1
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Karton A, Foller T, Joshi R. Catalyzing epoxy oxygen migration on the basal surface of graphene oxide using strong hydrogen-bond donors. Chem Commun (Camb) 2024. [PMID: 38895846 DOI: 10.1039/d4cc01911c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
High-level double-hybrid DFT simulations reveal that strong hydrogen-bond-donor catalysts (e.g., ethylene glycol, guanidine, and thiourea) significantly accelerate the migration of epoxy oxygen on the surface of graphene oxide, enhancing the reaction rate by 6-12 orders of magnitude. These results shed light on previously puzzling experimental observations.
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Affiliation(s)
- Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia.
| | - Tobias Foller
- School of Materials Science and Engineering, University of New South Wales Sydney, NSW, 2052, Australia
| | - Rakesh Joshi
- School of Materials Science and Engineering, University of New South Wales Sydney, NSW, 2052, Australia
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2
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Sadowska-Bartosz I, Bartosz G. Peroxiredoxin 2: An Important Element of the Antioxidant Defense of the Erythrocyte. Antioxidants (Basel) 2023; 12:antiox12051012. [PMID: 37237878 DOI: 10.3390/antiox12051012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/14/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Peroxiredoxin 2 (Prdx2) is the third most abundant erythrocyte protein. It was known previously as calpromotin since its binding to the membrane stimulates the calcium-dependent potassium channel. Prdx2 is present mostly in cytosol in the form of non-covalent dimers but may associate into doughnut-like decamers and other oligomers. Prdx2 reacts rapidly with hydrogen peroxide (k > 107 M-1 s-1). It is the main erythrocyte antioxidant that removes hydrogen peroxide formed endogenously by hemoglobin autoxidation. Prdx2 also reduces other peroxides including lipid, urate, amino acid, and protein hydroperoxides and peroxynitrite. Oxidized Prdx2 can be reduced at the expense of thioredoxin but also of other thiols, especially glutathione. Further reactions of Prdx2 with oxidants lead to hyperoxidation (formation of sulfinyl or sulfonyl derivatives of the peroxidative cysteine). The sulfinyl derivative can be reduced by sulfiredoxin. Circadian oscillations in the level of hyperoxidation of erythrocyte Prdx2 were reported. The protein can be subject to post-translational modifications; some of them, such as phosphorylation, nitration, and acetylation, increase its activity. Prdx2 can also act as a chaperone for hemoglobin and erythrocyte membrane proteins, especially during the maturation of erythrocyte precursors. The extent of Prdx2 oxidation is increased in various diseases and can be an index of oxidative stress.
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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, 4 Zelwerowicza St., 35-601 Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszów, 4 Zelwerowicza St., 35-601 Rzeszow, Poland
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3
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Montanhero Cabrera VI, do Nascimento Sividanes G, Quintiliano NF, Hikari Toyama M, Ghilardi Lago JH, de Oliveira MA. Exploring functional and structural features of chemically related natural prenylated hydroquinone and benzoic acid from Piper crassinervium (Piperaceae) on bacterial peroxiredoxin inhibition. PLoS One 2023; 18:e0281322. [PMID: 36827425 PMCID: PMC9956870 DOI: 10.1371/journal.pone.0281322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 02/26/2023] Open
Abstract
Multiple drug resistance (MDR) bacterial strains are responsible by 1.2 million of human deaths all over the world. The pathogens possess efficient enzymes which are able to mitigate the toxicity of reactive oxygen species (ROS) produced by some antibiotics and the host immune cells. Among them, the bacterial peroxiredoxin alkyl hydroperoxide reductase C (AhpC) is able to decompose efficiently several kinds of hydroperoxides. To decompose their substrates AhpC use a reactive cysteine residue (peroxidatic cysteine-CysP) that together with two other polar residues (Thr/Ser and Arg) comprise the catalytic triad of these enzymes and are involved in the substrate targeting/stabilization to allow a bimolecular nucleophilic substitution (SN2) reaction. Additionally to the high efficiency the AhpC is very abundant in the cells and present virulent properties in some bacterial species. Despite the importance of AhpC in bacteria, few studies aimed at using natural compounds as inhibitors of this class of enzymes. Some natural products were identified as human isoforms, presenting as common characteristics a bulk hydrophobic moiety and an α, β-unsaturated carbonylic system able to perform a thiol-Michael reaction. In this work, we evaluated two chemically related natural products: 1,4-dihydroxy-2-(3',7'-dimethyl-1'-oxo-2'E,6'-octadienyl) benzene (C1) and 4-hydroxy-2-(3',7'-dimethyl-1'-oxo-2'E,6'-octadienyl) benzoic acid (C2), both were isolated from branches Piper crassinervium (Piperaceae), over the peroxidase activity of AhpC from Pseudomonas aeruginosa (PaAhpC) and Staphylococcus epidermidis (SeAhpC). By biochemical assays we show that although both compounds can perform the Michael addition reaction, only compound C2 was able to inhibit the PaAhpC peroxidase activity but not SeAhpC, presenting IC50 = 20.3 μM. SDS-PAGE analysis revealed that the compound was not able to perform a thiol-Michael addition, suggesting another inhibition behavior. Using computer-assisted simulations, we also show that an acidic group present in the structure of compound C2 may be involved in the stabilization by polar interactions with the Thr and Arg residues from the catalytic triad and several apolar interactions with hydrophobic residues. Finally, C2 was not able to interfere in the peroxidase activity of the isoform Prx2 from humans or even the thiol proteins of the Trx reducing system from Escherichia coli (EcTrx and EcTrxR), indicating specificity for P. aeruginosa AhpC.
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Affiliation(s)
| | | | | | - Marcos Hikari Toyama
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente, SP, Brazil
| | - João Henrique Ghilardi Lago
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
- * E-mail: (MAO); (JHGL)
| | - Marcos Antonio de Oliveira
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente, SP, Brazil
- * E-mail: (MAO); (JHGL)
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4
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Auranofin and Pharmacologic Ascorbate as Radiomodulators in the Treatment of Pancreatic Cancer. Antioxidants (Basel) 2022; 11:antiox11050971. [PMID: 35624835 PMCID: PMC9137675 DOI: 10.3390/antiox11050971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/27/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer accounts for nearly one fourth of all new cancers worldwide. Little progress in the development of novel or adjuvant therapies has been made over the past few decades and new approaches to the treatment of pancreatic cancer are desperately needed. Pharmacologic ascorbate (P-AscH−, high-dose, intravenous vitamin C) is being investigated in clinical trials as an adjunct to standard-of-care chemoradiation treatments. In vitro, P-AscH− has been shown to sensitize cancer cells to ionizing radiation in a manner that is dependent on the generation of H2O2 while simultaneously protecting normal tissue from radiation damage. There is renewed interest in Auranofin (Au), an FDA-approved medication utilized in the treatment of rheumatoid arthritis, as an anti-cancer agent. Au inhibits the thioredoxin antioxidant system, thus increasing the overall peroxide burden on cancer cells. In support of current literature demonstrating Au’s effectiveness in breast, colon, lung, and ovarian cancer, we offer additional data that demonstrate the effectiveness of Au alone and in combination with P-AscH− and ionizing radiation in pancreatic cancer treatment. Combining P-AscH− and Au in the treatment of pancreatic cancer may confer multiple mechanisms to increase H2O2-dependent toxicity amongst cancer cells and provide a promising translatable avenue by which to enhance radiation effectiveness and improve patient outcomes.
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5
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Tairum CA, Santos MC, Breyer CA, de Oliveira ALP, Cabrera VIM, Toledo-Silva G, Mori GM, Toyama MH, Netto LES, de Oliveira MA. Effects of Serine or Threonine in the Active Site of Typical 2-Cys Prx on Hyperoxidation Susceptibility and on Chaperone Activity. Antioxidants (Basel) 2021; 10:1032. [PMID: 34202406 PMCID: PMC8300647 DOI: 10.3390/antiox10071032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 11/23/2022] Open
Abstract
Typical 2-Cys peroxiredoxins (2-Cys Prx) are ubiquitous Cys-based peroxidases, which are stable as decamers in the reduced state, and may dissociate into dimers upon disulfide bond formation. A peroxidatic Cys (CP) takes part of a catalytic triad, together with a Thr/Ser and an Arg. Previously, we described that the presence of Ser (instead of Thr) in the active site stabilizes yeast 2-Cys Prx as decamers. Here, we compared the hyperoxidation susceptibilities of yeast 2-Cys Prx. Notably, 2-Cys Prx containing Ser (named here Ser-Prx) were more resistant to hyperoxidation than enzymes containing Thr (Thr-Prx). In silico analysis revealed that Thr-Prx are more frequent in all domains of life, while Ser-Prx are more abundant in bacteria. As yeast 2-Cys Prx, bacterial Ser-Prx are more stable as decamers than Thr-Prx. However, bacterial Ser-Prx were only slightly more resistant to hyperoxidation than Thr-Prx. Furthermore, in all cases, organic hydroperoxide inhibited more the peroxidase activities of 2-Cys Prx than hydrogen peroxide. Moreover, bacterial Ser-Prx displayed increased thermal resistance and chaperone activity, which may be related with its enhanced stability as decamers compared to Thr-Prx. Therefore, the single substitution of Thr by Ser in the catalytic triad results in profound biochemical and structural differences in 2-Cys Prx.
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Affiliation(s)
- Carlos A. Tairum
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente 01049-010, Brazil; (C.A.T.); (M.C.S.); (C.A.B.); (A.L.P.d.O.); (V.I.M.C.); (M.H.T.)
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 01049-010, Brazil
| | - Melina Cardoso Santos
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente 01049-010, Brazil; (C.A.T.); (M.C.S.); (C.A.B.); (A.L.P.d.O.); (V.I.M.C.); (M.H.T.)
| | - Carlos Alexandre Breyer
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente 01049-010, Brazil; (C.A.T.); (M.C.S.); (C.A.B.); (A.L.P.d.O.); (V.I.M.C.); (M.H.T.)
| | - Ana Laura Pires de Oliveira
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente 01049-010, Brazil; (C.A.T.); (M.C.S.); (C.A.B.); (A.L.P.d.O.); (V.I.M.C.); (M.H.T.)
| | - Vitoria Isabela Montanhero Cabrera
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente 01049-010, Brazil; (C.A.T.); (M.C.S.); (C.A.B.); (A.L.P.d.O.); (V.I.M.C.); (M.H.T.)
| | - Guilherme Toledo-Silva
- Laboratório de Biomarcadores de Contaminação Aquática e Imunoquímica, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brazil;
| | - Gustavo Maruyama Mori
- Laboratório de Ecologia Molecular, Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente 01049-010, Brazil;
| | - Marcos Hikari Toyama
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente 01049-010, Brazil; (C.A.T.); (M.C.S.); (C.A.B.); (A.L.P.d.O.); (V.I.M.C.); (M.H.T.)
| | - Luis Eduardo Soares Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 01049-010, Brazil
| | - Marcos Antonio de Oliveira
- Instituto de Biociências, Universidade Estadual Paulista, UNESP, São Vicente 01049-010, Brazil; (C.A.T.); (M.C.S.); (C.A.B.); (A.L.P.d.O.); (V.I.M.C.); (M.H.T.)
