, Republic of Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea.
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17
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Singh A, Kumar N, Tomar PPS, Bhose S, Ghosh DK, Roy P, Sharma AK. Characterization of a bacterioferritin comigratory protein family 1-Cys peroxiredoxin from Candidatus Liberibacter asiaticus. PROTOPLASMA 2017; 254:1675-1691. [PMID: 27987036 DOI: 10.1007/s00709-016-1062-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/06/2016] [Indexed: 05/24/2023]
Abstract
To defend against the lethality of the reactive oxygen species (ROS), nature has armed microorganisms with a range of antioxidant proteins. These include peroxiredoxin (Prx) super family proteins which are ubiquitous cysteine-based non-heme peroxidases. The phytopathogenic bacterium Candidatus Liberibacter asiaticus (CLA), an etiological agent of citrus plants diseases, posses many genes for defense against oxidative stress. The bacterioferritin comigratory protein (BCP), a member of Prxs, is part of an oxidative stress defense system of CLA. The key residue of these enzymes is peroxidatic Cys (termed CPSH) which is contained within an absolutely conserved PXXX (T/S) XXC motif. In the present study, a 1-Cys Prx enzyme (CLa-BCP), having CPSH/sulfenic acid cysteine (C-46) but lacking the resolving cysteine (CRSH), was characterized from CLA. The peroxidase activity was demonstrated using a non-physiological electron donor DTT against varied substrates. The protein was shown to have the defensive role against peroxide-mediated cell killing and an antioxidant activity. In vitro DNA-binding studies showed that this protein can protect supercoiled DNA from oxidative damage. To the best of our knowledge, this is the first report on a 1-Cys BCPs to have an intracellular reactive oxygen species scavenging activity.
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Affiliation(s)
- Anamika Singh
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Narender Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Prabhat P S Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Sumit Bhose
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, 440 010, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, 440 010, India
| | - Partha Roy
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Ashwani K Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India.
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18
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Abstract
Peroxiredoxins (Prxs) are a large and conserved family of peroxidases that are considered to be the primary cellular guardians against oxidative stress in all living organisms. Prxs share a thioredoxin fold and contain a highly-reactive peroxidatic cysteine in a specialised active-site environment that is able to reduce their peroxide substrates. The minimal functional unit for Prxs are either monomers or dimers, but many dimers assemble into decameric rings. Ring structures can further form a variety of high molecular weight complexes. Many eukaryotic Prxs contain a conserved GGLG and C-terminal YF motif that confer sensitivity to elevated levels of peroxide, leading to hyperoxidation and inactivation. Inactive forms of Prxs can be re-reduced by the enzyme sulfiredoxin, in an ATP-dependent reaction. Cycles of hyperoxidation and reactivation are considered to play an integral role in a variety of H2O2-mediated cell signalling pathways in both stress and non-stress conditions. Prxs are also considered to exhibit chaperone-like properties when cells are under oxidative or thermal stress. The roles of various types of covalent modifications, e.g. acetylation and phosphorylation are also discussed. The ability of Prxs to assemble into ordered arrays such as nanotubes is currently being exploited in nanotechnology.
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Affiliation(s)
- Zhenbo Cao
- Institute of Molecular, Cell and Systems Biology, Davidson Building, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - John Gordon Lindsay
- Institute of Molecular, Cell and Systems Biology, Davidson Building, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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19
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Perkins A, Parsonage D, Nelson KJ, Ogba OM, Cheong PHY, Poole LB, Karplus PA. Peroxiredoxin Catalysis at Atomic Resolution. Structure 2016; 24:1668-1678. [PMID: 27594682 DOI: 10.1016/j.str.2016.07.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/24/2016] [Accepted: 07/17/2016] [Indexed: 12/23/2022]
Abstract
Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases that guard cells against oxidative damage, are virulence factors for pathogens, and are involved in eukaryotic redox regulatory pathways. We have analyzed catalytically active crystals to capture atomic resolution snapshots of a PrxQ subfamily enzyme (from Xanthomonas campestris) proceeding through thiolate, sulfenate, and sulfinate species. These analyses provide structures of unprecedented accuracy for seeding theoretical studies, and reveal conformational intermediates giving insight into the reaction pathway. Based on a highly non-standard geometry seen for the sulfenate intermediate, we infer that the sulfenate formation itself can strongly promote local unfolding of the active site to enhance productive catalysis. Further, these structures reveal that preventing local unfolding, in this case via crystal contacts, results in facile hyperoxidative inactivation even for Prxs normally resistant to such inactivation. This supports previous proposals that conformation-specific inhibitors may be useful for achieving selective inhibition of Prxs that are drug targets.
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Affiliation(s)
- Arden Perkins
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Kimberly J Nelson
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - O Maduka Ogba
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | | | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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20
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Kumar A, Balakrishna AM, Nartey W, Manimekalai MSS, Grüber G. Redox chemistry of Mycobacterium tuberculosis alkylhydroperoxide reductase E (AhpE): Structural and mechanistic insight into a mycoredoxin-1 independent reductive pathway of AhpE via mycothiol. Free Radic Biol Med 2016; 97:588-601. [PMID: 27417938 DOI: 10.1016/j.freeradbiomed.2016.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/07/2016] [Accepted: 07/09/2016] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has the ability to persist within the human host for a long time in a dormant stage and re-merges when the immune system is compromised. The pathogenic bacterium employs an elaborate antioxidant defence machinery composed of the mycothiol- and thioredoxin system in addition to a superoxide dismutase, a catalase, and peroxiredoxins (Prxs). Among the family of Peroxiredoxins, Mtb expresses a 1-cysteine peroxiredoxin, known as alkylhydroperoxide reductase E (MtAhpE), and defined as a potential tuberculosis drug target. The reduced MtAhpE (MtAhpE-SH) scavenges peroxides to become converted to MtAhpE-SOH. To provide continuous availability of MtAhpE-SH, MtAhpE-SOH has to become reduced. Here, we used NMR spectroscopy to delineate the reduced (MtAhpE-SH), sulphenic (MtAhpE-SOH) and sulphinic (MtAhpE-SO2H) states of MtAhpE through cysteinyl-labelling, and provide for the first time evidence of a mycothiol-dependent mechanism of MtAhpE reduction. This is confirmed by crystallographic studies, wherein MtAhpE was crystallized in the presence of mycothiol and the structure was solved at 2.43Å resolution. Combined with NMR-studies, the crystallographic structures reveal conformational changes of important residues during the catalytic cycle of MtAhpE. In addition, alterations of the overall protein in solution due to redox modulation are observed by small angle X-ray scattering (SAXS) studies. Finally, by employing SAXS and dynamic light scattering, insight is provided into the most probable physiological oligomeric state of MtAhpE necessary for activity, being also discussed in the context of concerted substrate binding inside the dimeric MtAhpE.
