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Schofield LC, Dialpuri JS, Murshudov GN, Agirre J. Post-translational modifications in the Protein Data Bank. Acta Crystallogr D Struct Biol 2024; 80:647-660. [PMID: 39207896 PMCID: PMC11394121 DOI: 10.1107/s2059798324007794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
Proteins frequently undergo covalent modification at the post-translational level, which involves the covalent attachment of chemical groups onto amino acids. This can entail the singular or multiple addition of small groups, such as phosphorylation; long-chain modifications, such as glycosylation; small proteins, such as ubiquitination; as well as the interconversion of chemical groups, such as the formation of pyroglutamic acid. These post-translational modifications (PTMs) are essential for the normal functioning of cells, as they can alter the physicochemical properties of amino acids and therefore influence enzymatic activity, protein localization, protein-protein interactions and protein stability. Despite their inherent importance, accurately depicting PTMs in experimental studies of protein structures often poses a challenge. This review highlights the role of PTMs in protein structures, as well as the prevalence of PTMs in the Protein Data Bank, directing the reader to accurately built examples suitable for use as a modelling reference.
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Affiliation(s)
- Lucy C Schofield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Jordan S Dialpuri
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Garib N Murshudov
- MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
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2
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Diemer V, Roy E, Agouridas V, Melnyk O. Protein desulfurization and deselenization. Chem Soc Rev 2024; 53:8521-8545. [PMID: 39010733 DOI: 10.1039/d4cs00135d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Methods enabling the dechalcogenation of thiols or selenols have been investigated and developed for a long time in fields of research as diverse as the study of prebiotic chemistry, the engineering of fuel processing techniques, the study of biomolecule structures and function or the chemical synthesis of biomolecules. The dechalcogenation of thiol or selenol amino acids is nowadays a particularly flourishing area of research for being a pillar of modern chemical protein synthesis, when used in combination with thiol or selenol-based chemoselective peptide ligation chemistries. This review offers a comprehensive and scholarly overview of the field, emphasizing emerging trends and providing a detailed and critical mechanistic discussion of the dechalcogenation methods developed so far. Taking advantage of recently published reports, it also clarifies some unexpected desulfurization reactions that were observed in the past and for which no explanation was provided at the time. Additionally, the review includes a discussion on principal desulfurization methods within the framework of newly introduced green chemistry metrics and toolkits, providing a well-rounded exploration of the subject.
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Affiliation(s)
- Vincent Diemer
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Eliott Roy
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
- Centrale Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
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3
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Noguchi N, Saito Y, Niki E. Actions of Thiols, Persulfides, and Polysulfides as Free Radical Scavenging Antioxidants. Antioxid Redox Signal 2023; 39:728-743. [PMID: 37154744 PMCID: PMC10619894 DOI: 10.1089/ars.2022.0191] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023]
Abstract
Significance: The essential roles of thiol compounds as redox signaling mediators and protectors have been established. Recently, the roles of persulfides and polysulfides as mediators involved in numerous physiological processes have been revealed. Recent Advances: Recently, it became possible to detect and measure persulfides and polysulfides in human fluids and tissues and their physiological functions, including cellular signaling and protection against oxidative stress, have been reported, but the underlying mechanisms and dynamics remain elusive. Critical Issues: Physiological functions of thiol compounds have been studied, focusing primarily on two-electron redox reactions. In contrast, the contribution of one-electron redox mechanisms, that is, free radical-mediated oxidation and antioxidation, has received much less attention. Considering the important effects of free radical-mediated oxidation of biological molecules on pathophysiology, the antioxidant functions of thiol compounds as free radical scavengers are challenging issues. Future Directions: The antioxidant actions and dynamics of thiols, hydropersulfides, and hydropolysulfides as free radical scavenging antioxidants and their physiological significance remain to be established. Antioxid. Redox Signal. 39, 728-743.
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Affiliation(s)
- Noriko Noguchi
- The Systems Life Sciences Laboratory, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Yoshiro Saito
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Etsuo Niki
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Meguro-ku, Japan
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4
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Koch CJ, Kim MM, Wiersma RD. Radiation-Chemical Oxygen Depletion Depends on Chemical Environment and Dose Rate: Implications for the FLASH Effect. Int J Radiat Oncol Biol Phys 2023; 117:214-222. [PMID: 37059234 DOI: 10.1016/j.ijrobp.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/27/2023] [Accepted: 04/01/2023] [Indexed: 04/16/2023]
Abstract
PURPOSE FLASH (dose rates >40 Gy/s) radiation therapy protects normal tissues from radiation damage, compared with conventional radiation therapy (∼Gy/m). Radiation-chemical oxygen depletion (ROD) occurs when oxygen reacts with radiation-induced free radicals, so a possible mechanism for FLASH involves radioprotection by the decreased oxygen as ROD occurs. High ROD rates would favor this mechanism, but prior studies have reported low ROD values (∼0.35 µM/Gy) in chemical environments such as water and protein/nutrient solutions. We proposed that intracellular ROD might be much larger, possibly promoted by its strongly reducing chemical environment. METHODS AND MATERIALS ROD was measured, using precision polarographic sensors, from ∼100 µM to zero in solutions containing intracellular reducing agents ± glycerol (1M), to simulate intracellular reducing and hydroxyl-radical-scavenging capacity. Cs irradiators and a research proton beamline allowed dose rates from 0.0085 to 100 Gy/s. RESULTS Reducing agents significantly altered ROD values. Most greatly increased ROD but some (eg, ascorbate) actually decreased ROD and additionally imposed an oxygen dependence of ROD at low oxygen concentrations. The highest values of ROD were found at low dose rates, but these montonically decreased with increasing dose rate. CONCLUSIONS ROD was greatly augmented by some intracellular reducing agents but others (eg, ascorbate) effectively reversed this effect. Ascorbate had its greatest effect at low oxygen concentrations. ROD decreased with increasing dose rate in most cases.