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6
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Peskin AV, Winterbourn CC. The Enigma of 2-Cys Peroxiredoxins: What Are Their Roles? BIOCHEMISTRY (MOSCOW) 2021; 86:84-91. [PMID: 33705284 DOI: 10.1134/s0006297921010089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
2-Cys peroxiredoxins are abundant thiol proteins that react efficiently with a wide range of peroxides. Unlike other enzymes, their exceptionally high reactivity does not rely on cofactors. The mechanism of oxidation and reduction of peroxiredoxins places them in a good position to act as antioxidants as well as key players in redox signaling. Understanding of the intimate details of peroxiredoxin functioning is important for translational research.
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Affiliation(s)
- Alexander V Peskin
- Centre for Free Radical Research, University of Otago Christchurch, Christchurch, Otago, 8140, New Zealand.
| | - Christine C Winterbourn
- Centre for Free Radical Research, University of Otago Christchurch, Christchurch, Otago, 8140, New Zealand
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7
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Peskin AV, Meotti FC, Kean KM, Göbl C, Peixoto AS, Pace PE, Horne CR, Heath SG, Crowther JM, Dobson RCJ, Karplus PA, Winterbourn CC. Modifying the resolving cysteine affects the structure and hydrogen peroxide reactivity of peroxiredoxin 2. J Biol Chem 2021; 296:100494. [PMID: 33667550 PMCID: PMC8049995 DOI: 10.1016/j.jbc.2021.100494] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 01/05/2023] Open
Abstract
Peroxiredoxin 2 (Prdx2) is a thiol peroxidase with an active site Cys (C52) that reacts rapidly with H2O2 and other peroxides. The sulfenic acid product condenses with the resolving Cys (C172) to form a disulfide which is recycled by thioredoxin or GSH via mixed disulfide intermediates or undergoes hyperoxidation to the sulfinic acid. C172 lies near the C terminus, outside the active site. It is not established whether structural changes in this region, such as mixed disulfide formation, affect H2O2 reactivity. To investigate, we designed mutants to cause minimal (C172S) or substantial (C172D and C172W) structural disruption. Stopped flow kinetics and mass spectrometry showed that mutation to Ser had minimal effect on rates of oxidation and hyperoxidation, whereas Asp and Trp decreased both by ∼100-fold. To relate to structural changes, we solved the crystal structures of reduced WT and C172S Prdx2. The WT structure is highly similar to that of the published hyperoxidized form. C172S is closely related but more flexible and as demonstrated by size exclusion chromatography and analytical ultracentrifugation, a weaker decamer. Size exclusion chromatography and analytical ultracentrifugation showed that the C172D and C172W mutants are also weaker decamers than WT, and small-angle X-ray scattering analysis indicated greater flexibility with partially unstructured regions consistent with C-terminal unfolding. We propose that these structural changes around C172 negatively impact the active site geometry to decrease reactivity with H2O2. This is relevant for Prdx turnover as intermediate mixed disulfides with C172 would also be disruptive and could potentially react with peroxides before resolution is complete.
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Affiliation(s)
- Alexander V Peskin
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Flavia C Meotti
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Kelsey M Kean
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Christoph Göbl
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Albert Souza Peixoto
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Paul E Pace
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Christopher R Horne
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sarah G Heath
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Jennifer M Crowther
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA.
| | - Christine C Winterbourn
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand.
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8
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Nagy P, Dóka É, Ida T, Akaike T. Measuring Reactive Sulfur Species and Thiol Oxidation States: Challenges and Cautions in Relation to Alkylation-Based Protocols. Antioxid Redox Signal 2020; 33:1174-1189. [PMID: 32631072 DOI: 10.1089/ars.2020.8077] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Significance: Redox biology is gaining ground in research related to human physiology (metabolism, signaling), pathophysiology (cancer, cardiovascular disease, neurodegeneration), and toxicology (radiation- or xenobiotic-induced damage). A major hurdle in advancing redox medicine is the current lack of understanding the mechanisms underpinning the observed detrimental or beneficial in vivo effects. To gain deeper insights into the underlying molecular pathways of redox regulation, we need to appreciate the strengths and limitations of the currently available methods. Recent Advances: Reactive sulfur species (RSS), including cysteine derivatives of peptides and proteins along with small molecules such as hydrogen sulfide or inorganic polysulfides, are major players in redox biology. RSS-mediated regulation of protein functions is a widely studied mechanism in the field, and considerable efforts have been devoted to the development of selective detection methods. Critical Issues: A large number of available methods rely on an alkylation step to freeze the dynamism of consecutive oxidation and reduction events among RSS at a particular time point inside the cell. This process uses the assumption that alkylation blocks all redox events instantaneously. We argue that unfortunately this is often not the case, which could have serious impacts on detected sulfur species speciation and confound experimental results. Future Directions: Novel technologies and prudent optimization of existing methods to accurately characterize the dynamic redox status of the thiol proteome as well as detailed understanding of regulatory and signaling capacities of protein polysulfidation are crucial to open new routes toward therapeutic interventions.
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Affiliation(s)
- Péter Nagy
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary
| | - Éva Dóka
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary
| | - Tomoaki Ida
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
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9
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Abstract
Significance: In humans, imbalances in the reduction-oxidation (redox) status of cells are associated with many pathological states. In addition, many therapeutics and prophylactics used as interventions for diverse pathologies either directly modulate oxidant levels or otherwise influence endogenous cellular redox systems. Recent Advances: The cellular machineries that maintain redox homeostasis or that function within antioxidant defense systems rely heavily on the regulated reactivities of sulfur atoms either within or derived from the amino acids cysteine and methionine. Recent advances have substantially advanced our understanding of the complex and essential chemistry of biological sulfur-containing molecules. Critical Issues: The redox machineries that maintain cellular homeostasis under diverse stresses can consume large amounts of energy to generate reducing power and/or large amounts of sulfur-containing nutrients to replenish or sustain intracellular stores. By understanding the metabolic pathways underlying these responses, one can better predict how to protect cells from specific stresses. Future Directions: Here, we summarize the current state of knowledge about the impacts of different stresses on cellular metabolism of sulfur-containing molecules. This analysis suggests that there remains more to be learned about how cells use sulfur chemistry to respond to stresses, which could in turn lead to advances in therapeutic interventions for some exposures or conditions.
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Affiliation(s)
- Colin G Miller
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, USA
| | - Edward E Schmidt
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, USA
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10
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A comparison of the chemical biology of hydropersulfides (RSSH) with other protective biological antioxidants and nucleophiles. Nitric Oxide 2020; 107:46-57. [PMID: 33253886 DOI: 10.1016/j.niox.2020.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/05/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022]
Abstract
The hydropersulfide (RSSH) functional group has received significant recent interest due to its unique chemical properties that set it apart from other biological species. The chemistry of RSSH predicts that one possible biological role may be as a protectant against cellular oxidative and electrophilic stress. That is, RSSH has reducing and nucleophilic properties that may combat the potentially destructive biochemistry of toxicologically relevant oxidants and electrophiles. However, there are currently numerous other molecules that have established roles in this regard. For example, ascorbate and tocopherols are potent antioxidants that quench deleterious oxidative reactions and glutathione (GSH) is a well-established and highly prevalent biological protectant against electrophile toxicity. Thus, in order to begin to understand the possible role of RSSH species as protectants against oxidative/electrophilic stress, the inherent chemical properties of RSSH versus these other protectants will be discussed and contrasted.
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11
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Peskin AV, Meotti FC, de Souza LF, Anderson RF, Winterbourn CC, Salvador A. Intra-dimer cooperativity between the active site cysteines during the oxidation of peroxiredoxin 2. Free Radic Biol Med 2020; 158:115-125. [PMID: 32702382 DOI: 10.1016/j.freeradbiomed.2020.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 01/02/2023]
Abstract
Peroxiredoxin 2 (Prdx2) and other typical 2-Cys Prdxs function as homodimers in which hydrogen peroxide oxidizes each active site cysteine to a sulfenic acid which then condenses with the resolving cysteine on the alternate chain. Previous kinetic studies have considered both sites as equally reactive. Here we have studied Prdx2 using a combination of non-reducing SDS-PAGE to separate reduced monomers and dimers with one and two disulfide bonds, and stopped flow analysis of tryptophan fluorescence, to investigate whether there is cooperativity between the sites. We have observed positive cooperativity when H2O2 is added as a bolus and oxidation of the second site occurs while the first site is present as a sulfenic acid. Modelling of this reaction showed that the second site reacts 2.2 ± 0.1 times faster. In contrast, when H2O2 was generated slowly and the first active site condensed to a disulfide before the second site reacted, no cooperativity was evident. Conversion of the sulfenic acid to the disulfide showed negative cooperativity, with modelling of the exponential rise in tryptophan fluorescence yielding a rate constant of 0.75 ± 0.08 s-1 when the alternate active site was present as a sulfenic acid and 2.29 ± 0.08-fold lower when it was a disulfide. No difference in the rate of hyperoxidation at the two sites was detected. Our findings imply that oxidation of one active site affects the conformation of the second site and influences which intermediate forms of the protein are favored under different cellular conditions.
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Affiliation(s)
- Alexander V Peskin
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Flávia C Meotti
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo-SP, Brazil
| | - Luiz F de Souza
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo-SP, Brazil
| | - Robert F Anderson
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Christine C Winterbourn
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand.
| | - Armindo Salvador
- CNC - Centre for Neuroscience Cell Biology, University of Coimbra, Coimbra, Portugal; CQC, Department of Chemistry, And University of Coimbra, Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.
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12
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Mohammad A, Saini RV, Kumar R, Sharma D, Saini NK, Gupta A, Thakur P, Winterbourn CC, Saini AK. A curious case of cysteines in human peroxiredoxin I. Redox Biol 2020; 37:101738. [PMID: 33011678 PMCID: PMC7530344 DOI: 10.1016/j.redox.2020.101738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/08/2020] [Accepted: 09/19/2020] [Indexed: 01/06/2023] Open
Abstract
Peroxiredoxins (Prxs) are antioxidant proteins that are involved in cellular defence against reactive oxygen species and reactive nitrogen species. Humans have six peroxiredoxins, hPrxI-VI, out of which hPrxI and hPrxII belongs to the typical 2-Cys class sharing 90% conservation in their amino acid sequence including catalytic residues required to carry out their peroxidase and chaperone activities. Despite the high conservation between hPrxI and hPrxII, hPrxI behaves differently from hPrxII in its peroxidase and chaperone activity. We recently showed in yeast that in the absence of Tsa1 and Tsa2 (orthologs of hPrx) hPrxI protects the cells against different stressors whereas hPrxII does not. To understand this difference, we expressed catalytic mutants of hPrxI in yeast cells lacking the orthologs of hPrxI/II. We found that the catalytic mutants lacking peroxidase function including hPrxIC52S, hPrxIC173S, hPrxIT49A, hPrxIP45A and hPrxIR128A were not able to grow on media with nitrosative stressor (sodium nitroprusside) and unable to withstand heat stress, but surprisingly they were able to grow on an oxidative stressor (H2O2). Interestingly, we found that hPrxI increases the expression of antioxidant genes, GPX1 and SOD1, and this is also seen in the case of a catalytic mutant, indicating hPrxI can indirectly reduce oxidative stress independently of its own peroxidase function and thus suggesting a novel role of hPrxI in altering the expression of other antioxidant genes. Furthermore, hPrxIC83T was resistant to hyperoxidation and formation of stable high molecular weight oligomers, which is suggestive of impaired chaperone activity. Our results suggest that the catalytic residues of hPrxI are essential to counter the nitrosative stress whereas Cys83 in hPrxI plays a critical role in hyperoxidation of hPrxI.