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Affiliation(s)
- Arvind Kumar
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Asha Manikkoth Balakrishna
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | | | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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21
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van Bergen LAH, Alonso M, Palló A, Nilsson L, De Proft F, Messens J. Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE. Sci Rep 2016; 6:30369. [PMID: 27468924 PMCID: PMC4965862 DOI: 10.1038/srep30369] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/30/2016] [Indexed: 01/12/2023] Open
Abstract
In many established methods, identification of hydrogen bonds (H-bonds) is primarily based on pairwise comparison of distances between atoms. These methods often give rise to systematic errors when sulfur is involved. A more accurate method is the non-covalent interaction index, which determines the strength of the H-bonds based on the associated electron density and its gradient. We applied the NCI index on the active site of a single-cysteine peroxiredoxin. We found a different sulfur hydrogen-bonding network to that typically found by established methods, and we propose a more accurate equation for determining sulfur H-bonds based on geometrical criteria. This new algorithm will be implemented in the next release of the widely-used CHARMM program (version 41b), and will be particularly useful for analyzing water molecule-mediated H-bonds involving different atom types. Furthermore, based on the identification of the weakest sulfur-water H-bond, the location of hydrogen peroxide for the nucleophilic attack by the cysteine sulfur can be predicted. In general, current methods to determine H-bonds will need to be reevaluated, thereby leading to better understanding of the catalytic mechanisms in which sulfur chemistry is involved.
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Affiliation(s)
- Laura A H van Bergen
- Research Group of General Chemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Structural Biology Research Center, VIB, 1050 Brussels, Belgium.,Brussels Center for Redox Biology, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Mercedes Alonso
- Research Group of General Chemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Anna Palló
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium.,Brussels Center for Redox Biology, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14183 Huddinge, Sweden
| | - Frank De Proft
- Research Group of General Chemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium.,Brussels Center for Redox Biology, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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22
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Kim KH, Lee W, Kim EE. Crystal structures of human peroxiredoxin 6 in different oxidation states. Biochem Biophys Res Commun 2016; 477:717-722. [PMID: 27353378 DOI: 10.1016/j.bbrc.2016.06.125] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/24/2016] [Indexed: 11/27/2022]
Abstract
Peroxiredoxins (Prxs) are a family of antioxidant enzymes found ubiquitously. Prxs function not only as H2O2 scavengers but also as highly sensitive H2O2 sensors and signal transducers. Since reactive oxygen species are involved in many cellular metabolic and signaling processes, Prxs play important roles in various diseases. Prxs can be hyperoxidized to the sulfinic acid (SO2H) or sulfonic acid (SO3H) forms in the presence of high concentrations of H2O2. It is known that oligomerization of Prx is changed accompanying oxidation states, and linked to the function. Among the six Prxs in mammals, Prx6 is the only 1-Cys Prx. It is found in all organs in humans, unlike some 2-Cys Prxs, and is present in all species from bacteria to humans. In addition, Prx6 has Ca(2+)-independent phospholipase A2 (PLA2) activity. Thus far only the crystal structure of Prx in the oxidized state has been reported. In this study, we present the crystal structures of human Prx6 in the reduced (SH) and the sulfinic acid (SO2H) forms.
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Affiliation(s)
- Kyung Hee Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.
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23
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Touw WG, Joosten RP, Vriend G. New Biological Insights from Better Structure Models. J Mol Biol 2016; 428:1375-1393. [PMID: 26869101 DOI: 10.1016/j.jmb.2016.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 01/04/2016] [Accepted: 02/01/2016] [Indexed: 02/01/2023]
Abstract
Structure validation is a key component of all steps in the structure determination process, from structure building, refinement, deposition, and evaluation all the way to post-deposition optimisation of structures in the Protein Data Bank (PDB) by re-refinement and re-building. Today, many aspects of protein structures are understood better than 10years ago, and combined with improved software and more computing power, the automated PDB_REDO procedure can significantly improve about 85% of all X-ray structures ever deposited in the PDB. We review structure validation, structure improvement, and a series of validation resources and facilities that give access to improved PDB files and to reports on the quality of the original and the improved structures. Post-deposition optimisation generally leads to improved protein structures and a series of examples will illustrate how that, in turn, leads to improved or even novel biological insights.
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Affiliation(s)
- Wouter G Touw
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
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24
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Zeida A, Reyes AM, Lichtig P, Hugo M, Vazquez DS, Santos J, González Flecha FL, Radi R, Estrin DA, Trujillo M. Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis. Biochemistry 2015; 54:7237-47. [DOI: 10.1021/acs.biochem.5b00758] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
| | - Aníbal M. Reyes
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | - Martín Hugo
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | | | | | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | | | - Madia Trujillo
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
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25
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Gadd MS, Bulatov E, Ciulli A. Serendipitous SAD Solution for DMSO-Soaked SOCS2-ElonginC-ElonginB Crystals Using Covalently Incorporated Dimethylarsenic: Insights into Substrate Receptor Conformational Flexibility in Cullin RING Ligases. PLoS One 2015; 10:e0131218. [PMID: 26121586 PMCID: PMC4486172 DOI: 10.1371/journal.pone.0131218] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/29/2015] [Indexed: 11/18/2022] Open
Abstract
Suppressor of cytokine signalling 2 (SOCS2) is the substrate-binding component of a Cullin-RING E3 ubiquitin ligase (CRL) complex that targets phosphorylated hormone receptors for degradation by the ubiquitin-proteasome system. As a key regulator of the transcriptional response to growth signals, SOCS2 and its protein complex partners are potential targets for small molecule development. We found that crystals of SOCS2 in complex with its adaptor proteins, Elongin C and Elongin B, underwent a change in crystallographic parameters when treated with dimethyl sulfoxide during soaking experiments. To solve the phase problem for the new crystal form we identified the presence of arsenic atoms in the crystals, a result of covalent modification of cysteines by cacodylate, and successfully extracted anomalous signal from these atoms for experimental phasing. The resulting structure provides a means for solving future structures where the crystals must be treated with DMSO for ligand soaking approaches. Additionally, the conformational changes induced in this structure reveal flexibility within SOCS2 that match those postulated by previous molecular dynamics simulations. This conformational flexibility illustrates how SOCS2 can orient its substrates for successful ubiquitination by other elements of the CRL complex.