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Affiliation(s)
- Cameron J Koch
- Radiation Oncology Department, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Michele M Kim
- Radiation Oncology Department, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rodney D Wiersma
- Radiation Oncology Department, University of Pennsylvania, Philadelphia, Pennsylvania
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5
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Wardman P. Factors Important in the Use of Fluorescent or Luminescent Probes and Other Chemical Reagents to Measure Oxidative and Radical Stress. Biomolecules 2023; 13:1041. [PMID: 37509077 PMCID: PMC10377120 DOI: 10.3390/biom13071041] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/20/2023] [Accepted: 06/24/2023] [Indexed: 07/30/2023] Open
Abstract
Numerous chemical probes have been used to measure or image oxidative, nitrosative and related stress induced by free radicals in biology and biochemistry. In many instances, the chemical pathways involved are reasonably well understood. However, the rate constants for key reactions involved are often not yet characterized, and thus it is difficult to ensure the measurements reflect the flux of oxidant/radical species and are not influenced by competing factors. Key questions frequently unanswered are whether the reagents are used under 'saturating' conditions, how specific probes are for particular radicals or oxidants and the extent of the involvement of competing reactions (e.g., with thiols, ascorbate and other antioxidants). The commonest-used probe for 'reactive oxygen species' in biology actually generates superoxide radicals in producing the measured product in aerobic systems. This review emphasizes the need to understand reaction pathways and in particular to quantify the kinetic parameters of key reactions, as well as measure the intracellular levels and localization of probes, if such reagents are to be used with confidence.
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Affiliation(s)
- Peter Wardman
- Formerly of the Gray Cancer Institute, Mount Vernon Hospital/University of Oxford, UK
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6
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Hu A, Qiu R, Li WB, Zhou W, Wu Z, Zhang H, Li J. Radical recombination and antioxidants: a hypothesis on the FLASH effect mechanism. Int J Radiat Biol 2023; 99:620-628. [PMID: 35938944 DOI: 10.1080/09553002.2022.2110307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
PURPOSE FLASH (ultra-high dose rate) radiotherapy spares normal tissue while keeping tumor control. However, the mechanism of the FLASH effect remains unclear and may have consequences beyond the irradiated area. MATERIALS AND METHODS We reanalyze the available results of ultra-high-dose-rate-related experiments to find out the key points of the mechanism of the FLASH effect. Then, we present a hypothesis on the mechanism of the FLASH effect: FLASH beams generate a high transient concentration of peroxyl radicals leading to a high fraction of radical recombination, which results in less oxidation damage to normal tissue. For the cells containing higher concentrations of antioxidants, the fractions of radical recombination are smaller because the antioxidants compete to react with peroxyl radicals. Therefore the damages by different dose rate beams differ slightly in this condition. Since some tumors contain a higher level of antioxidants, this may be the reason for the loss of the protective effect in tumors irradiated by FLASH beams. The high concentration of antioxidants in tumors results in slight radiolytic oxygen consumption, and consequently the protective effect observed in in vitro experiment cannot be observed in in vivo experiment. To quantitatively elaborate our hypothesis, a kinetic model is implemented to simulate the reactions induced by irradiation. Two parameters are defined to abstractly study the factors affecting the reaction, such as dose rate, antioxidants, total dose and reaction rate constants. RESULTS AND CONCLUSIONS We find that the explanation of the difference between in vivo and in vitro experiments is crucial to understanding the mechanism of the FLASH effect. Our hypothesis agrees with the results of related experiments. Based on the kinetic model, the effects of these factors on the FLASH effect are quantitatively investigated.