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Affiliation(s)
- Ashu Mohammad
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India; Faculty of Applied Science and Biotechnology, Shoolini University, Solan, 173229, India
| | - Reena V Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Rakesh Kumar
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Neeraj K Saini
- Department of Biotechnology, Jawaharlal Nehru University, Delhi, 110067, India
| | - Arpit Gupta
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Priyanka Thakur
- Faculty of Sciences, Shoolini University, Solan, 173229, India
| | - Christine C Winterbourn
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Adesh K Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India; Maharishi Markandeshwar (Deemed to Be University), Solan, HP, 173212, India.
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13
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Cobley JN, Husi H. Immunological Techniques to Assess Protein Thiol Redox State: Opportunities, Challenges and Solutions. Antioxidants (Basel) 2020; 9:E315. [PMID: 32326525 PMCID: PMC7222201 DOI: 10.3390/antiox9040315] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
To understand oxidative stress, antioxidant defense, and redox signaling in health and disease it is essential to assess protein thiol redox state. Protein thiol redox state is seldom assessed immunologically because of the inability to distinguish reduced and reversibly oxidized thiols by Western blotting. An underappreciated opportunity exists to use Click PEGylation to realize the transformative power of simple, time and cost-efficient immunological techniques. Click PEGylation harnesses selective, bio-orthogonal Click chemistry to separate reduced and reversibly oxidized thiols by selectively ligating a low molecular weight polyethylene glycol moiety to the redox state of interest. The resultant ability to disambiguate reduced and reversibly oxidized species by Western blotting enables Click PEGylation to assess protein thiol redox state. In the present review, to enable investigators to effectively harness immunological techniques to assess protein thiol redox state we critique the chemistry, promise and challenges of Click PEGylation.
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Affiliation(s)
- James Nathan Cobley
- Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK;
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14
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Truzzi DR, Alves SV, Netto LES, Augusto O. The Peroxidatic Thiol of Peroxiredoxin 1 is Nitrosated by Nitrosoglutathione but Coordinates to the Dinitrosyl Iron Complex of Glutathione. Antioxidants (Basel) 2020; 9:antiox9040276. [PMID: 32218363 PMCID: PMC7222187 DOI: 10.3390/antiox9040276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022] Open
Abstract
Protein S-nitrosation is an important consequence of NO●·metabolism with implications in physiology and pathology. The mechanisms responsible for S-nitrosation in vivo remain debatable and kinetic data on protein S-nitrosation by different agents are limited. 2-Cys peroxiredoxins, in particular Prx1 and Prx2, were detected as being S-nitrosated in multiple mammalian cells under a variety of conditions. Here, we investigated the kinetics of Prx1 S-nitrosation by nitrosoglutathione (GSNO), a recognized biological nitrosating agent, and by the dinitrosyl-iron complex of glutathione (DNIC-GS; [Fe(NO)2(GS)2]−), a hypothetical nitrosating agent. Kinetics studies following the intrinsic fluorescence of Prx1 and its mutants (C83SC173S and C52S) were complemented by product analysis; all experiments were performed at pH 7.4 and 25 ℃. The results show GSNO-mediated nitrosation of Prx1 peroxidatic residue (k+NOCys52 = 15.4 ± 0.4 M−1. s−1) and of Prx1 Cys83 residue (k+NOCys83 = 1.7 ± 0.4 M−1. s−1). The reaction of nitrosated Prx1 with GSH was also monitored and provided a second-order rate constant for Prx1Cys52NO denitrosation of k−NOCys52 = 14.4 ± 0.3 M−1. s−1. In contrast, the reaction of DNIC-GS with Prx1 did not nitrosate the enzyme but formed DNIC-Prx1 complexes. The peroxidatic Prx1 Cys was identified as the residue that more rapidly replaces the GS ligand from DNIC-GS (kDNICCys52 = 7.0 ± 0.4 M−1. s−1) to produce DNIC-Prx1 ([Fe(NO)2(GS)(Cys52-Prx1)]−). Altogether, the data showed that in addition to S-nitrosation, the Prx1 peroxidatic residue can replace the GS ligand from DNIC-GS, forming stable DNIC-Prx1, and both modifications disrupt important redox switches.
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Affiliation(s)
- Daniela R. Truzzi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil;
- Correspondence:
| | - Simone V. Alves
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil; (S.V.A.); (L.E.S.N.)
| | - Luis E. S. Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil; (S.V.A.); (L.E.S.N.)
| | - Ohara Augusto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil;
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15
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Dóka É, Ida T, Dagnell M, Abiko Y, Luong NC, Balog N, Takata T, Espinosa B, Nishimura A, Cheng Q, Funato Y, Miki H, Fukuto JM, Prigge JR, Schmidt EE, Arnér ESJ, Kumagai Y, Akaike T, Nagy P. Control of protein function through oxidation and reduction of persulfidated states. SCIENCE ADVANCES 2020; 6:eaax8358. [PMID: 31911946 PMCID: PMC6938701 DOI: 10.1126/sciadv.aax8358] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 11/05/2019] [Indexed: 05/17/2023]
Abstract
Irreversible oxidation of Cys residues to sulfinic/sulfonic forms typically impairs protein function. We found that persulfidation (CysSSH) protects Cys from irreversible oxidative loss of function by the formation of CysSSO1-3H derivatives that can subsequently be reduced back to native thiols. Reductive reactivation of oxidized persulfides by the thioredoxin system was demonstrated in albumin, Prx2, and PTP1B. In cells, this mechanism protects and regulates key proteins of signaling pathways, including Prx2, PTEN, PTP1B, HSP90, and KEAP1. Using quantitative mass spectrometry, we show that (i) CysSSH and CysSSO3H species are abundant in mouse liver and enzymatically regulated by the glutathione and thioredoxin systems and (ii) deletion of the thioredoxin-related protein TRP14 in mice altered CysSSH levels on a subset of proteins, predicting a role for TRP14 in persulfide signaling. Furthermore, selenium supplementation, polysulfide treatment, or knockdown of TRP14 mediated cellular responses to EGF, suggesting a role for TrxR1/TRP14-regulated oxidative persulfidation in growth factor responsiveness.
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Affiliation(s)
- É. Dóka
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, 1122 Budapest, Hungary
| | - T. Ida
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, 980-8575 Sendai, Japan
| | - M. Dagnell
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Y. Abiko
- Environmental Biology Section, Faculty of Medicine, University of Tsukuba, 305-8575 Tsukuba, Japan
| | - N. C. Luong
- Environmental Biology Section, Faculty of Medicine, University of Tsukuba, 305-8575 Tsukuba, Japan
- Faculty of Pharmacy, Hue University of Medicine and Pharmacy, Hue University, 06 Ngo Quyen, Hue, Vietnam
| | - N. Balog
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, 1122 Budapest, Hungary
| | - T. Takata
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, 980-8575 Sendai, Japan
| | - B. Espinosa
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - A. Nishimura
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, 980-8575 Sendai, Japan
| | - Q. Cheng
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Y. Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - H. Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - J. M. Fukuto
- Department of Chemistry, Sonoma State University, Rohnert Park, Sonoma, CA 94928, USA
| | - J. R. Prigge
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - E. E. Schmidt
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - E. S. J. Arnér
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Y. Kumagai
- Environmental Biology Section, Faculty of Medicine, University of Tsukuba, 305-8575 Tsukuba, Japan
| | - T. Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, 980-8575 Sendai, Japan
| | - P. Nagy
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, 1122 Budapest, Hungary
- Corresponding author.
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16
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Abstract
Peroxiredoxins are ubiquitous antioxidant proteins that exhibit a striking variety of quaternary structures, making them appealing building blocks with which nanoscale architectures are created for applications in nanotechnology. The solution environment of the protein, as well as protein sequence, influences the presentation of a particular structure, thereby enabling mesoscopic manipulations that affect arrangments at the nanoscale. This chapter will equip us with the knowledge necessary to not only produce and manipulate peroxiredoxin proteins into desired structures but also to characterize the different structures using dynamic light scattering, analytical centrifugation, and negative stain transmission electron microscopy, thereby setting the stage for us to use these proteins for applications in nanotechnology.
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Affiliation(s)
- Frankie Conroy
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - N Amy Yewdall
- Bio-Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
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17
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Kumar R, Mohammad A, Saini RV, Chahal A, Wong CM, Sharma D, Kaur S, Kumar V, Winterbourn CC, Saini AK. Deciphering the in vivo redox behavior of human peroxiredoxins I and II by expressing in budding yeast. Free Radic Biol Med 2019; 145:321-329. [PMID: 31580947 DOI: 10.1016/j.freeradbiomed.2019.09.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 01/18/2019] [Accepted: 09/27/2019] [Indexed: 01/06/2023]
Abstract
Peroxiredoxins (Prxs), scavenge cellular peroxides by forming recyclable disulfides but under high oxidative stress, hyperoxidation of their active-site Cys residue results in loss of their peroxidase activity. Saccharomyces cerevisiae deficient in human Prx (hPrx) orthologue TSA1 show growth defects under oxidative stress. They can be complemented with hPRXI but not by hPRXII, but it is not clear how the disulfide and hyperoxidation states of the hPrx vary in yeast under oxidative stress. To understand this, we used oxidative-stress sensitive tsa1tsa2Δ yeast strain to express hPRXI or hPRXII. We found that hPrxI in yeast exists as a mixture of disulfide-linked dimer and reduced monomer but becomes hyperoxidized upon elevated oxidative stress as analyzed under denaturing conditions (SDS-PAGE). In contrast, hPrxII was present predominantly as the disulfide in unstressed cells and readily converted to its hyperoxidized, peroxidase-inactive form even with mild oxidative stress. Interestingly, we found that plant extracts containing polyphenol antioxidants provided further protection against the growth defects of the tsa1tsa2Δ strain expressing hPrx and preserved the peroxidase-active forms of the Prxs. The extracts also helped to protect against hyperoxidation of hPrxs in HeLa cells. Based on these findings we can conclude that resistance to oxidative stress of yeast cells expressing individual hPrxs requires the hPrx to be maintained in a redox state that permits redox cycling and peroxidase activity. Peroxidase activity decreases as the hPrx becomes hyperoxidized and the limited protection by hPrxII compared with hPrxI can be explained by its greater sensitivity to hyperoxidation.