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Affiliation(s)
- Morgan S. Gadd
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, United Kingdom
| | - Emil Bulatov
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, United Kingdom
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, United Kingdom
- * E-mail:
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26
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Kwon T, Rho JK, Lee JC, Park YH, Shin HJ, Cho S, Kang YK, Kim BY, Yoon DY, Yu DY. An important role for peroxiredoxin II in survival of A549 lung cancer cells resistant to gefitinib. Exp Mol Med 2015; 47:e165. [PMID: 26021759 PMCID: PMC4454996 DOI: 10.1038/emm.2015.24] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/22/2014] [Accepted: 01/19/2015] [Indexed: 12/27/2022] Open
Abstract
Redox adaptation is an important concept that explains the mechanisms by which cancer cells survive under persistent endogenous oxidative stress and become resistant to certain anticancer agents. To investigate this concept, we determined the expression levels of peroxiredoxins (Prxs), antioxidant enzymes in drug-resistant non-small cell lung carcinoma cells. Prx II was remarkably increased only in A549/GR (gefitinib-resistant) cells compared with A549 cells, consistent with methylation/demethylation. Prx II was highly methylated in the A549 cells but was demethylated in the A549/GR cells. The elevated expression of Prx II resulted in the downregulation of reactive oxygen species (ROS) and cell death and upregulation of cell cycle progression in the A549/GR cells. When Prx II mRNA in the A549/GR cells was knocked down, the levels of ROS and apoptosis were significantly recovered to the levels of the controls. In addition, signaling molecules involved in apoptosis were increased in the A549/GR-shPrx II cells. There was no difference in the expression of MAPK/ERK between the A549/GR cells and A549/GR-shPrx II cells, but the phosphorylation of JNK was increased in the A549/GR cells and was markedly decreased in the A549/GR-shPrx II cells. Colony number and tumor growth were significantly decreased in the A549/GR-shPrx II cells compared with the A549/GR cells. Our findings suggest that Prx II has an important role in cancer cell survival via the modulation of signaling molecules involved in apoptosis and the phosphorylation of JNK by the downregulation of ROS levels in A549/GR cells.
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Affiliation(s)
- Taeho Kwon
- 1] Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea [2] Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
| | - Jin Kyung Rho
- Asan Institute for Life Sciences, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Korea
| | - Jae Cheol Lee
- Asan Institute for Life Sciences, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Korea
| | - Young-Ho Park
- Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Hye-Jun Shin
- Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Sunwha Cho
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Bo-Yeon Kim
- World Class Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Chungbuk, Korea
| | - Do-Young Yoon
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
| | - Dae-Yeul Yu
- Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
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Cao Z, McGow DP, Shepherd C, Lindsay JG. Improved Catenated Structures of Bovine Peroxiredoxin III F190L Reveal Details of Ring-Ring Interactions and a Novel Conformational State. PLoS One 2015; 10:e0123303. [PMID: 25906064 PMCID: PMC4407889 DOI: 10.1371/journal.pone.0123303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/03/2015] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial 2-cys peroxiredoxin III (PrxIII) is a key player in antioxidant defence reducing locally-generated H2O2 to H2O. A Phe to Leu (F190L) mutation in the C-terminal α-helix of PrxIII, mimicking that found in some bacteria and parasites, increases its resistance to hyperoxidation but has no obvious influence on peroxidase activity. Here we report on the oxidized and reduced crystal structures of bovine PrxIII F190L at 2.4 Å and 2.2 Å, respectively. Both structures exist as two-ring catenanes with their dodecameric rings inclined at 55o to each other, similar to that previously reported for PrxIII C168S. The new higher-resolution structures reveal details of the complex network of H-bonds stabilising the inter-toroid contacts. In addition, Arg123, the key conserved residue, that normally interacts with the catalytic cys (Cp, cys 47) is found in a distinct conformation extending away from the Cp while the characteristic Arg-Glu-Arg network, underpinning the active-site geometry also displays a distinctive arrangement, not observed previously. This novel active-site organisation may provide new insights into the dynamics of the large-scale conformational changes occurring between oxidized and reduced states.
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Affiliation(s)
- Zhenbo Cao
- From the Institute of Molecular, Cell and Systems Biology, CMVLS, University of Glasgow, Glasgow, United Kingdom
| | - Donna P. McGow
- From the Institute of Molecular, Cell and Systems Biology, CMVLS, University of Glasgow, Glasgow, United Kingdom
| | - Colin Shepherd
- From the Institute of Molecular, Cell and Systems Biology, CMVLS, University of Glasgow, Glasgow, United Kingdom
| | - J. Gordon Lindsay
- From the Institute of Molecular, Cell and Systems Biology, CMVLS, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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Abstract
Peroxiredoxins were not recognized as a family of enzymes until the 1990s but are now known to be the dominant peroxidases in most organisms. Here, the history and fundamental properties of peroxiredoxins are briefly reviewed, with a special focus on describing how an exquisitely tunable balance between fully folded and locally unfolded conformations plays a large role in peroxiredoxin catalytic properties.
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Affiliation(s)
- P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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Kaihami GH, de Almeida JRF, dos Santos SS, Netto LES, de Almeida SR, Baldini RL. Involvement of a 1-Cys peroxiredoxin in bacterial virulence. PLoS Pathog 2014; 10:e1004442. [PMID: 25329795 PMCID: PMC4199769 DOI: 10.1371/journal.ppat.1004442] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 09/02/2014] [Indexed: 12/31/2022] Open
Abstract
The killing of bacterial pathogens by macrophages occurs via the oxidative burst and bacteria have evolved to overcome this challenge and survive, using several virulence and defense strategies, including antioxidant mechanisms. We show here that the 1-Cys peroxiredoxin LsfA from the opportunistic pathogen Pseudomonas aeruginosa is endowed with thiol-dependent peroxidase activity that protects the bacteria from H(2)O(2) and that this protein is implicated in pathogenicity. LsfA belongs to the poorly studied Prx6 subfamily of peroxiredoxins. The function of these peroxiredoxins has not been characterized in bacteria, and their contribution to host-pathogen interactions remains unknown. Infection of macrophages with the lsfA mutant strains resulted in higher levels of the cytokine TNF-α production due to the activation of the NF-kB and MAPK pathways, that are partially inhibited by the wild-type P. aeruginosa strain. A redox fluorescent probe was more oxidized in the lsfA mutant-infected macrophages than it was in the macrophages infected with the wild-type strain, suggesting that the oxidative burst was overstimulated in the absence of LsfA. Although no differences in the phagocytosis rates were observed when macrophages were infected with wild-type and mutant bacteria in a gentamicin exclusion assay, a higher number of wild-type bacterial cells was found in the supernatant. This difference was not observed when macrophages were pre-treated with a NADPH oxidase inhibitor, confirming the role of LsfA in the bacterial resistance to ROS generated via NADPH oxidase. In an acute pneumonia model, mice infected with the mutant strains presented higher cytokine release in the lungs and increased activated neutrophil recruitment, with reduced bacterial burden and improved survival rates compared to mice infected with the wild-type bacteria. LsfA is the first bacterial 1-Cys Prx shown to modulate host immune responses and its characterization will allow a better understanding of the role of redox signaling in host-pathogen interactions.