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Affiliation(s)
- Ankang Hu
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Key Laboratory of Particle & Radiation Imaging, Tsinghua University, Ministry of Education, Beijing, China
| | - Rui Qiu
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Key Laboratory of Particle & Radiation Imaging, Tsinghua University, Ministry of Education, Beijing, China
| | - Wei Bo Li
- Institute of Radiation Medicine, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Wanyi Zhou
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Key Laboratory of Particle & Radiation Imaging, Tsinghua University, Ministry of Education, Beijing, China
| | - Zhen Wu
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Nuctech Company Limited, Beijing, China
| | - Hui Zhang
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Key Laboratory of Particle & Radiation Imaging, Tsinghua University, Ministry of Education, Beijing, China
| | - Junli Li
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Key Laboratory of Particle & Radiation Imaging, Tsinghua University, Ministry of Education, Beijing, China
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7
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Ventura ON, Segovia M, Vega-Teijido M, Katz A, Kieninger M, Tasinato N, Salta Z. Correcting the Experimental Enthalpies of Formation of Some Members of the Biologically Significant Sulfenic Acids Family. J Phys Chem A 2022; 126:6091-6109. [PMID: 36044372 DOI: 10.1021/acs.jpca.2c04235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulfenic acids are important intermediates in the oxidation of cysteine thiol groups in proteins by reactive oxygen species. The mechanism is influenced heavily by the presence of polar groups, other thiol groups, and solvent, all of which determines the need to compute precisely the energies involved in the process. Surprisingly, very scarce experimental information exists about a very basic property of sulfenic acids, the enthalpies of formation. In this Article, we use high level quantum chemical methods to derive the enthalpy of formation at 298.15 K of methane-, ethene-, ethyne-, and benzenesulfenic acids, the only ones for which some experimental information exists. The methods employed were tested against well-known experimental data of related species and extensive CCSD(T) calculations. Our best results consistently point out to a much lower enthalpy of formation of methanesulfenic acid, CH3SOH (ΔfH0(298.15K) = -35.1 ± 0.4 kcal mol-1), than the one reported in the NIST thermochemical data tables. The enthalpies of formation derived for ethynesulfenic acid, HC≡CSOH, +32.9 ± 1.0 kcal/mol, and benzenesulfenic acid, C6H5SOH, -2.6 ± 0.6 kcal mol-1, also differ markedly from the experimental values, while the enthalpy of formation of ethenesulfenic acid CH2CHSOH, not available experimentally, was calculated as -11.2 ± 0.7 kcal mol-1.
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Affiliation(s)
- Oscar N Ventura
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Marc Segovia
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Mauricio Vega-Teijido
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Aline Katz
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Martina Kieninger
- Computational Chemistry and Biology Group, CCBG, DETEMA, Facultad de Química, Universidad de la República, 11400 Montevideo, Uruguay
| | - Nicola Tasinato
- SMART Lab, Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Zoi Salta
- SMART Lab, Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy
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8
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Wardman P. Approaches to modeling chemical reaction pathways in radiobiology. Int J Radiat Biol 2022; 98:1399-1413. [DOI: 10.1080/09553002.2022.2033342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Peter Wardman
- 20 Highover Park, Amersham, Buckinghamshire HP7 0BN, United Kingdom
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9
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Fuentes-Lemus E, Jiang S, Hägglund P, Davies MJ. High concentrations of casein proteins exacerbate radical chain reactions and increase the extent of oxidative damage. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.107060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Görüşük EM, Bekdeşer B, Bener M, Apak R. ABTS radical-based single reagent assay for simultaneous determination of biologically important thiols and disulfides. Talanta 2020; 218:121212. [PMID: 32797935 DOI: 10.1016/j.talanta.2020.121212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/20/2022]
Abstract
Both the total amount of biothiols and thiol/disulfide ratio are wellness indicators of oxidative balance that play an important role in antioxidant defense system. Oxidized biothiols in disulfide form cannot be determined by conventional ABTS assay due to the biphasic kinetic pattern of the reaction between biothiols and ABTS radical cation (ABTS•+), necessitating the initial reduction of disulfides to thiols prior to measurement. In this study, direct simultaneous determination of biothiols (RSH) and their disulfides (RSSR) by using a single reagent of ABTS•+ was achieved without preliminary chemical reduction. Thus, conventional problems of preliminary operations arising from direct borohydride reduction of disulfides to thiols, followed by formaldehyde removal of borohydride excess and complications caused by formaldehyde-thiol reactions were effectively overcome with the use of a single reagent (ABTS•+). Box-Behnken statistical experimental design was employed to specify the optimal incubation temperature and time as 60 °C and 60 min, respectively. The detection limits (LOD) of the proposed assay for biothiols were compared to those of the widely used DTNB (Ellman) reference assay known to be nonresponsive to disulfides, and were found to be much lower (4-70 times). The proposed biothiol assay was successfully applied to some pharmaceutical samples and synthetic serum without preliminary treatment, and the results were highly compatible with the HPLC findings. The proposed assay was demonstrated to have superior features such as simplicity, rapidity and higher sensitivity over the widely applied Ellman thiols assay.
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Affiliation(s)
- Emine Münevver Görüşük
- Istanbul University-Cerrahpasa, Faculty of Engineering, Department of Chemistry, Avcilar, 34320, Istanbul, Turkey
| | - Burcu Bekdeşer
- Istanbul University-Cerrahpasa, Faculty of Engineering, Department of Chemistry, Avcilar, 34320, Istanbul, Turkey
| | - Mustafa Bener
- Istanbul University-Cerrahpasa, Faculty of Engineering, Department of Chemistry, Avcilar, 34320, Istanbul, Turkey
| | - Reşat Apak
- Istanbul University-Cerrahpasa, Faculty of Engineering, Department of Chemistry, Avcilar, 34320, Istanbul, Turkey.
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11
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Wardman P. Radiotherapy Using High-Intensity Pulsed Radiation Beams (FLASH): A Radiation-Chemical Perspective. Radiat Res 2020; 194:607-617. [DOI: 10.1667/rade-19-00016] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 11/03/2022]
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12
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Antioxidants and radical damage in a hydrophilic environment: chemical reactions and concepts. Essays Biochem 2019; 64:67-74. [DOI: 10.1042/ebc20190063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022]
Abstract
AbstractKnown endogenous antioxidants are unlikely to prevent radical damage due to oxidative stress or achieve complete repair by established reaction mechanisms. While near complete prevention seems very unrealistic, some of the initial damage can be repaired. Depending on tissue, this may be even a large fraction. Antioxidants, however, will efficiently break radical reaction chains and, therefore, certainly limit the damage caused by radicals. It is not clear if chemical antioxidant action is strictly limited to electron-transfer processes or if additional reaction mechanisms may contribute.