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Affiliation(s)
- Rakesh Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, India
| | - Ashu Mohammad
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, India
| | - Reena V Saini
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, India
| | - Anterpreet Chahal
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, India
| | - Chi-Ming Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Special Administrative Region, People's Republic of China
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Sukhvir Kaur
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, India
| | - Vikas Kumar
- Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Christine C Winterbourn
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Adesh K Saini
- Faculty of Basic Sciences Shoolini University, Solan, India.
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18
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Yu MJ, Wu J, Chen SL. Mechanism and Inhibitor Exploration with Binuclear Mg Ketol-Acid Reductoisomerase: Targeting the Biosynthetic Pathway of Branched-Chain Amino Acids. Chembiochem 2019; 21:381-391. [PMID: 31309701 DOI: 10.1002/cbic.201900363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 01/01/2023]
Abstract
Binuclear Mg ketol-acid reductoisomerase (KARI), which converts (S)-2-acetolactate into (R)-2,3-dihydroxyisovalerate, is responsible for the second step of the biosynthesis of branched-chain amino acids in plants and microorganisms and thus serves as a key inhibition target potentially without effects on mammals. Here, through the use of density functional calculations and a chemical model, the KARI-catalyzed reaction has been demonstrated to include the initial deprotonation of the substrate C2 hydroxy group, bridged by the two Mg ions, alkyl migration from the C2-alkoxide carbon atom to the C3-carbonyl carbon atom, and hydride transfer from a nicotinamide adenine dinucleotide phosphate [NAD(P)H] cofactor to C2. A dead-end mechanism with a hydride transferred to the C3 carbonyl group has been ruled out. The nucleophilicity (migratory aptitude) of the migrating carbon atom and the provision of additional negative charge to the di-Mg coordination sphere have significant effects on the steps of alkyl migration and hydride transfer, respectively. Other important mechanistic characteristics are also revealed. Inspired by the mechanism, an inhibitor (2-carboxylate-lactic acid) was designed and predicted by barrier analysis to be effective in inactivating KARI, hence probably enriching the antifungal and antibacterial library. Two types of slow substrate analogues (2-trihalomethyl acetolactic acids and 2-glutaryl lactic acid) were also found.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Jue Wu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
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19
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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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20
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Randall LM, Dalla Rizza J, Parsonage D, Santos J, Mehl RA, Lowther WT, Poole LB, Denicola A. Unraveling the effects of peroxiredoxin 2 nitration; role of C-terminal tyrosine 193. Free Radic Biol Med 2019; 141:492-501. [PMID: 31323313 PMCID: PMC6749834 DOI: 10.1016/j.freeradbiomed.2019.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022]
Abstract
Peroxiredoxins (Prx) are enzymes that efficiently reduce hydroperoxides through active participation of cysteine residues (CP, CR). The first step in catalysis, the reduction of peroxide substrate, is fast, 107 - 108 M-1s-1 for human Prx2. In addition, the high intracellular concentration of Prx positions them not only as good antioxidants but also as central players in redox signaling pathways. These biological functions can be affected by post-translational modifications that could alter the peroxidase activity and/or interaction with other proteins. In particular, inactivation by hyperoxidation of CP, which occurs when a second molecule of peroxide reacts with the CP in the sulfenic acid form, modulates their participation in redox signaling pathways. The higher sensitivity to hyperoxidation of some Prx has been related to the presence of structural motifs that disfavor disulfide formation at the active site, making the CP sulfenic acid more available for hyperoxidation or interaction with a redox protein target. We previously reported that treatment of human Prx2 with peroxynitrite results in tyrosine nitration, a post-translational modification on non-catalytic residues, yielding a more active peroxidase with higher resistance to hyperoxidation. In this work, studies on various mutants of hPrx2 confirm that the presence of the tyrosyl side-chain of Y193, belonging to the C-terminal YF motif of eukaryotic Prx, is necessary to observe the increase in Prx2 resistance to hyperoxidation. Moreover, our results underline the critical role of this structural motif on the rate of disulfide formation that determines the differential participation of Prx in redox signaling pathways.
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Affiliation(s)
- Lía M Randall
- Laboratorio I+D de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay; Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay
| | - Joaquín Dalla Rizza
- Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay
| | - Derek Parsonage
- Department of Biochemistry and Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas (UBA-CONICET), Buenos Aires, Argentina
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - W Todd Lowther
- Department of Biochemistry and Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Leslie B Poole
- Department of Biochemistry and Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay.
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21
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Zaffagnini M, Fermani S, Marchand CH, Costa A, Sparla F, Rouhier N, Geigenberger P, Lemaire SD, Trost P. Redox Homeostasis in Photosynthetic Organisms: Novel and Established Thiol-Based Molecular Mechanisms. Antioxid Redox Signal 2019; 31:155-210. [PMID: 30499304 DOI: 10.1089/ars.2018.7617] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Significance: Redox homeostasis consists of an intricate network of reactions in which reactive molecular species, redox modifications, and redox proteins act in concert to allow both physiological responses and adaptation to stress conditions. Recent Advances: This review highlights established and novel thiol-based regulatory pathways underlying the functional facets and significance of redox biology in photosynthetic organisms. In the last decades, the field of redox regulation has largely expanded and this work is aimed at giving the right credit to the importance of thiol-based regulatory and signaling mechanisms in plants. Critical Issues: This cannot be all-encompassing, but is intended to provide a comprehensive overview on the structural/molecular mechanisms governing the most relevant thiol switching modifications with emphasis on the large genetic and functional diversity of redox controllers (i.e., redoxins). We also summarize the different proteomic-based approaches aimed at investigating the dynamics of redox modifications and the recent evidence that extends the possibility to monitor the cellular redox state in vivo. The physiological relevance of redox transitions is discussed based on reverse genetic studies confirming the importance of redox homeostasis in plant growth, development, and stress responses. Future Directions: In conclusion, we can firmly assume that redox biology has acquired an established significance that virtually infiltrates all aspects of plant physiology.
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Affiliation(s)
- Mirko Zaffagnini
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | - Simona Fermani
- 2 Department of Chemistry Giacomo Ciamician, University of Bologna, Bologna, Italy
| | - Christophe H Marchand
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Alex Costa
- 4 Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Sparla
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | | | - Peter Geigenberger
- 6 Department Biologie I, Ludwig-Maximilians-Universität München, LMU Biozentrum, Martinsried, Germany
| | - Stéphane D Lemaire
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Paolo Trost
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
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22
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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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23
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Dagnell M, Cheng Q, Rizvi SHM, Pace PE, Boivin B, Winterbourn CC, Arnér ESJ. Bicarbonate is essential for protein-tyrosine phosphatase 1B (PTP1B) oxidation and cellular signaling through EGF-triggered phosphorylation cascades. J Biol Chem 2019; 294:12330-12338. [PMID: 31197039 DOI: 10.1074/jbc.ra119.009001] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/06/2019] [Indexed: 12/13/2022] Open
Abstract
Protein-tyrosine phosphatases (PTPs) counteract protein tyrosine phosphorylation and cooperate with receptor-tyrosine kinases in the regulation of cell signaling. PTPs need to undergo oxidative inhibition for activation of cellular cascades of protein-tyrosine kinase phosphorylation following growth factor stimulation. It has remained enigmatic how such oxidation can occur in the presence of potent cellular reducing systems. Here, using in vitro biochemical assays with purified, recombinant protein, along with experiments in the adenocarcinoma cell line A431, we discovered that bicarbonate, which reacts with H2O2 to form the more reactive peroxymonocarbonate, potently facilitates H2O2-mediated PTP1B inactivation in the presence of thioredoxin reductase 1 (TrxR1), thioredoxin 1 (Trx1), and peroxiredoxin 2 (Prx2) together with NADPH. The cellular experiments revealed that intracellular bicarbonate proportionally dictates total protein phosphotyrosine levels obtained after stimulation with epidermal growth factor (EGF) and that bicarbonate levels directly correlate with the extent of PTP1B oxidation. In fact, EGF-induced cellular oxidation of PTP1B was completely dependent on the presence of bicarbonate. These results provide a plausible mechanism for PTP inactivation during cell signaling and explain long-standing observations that growth factor responses and protein phosphorylation cascades are intimately linked to the cellular acid-base balance.
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Affiliation(s)
- Markus Dagnell
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | | | - Paul E Pace
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand
| | - Benoit Boivin
- Department of Nanobioscience, SUNY Polytechnic Institute, Albany, New York 12203
| | - Christine C Winterbourn
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand.
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
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24
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Muralidharan M, Bhat V, Bindu YS, Mandal AK. Glycation profile of minor abundant erythrocyte proteome across varying glycemic index in diabetes mellitus. Anal Biochem 2019; 573:37-43. [PMID: 30831097 DOI: 10.1016/j.ab.2019.02.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 11/26/2022]
Abstract
PURPOSE Long-term glycemic index in patients with diabetes mellitus (DM) is measured by glycated hemoglobin (HbA1c) besides blood glucose. In DM, the primary amino groups of proteins get glycated via non-enzymatic post-translational modification. This study aims at identifying and characterizing site-specific glycation of erythrocyte proteome across varying glycemic index in patients with DM. EXPERIMENTS We isolated the glycated erythrocyte proteome devoid of hemoglobin from control and diabetic samples using boronate affinity chromatography. Proteomic analysis was performed using nanoLC/ESI-MS proteomics platform. The site-specific modification on different proteins was deciphered using a customized database. RESULTS We report 37 glycated proteins identified and characterized from samples with HbA1c of 6%, 8%, 12%, and 16%. Our results show that both extent and site-specific modification of proteins increased with increasing HbA1c. The observed residue-specific modifications of catalase, peroxiredoxin, carbonic anhydrase, lactate dehydrogenase B and delta-aminolevulinic acid dehydratase were correlated with the literature report on their functional disorder in DM. CONCLUSIONS and clinical relevance: 37 glycated erythrocyte proteins apart from hemoglobin were characterized from DM patient samples with varying HbA1c values. We correlated the site-specific glycation and associated functional disorder of five representative proteins. However, the clinical correlation with the observed modifications needs further investigation.
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Affiliation(s)
- Monita Muralidharan
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences, 100ft Road, Koramangala, Bangalore, 560034, India
| | - Vijay Bhat
- Manipal Hospital, Department of Biochemistry, Old Airport Road, Bangalore, 560017, India
| | - Y S Bindu
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences, 100ft Road, Koramangala, Bangalore, 560034, India
| | - Amit Kumar Mandal
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences, 100ft Road, Koramangala, Bangalore, 560034, India.