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Affiliation(s)
- Gilberto Hideo Kaihami
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Suelen Silvana dos Santos
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Luis Eduardo Soares Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Sandro Rogério de Almeida
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Regina Lúcia Baldini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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Zeida A, Reyes AM, Lebrero MCG, Radi R, Trujillo M, Estrina DA. The extraordinary catalytic ability of peroxiredoxins: a combined experimental and QM/MM study on the fast thiol oxidation step. Chem Commun (Camb) 2014; 50:10070-3. [PMID: 25045760 PMCID: PMC4336542 DOI: 10.1039/c4cc02899f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peroxiredoxins (Prxs) catalyze the reduction of peroxides, a process of key relevance in a variety of cellular processes. The first step in the catalytic cycle of all Prxs is the oxidation of a cysteine residue to sulfenic acid, which occurs 10(3)-10(7) times faster than in free cysteine. We present an experimental kinetics and hybrid QM/MM investigation to explore the reaction of Prxs with H2O2 using alkyl hydroperoxide reductase E from Mycobacterium tuberculosis as a Prx model. We report for the first time the thermodynamic activation parameters of H2O2 reduction using Prx, which show that protein significantly lowers the activation enthalpy, with an unfavourable entropic effect, compared to the uncatalyzed reaction. The QM/MM simulations show that the remarkable catalytic effects responsible for the fast H2O2 reduction in Prxs are mainly due to an active-site arrangement, which establishes a complex hydrogen bond network activating both reactive species.
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Affiliation(s)
- Ari Zeida
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina
| | - Anibal M. Reyes
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Mariano C. G. Lebrero
- IQUIFIB-Dpto. Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral Flores 2125, CP 11800, Montevideo, Uruguay
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Furdui CM, Poole LB. Chemical approaches to detect and analyze protein sulfenic acids. MASS SPECTROMETRY REVIEWS 2014; 33:126-46. [PMID: 24105931 PMCID: PMC3946320 DOI: 10.1002/mas.21384] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 04/03/2013] [Accepted: 04/04/2013] [Indexed: 05/08/2023]
Abstract
Orchestration of many processes relying on intracellular signal transduction is recognized to require the generation of hydrogen peroxide as a second messenger, yet relatively few molecular details of how this oxidant acts to regulate protein function are currently understood. This review describes emerging chemical tools and approaches that can be applied to study protein oxidation in biological systems, with a particular emphasis on a key player in protein redox regulation, cysteine sulfenic acid. While sulfenic acids (within purified proteins or simple mixtures) are detectable by physical approaches like X-ray crystallography, nuclear magnetic resonance and mass spectrometry, the propensity of these moieties to undergo further modification in complex biological systems has necessitated the development of chemical probes, reporter groups and analytical approaches to allow for their selective detection and quantification. Provided is an overview of techniques that are currently available for the study of sulfenic acids, and some of the biologically meaningful data that have been collected using such approaches.
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Affiliation(s)
- Cristina M. Furdui
- Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
- Correspondence to: Leslie B. Poole, Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157; ; telephone: 336-716-6711
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Hugo M, Van Laer K, Reyes AM, Vertommen D, Messens J, Radi R, Trujillo M. Mycothiol/mycoredoxin 1-dependent reduction of the peroxiredoxin AhpE from Mycobacterium tuberculosis. J Biol Chem 2013; 289:5228-39. [PMID: 24379404 DOI: 10.1074/jbc.m113.510248] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis), the pathogen responsible for tuberculosis, detoxifies cytotoxic peroxides produced by activated macrophages. M. tuberculosis expresses alkyl hydroxyperoxide reductase E (AhpE), among other peroxiredoxins. So far the system that reduces AhpE was not known. We identified M. tuberculosis mycoredoxin-1 (MtMrx1) acting in combination with mycothiol and mycothiol disulfide reductase (MR), as a biologically relevant reducing system for MtAhpE. MtMrx1, a glutaredoxin-like, mycothiol-dependent oxidoreductase, directly reduces the oxidized form of MtAhpE, through a protein mixed disulfide with the N-terminal cysteine of MtMrx1 and the sulfenic acid derivative of the peroxidatic cysteine of MtAhpE. This disulfide is then reduced by the C-terminal cysteine in MtMrx1. Accordingly, MtAhpE catalyzes the oxidation of wt MtMrx1 by hydrogen peroxide but not of MtMrx1 lacking the C-terminal cysteine, confirming a dithiolic mechanism. Alternatively, oxidized MtAhpE forms a mixed disulfide with mycothiol, which in turn is reduced by MtMrx1 using a monothiolic mechanism. We demonstrated the H2O2-dependent NADPH oxidation catalyzed by MtAhpE in the presence of MR, Mrx1, and mycothiol. Disulfide formation involving mycothiol probably competes with the direct reduction by MtMrx1 in aqueous intracellular media, where mycothiol is present at millimolar concentrations. However, MtAhpE was found to be associated with the membrane fraction, and since mycothiol is hydrophilic, direct reduction by MtMrx1 might be favored. The results reported herein allow the rationalization of peroxide detoxification actions inferred for mycothiol, and more recently, for Mrx1 in cellular systems. We report the first molecular link between a thiol-dependent peroxidase and the mycothiol/Mrx1 pathway in Mycobacteria.