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13
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Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions. Amino Acids 2019; 51:1409-1431. [DOI: 10.1007/s00726-019-02787-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/07/2019] [Indexed: 12/12/2022]
Abstract
AbstractPeptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.
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14
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Close DM, Bernhard WA. Comprehensive model for X-ray-induced damage in protein crystallography. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:945-957. [PMID: 31274416 DOI: 10.1107/s1600577519005083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Acquisition of X-ray crystallographic data is always accompanied by structural degradation owing to the absorption of energy. The application of high-fluency X-ray sources to large biomolecules has increased the importance of finding ways to curtail the onset of X-ray-induced damage. A significant effort has been under way with the aim of identifying strategies for protecting protein structure. A comprehensive model is presented that has the potential to explain, both qualitatively and quantitatively, the structural changes induced in crystalline protein at ∼100 K. The first step is to consider the qualitative question: what are the radiation-induced intermediates and expected end products? The aim of this paper is to assist in optimizing these strategies through a fundamental understanding of radiation physics and chemistry, with additional insight provided by theoretical calculations performed on the many schemes presented.
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Affiliation(s)
- David M Close
- Department of Physics, East Tennessee State University, Box 70652, Johnson City, TN 37614, USA
| | - William A Bernhard
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
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15
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Frank P, Sarangi R, Hedman B, Hodgson KO. Synchrotron X-radiolysis of l-cysteine at the sulfur K-edge: Sulfurous products, experimental surprises, and dioxygen as an oxidoreductant. J Chem Phys 2019; 150:105101. [PMID: 30876351 PMCID: PMC7791807 DOI: 10.1063/1.5079419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/12/2019] [Indexed: 11/14/2022] Open
Abstract
In situ inventory of sulfurous products from the sulfur K-edge synchrotron X-radiolysis of l-cysteine in solid-phase and anaerobic (pH 5) and air-saturated (pH 5, 7, and 9) solutions without and with 40% glycerol is reported. Sequential K-edge X-ray Absorption Spectroscopic (XAS) spectra were acquired. l-cysteine degraded systematically in the X-ray beam. Radiolytic products were inventoried by fits using the XAS spectra of sulfur model compounds. Solid l-cysteine declined to 92% fraction after a single K-edge XAS scan. After six scans, 60% remained, accompanied by 14% cystine, 16% thioether, 5.4% elemental sulfur, and smaller fractions of more highly oxidized products. In air-saturated pH 5 solution, 73% of l-cysteine remained after ten scans, with 2% cystine and 19% elemental sulfur. Oxidation increased with 40% glycerol, yielding 67%, 5%, and 23% fractions, respectively, after ten scans. Higher pH solutions exhibited less radiolytic chemistry. All the reactivity followed first-order kinetics. The anaerobic experiment displayed two reaction phases, with sharp changes in kinetics and radiolytic chemistry. Unexpectedly, the radiolytic oxidation of l-cysteine was increased in anaerobic solution. After ten scans, only 60% of the l-cysteine remained, along with 17% cystine, 22% elemental sulfur, and traces of more highly oxidized products. A new aerobic reaction cycle is hypothesized, wherein dissolved dioxygen captures radiolytic H• or eaq -, enters HO2 •/O2 •-, reductively quenches cysteine thiyl radicals, and cycles back to O2. This cycle is suggested to suppress the radiolytic production of cystine in aerobic solution.
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Affiliation(s)
- Patrick Frank
- Author to whom correspondence should be addressed: . Tel.: 650-723-2479
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, USA
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16
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Taysi S, Tascan AS, Ugur MG, Demir M. Radicals, Oxidative/Nitrosative Stress and Preeclampsia. Mini Rev Med Chem 2019; 19:178-193. [DOI: 10.2174/1389557518666181015151350] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 11/01/2016] [Accepted: 02/28/2017] [Indexed: 12/23/2022]
Abstract
Preeclampsia (PE) has a profound effect in increasing both maternal and fetal morbidity and
mortality especially in third World. Disturbances of extravillous trophoblast migration toward uterine
spiral arteries is characteristic feature of PE, which, in turn, leads to increased uteroplacental vascular
resistance and by vascular dysfunction resulting in reduced systemic vasodilatory properties. Underlying
pathogenesis appeared to be an altered bioavailability of nitric oxide (NO•) and tissue damage
caused by increased levels of reactive oxygen species (ROS) and reactive nitrogen species (RNS). The
increase in ROS and RNS production or the decrease in antioxidant mechanisms generates a condition
called oxidative and nitrosative stress, respectively, defined as the imbalance between pro- and antioxidants
in favor of the oxidants. Additionally, ROS might trigger platelet adhesion and aggregation
leading to intravascular coagulopathy. ROS-induced coagulopathy causes placental infarction and impairs
the uteroplacental blood flow in PE. As a consequence of these disorders could result in deficiencies
in oxygen and nutrients required for normal fetal development resulting in fetal growth restriction.
On the one hand, enzymatic and nonenzymatic antioxidants scavenge ROS and protect tissues against
oxidative damage. More specifically, placental antioxidant enzymes including catalase, superoxide
dismutase (SOD), and glutathione peroxidase (GSH-Px) protect the vasculature from ROS, maintaining
the vascular function. On the other hand, ischemia in placenta in PE reduces the antioxidant activity.