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25
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Miller CG, Schmidt EE. Disulfide reductase systems in liver. Br J Pharmacol 2019; 176:532-543. [PMID: 30221761 PMCID: PMC6346074 DOI: 10.1111/bph.14498] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/03/2018] [Accepted: 08/18/2018] [Indexed: 12/18/2022] Open
Abstract
Intermediary metabolism and detoxification place high demands on the disulfide reductase systems in most hepatocyte subcellular compartments. Biosynthetic, metabolic, cytoprotective and signalling activities in the cytosol; regulation of transcription in nuclei; respiration in mitochondria; and protein folding in endoplasmic reticulum all require resident disulfide reductase activities. In the cytosol, two NADPH-dependent enzymes, glutathione reductase and thioredoxin reductase, as well as a recently identified NADPH-independent system that uses catabolism of methionine to maintain pools of reduced glutathione, supply disulfide reducing power. However the necessary discontinuity between the cytosol and the interior of organelles restricts the ability of the cytosolic systems to support needs in other compartments. Maintenance of molecular- and charge-gradients across the inner-mitochondrial membrane, which is needed for oxidative phosphorylation, mandates that the matrix maintain an autonomous set of NADPH-dependent disulfide reductase systems. Elsewhere, complex mechanisms mediate the transfer of cytosolic reducing power into specific compartments. The redox needs in each compartment also differ, with the lumen of the endoplasmic reticulum, the mitochondrial inter-membrane space and some signalling proteins in the cytosol each requiring different levels of protein oxidation. Here, we present an overview of the current understanding of the disulfide reductase systems in major subcellular compartments of hepatocytes, integrating knowledge obtained from direct analyses on liver with inferences from other model systems. Additionally, we discuss relevant advances in the expanding field of redox signalling. LINKED ARTICLES: This article is part of a themed section on Chemical Biology of Reactive Sulfur Species. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.4/issuetoc.
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Affiliation(s)
- Colin G Miller
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMTUSA
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Edward E Schmidt
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
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26
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De Armas MI, Esteves R, Viera N, Reyes AM, Mastrogiovanni M, Alegria TGP, Netto LES, Tórtora V, Radi R, Trujillo M. Rapid peroxynitrite reduction by human peroxiredoxin 3: Implications for the fate of oxidants in mitochondria. Free Radic Biol Med 2019; 130:369-378. [PMID: 30391677 DOI: 10.1016/j.freeradbiomed.2018.10.451] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Mitochondria are main sites of peroxynitrite formation. While at low concentrations mitochondrial peroxynitrite has been associated with redox signaling actions, increased levels can disrupt mitochondrial homeostasis and lead to pathology. Peroxiredoxin 3 is exclusively located in mitochondria, where it has been previously shown to play a major role in hydrogen peroxide reduction. In turn, reduction of peroxynitrite by peroxiredoxin 3 has been inferred from its protective actions against tyrosine nitration and neurotoxicity in animal models, but was not experimentally addressed so far. Herein, we demonstrate the human peroxiredoxin 3 reduces peroxynitrite with a rate constant of 1 × 107 M-1 s-1 at pH 7.8 and 25 °C. Reaction with hydroperoxides caused biphasic changes in the intrinsic fluorescence of peroxiredoxin 3: the first phase corresponded to the peroxidatic cysteine oxidation to sulfenic acid. Peroxynitrite in excess led to peroxiredoxin 3 hyperoxidation and tyrosine nitration, oxidative post-translational modifications that had been previously identified in vivo. A significant fraction of the oxidant is expected to react with CO2 and generate secondary radicals, which participate in further oxidation and nitration reactions, particularly under metabolic conditions of active oxidative decarboxylations or increased hydroperoxide formation. Our results indicate that both peroxiredoxin 3 and 5 should be regarded as main targets for peroxynitrite in mitochondria.
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Affiliation(s)
- María Inés De Armas
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Romina Esteves
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Nicolás Viera
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Aníbal M Reyes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Mauricio Mastrogiovanni
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Thiago G P Alegria
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Luis E S Netto
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Verónica Tórtora
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Center For Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Uruguay.
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27
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Zadeh-Esmaeel MM, Rezaei-Tavirani M, Ali Ahmadi N, Vafae R. Evaluation of gene expression change in eosinophilic gastroenteritis. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2019; 12:239-245. [PMID: 31528308 PMCID: PMC6668767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/18/2018] [Indexed: 11/01/2022]
Abstract
AIM Screening differentially expressed genes (DEGs) related to Eosinophilic gastroenteritis (EG) to introduce possible biomarkers. BACKGROUND EG as a rare gastrointestinal disorder is characterized with gastrointestinal bleeding, crampy generalized abdominal pain, diarrhea, nausea, vomiting, and weight loss. In this study gene expression profile of patients is analysis via protein-protein interaction (PPI) analysis to reveal new prospective of disease. METHODS Top significant genes of gene expression profiles of 5 gastric antrum EG patients and 5gastric antrum control from GEO which were matched via boxplot analysis were screened via PPI network by using Cytoscape software and STRING database. Numbers of 20 top nodes of query DEGs based on degree value were introduced as central nodes which 7 critical central genes among them were identified. Gene ontology enrichment for the 20 central genes was done by using CluGO. Action map for the central genes was performed by applying CluePedia. RESULTS Among 20 central nodes, TXN, PRDX2, NR3C1, GRB2, PIK3C3, AP2B1 and REPS1 were recognized as critical central genes. Nine biological terms were determined that most of them were involved in the transport processes. CONCLUSION The introduced possible biomarkers can be used in the differential diagnosis of the disease and also in treatment of disorder.
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Affiliation(s)
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nayeb Ali Ahmadi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Vafae
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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28
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Pace PE, Peskin AV, Konigstorfer A, Jasoni CJ, Winterbourn CC, Hampton MB. Peroxiredoxin interaction with the cytoskeletal-regulatory protein CRMP2: Investigation of a putative redox relay. Free Radic Biol Med 2018; 129:383-393. [PMID: 30315937 DOI: 10.1016/j.freeradbiomed.2018.10.407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/14/2018] [Accepted: 10/03/2018] [Indexed: 12/22/2022]
Abstract
Hydrogen peroxide (H2O2) acts as a signaling molecule in cells by oxidising cysteine residues in regulatory proteins such as phosphatases, kinases and transcription factors. It is unclear exactly how many of these proteins are specifically targeted by H2O2 because they appear too unreactive to be directly oxidised. One proposal is that peroxiredoxins (Prxs) initially react with H2O2 and then oxidise adjacent proteins via a thiol relay mechanism. The aim of this study was to identify constitutive interaction partners of Prx2 in Jurkat T-lymphoma cells, in which thiol protein oxidation occurs at low micromolar concentrations of H2O2. Immunoprecipitation and proximity ligation assays identified a physical interaction between collapsin response mediator protein 2 (CRMP2) and cytoplasmic Prx2. CRMP2 regulates microtubule structure during lymphocyte migration and neuronal development. Exposure of Jurkat cells to low micromolar levels of H2O2 caused rapid and reversible oxidation of CRMP2, in parallel with Prx2 oxidation, despite purified recombinant CRMP2 protein reacting slowly with H2O2 (k~1 M-1s-1). Lowering Prx expression should inhibit oxidation of proteins oxidised by a relay mechanism, however knockout of Prx2 had no effect on CRMP2 oxidation. CRMP2 also interacted with Prx1, suggesting redundancy in single knockout cells. Prx 1 and 2 double knockout Jurkat cells were not viable. An interaction between Prx2 and CRMP2 was also detected in other human and rodent cells, including primary neurons. However, low concentrations of H2O2 did not cause CRMP2 oxidation in these cells. This indicates a cell-type specific mechanism for promoting CRMP2 oxidation in Jurkat cells, with insufficient evidence to attribute oxidation to a Prx-dependent redox relay.
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Affiliation(s)
- Paul E Pace
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Alexander V Peskin
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Andreas Konigstorfer
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Christine J Jasoni
- Department of Anatomy and Centre for Neuroendocrinology, University of Otago, School of Biomedical Sciences, Dunedin, New Zealand
| | - Christine C Winterbourn
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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29
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Piecing Together How Peroxiredoxins Maintain Genomic Stability. Antioxidants (Basel) 2018; 7:antiox7120177. [PMID: 30486489 PMCID: PMC6316004 DOI: 10.3390/antiox7120177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022] Open
Abstract
Peroxiredoxins, a highly conserved family of thiol oxidoreductases, play a key role in oxidant detoxification by partnering with the thioredoxin system to protect against oxidative stress. In addition to their peroxidase activity, certain types of peroxiredoxins possess other biochemical activities, including assistance in preventing protein aggregation upon exposure to high levels of oxidants (molecular chaperone activity), and the transduction of redox signals to downstream proteins (redox switch activity). Mice lacking the peroxiredoxin Prdx1 exhibit an increased incidence of tumor formation, whereas baker's yeast (Saccharomyces cerevisiae) lacking the orthologous peroxiredoxin Tsa1 exhibit a mutator phenotype. Collectively, these findings suggest a potential link between peroxiredoxins, control of genomic stability, and cancer etiology. Here, we examine the potential mechanisms through which Tsa1 lowers mutation rates, taking into account its diverse biochemical roles in oxidant defense, protein homeostasis, and redox signaling as well as its interplay with thioredoxin and thioredoxin substrates, including ribonucleotide reductase. More work is needed to clarify the nuanced mechanism(s) through which this highly conserved peroxidase influences genome stability, and to determine if this mechanism is similar across a range of species.
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30
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Miller CG, Holmgren A, Arnér ESJ, Schmidt EE. NADPH-dependent and -independent disulfide reductase systems. Free Radic Biol Med 2018; 127:248-261. [PMID: 29609022 PMCID: PMC6165701 DOI: 10.1016/j.freeradbiomed.2018.03.051] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022]
Abstract
Over the past seven decades, research on autotrophic and heterotrophic model organisms has defined how the flow of electrons ("reducing power") from high-energy inorganic sources, through biological systems, to low-energy inorganic products like water, powers all of Life's processes. Universally, an initial major biological recipient of these electrons is nicotinamide adenine dinucleotide-phosphate, which thereby transits from an oxidized state (NADP+) to a reduced state (NADPH). A portion of this reducing power is then distributed via the cellular NADPH-dependent disulfide reductase systems as sequential reductions of disulfide bonds. Along the disulfide reduction pathways, some enzymes have active sites that use the selenium-containing amino acid, selenocysteine, in place of the common but less reactive sulfur-containing cysteine. In particular, the mammalian/metazoan thioredoxin systems are usually selenium-dependent as, across metazoan phyla, most thioredoxin reductases are selenoproteins. Among the roles of the NADPH-dependent disulfide reductase systems, the most universal is that they provide the reducing power for the production of DNA precursors by ribonucleotide reductase (RNR). Some studies, however, have uncovered examples of NADPH-independent disulfide reductase systems that can also support RNR. These systems are summarized here and their implications are discussed.
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Affiliation(s)
- Colin G Miller
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Arne Holmgren
- Division of Biochemistry, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Edward E Schmidt
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA.