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Pallotta V, D’Alessandro A, Rinalducci S, Zolla L. Native Protein Complexes in the Cytoplasm of Red Blood Cells. J Proteome Res 2013; 12:3529-46. [DOI: 10.1021/pr400431b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Valeria Pallotta
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Angelo D’Alessandro
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Sara Rinalducci
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Lello Zolla
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
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Van Laer K, Buts L, Foloppe N, Vertommen D, Van Belle K, Wahni K, Roos G, Nilsson L, Mateos LM, Rawat M, van Nuland NAJ, Messens J. Mycoredoxin-1 is one of the missing links in the oxidative stress defence mechanism of Mycobacteria. Mol Microbiol 2012; 86:787-804. [DOI: 10.1111/mmi.12030] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2012] [Indexed: 01/02/2023]
Affiliation(s)
| | | | - Nicolas Foloppe
- Department of Biosciences and Nutrition; Karolinska Institutet; Huddinge; SE-171 77; Sweden
| | - Didier Vertommen
- de Duve Institute; Université catholique de Louvain; Brussels; 1200; Belgium
| | | | | | | | - Lennart Nilsson
- Department of Biosciences and Nutrition; Karolinska Institutet; Huddinge; SE-171 77; Sweden
| | - Luis M. Mateos
- Department of Molecular Biology; Area of Microbiology; University of León; León; 24006; Spain
| | - Mamta Rawat
- Department of Biology; California State University; Fresno; CA; 93740; USA
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Gretes MC, Poole LB, Karplus PA. Peroxiredoxins in parasites. Antioxid Redox Signal 2012; 17:608-33. [PMID: 22098136 PMCID: PMC3373223 DOI: 10.1089/ars.2011.4404] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 11/18/2011] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Parasite survival and virulence relies on effective defenses against reactive oxygen and nitrogen species produced by the host immune system. Peroxiredoxins (Prxs) are ubiquitous enzymes now thought to be central to such defenses and, as such, have potential value as drug targets and vaccine antigens. RECENT ADVANCES Plasmodial and kinetoplastid Prx systems are the most extensively studied, yet remain inadequately understood. For many other parasites our knowledge is even less well developed. Through parasite genome sequencing efforts, however, the key players are being discovered and characterized. Here we describe what is known about the biochemistry, regulation, and cell biology of Prxs in parasitic protozoa, helminths, and fungi. At least one Prx is found in each parasite with a sequenced genome, and a notable theme is the common patterns of expression, localization, and functionality among sequence-similar Prxs in related species. CRITICAL ISSUES The nomenclature of Prxs from parasites is in a state of disarray, causing confusion and making comparative inferences difficult. Here we introduce a systematic Prx naming convention that is consistent between organisms and informative about structural and evolutionary relationships. FUTURE DIRECTIONS The new nomenclature should stimulate the crossfertilization of ideas among parasitologists and with the broader redox research community. The diverse parasite developmental stages and host environments present complex systems in which to explore the variety of roles played by Prxs, with a view toward parlaying what is learned into novel therapies and vaccines that are urgently needed.
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Affiliation(s)
- Michael C. Gretes
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - P. Andrew Karplus
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
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Hassan S, Debnath A, Mahalingam V, Hanna LE. Computational structural analysis of proteins of Mycobacterium tuberculosis and a resource for identifying off-targets. J Mol Model 2012; 18:3993-4004. [DOI: 10.1007/s00894-012-1412-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 03/20/2012] [Indexed: 10/28/2022]
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Qiu W, Dong A, Pizarro JC, Botchkarsev A, Min J, Wernimont AK, Hills T, Hui R, Artz JD. Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding. BMC STRUCTURAL BIOLOGY 2012; 12:2. [PMID: 22429898 PMCID: PMC3337327 DOI: 10.1186/1472-6807-12-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 03/19/2012] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Plasmodium falciparum is the protozoan parasite primarily responsible for more than one million malarial deaths, annually, and is developing resistance to current therapies. Throughout its lifespan, the parasite is subjected to oxidative attack, so Plasmodium antioxidant defences are essential for its survival and are targets for disease control.
Results
To further understand the molecular aspects of the Plasmodium redox system, we solved 4 structures of Plasmodium peroxiredoxins (Prx). Our study has confirmed Pv Trx-Px1 to be a hydrogen peroxide (H2O2)-sensitive peroxiredoxin. We have identified and characterized the novel toroid octameric oligomer of Py Trx-Px1, which may be attributed to the interplay of several factors including: (1) the orientation of the conserved surface/buried arginine of the NNLA(I/L)GRS-loop; and (2) the C-terminal tail positioning (also associated with the aforementioned conserved loop) which facilitates the intermolecular hydrogen bond between dimers (in an A-C fashion). In addition, a notable feature of the disulfide bonds in some of the Prx crystal structures is discussed. Finally, insight into the latter stages of the peroxiredoxin reaction coordinate is gained. Our structure of Py Prx6 is not only in the sulfinic acid (RSO2H) form, but it is also with glycerol bound in a way (not previously observed) indicative of product binding.
Conclusions
The structural characterization of Plasmodium peroxiredoxins provided herein provides insight into their oligomerization and product binding which may facilitate the targeting of these antioxidant defences. Although the structural basis for the octameric oligomerization is further understood, the results yield more questions about the biological implications of the peroxiredoxin oligomerization, as multiple toroid configurations are now known. The crystal structure depicting the product bound active site gives insight into the overoxidation of the active site and allows further characterization of the leaving group chemistry.
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Trivedi A, Singh N, Bhat SA, Gupta P, Kumar A. Redox biology of tuberculosis pathogenesis. Adv Microb Physiol 2012; 60:263-324. [PMID: 22633061 DOI: 10.1016/b978-0-12-398264-3.00004-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most successful human pathogens. Mtb is persistently exposed to numerous oxidoreductive stresses during its pathogenic cycle of infection and transmission. The distinctive ability of Mtb, not only to survive the redox stress manifested by the host but also to use it for synchronizing the metabolic pathways and expression of virulence factors, is central to its success as a pathogen. This review describes the paradigmatic redox and hypoxia sensors employed by Mtb to continuously monitor variations in the intracellular redox state and the surrounding microenvironment. Two component proteins, namely, DosS and DosT, are employed by Mtb to sense changes in oxygen, nitric oxide, and carbon monoxide levels, while WhiB3 and anti-sigma factor RsrA are used to monitor changes in intracellular redox state. Using these and other unidentified redox sensors, Mtb orchestrates its metabolic pathways to survive in nutrient-deficient, acidic, oxidative, nitrosative, and hypoxic environments inside granulomas or infectious lesions. A number of these metabolic pathways are unique to mycobacteria and thus represent potential drug targets. In addition, Mtb employs versatile machinery of the mycothiol and thioredoxin systems to ensure a reductive intracellular environment for optimal functioning of its proteins even upon exposure to oxidative stress. Mtb also utilizes a battery of protective enzymes, such as superoxide dismutase (SOD), catalase (KatG), alkyl hydroperoxidase (AhpC), and peroxiredoxins, to neutralize the redox stress generated by the host immune system. This chapter reviews the current understanding of mechanisms employed by Mtb to sense and neutralize redox stress and their importance in TB pathogenesis and drug development.