Collectively, the extent of oxidative stress would increase and therefore leads to the development
of the pathological findings of PE including hypertension and proteinuria. Our goal in this article is to
review current literature about researches demonstrating the interplay between oxidative, nitrosative
stresses and PE, about their roles in the pathophysiology of PE and also about the outcomes of current
clinical trials aiming to prevent PE with antioxidant supplementation.
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Affiliation(s)
- Seyithan Taysi
- Department of Medical Biochemistry, Gaziantep University, Medical School, Gaziantep, Turkey
| | - Ayse Saglam Tascan
- Department of Medical Biochemistry, Gaziantep University, Medical School, Gaziantep, Turkey
| | - Mete Gurol Ugur
- Obstetrics and Gynecology, Gaziantep University, Medical School, Gaziantep, Turkey
| | - Mustafa Demir
- Division of Obstetrics and Gynecology, Golbasi State Hospital, Adiyaman, Turkey
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Proteomic profiling of oxidized cysteine and methionine residues by hydroxyl radicals in myosin of pork. Food Chem 2018; 243:277-284. [DOI: 10.1016/j.foodchem.2017.09.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/11/2017] [Accepted: 09/14/2017] [Indexed: 11/22/2022]
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18
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Akhtar MJ, Ahamed M, Alhadlaq HA, Alshamsan A. Mechanism of ROS scavenging and antioxidant signalling by redox metallic and fullerene nanomaterials: Potential implications in ROS associated degenerative disorders. Biochim Biophys Acta Gen Subj 2017; 1861:802-813. [PMID: 28115205 DOI: 10.1016/j.bbagen.2017.01.018] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/21/2016] [Accepted: 01/09/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND The balance between oxidation and anti-oxidation is believed to be critical in maintaining healthy biological systems. However, our endogenous antioxidant defense systems are incomplete without exogenous antioxidants and, therefore, there is a continuous demand for exogenous antioxidants to prevent stress and ageing associated disorders. Nanotechnology has yielded enormous variety of nanomaterials (NMs) of which metallic and carbonic (mainly fullerenes) NMs, with redox property, have been found to be strong scavengers of ROS and antioxidants in preclinical in vitro and in vivo models. SCOPE OF REVIEW Redox activity of metal based NMs and membrane translocation time of fullerene NMs seem to be the major determinants in ROS scavenging potential exhibited by these NMs. A comprehensive knowledge about the effects of ROS scavenging NMs in cellular antioxidant signalling is largely lacking. This review compiles the mechanisms of ROS scavenging as well as antioxidant signalling of the aforementioned metallic and fullerene NMs. MAJOR CONCLUSIONS Direct interaction between NMs and proteins does greatly affect the corona/adsorption formation dynamics but such interaction does not provide the explanation behind diverse biological outcomes induced by NMs. Indirect interaction, however, that could occur via NMs uptake and dissolution, NMs ROS induction and ROS scavenging property, and NMs membrane translocation time seem to work as a central mode of interaction. GENERAL SIGNIFICANCE The usage of potential antioxidant NMs in biological systems would greatly impact the field of nanomedicine. ROS scavenging NMs hold great promise in the future treatment of ROS related degenerative disorders.
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Affiliation(s)
- Mohd Javed Akhtar
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia.
| | - Maqusood Ahamed
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
| | - Hisham A Alhadlaq
- Department of Physics and Astronomy, College of Sciences, King Saud University, Riyadh, Saudi Arabia; King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
| | - Aws Alshamsan
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia; Nanomedicine Research Unit, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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19
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Short JD, Downs K, Tavakoli S, Asmis R. Protein Thiol Redox Signaling in Monocytes and Macrophages. Antioxid Redox Signal 2016; 25:816-835. [PMID: 27288099 PMCID: PMC5107717 DOI: 10.1089/ars.2016.6697] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SIGNIFICANCE Monocyte and macrophage dysfunction plays a critical role in a wide range of inflammatory disease processes, including obesity, impaired wound healing diabetic complications, and atherosclerosis. Emerging evidence suggests that the earliest events in monocyte or macrophage dysregulation include elevated reactive oxygen species production, thiol modifications, and disruption of redox-sensitive signaling pathways. This review focuses on the current state of research in thiol redox signaling in monocytes and macrophages, including (i) the molecular mechanisms by which reversible protein-S-glutathionylation occurs, (ii) the identification of bona fide S-glutathionylated proteins that occur under physiological conditions, and (iii) how disruptions of thiol redox signaling affect monocyte and macrophage functions and contribute to atherosclerosis. Recent Advances: Recent advances in redox biochemistry and biology as well as redox proteomic techniques have led to the identification of many new thiol redox-regulated proteins and pathways. In addition, major advances have been made in expanding the list of S-glutathionylated proteins and assessing the role that protein-S-glutathionylation and S-glutathionylation-regulating enzymes play in monocyte and macrophage functions, including monocyte transmigration, macrophage polarization, foam cell formation, and macrophage cell death. CRITICAL ISSUES Protein-S-glutathionylation/deglutathionylation in monocytes and macrophages has emerged as a new and important signaling paradigm, which provides a molecular basis for the well-established relationship between metabolic disorders, oxidative stress, and cardiovascular diseases. FUTURE DIRECTIONS The identification of specific S-glutathionylated proteins as well as the mechanisms that control this post-translational protein modification in monocytes and macrophages will facilitate the development of new preventive and therapeutic strategies to combat atherosclerosis and other metabolic diseases. Antioxid. Redox Signal. 25, 816-835.