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31
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Abstract
Hydrogen peroxide (H2O2) is generated in numerous biological processes. It transmits cellular signals, contributes to oxidative folding of exported proteins, and, in excess, can be damaging to cells and tissues. Although a strong oxidant, high activation energy barriers make it unreactive with most biological molecules. Its main reactions are with transition metal centers, selenoproteins and selected thiol proteins, with glutathione peroxidases (GPxs) and peroxiredoxins (Prxs) being major targets. It reacts slowly with most thiol proteins, and how they become oxidized during redox signal transmission is not well understood. Recent Advances: Kinetic analysis indicates that Prxs and GPxs are overwhelmingly favored as targets for H2O2 in cells. Studies with localized probes indicate that H2O2 can be produced in cellular microdomains and be consumed by highly reactive targets before it can diffuse to other parts of the cell. Inactivation of these targets alone will not confine it to its site of production. Kinetic data indicate that oxidation of regulatory thiol proteins by H2O2 requires a facilitated mechanism such as directed transfer from source to target or a relay mediated through a highly reactive sensor. Critical Issues and Future Directions: Absolute rates of H2O2 production and steady-state concentrations in cells still need to be characterized. More information on cellular sites of production and action is required, and specific mechanisms of oxidation of regulatory proteins during redox signaling require further characterization. Antioxid. Redox Signal. 29, 541-551.
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Affiliation(s)
- Christine C Winterbourn
- Department of Pathology, Centre for Free Radical Research, University of Otago Christchurch , Christchurch, New Zealand
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32
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Roos G, Miranda-Quintana RA, Martínez González M. How Biochemical Environments Fine-Tune a Redox Process: From Theoretical Models to Practical Applications. J Phys Chem B 2018; 122:8157-8165. [PMID: 30040409 DOI: 10.1021/acs.jpcb.8b04736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this study, we give a new physical insight into how enzymatic environments influence a redox process. This is particularly important in a biochemical context, in which oxidoreductase enzymes and low-molecular-weight cofactors create a microenvironment, fine-tuning their specific redox potential. We present a new theoretical model, quantitatively backed up by quantum chemically calculated data obtained for key biological sulfur-based model reactions involved in preserving the cellular redox homeostasis during oxidative stress. We show that environmental effects can be quantitatively predicted from the thermodynamic cycle linking ΔΔ G(OX/RED)ref-ligand values to the differential interaction energy ΔΔ Gint of the reduced and oxidized species with the environment. Our obtained data can be linked to hydrogen-bond patterns found in protein active sites. The thermodynamic model is further understood in the framework of molecular orbital theory. The key insight of this work is that the intrinsic properties of neither a redox couple nor the interacting environment (e.g., ligand) are enough by themselves to uniquely predict reduction potentials. Instead, system-environment interactions need to be considered. This study is of general interest as redox processes are pivotal to empower, protect, or damage organisms. Our presented thermodynamic model allows a pragmatically evaluation on the expected influence of a particular environment on a redox process, necessary to fully understand how redox processes take place in living organisms.
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Affiliation(s)
- Goedele Roos
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) , Université de Lille , 1 Sciences et Technologies 50 Avenue de Halley BP 70478, 59658 Villeneuve d'Ascq Cedex, France
| | | | - Marco Martínez González
- Laboratory of Computational and Theoretical Chemistry, Faculty of Chemistry , University of Havana , 10400 Havana , Cuba.,Departamento de Química, y Centro de Química , Universidade de Coimbra , 3004-535 Coimbra , Portugal
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33
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Detienne G, De Haes W, Mergan L, Edwards SL, Temmerman L, Van Bael S. Beyond ROS clearance: Peroxiredoxins in stress signaling and aging. Ageing Res Rev 2018; 44:33-48. [PMID: 29580920 DOI: 10.1016/j.arr.2018.03.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
Abstract
Antioxidants were long predicted to have lifespan-promoting effects, but in general this prediction has not been well supported. While some antioxidants do seem to have a clear effect on longevity, this may not be primarily as a result of their role in the removal of reactive oxygen species, but rather mediated by other mechanisms such as the modulation of intracellular signaling. In this review we discuss peroxiredoxins, a class of proteinaceous antioxidants with redox signaling and chaperone functions, and their involvement in regulating longevity and stress resistance. Peroxiredoxins have a clear role in the regulation of lifespan and survival of many model organisms, including the mouse, Caenorhabditis elegans and Drosophila melanogaster. Recent research on peroxiredoxins - in these models and beyond - has revealed surprising new insights regarding the interplay between peroxiredoxins and longevity signaling, which will be discussed here in detail. As redox signaling is emerging as a potentially important player in the regulation of longevity and aging, increased knowledge of these fascinating antioxidants and their mode(s) of action is paramount.
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Affiliation(s)
- Giel Detienne
- Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Wouter De Haes
- Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Lucas Mergan
- Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Samantha L Edwards
- Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Liesbet Temmerman
- Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Sven Van Bael
- Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
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34
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Cobley JN, Fiorello ML, Bailey DM. 13 reasons why the brain is susceptible to oxidative stress. Redox Biol 2018; 15:490-503. [PMID: 29413961 PMCID: PMC5881419 DOI: 10.1016/j.redox.2018.01.008] [Citation(s) in RCA: 659] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/12/2022] Open
Abstract
The human brain consumes 20% of the total basal oxygen (O2) budget to support ATP intensive neuronal activity. Without sufficient O2 to support ATP demands, neuronal activity fails, such that, even transient ischemia is neurodegenerative. While the essentiality of O2 to brain function is clear, how oxidative stress causes neurodegeneration is ambiguous. Ambiguity exists because many of the reasons why the brain is susceptible to oxidative stress remain obscure. Many are erroneously understood as the deleterious result of adventitious O2 derived free radical and non-radical species generation. To understand how many reasons underpin oxidative stress, one must first re-cast free radical and non-radical species in a positive light because their deliberate generation enables the brain to achieve critical functions (e.g. synaptic plasticity) through redox signalling (i.e. positive functionality). Using free radicals and non-radical derivatives to signal sensitises the brain to oxidative stress when redox signalling goes awry (i.e. negative functionality). To advance mechanistic understanding, we rationalise 13 reasons why the brain is susceptible to oxidative stress. Key reasons include inter alia unsaturated lipid enrichment, mitochondria, calcium, glutamate, modest antioxidant defence, redox active transition metals and neurotransmitter auto-oxidation. We review RNA oxidation as an underappreciated cause of oxidative stress. The complex interplay between each reason dictates neuronal susceptibility to oxidative stress in a dynamic context and neural identity dependent manner. Our discourse sets the stage for investigators to interrogate the biochemical basis of oxidative stress in the brain in health and disease.
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Affiliation(s)
- James Nathan Cobley
- Free Radical Laboratory, Departments of Diabetes and Cardiovascular Sciences, Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3HJ, UK.
| | - Maria Luisa Fiorello
- Free Radical Laboratory, Departments of Diabetes and Cardiovascular Sciences, Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3HJ, UK
| | - Damian Miles Bailey
- Neurovascular Research Laboratory, Faculty of Life Sciences and Education, University of South Wales, Wales, CF37 4AT, UK
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Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. Active site C P-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins. Free Radic Biol Med 2018; 118:59-70. [PMID: 29474868 DOI: 10.1016/j.freeradbiomed.2018.02.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/12/2018] [Accepted: 02/17/2018] [Indexed: 01/20/2023]
Abstract
Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (CP) located in a conserved sequence Pxxx(T/S)xxCP motif known as CP-loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the CP-loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the CP-loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the CP-loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the CP-loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the CP-loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted CP-loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the CP-loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles.
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Affiliation(s)
- Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Computer Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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36
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Portillo-Ledesma S, Randall LM, Parsonage D, Dalla Rizza J, Karplus PA, Poole LB, Denicola A, Ferrer-Sueta G. Differential Kinetics of Two-Cysteine Peroxiredoxin Disulfide Formation Reveal a Novel Model for Peroxide Sensing. Biochemistry 2018; 57:3416-3424. [PMID: 29553725 DOI: 10.1021/acs.biochem.8b00188] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Two-cysteine peroxiredoxins (Prx) have a three-step catalytic cycle consisting of (1) reduction of peroxide and formation of sulfenic acid on the enzyme, (2) condensation of the sulfenic acid with a thiol to form disulfide, also known as resolution, and (3) reduction of the disulfide by a reductant protein. By following changes in protein fluorescence, we have studied the pH dependence of reaction 2 in human peroxiredoxins 1, 2, and 5 and in Salmonella typhimurium AhpC and obtained rate constants for the reaction and p Ka values of the thiol and sulfenic acid involved for each system. The observed reaction 2 rate constant spans 2 orders of magnitude, but in all cases, reaction 2 appears to be slow compared to the same reaction in small-molecule systems, making clear the rates are limited by conformational features of the proteins. For each Prx, reaction 2 will become rate-limiting at some critical steady-state concentration of H2O2 producing the accumulation of Prx as sulfenic acid. When this happens, an alternative and faster-resolving Prx (or other peroxidase) may take over the antioxidant role. The accumulation of sulfenic acid Prx at distinct concentrations of H2O2 is embedded in the kinetic limitations of the catalytic cycle and may constitute the basis of a H2O2-mediated redox signal transduction pathway requiring neither inactivation nor posttranslational modification. The differences in the rate constants of resolution among Prx coexisting in the same compartment may partially explain their complementation in antioxidant function and stepwise sensing of H2O2 concentration.
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Affiliation(s)
| | - Lía M Randall
- Laboratorio de I+D de Moléculas Bioactivas, CENUR Litoral Norte , Universidad de la República , Paysandú , Uruguay
| | - Derek Parsonage
- Department of Biochemistry and Centers for Structural Biology and for Redox Biology and Medicine , Wake Forest School of Medicine , Winston-Salem , North Carolina 27157 , United States
| | | | - P Andrew Karplus
- Department of Biochemistry and Biophysics , Oregon State University , 2011 Agricultural & Life Sciences Building , Corvallis , Oregon 97331 , United States
| | - Leslie B Poole
- Department of Biochemistry and Centers for Structural Biology and for Redox Biology and Medicine , Wake Forest School of Medicine , Winston-Salem , North Carolina 27157 , United States
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37
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Nelson KJ, Perkins A, Van Swearingen AED, Hartman S, Brereton AE, Parsonage D, Salsbury FR, Karplus PA, Poole LB. Experimentally Dissecting the Origins of Peroxiredoxin Catalysis. Antioxid Redox Signal 2018; 28:521-536. [PMID: 28375740 PMCID: PMC5806077 DOI: 10.1089/ars.2016.6922] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AIMS Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases involved in oxidant defense and signal transduction. Despite much study, the precise roles of conserved residues remain poorly defined. In this study, we carried out extensive functional and structural characterization of 10 variants of such residues in a model decameric bacterial Prx. RESULTS Three active site proximal mutations of Salmonella typhimurium AhpC, T43V, R119A, and E49Q, lowered catalytic efficiency with hydrogen peroxide by 4-5 orders of magnitude, but did not affect reactivity toward their reductant, AhpF. pKa values of the peroxidatic cysteine were also shifted up by 1-1.3 pH units for these and a decamer disruption mutant, T77I. Except for the decamer-stabilizing T77V, all mutations destabilized decamers in the reduced form. In the oxidized form, three mutants-T77V, T43A, and T43S-exhibited stabilized decamers and were more efficiently reduced by AhpF than wild-type AhpC. Crystal structures of most mutants were solved and many showed alterations in stability of the fully folded active site loop. INNOVATION This is the first study of Prx mutants to comprehensively assess the effects of mutations on catalytic activities, the active site cysteine pKa, and the protein structure and oligomeric status. CONCLUSION The Arg119 side chain must be properly situated for efficient catalysis, but for other debilitating variants, the functional defects could be explained by structural perturbations and/or associated decamer destabilization rather than direct effects. This underscores the importance of our comprehensive approach. A remarkable new finding was the preference of the reductant for decamers. Antioxid. Redox Signal. 28, 521-536.