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Hall A, Nelson K, Poole LB, Karplus PA. Structure-based insights into the catalytic power and conformational dexterity of peroxiredoxins. Antioxid Redox Signal 2011; 15:795-815. [PMID: 20969484 PMCID: PMC3125576 DOI: 10.1089/ars.2010.3624] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/01/2010] [Accepted: 10/24/2010] [Indexed: 12/25/2022]
Abstract
Peroxiredoxins (Prxs), some of nature's dominant peroxidases, use a conserved Cys residue to reduce peroxides. They are highly expressed in organisms from all kingdoms, and in eukaryotes they participate in hydrogen peroxide signaling. Seventy-two Prx structures have been determined that cover much of the diversity of the family. We review here the current knowledge and show that Prxs can be effectively classified by a structural/evolutionary organization into six subfamilies followed by specification of a 1-Cys or 2-Cys mechanism, and for 2-Cys Prxs, the structural location of the resolving Cys. We visualize the varied catalytic structural transitions and highlight how they differ depending on the location of the resolving Cys. We also review new insights into the question of how Prxs are such effective catalysts: the enzyme activates not only the conserved Cys thiolate but also the peroxide substrate. Moreover, the hydrogen-bonding network created by the four residues conserved in all Prx active sites stabilizes the transition state of the peroxidatic S(N)2 displacement reaction. Strict conservation of the peroxidatic active site along with the variation in structural transitions provides a fascinating picture of how the diverse Prxs function to break down peroxide substrates rapidly.
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Affiliation(s)
- Andrea Hall
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
| | - Kimberly Nelson
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - P. Andrew Karplus
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
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40
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Poole LB, Hall A, Nelson KJ. Overview of peroxiredoxins in oxidant defense and redox regulation. CURRENT PROTOCOLS IN TOXICOLOGY 2011; Chapter 7:Unit7.9. [PMID: 21818754 PMCID: PMC3156475 DOI: 10.1002/0471140856.tx0709s49] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Peroxiredoxins are important hydroperoxide detoxification enzymes, yet have only come to the fore in recent years relative to the other major players in peroxide detoxification, heme-containing catalases and peroxidases and glutathione peroxidases. These cysteine-dependent peroxidases exhibit high reactivity with hydrogen peroxide, organic hydroperoxides, and peroxynitrite and play major roles not only in peroxide defense, but also in regulating peroxide-mediated cell signaling. This overview focuses on important peroxiredoxin features that have emerged over the past several decades with an emphasis on catalytic mechanism, regulation, and biological function.
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Affiliation(s)
- Leslie B. Poole
- Dept. of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - Andrea Hall
- Dept. of Biochemistry and Biophysics, Oregon State University, Corvallis, OR
| | - Kimberly J. Nelson
- Dept. of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157
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Reyes AM, Hugo M, Trostchansky A, Capece L, Radi R, Trujillo M. Oxidizing substrate specificity of Mycobacterium tuberculosis alkyl hydroperoxide reductase E: kinetics and mechanisms of oxidation and overoxidation. Free Radic Biol Med 2011; 51:464-73. [PMID: 21571062 DOI: 10.1016/j.freeradbiomed.2011.04.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 04/07/2011] [Accepted: 04/12/2011] [Indexed: 11/17/2022]
Abstract
Alkyl hydroperoxide reductase E (AhpE), a novel subgroup of the peroxiredoxin family, comprises Mycobacterium tuberculosis AhpE (MtAhpE) and AhpE-like proteins present in many bacteria and archaea, for which functional characterization is scarce. We previously reported that MtAhpE reacted ~10(3) times faster with peroxynitrite than with hydrogen peroxide, but the molecular reasons for that remained unknown. Herein, we investigated the oxidizing substrate specificity and the oxidative inactivation of the enzyme. In most cases, both peroxidatic thiol oxidation and sulfenic acid overoxidation followed a trend in which those peroxides with the lower leaving-group pK(a) reacted faster than others. These data are in agreement with the accepted mechanisms of thiol oxidation and support that overoxidation occurs through sulfenate anion reaction with the protonated peroxide. However, MtAhpE oxidation and overoxidation by fatty acid-derived hydroperoxides (~10(8) and 10(5) M(-1) s(-1), respectively, at pH 7.4 and 25°C) were much faster than expected according to the Brønsted relationship with leaving-group pK(a). A stoichiometric reduction of the arachidonic acid hydroperoxide 15-HpETE to its corresponding alcohol was confirmed. Interactions of fatty acid hydroperoxides with a hydrophobic groove present on the reduced MtAhpE surface could be the basis of their surprisingly fast reactivity.
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Affiliation(s)
- Aníbal M Reyes
- Departamento de Bioquímica, Universidad de la República, 11800 Montevideo, Uruguay
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Rinalducci S, D'Amici GM, Blasi B, Zolla L. Oxidative stress-dependent oligomeric status of erythrocyte peroxiredoxin II (PrxII) during storage under standard blood banking conditions. Biochimie 2011; 93:845-53. [PMID: 21354257 DOI: 10.1016/j.biochi.2011.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 02/14/2011] [Indexed: 12/14/2022]
Abstract
Although biochemical properties of 2-Cys peroxiredoxins have been extensively studied in various cell lines and organisms, redox-induced structural transitions of peroxiredoxin II (PrxII) in human erythrocytes certainly warrant further investigation. In this work, cytosol and membrane ghosts of both fresh erythrocytes (cells obtained just after blood collection) and 28-day stored erythrocytes were analyzed by proteomics tools. We demonstrated that in fresh red blood cells PrxII exhibits four different oligomeric states in cytosol, whereas no PrxII complexes are in the membrane. The highest molecular weight PrxII protein complex (440 kDa) was proven to derive from the association between tetrameric catalase (CAT, 232 kDa) and decameric PrxII, whereas oligomers at 140, 100 and 67 kDa resulted to be homo-polymeric complexes composed of variable copies of PrxII monomeric subunits. Interestingly, the 440 kDa complex contained both reduced and oxidized (disulphide-linked dimers) PrxII decamers. Upon oxidative stress (28-day storage), the PrxII oligomers at 100 kDa in the cytosol disappeared and the CAT-PrxII hetero-oligomeric complex at 440 kDa is converted to a higher molecular weight structure (480 kDa) due to the presence therein of cross-linked species of PrxII and hemoglobin. More interestingly, oxidized red cell membranes contained the CAT-PrxII complex detected in 0-day cytosol as a consequence of protein recruitments induced by oxidative stress, however it showed a greater percentage of PrxII dimers. Finally, since the adoption of distinct PrxII structures is known to be closely related to different functions, peroxidase activity assays were performed demonstrating a positive reaction for oligomers at 440 kDa (both in cytosol and membrane compartment) and at 140 kDa. Our results contribute to clarify structural and functional switching of peroxiredoxin II in erythrocytes, thus possibly opening new scenarios in the biological roles played by this protein in defense mechanisms against oxidative stress, especially with the reference to red cell storage lesions.