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Affiliation(s)
- John D Short
- 1 Department of Pharmacology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Kevin Downs
- 2 Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Sina Tavakoli
- 3 Department of Radiology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Reto Asmis
- 4 Department of Clinical Laboratory Sciences, University of Texas Health Science Center at San Antonio , San Antonio, Texas.,5 Department of Biochemistry, University of Texas Health Science Center at San Antonio , San Antonio, Texas
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20
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Abstract
Amino acid and protein hydroperoxides can constitute a significant hazard if formed in vivo. It has been suggested that cysteine can form hydroperoxides after intramolecular hydrogen transfer to the commonly produced cysteine sulfur-centered radical. The resultant cysteine-derived carbon-centered radicals can react with oxygen at almost diffusion-controlled rate, forming peroxyl radicals which can oxidize other molecules and be reduced to hydroperoxides in the process. No cysteine hydroperoxides have been found so far. In this study, dilute air-saturated cysteine solutions were exposed to radicals generated by ionizing radiation and the hydroperoxides measured by an iodide assay. Of the three primary radicals present, the hydroxyl, hydrogen atoms and hydrated electrons, the first two were ineffective. However, electrons did initiate the generation of hydroperoxides by removing the -SH group and forming cysteine-derived carbon radicals. Under optimal conditions, 100% of the electrons reacting with cysteine produced the hydroperoxides with a 1:1 stoichiometry. Maximum hydroperoxide yields were at pH 5.5, with fairly rapid decline under more acid or alkaline conditions. The hydroperoxides were stable between pH 3 and 7.5, and decomposed in alkaline solutions. The results suggest that formation of cysteine hydroperoxides initiated by electrons is an unlikely event under physiological conditions.
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Affiliation(s)
- Janusz M Gebicki
- a Department of Biological Sciences , Macquarie University , Sydney , NSW , Australia
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21
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Winterbourn CC. Revisiting the reactions of superoxide with glutathione and other thiols. Arch Biochem Biophys 2016; 595:68-71. [DOI: 10.1016/j.abb.2015.11.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/01/2015] [Accepted: 09/16/2015] [Indexed: 01/17/2023]
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Abstract
Proteins are major targets for radicals and two-electron oxidants in biological systems due to their abundance and high rate constants for reaction. With highly reactive radicals damage occurs at multiple side-chain and backbone sites. Less reactive species show greater selectivity with regard to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners and modified turnover. In the presence of O2, high yields of peroxyl radicals and peroxides (protein peroxidation) are formed; the latter account for up to 70% of the initial oxidant flux. Protein peroxides can oxidize both proteins and other targets. One-electron reduction results in additional radicals and chain reactions with alcohols and carbonyls as major products; the latter are commonly used markers of protein damage. Direct oxidation of cysteine (and less commonly) methionine residues is a major reaction; this is typically faster than with H2O2, and results in altered protein activity and function. Unlike H2O2, which is rapidly removed by protective enzymes, protein peroxides are only slowly removed, and catabolism is a major fate. Although turnover of modified proteins by proteasomal and lysosomal enzymes, and other proteases (e.g. mitochondrial Lon), can be efficient, protein hydroperoxides inhibit these pathways and this may contribute to the accumulation of modified proteins in cells. Available evidence supports an association between protein oxidation and multiple human pathologies, but whether this link is causal remains to be established.
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Affiliation(s)
- Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
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23
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Plegaria JS, Herrero C, Quaranta A, Pecoraro VL. Electron transfer activity of a de novo designed copper center in a three-helix bundle fold. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:522-530. [PMID: 26427552 DOI: 10.1016/j.bbabio.2015.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/18/2015] [Indexed: 11/29/2022]
Abstract
In this work, we characterized the intermolecular electron transfer (ET) properties of a de novo designed metallopeptide using laser-flash photolysis. α3D-CH3 is three helix bundle peptide that was designed to contain a copper ET site that is found in the β-barrel fold of native cupredoxins. The ET activity of Cuα3D-CH3 was determined using five different photosensitizers. By exhibiting a complete depletion of the photo-oxidant and the successive formation of a Cu(II) species at 400 nm, the transient and generated spectra demonstrated an ET transfer reaction between the photo-oxidant and Cu(I)α3D-CH3. This observation illustrated our success in integrating an ET center within a de novo designed scaffold. From the kinetic traces at 400 nm, first-order and bimolecular rate constants of 10(5) s(-1) and 10(8) M(-1) s(-1) were derived. Moreover, a Marcus equation analysis on the rate versus driving force study produced a reorganization energy of 1.1 eV, demonstrating that the helical fold of α3D requires further structural optimization to efficiently perform ET. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Jefferson S Plegaria
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Christian Herrero
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris Sud, CNRS, 91405 Orsay Cedex, France
| | | | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States.