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Affiliation(s)
- Kimberly J Nelson
- 1 Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina.,2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
| | - Arden Perkins
- 3 Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon
| | - Amanda E D Van Swearingen
- 1 Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina.,2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
| | - Steven Hartman
- 3 Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon
| | - Andrew E Brereton
- 3 Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon
| | - Derek Parsonage
- 1 Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina.,2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
| | - Freddie R Salsbury
- 2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina.,4 Department of Physics, Wake Forest University , Winston-Salem, North Carolina
| | - P Andrew Karplus
- 3 Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon
| | - Leslie B Poole
- 1 Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina.,2 Center for Redox Biology and Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
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38
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Abstract
Hydrogen peroxide (H2O2) is produced on stimulation of many cell surface receptors and serves as an intracellular messenger in the regulation of diverse physiological events, mostly by oxidizing cysteine residues of effector proteins. Mammalian cells express multiple H2O2-eliminating enzymes, including catalase, glutathione peroxidase (GPx), and peroxiredoxin (Prx). A conserved cysteine in Prx family members is the site of oxidation by H2O2. Peroxiredoxins possess a high-affinity binding site for H2O2 that is lacking in catalase and GPx and which renders the catalytic cysteine highly susceptible to oxidation, with a rate constant several orders of magnitude greater than that for oxidation of cysteine in most H2O2 effector proteins. Moreover, Prxs are abundant and present in all subcellular compartments. The cysteines of most H2O2 effectors are therefore at a competitive disadvantage for reaction with H2O2. Recent Advances: Here we review intracellular sources of H2O2 as well as H2O2 target proteins classified according to biochemical and cellular function. We then highlight two strategies implemented by cells to overcome the kinetic disadvantage of most target proteins with regard to H2O2-mediated oxidation: transient inactivation of local Prx molecules via phosphorylation, and indirect oxidation of target cysteines via oxidized Prx. Critical Issues and Future Directions: Recent studies suggest that only a small fraction of the total pools of Prxs and H2O2 effector proteins localized in specific subcellular compartments participates in H2O2 signaling. Development of sensitive tools to selectively detect phosphorylated Prxs and oxidized effector proteins is needed to provide further insight into H2O2 signaling. Antioxid. Redox Signal. 28, 537-557.
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Affiliation(s)
- Sue Goo Rhee
- 1 Yonsei Biomedical Research Institute, Yonsei University College of Medicine , Seoul, Korea
| | - Hyun Ae Woo
- 2 College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul, Korea
| | - Dongmin Kang
- 3 Department of Life Science, Ewha Womans University , Seoul, Korea
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39
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The Role of Free Radicals in Autophagy Regulation: Implications for Ageing. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:2450748. [PMID: 29682156 PMCID: PMC5846360 DOI: 10.1155/2018/2450748] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 01/05/2018] [Accepted: 01/16/2018] [Indexed: 12/19/2022]
Abstract
Reactive oxygen and nitrogen species (ROS and RNS, resp.) have been traditionally perceived solely as detrimental, leading to oxidative damage of biological macromolecules and organelles, cellular demise, and ageing. However, recent data suggest that ROS/RNS also plays an integral role in intracellular signalling and redox homeostasis (redoxtasis), which are necessary for the maintenance of cellular functions. There is a complex relationship between cellular ROS/RNS content and autophagy, which represents one of the major quality control systems in the cell. In this review, we focus on redox signalling and autophagy regulation with a special interest on ageing-associated changes. In the last section, we describe the role of autophagy and redox signalling in the context of Alzheimer's disease as an example of a prevalent age-related disorder.
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40
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Yewdall NA, Peskin AV, Hampton MB, Goldstone DC, Pearce FG, Gerrard JA. Quaternary structure influences the peroxidase activity of peroxiredoxin 3. Biochem Biophys Res Commun 2018; 497:558-563. [PMID: 29438714 DOI: 10.1016/j.bbrc.2018.02.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/09/2018] [Indexed: 12/16/2022]
Abstract
Peroxiredoxins are abundant peroxidase enzymes that are key regulators of the cellular redox environment. A major subgroup of these proteins, the typical 2-Cys peroxiredoxins, can switch between dimers and decameric or dodecameric rings, during the catalytic cycle. The necessity of this change in quaternary structure for function as a peroxidase is not fully understood. In order to explore this, human peroxiredoxin 3 (Prx3) protein was engineered to form both obligate dimers (S75E Prx3) and stabilised dodecameric rings (S78C Prx3), uncoupling structural transformations from the catalytic cycle. The obligate dimer, S75E Prx3, retained catalytic activity towards hydrogen peroxide, albeit significantly lower than the wildtype and S78C proteins, suggesting an evolutionary advantage of having higher order self-assemblies.
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Affiliation(s)
- N Amy Yewdall
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand; Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Alexander V Peskin
- Centre for Free Radical Research, Department of Pathology, University of Otago Christchurch, Christchurch 8011, New Zealand
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology, University of Otago Christchurch, Christchurch 8011, New Zealand
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Juliet A Gerrard
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University, Wellington 6140, New Zealand; School of Chemical Sciences, University of Auckland, Auckland 1010, New Zealand.
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41
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Peixoto ÁS, Geyer RR, Iqbal A, Truzzi DR, Soares Moretti AI, Laurindo FRM, Augusto O. Peroxynitrite preferentially oxidizes the dithiol redox motifs of protein-disulfide isomerase. J Biol Chem 2018; 293:1450-1465. [PMID: 29191937 PMCID: PMC5787819 DOI: 10.1074/jbc.m117.807016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/29/2017] [Indexed: 12/22/2022] Open
Abstract
Protein-disulfide isomerase (PDI) is a ubiquitous dithiol-disulfide oxidoreductase that performs an array of cellular functions, such as cellular signaling and responses to cell-damaging events. PDI can become dysfunctional by post-translational modifications, including those promoted by biological oxidants, and its dysfunction has been associated with several diseases in which oxidative stress plays a role. Because the kinetics and products of the reaction of these oxidants with PDI remain incompletely characterized, we investigated the reaction of PDI with the biological oxidant peroxynitrite. First, by determining the rate constant of the oxidation of PDI's redox-active Cys residues (Cys53 and Cys397) by hydrogen peroxide (k = 17.3 ± 1.3 m-1 s-1 at pH 7.4 and 25 °C), we established that the measured decay of the intrinsic PDI fluorescence is appropriate for kinetic studies. The reaction of these PDI residues with peroxynitrite was considerably faster (k = (6.9 ± 0.2) × 104 m-1 s-1), and both Cys residues were kinetically indistinguishable. Limited proteolysis, kinetic simulations, and MS analyses confirmed that peroxynitrite preferentially oxidizes the redox-active Cys residues of PDI to the corresponding sulfenic acids, which reacted with the resolving thiols at the active sites to produce disulfides (i.e. Cys53-Cys56 and Cys397-Cys400). A fraction of peroxynitrite, however, decayed to radicals that hydroxylated and nitrated other active-site residues (Trp52, Trp396, and Tyr393). Excess peroxynitrite promoted further PDI oxidation, nitration, inactivation, and covalent oligomerization. We conclude that these PDI modifications may contribute to the pathogenic mechanism of several diseases associated with dysfunctional PDI.
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Affiliation(s)
- Álbert Souza Peixoto
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
| | - R Ryan Geyer
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
| | - Asif Iqbal
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
| | - Daniela R Truzzi
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
| | - Ana I Soares Moretti
- Vascular Biology Laboratory, Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, CEP 05403-000, Brazil
| | - Francisco R M Laurindo
- Vascular Biology Laboratory, Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, CEP 05403-000, Brazil
| | - Ohara Augusto
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
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42
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Dagnell M, Pace PE, Cheng Q, Frijhoff J, Östman A, Arnér ESJ, Hampton MB, Winterbourn CC. Thioredoxin reductase 1 and NADPH directly protect protein tyrosine phosphatase 1B from inactivation during H 2O 2 exposure. J Biol Chem 2017; 292:14371-14380. [PMID: 28684416 DOI: 10.1074/jbc.m117.793745] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/26/2017] [Indexed: 02/06/2023] Open
Abstract
Regulation of growth factor signaling involves reversible inactivation of protein tyrosine phosphatases (PTPs) through the oxidation and reduction of their active site cysteine. However, there is limited mechanistic understanding of these redox events and their co-ordination in the presence of cellular antioxidant networks. Here we investigated interactions between PTP1B and the peroxiredoxin 2 (Prx2)/thioredoxin 1 (Trx1)/thioredoxin reductase 1 (TrxR1) network. We found that Prx2 becomes oxidized in PDGF-treated fibroblasts, but only when TrxR1 has first been inhibited. Using purified proteins, we also found that PTP1B is relatively insensitive to inactivation by H2O2 but found no evidence for a relay mechanism in which Prx2 or Trx1 facilitates PTP1B oxidation. Instead, these proteins prevented PTP1B inactivation by H2O2 Intriguingly, we discovered that TrxR1/NADPH directly protects PTP1B from inactivation when present during the H2O2 exposure. This protection was dependent on the concentration of TrxR1 and independent of Trx1 and Prx2. The protection was blocked by auranofin and required an intact selenocysteine residue in TrxR1. This activity likely involves reduction of the sulfenic acid intermediate form of PTP1B by TrxR1 and is therefore distinct from the previously described reactivation of end-point oxidized PTP1B, which requires both Trx1 and TrxR1. The ability of TrxR1 to directly reduce an oxidized phosphatase is a novel activity that can help explain previously observed increases in PTP1B oxidation and PDGF receptor phosphorylation in TrxR1 knockout cells. The activity of TrxR1 is therefore of potential relevance for understanding the mechanisms of redox regulation of growth factor signaling pathways.