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Affiliation(s)
- Sara Rinalducci
- Department of Environmental Sciences, University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy
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43
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Exploring the catalytic mechanism of the first dimeric Bcp: Functional, structural and docking analyses of Bcp4 from Sulfolobus solfataricus. Biochimie 2010; 92:1435-44. [DOI: 10.1016/j.biochi.2010.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 07/06/2010] [Indexed: 11/17/2022]
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44
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Hall A, Parsonage D, Poole LB, Karplus PA. Structural evidence that peroxiredoxin catalytic power is based on transition-state stabilization. J Mol Biol 2010; 402:194-209. [PMID: 20643143 PMCID: PMC2941395 DOI: 10.1016/j.jmb.2010.07.022] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 07/08/2010] [Accepted: 07/08/2010] [Indexed: 11/18/2022]
Abstract
Peroxiredoxins (Prxs) are important peroxidases associated with both antioxidant protection and redox signaling. They use a conserved Cys residue to reduce peroxide substrates. The Prxs have a remarkably high catalytic efficiency that makes them a dominant player in cell-wide peroxide reduction, but the origins of their high activity have been mysterious. We present here a novel structure of human PrxV at 1.45 A resolution that has a dithiothreitol bound in the active site with its diol moiety mimicking the two oxygens of a peroxide substrate. This suggests diols and similar di-oxygen compounds as a novel class of competitive inhibitors for the Prxs. Common features of this and other structures containing peroxide, peroxide-mimicking ligands, or peroxide-mimicking water molecules reveal hydrogen bonding and steric factors that promote its high reactivity by creating an oxygen track along which the peroxide oxygens move as the reaction proceeds. Key insights include how the active-site microenvironment activates both the peroxidatic cysteine side chain and the peroxide substrate and how it is exquisitely well suited to stabilize the transition state of the in-line S(N)2 substitution reaction that is peroxidation.
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Affiliation(s)
- Andrea Hall
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - P. Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
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45
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Wang X, Chen G, Liu H, Zhao Z, Li Z. Four-Dimensional Orthogonal Electrophoresis System for Screening Protein Complexes and Protein−Protein Interactions Combined with Mass Spectrometry. J Proteome Res 2010; 9:5325-34. [DOI: 10.1021/pr100581x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaodong Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Guoqiang Chen
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Hui Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Zhiyun Zhao
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Zhili Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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An extracellular disulfide bond forming protein (DsbF) from Mycobacterium tuberculosis: structural, biochemical, and gene expression analysis. J Mol Biol 2010; 396:1211-26. [PMID: 20060836 DOI: 10.1016/j.jmb.2009.12.060] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 12/03/2009] [Accepted: 12/29/2009] [Indexed: 12/21/2022]
Abstract
Disulfide bond forming (Dsb) proteins ensure correct folding and disulfide bond formation of secreted proteins. Previously, we showed that Mycobacterium tuberculosis DsbE (Mtb DsbE, Rv2878c) aids in vitro oxidative folding of proteins. Here, we present structural, biochemical, and gene expression analyses of another putative Mtb secreted disulfide bond isomerase protein homologous to Mtb DsbE, Mtb DsbF (Rv1677). The X-ray crystal structure of Mtb DsbF reveals a conserved thioredoxin fold although the active-site cysteines may be modeled in both oxidized and reduced forms, in contrast to the solely reduced form in Mtb DsbE. Furthermore, the shorter loop region in Mtb DsbF results in a more solvent-exposed active site. Biochemical analyses show that, similar to Mtb DsbE, Mtb DsbF can oxidatively refold reduced, unfolded hirudin and has a comparable pK(a) for the active-site solvent-exposed cysteine. However, contrary to Mtb DsbE, the Mtb DsbF redox potential is more oxidizing and its reduced state is more stable. From computational genomics analysis of the M. tuberculosis genome, we identified a potential Mtb DsbF interaction partner, Rv1676, a predicted peroxiredoxin. Complex formation is supported by protein coexpression studies and inferred by gene expression profiles, whereby Mtb DsbF and Rv1676 are upregulated under similar environments. Additionally, comparison of Mtb DsbF and Mtb DsbE gene expression data indicates anticorrelated gene expression patterns, suggesting that these two proteins and their functionally linked partners constitute analogous pathways that may function under different conditions.
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Hugo M, Turell L, Manta B, Botti H, Monteiro G, Netto LES, Alvarez B, Radi R, Trujillo M. Thiol and sulfenic acid oxidation of AhpE, the one-cysteine peroxiredoxin from Mycobacterium tuberculosis: kinetics, acidity constants, and conformational dynamics. Biochemistry 2009; 48:9416-26. [PMID: 19737009 DOI: 10.1021/bi901221s] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug resistance and virulence of Mycobacterium tuberculosis are partially related to the pathogen's antioxidant systems. Peroxide detoxification in this bacterium is achieved by the heme-containing catalase peroxidase and different two-cysteine peroxiredoxins. M. tuberculosis genome also codifies for a putative one-cysteine peroxiredoxin, alkyl hydroperoxide reductase E (MtAhpE). Its expression was previously demonstrated at a transcriptional level, and the crystallographic structure of the recombinant protein was resolved under reduced and oxidized states. Herein, we report that the conformation of MtAhpE changed depending on its single cysteine redox state, as reflected by different tryptophan fluorescence properties and changes in quaternary structure. Dynamics of fluorescence changes, complemented by competition kinetic assays, were used to perform protein functional studies. MtAhpE reduced peroxynitrite 2 orders of magnitude faster than hydrogen peroxide (1.9 x 10(7) M(-1) s(-1) vs 8.2 x 10(4) M(-1) s(-1) at pH 7.4 and 25 degrees C, respectively). The latter also caused cysteine overoxidation to sulfinic acid, but at much slower rate constant (40 M(-1) s(-1)). The pK(a) of the thiol in the reduced enzyme was 5.2, more than one unit lower than that of the sulfenic acid in the oxidized enzyme. The pH profile of hydrogen peroxide-mediated thiol and sulfenic acid oxidations indicated thiolate and sulfenate as the reacting species. The formation of sulfenic acid as well as the catalytic peroxidase activity of MtAhpE was demonstrated using the artificial reducing substrate thionitrobenzoate. Taken together, our results indicate that MtAhpE is a relevant component in the antioxidant repertoire of M. tuberculosis probably involved in peroxide and specially peroxynitrite detoxification.