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24
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Abstract
The cysteine (Cys) proteome is a major component of the adaptive interface between the genome and the exposome. The thiol moiety of Cys undergoes a range of biologic modifications enabling biological switching of structure and reactivity. These biological modifications include sulfenylation and disulfide formation, formation of higher oxidation states, S-nitrosylation, persulfidation, metalation, and other modifications. Extensive knowledge about these systems and their compartmentalization now provides a foundation to develop advanced integrative models of Cys proteome regulation. In particular, detailed understanding of redox signaling pathways and sensing networks is becoming available to allow the discrimination of network structures. This research focuses attention on the need for atlases of Cys modifications to develop systems biology models. Such atlases will be especially useful for integrative studies linking the Cys proteome to imaging and other omics platforms, providing a basis for improved redox-based therapeutics. Thus, a framework is emerging to place the Cys proteome as a complement to the quantitative proteome in the omics continuum connecting the genome to the exposome.
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Affiliation(s)
- Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Joshua D Chandler
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA.
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25
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Carroll L, Davies MJ, Pattison DI. Reaction of low-molecular-mass organoselenium compounds (and their sulphur analogues) with inflammation-associated oxidants. Free Radic Res 2015; 49:750-67. [PMID: 25854915 DOI: 10.3109/10715762.2015.1018247] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Selenium is an essential trace element in mammals, with the majority specifically encoded as seleno-L-cysteine into a range of selenoproteins. Many of these proteins play a key role in modulating oxidative stress, via either direct detoxification of biological oxidants, or repair of oxidised residues. Both selenium- and sulphur-containing residues react readily with the wide range of oxidants (including hydrogen peroxide, radicals, singlet oxygen and hypochlorous, hypobromous, hypothiocyanous and peroxynitrous acids) that are produced during inflammation and have been implicated in the development of a range of inflammatory diseases. Whilst selenium has similar properties to sulphur, it typically exhibits greater reactivity with most oxidants, and there are considerable differences in the subsequent reactivity and ease of repair of the oxidised species that are formed. This review discusses the chemistry of low-molecular-mass organoselenium compounds (e.g. selenoethers, diselenides and selenols) with inflammatory oxidants, with a particular focus on the reaction kinetics and product studies, with the differences in reactivity between selenium and sulphur analogues described in the selected examples. These data provide insight into the therapeutic potential of low-molecular-mass selenium-containing compounds to modulate the activity of both radical and molecular oxidants and provide protection against inflammation-induced damage. Progress in their therapeutic development (including modulation of potential selenium toxicity by strategic design) is demonstrated by a brief summary of some recent studies where novel organoselenium compounds have been used as wound healing or radioprotection agents and in the prevention of cardiovascular disease.
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Affiliation(s)
- L Carroll
- The Heart Research Institute , Newtown, Sydney , Australia
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26
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Perna A, Intaglietta I, Simonetti A, Gambacorta E. Donkey Milk for Manufacture of Novel Functional Fermented Beverages. J Food Sci 2015; 80:S1352-9. [PMID: 25962497 DOI: 10.1111/1750-3841.12862] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/22/2015] [Indexed: 12/31/2022]
Abstract
The aim of this work was to investigate on the functional features of a donkey milk probiotic berevage as a novel food. Particularly, it was to study the decrease of lactose content and the antioxidant activity of standard yogurt (YC) and probiotic yogurt (YP; Lactobacillus acidophilus, Lactobacillus casei) from donkey milk during the storage up to 30 d at 4 ºC. The evolution of lactose content using enzymatic-spectrophotometric kits was analyzed. Antioxidant activity of yogurt was measured using 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS), ferric reducing antioxidant power (FRAP), and thiol assays. Parallel consumer sensory studies were carried out as consumer test in order to gain information about the impact of these novel fermented beverages on sensory perceptions. The statistical analysis has shown significant effect of studied factors. The results showed that the lactose content gradually decreased during storage in both yogurts, reaching values of 2.36% and 2.10% in YC and YP, respectively, at 30 d (P < 0.05). During storage of both yogurt types, the antioxidant activity increased, but YP showed a higher antioxidant activity than YC. The results suggest that the antioxidant activity of yogurt samples was affected by cultures of lactic acid bacteria (LAB). We conclude that the fermented donkey milk could be configured as health and nutraceutical food, which aims to meet nutritional requirements of certain consumers groups with lactose or cow milk protein intolerance.
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Affiliation(s)
- Annamaria Perna
- Authors are with School of Agricultural, Forestry, Food and Environmental Sciences, Univ. of Basilicata, Potenza, Viale dell'Ateneo Lucano, 10-85100, Italy
| | - Immacolata Intaglietta
- Authors are with School of Agricultural, Forestry, Food and Environmental Sciences, Univ. of Basilicata, Potenza, Viale dell'Ateneo Lucano, 10-85100, Italy
| | - Amalia Simonetti
- Authors are with School of Agricultural, Forestry, Food and Environmental Sciences, Univ. of Basilicata, Potenza, Viale dell'Ateneo Lucano, 10-85100, Italy
| | - Emilio Gambacorta
- Authors are with School of Agricultural, Forestry, Food and Environmental Sciences, Univ. of Basilicata, Potenza, Viale dell'Ateneo Lucano, 10-85100, Italy
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27
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Mangiferin as chain transfer agent: effect on the molecular weight of poly(methyl methacrylate) and polystyrene. Polym Bull (Berl) 2015. [DOI: 10.1007/s00289-015-1343-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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Winterbourn CC. Are free radicals involved in thiol-based redox signaling? Free Radic Biol Med 2015; 80:164-70. [PMID: 25277419 DOI: 10.1016/j.freeradbiomed.2014.08.017] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 08/12/2014] [Accepted: 08/18/2014] [Indexed: 12/27/2022]
Abstract
Cells respond to many stimuli by transmitting signals through redox-regulated pathways. It is generally accepted that in many instances signal transduction is via reversible oxidation of thiol proteins, although there is uncertainty about the specific redox transformations involved. The prevailing view is that thiol oxidation occurs by a two electron mechanism, most commonly involving hydrogen peroxide. Free radicals, on the other hand, are considered as damaging species and not generally regarded as important in cell signaling. This paper examines whether it is justified to dismiss radicals or whether they could have a signaling role. Although there is no direct evidence that radicals are involved in transmitting thiol-based redox signals, evidence is presented that they are generated in cells when these signaling pathways are activated. Radicals produce the same thiol oxidation products as two electron oxidants, although by a different mechanism, and at this point radical-mediated pathways should not be dismissed. There are unresolved issues about how radical mechanisms could achieve sufficient selectivity, but this could be possible through colocalization of radical-generating and signal-transducing proteins. Colocalization is also likely to be important for nonradical signaling mechanisms and identification of such associations should be a priority for advancing the field.