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Affiliation(s)
- Markus Dagnell
- From the Centre for Free Radical Research, Department of Pathology, University of Otago, Christchurch 8041, New Zealand.,the Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Paul E Pace
- From the Centre for Free Radical Research, Department of Pathology, University of Otago, Christchurch 8041, New Zealand
| | - Qing Cheng
- the Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jeroen Frijhoff
- the Faculty of Health, Medicine and Life Sciences, Cardiovascular Research Institute Maastricht University, 6229 ER Maastricht, The Netherlands, and
| | - Arne Östman
- the Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Elias S J Arnér
- the Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mark B Hampton
- From the Centre for Free Radical Research, Department of Pathology, University of Otago, Christchurch 8041, New Zealand
| | - Christine C Winterbourn
- From the Centre for Free Radical Research, Department of Pathology, University of Otago, Christchurch 8041, New Zealand,
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43
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Bonanata J, Turell L, Antmann L, Ferrer-Sueta G, Botasini S, Méndez E, Alvarez B, Coitiño EL. The thiol of human serum albumin: Acidity, microenvironment and mechanistic insights on its oxidation to sulfenic acid. Free Radic Biol Med 2017; 108:952-962. [PMID: 28438657 DOI: 10.1016/j.freeradbiomed.2017.04.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/14/2017] [Accepted: 04/17/2017] [Indexed: 01/02/2023]
Abstract
Human serum albumin (HSA) has a single reduced cysteine residue, Cys34, whose acidity has been controversial. Three experimental approaches (pH-dependence of reactivity towards hydrogen peroxide, ultraviolet titration and infrared spectroscopy) are used to determine that the pKa value in delipidated HSA is 8.1±0.2 at 37°C and 0.1M ionic strength. Molecular dynamics simulations of HSA in the sub-microsecond timescale show that while sulfur exposure to solvent is limited and fluctuating in the thiol form, it increases in the thiolate, stabilized by a persistent hydrogen-bond (HB) network involving Tyr84 and bridging waters to Asp38 and Gln33 backbone. Insight into the mechanism of Cys34 oxidation by H2O2 is provided by ONIOM(QM:MM) modeling including quantum water molecules. The reaction proceeds through a slightly asynchronous SN2 transition state (TS) with calculated Δ‡G and Δ‡H barriers at 298K of respectively 59 and 54kJmol-1 (the latter within chemical accuracy from the experimental value). A post-TS proton transfer leads to HSA-SO- and water as products. The structured reaction site cages H2O2, which donates a strong HB to the thiolate. Loss of this HB before reaching the TS modulates Cys34 nucleophilicity and contributes to destabilize H2O2. The lack of reaction-site features required for differential stabilization of the TS (positive charges, H2O2 HB strengthening) explains the striking difference in kinetic efficiency for the same reaction in other proteins (e.g. peroxiredoxins). The structured HB network surrounding HSA-SH with sequestered waters carries an entropic penalty on the barrier height. These studies contribute to deepen the understanding of the reactivity of HSA-SH, the most abundant thiol in human plasma, and in a wider perspective, provide clues on the key aspects that modulate thiol reactivity against H2O2.
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Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional (LQTC), Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay; Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Lucía Turell
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Laura Antmann
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Santiago Botasini
- Laboratorio de Biomateriales, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Eduardo Méndez
- Laboratorio de Biomateriales, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay.
| | - E Laura Coitiño
- Laboratorio de Química Teórica y Computacional (LQTC), Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay.
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44
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Dokainish HM, Simard DJ, Gauld JW. A Pseudohypervalent Sulfur Intermediate as an Oxidative Protective Mechanism in the Archaea Peroxiredoxin Enzyme ApTPx. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b04671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hisham M. Dokainish
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Daniel J. Simard
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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45
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Carvalho LAC, Truzzi DR, Fallani TS, Alves SV, Toledo JC, Augusto O, Netto LES, Meotti FC. Urate hydroperoxide oxidizes human peroxiredoxin 1 and peroxiredoxin 2. J Biol Chem 2017; 292:8705-8715. [PMID: 28348082 DOI: 10.1074/jbc.m116.767657] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/27/2017] [Indexed: 12/24/2022] Open
Abstract
Urate hydroperoxide is a product of the oxidation of uric acid by inflammatory heme peroxidases. The formation of urate hydroperoxide might be a key event in vascular inflammation, where there is large amount of uric acid and inflammatory peroxidases. Urate hydroperoxide oxidizes glutathione and sulfur-containing amino acids and is expected to react fast toward reactive thiols from peroxiredoxins (Prxs). The kinetics for the oxidation of the cytosolic 2-Cys Prx1 and Prx2 revealed that urate hydroperoxide oxidizes these enzymes at rates comparable with hydrogen peroxide. The second-order rate constants of these reactions were 4.9 × 105 and 2.3 × 106 m-1 s-1 for Prx1 and Prx2, respectively. Kinetic and simulation data suggest that the oxidation of Prx2 by urate hydroperoxide occurs by a three-step mechanism, where the peroxide reversibly associates with the enzyme; then it oxidizes the peroxidatic cysteine, and finally, the rate-limiting disulfide bond is formed. Of relevance, the disulfide bond formation was much slower in Prx2 (k3 = 0.31 s-1) than Prx1 (k3 = 14.9 s-1). In addition, Prx2 was more sensitive than Prx1 to hyperoxidation caused by both urate hydroperoxide and hydrogen peroxide. Urate hydroperoxide oxidized Prx2 from intact erythrocytes to the same extent as hydrogen peroxide. Therefore, Prx1 and Prx2 are likely targets of urate hydroperoxide in cells. Oxidation of Prxs by urate hydroperoxide might affect cell function and be partially responsible for the pro-oxidant and pro-inflammatory effects of uric acid.
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Affiliation(s)
| | - Daniela R Truzzi
- From the Departamento de Bioquímica, Instituto de Química (IQUSP)
| | | | - Simone V Alves
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências (IB-USP), and
| | - José Carlos Toledo
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo-SP CEP 05508-000, Brazil
| | - Ohara Augusto
- From the Departamento de Bioquímica, Instituto de Química (IQUSP)
| | - Luís E S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências (IB-USP), and
| | - Flavia C Meotti
- From the Departamento de Bioquímica, Instituto de Química (IQUSP),
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46
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Abstract
Peroxiredoxins (Prxs) constitute a major family of peroxidases, with mammalian cells expressing six Prx isoforms (PrxI to PrxVI). Cells produce hydrogen peroxide (H2O2) at various intracellular locations where it can serve as a signaling molecule. Given that Prxs are abundant and possess a structure that renders the cysteine (Cys) residue at the active site highly sensitive to oxidation by H2O2, the signaling function of this oxidant requires extensive and highly localized regulation. Recent findings on the reversible regulation of PrxI through phosphorylation at the centrosome and on the hyperoxidation of the Cys at the active site of PrxIII in mitochondria are described in this review as examples of such local regulation of H2O2 signaling. Moreover, their high affinity for and sensitivity to oxidation by H2O2 confer on Prxs the ability to serve as sensors and transducers of H2O2 signaling through transfer of their oxidation state to bound effector proteins.
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Affiliation(s)
- Sue Goo Rhee
- Yonsei Biomedical Research Institute, Yonsei University College of Medicine, Seoul 120-752, Korea;
| | - In Sup Kil
- Yonsei Biomedical Research Institute, Yonsei University College of Medicine, Seoul 120-752, Korea;
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47
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Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput Biol 2017; 13:e1005284. [PMID: 28187133 PMCID: PMC5302317 DOI: 10.1371/journal.pcbi.1005284] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/06/2016] [Indexed: 12/15/2022] Open
Abstract
Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique). MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially-MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method's novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is demonstrated by the Prx superfamily results, laying the foundation for potential functionally relevant clustering of the universe of protein sequences.
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Affiliation(s)
- Angela F. Harper
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Janelle B. Leuthaeuser
- Department of Molecular Genetics and Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco School of Pharmacy, San Francisco, California, United States of America
| | - John H. Morris
- Department of Pharmaceutical Chemistry, University of California San Francisco School of Pharmacy, San Francisco, California, United States of America
| | - Thomas E. Ferrin
- Department of Pharmaceutical Chemistry, University of California San Francisco School of Pharmacy, San Francisco, California, United States of America
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jacquelyn S. Fetrow
- Department of Chemistry, University of Richmond, Richmond, Virginia, United States of America
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48
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An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase. Sci Rep 2017; 7:40517. [PMID: 28098177 PMCID: PMC5241826 DOI: 10.1038/srep40517] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023] Open
Abstract
The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.
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49
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Karimi M, Ignasiak MT, Chan B, Croft AK, Radom L, Schiesser CH, Pattison DI, Davies MJ. Reactivity of disulfide bonds is markedly affected by structure and environment: implications for protein modification and stability. Sci Rep 2016; 6:38572. [PMID: 27941824 PMCID: PMC5150571 DOI: 10.1038/srep38572] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/09/2016] [Indexed: 11/09/2022] Open
Abstract
Disulfide bonds play a key role in stabilizing protein structures, with disruption strongly associated with loss of protein function and activity. Previous data have suggested that disulfides show only modest reactivity with oxidants. In the current study, we report kinetic data indicating that selected disulfides react extremely rapidly, with a variation of 104 in rate constants. Five-membered ring disulfides are particularly reactive compared with acyclic (linear) disulfides or six-membered rings. Particular disulfides in proteins also show enhanced reactivity. This variation occurs with multiple oxidants and is shown to arise from favorable electrostatic stabilization of the incipient positive charge on the sulfur reaction center by remote groups, or by the neighboring sulfur for conformations in which the orbitals are suitably aligned. Controlling these factors should allow the design of efficient scavengers and high-stability proteins. These data are consistent with selective oxidative damage to particular disulfides, including those in some proteins.
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Affiliation(s)
- Maryam Karimi
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia.,Faculty of Medicine, University of Sydney, NSW, 2006, Australia
| | - Marta T Ignasiak
- Department of Biomedical Science, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Bun Chan
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, Great Britain
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Carl H Schiesser
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - David I Pattison
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia.,Faculty of Medicine, University of Sydney, NSW, 2006, Australia
| | - Michael J Davies
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia.,Faculty of Medicine, University of Sydney, NSW, 2006, Australia.,Department of Biomedical Science, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
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50
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Bayer SB, Low FM, Hampton MB, Winterbourn CC. Interactions between peroxiredoxin 2, hemichrome and the erythrocyte membrane. Free Radic Res 2016; 50:1329-1339. [DOI: 10.1080/10715762.2016.1241995] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Simone B. Bayer
- Department of Pathology, Centre for Free Radical Research, University of Otago, Christchurch, New Zealand
| | - Felicia M. Low
- Department of Pathology, Centre for Free Radical Research, University of Otago, Christchurch, New Zealand
| | - Mark B. Hampton
- Department of Pathology, Centre for Free Radical Research, University of Otago, Christchurch, New Zealand
| | - Christine C. Winterbourn
- Department of Pathology, Centre for Free Radical Research, University of Otago, Christchurch, New Zealand
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