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Affiliation(s)
- Martín Hugo
- Departamento de Bioqumica, Facultad de Medicina, Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
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48
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D'Ambrosio K, Limauro D, Pedone E, Galdi I, Pedone C, Bartolucci S, De Simone G. Insights into the catalytic mechanism of the Bcp family: functional and structural analysis of Bcp1 from Sulfolobus solfataricus. Proteins 2009; 76:995-1006. [PMID: 19338062 DOI: 10.1002/prot.22408] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bcps constitute a group of antioxidant enzymes, belonging to the Prx family, that are widely distributed in bacteria, plants, and fungi. These proteins can contain two conserved cysteines within the CXXXXC motif. Recent studies demonstrated that though the role of the first cysteine is well defined, being the catalytic peroxidatic cysteine in all the members of this protein family, data on the function of the second cysteine are controversial and require further investigation. In this article, we report on the functional and structural characterization of Bcp1, an archaeal Bcp isolated from Sulfolobus solfataricus, which presents two conserved cysteine residues at positions 45 and 50. Functional studies revealed that this enzyme performs the catalytic reaction using an atypical 2-Cys mechanism, where Cys45 is the peroxidatic and Cys50 is the resolving cysteine. The X-ray structure of the double mutant C45S/C50S, representative of the fully reduced enzyme state, was determined at a resolution of 2.15 A, showing a Trx fold similar to that of other Prxs. Superposition with a structural homologue in the oxidized state provided, for the first time, a detailed description of the structural rearrangement necessary for a member of the Bcp family to perform the catalytic reaction. From this structural analysis, it emerges that a significant conformational change from a fully folded, to a locally unfolded form is required to form the intramolecular disulfide bond upon oxidation, according to the proposed reaction mechanism. Two residues, namely Arg53 and Asp54, which could play a role in this rearrangement, were also identified.
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Affiliation(s)
- Katia D'Ambrosio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
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Lee HL, Kim YS, Park JH, Chung WY, Lee KS, Oh YJ, Sheen SS, Park KJ, Hwang SC. Selectively decreased expression of peroxiredoxins induced by silica in pulmonary epithelial cells. Korean J Intern Med 2009; 24:220-6. [PMID: 19721858 PMCID: PMC2732781 DOI: 10.3904/kjim.2009.24.3.220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 11/28/2008] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND/AIMS Peroxiredoxin (Prx) belongs to a ubiquitous family of antioxidant enzymes that regulates many cellular processes through intracellular oxidative signal transduction pathways. Silica-induced lung damage involves reactive oxygen species (ROS) that trigger subsequent toxic effects and inflammatory responses in alveolar epithelial cells resulting in fibrosis. Therefore, we investigated the role of Prx in the development of lung oxidant injury caused by silicosis, and determined the implication of ROS in that process. METHODS Lung epithelial cell lines A549 and WI26 were treated with 1% silica for 0, 24, or 48 hours, following pretreatment of the A549 cells with N-acetyl-L-cysteine and diphenylene iodonium and no pretreatment of the WI26 cells. We transfected an HA-ubiquitin construct into the A549 cell line and then analyzed the cells via Western blotting and co-immunoprecipitation. RESULTS Silica treatment induced cell death in the A549 lung epithelial cell line and selectively degraded Prx I without impairing protein synthesis in the A549 cells, even when the ROS effect was blocked chemically by N-acetyl-L-cysteine. A co-immunoprecipitation study revealed that Prx I did not undergo ubiquitination. CONCLUSIONS Silica treatment induces a decrease of Prx I expression in lung epithelial cell lines regardless of the presence of ROS. The silica-induced degradation of Prx does not involve the ubiquitin-proteasomal pathway.
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Affiliation(s)
- Hye Lim Lee
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Young Sun Kim
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Joo Hun Park
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Wou Young Chung
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Kyu Sung Lee
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Yoon Jung Oh
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Seung Soo Sheen
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Kwang Joo Park
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Sung Chul Hwang
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
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50
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Machado CX, Pinto PM, Zaha A, Ferreira HB. A peroxiredoxin from Mycoplasma hyopneumoniae with a possible role in H2O2 detoxification. MICROBIOLOGY-SGM 2009; 155:3411-3419. [PMID: 19589831 DOI: 10.1099/mic.0.030643-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia, which affects pig farms worldwide, causing heavy economic losses. In the infection process, this bacterium is exposed to reactive oxygen species (ROS) from its own metabolism or generated by the host as one of the strategies used to neutralize the pathogen. Although the presence of classical antioxidant enzymes would be expected in M. hyopneumoniae, important genes directly related to protection against ROS, such as superoxide dismutase, catalases and glutathione peroxidase, have not been identified by sequence homology in the genome sequence annotation. Among the few identified M. hyopneumoniae genes coding for proteins possibly involved with suppression of ROS-mediated damage, one (tpx) coding for a peroxiredoxin (MhPrx) has been recognized. The sequence and phylogenetic analyses perfomed in this study indicate that MhPrx is closely related to the atypical 2-Cys peroxiredoxin subfamily, although it has only one cysteine in its sequence. The MhPrx coding DNA sequence was cloned and expressed in Escherichia coli to produce a recombinant MhPrx (rMhPrx), which was purified and used to immunize mice and produce an anti-MhPrx polyclonal antiserum. Probing of M. hyopneumoniae extracts with this antiserum demonstrated that MhPrx is expressed in all three tested strains (J, 7422 and 7448). Cross-linking assays and size-exclusion chromatography indicate that rMhPrx forms dimers, as has been established for atypical 2-Cys peroxiredoxins. Furthermore, a metal-catalysed oxidation system was used to assay the activity of rMhPrx, showing that it can protect DNA from ROS-mediated damage and may play an essential role during infection.
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Affiliation(s)
- Cláudio X Machado
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Paulo M Pinto
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Arnaldo Zaha
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre-RS, Brazil.,Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Henrique B Ferreira
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre-RS, Brazil.,Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
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