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Affiliation(s)
- Christine C Winterbourn
- Centre for Free Radical Research, Department of Pathology, University of Otago, P.O. Box 4345, Christchurch, New Zealand.
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29
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Pereira JCM, Iretskii AV, Han RM, Ford PC. Dinitrosyl Iron Complexes with Cysteine. Kinetics Studies of the Formation and Reactions of DNICs in Aqueous Solution. J Am Chem Soc 2014; 137:328-36. [DOI: 10.1021/ja510393q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- José Clayston Melo Pereira
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, Santa
Barbara, California 93106-9510, United States
- Departamento
de Química Geral e Inorgânica, Instituto de Química
de Araraquara, UNESP − Universidade Estadual Paulista, Araraquara, São Paulo 14801−970, Brazil
| | - Alexei V. Iretskii
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, Santa
Barbara, California 93106-9510, United States
- Department
of Chemistry and Environmental Sciences, Lake Superior State University, Sault Sainte Marie, Michigan 49783, United States
| | - Rui-Min Han
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, Santa
Barbara, California 93106-9510, United States
- Department
of Chemistry, Renmin University of China, 59 ZhongGuanCun St., Beijing, 100872, China
| | - Peter C. Ford
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, Santa
Barbara, California 93106-9510, United States
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30
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Adhikary A, Kumar A, Rayala R, Hindi RM, Adhikary A, Wnuk SF, Sevilla MD. One-electron oxidation of gemcitabine and analogs: mechanism of formation of C3' and C2' sugar radicals. J Am Chem Soc 2014; 136:15646-53. [PMID: 25296262 PMCID: PMC4227712 DOI: 10.1021/ja5083156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gemcitabine is a modified cytidine analog having two fluorine atoms at the 2'-position of the ribose ring. It has been proposed that gemcitabine inhibits RNR activity by producing a C3'• intermediate via direct H3'-atom abstraction followed by loss of HF to yield a C2'• with 3'-keto moiety. Direct detection of C3'• and C2'• during RNR inactivation by gemcitabine still remains elusive. To test the influence of 2'- substitution on radical site formation, electron spin resonance (ESR) studies are carried out on one-electron oxidized gemcitabine and other 2'-modified analogs, i.e., 2'-deoxy-2'-fluoro-2'-C-methylcytidine (MeFdC) and 2'-fluoro-2'-deoxycytidine (2'-FdC). ESR line components from two anisotropic β-2'-F-atom hyperfine couplings identify the C3'• formation in one-electron oxidized gemcitabine, but no further reaction to C2'• is found. One-electron oxidized 2'-FdC is unreactive toward C3'• or C2'• formation. In one-electron oxidized MeFdC, ESR studies show C2'• production presumably from a very unstable C3'• precursor. The experimentally observed hyperfine couplings for C2'• and C3'• match well with the theoretically predicted ones. C3'• to C2'• conversion in one-electron oxidized gemcitabine and MeFdC has theoretically been modeled by first considering the C3'• and H3O(+) formation via H3'-proton deprotonation and the subsequent C2'• formation via HF loss induced by this proximate H3O(+). Theoretical calculations show that in gemcitabine, C3'• to C2'• conversion in the presence of a proximate H3O(+) has a barrier in agreement with the experimentally observed lack of C3'• to C2'• conversion. In contrast, in MeFdC, the loss of HF from C3'• in the presence of a proximate H3O(+) is barrierless resulting in C2'• formation which agrees with the experimentally observed rapid C2'• formation.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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31
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Kaludercic N, Deshwal S, Di Lisa F. Reactive oxygen species and redox compartmentalization. Front Physiol 2014; 5:285. [PMID: 25161621 PMCID: PMC4130307 DOI: 10.3389/fphys.2014.00285] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/11/2014] [Indexed: 01/01/2023] Open
Abstract
Reactive oxygen species (ROS) formation and signaling are of major importance and regulate a number of processes in physiological conditions. A disruption in redox status regulation, however, has been associated with numerous pathological conditions. In recent years it has become increasingly clear that oxidative and reductive modifications are confined in a spatio-temporal manner. This makes ROS signaling similar to that of Ca(2+) or other second messengers. Some subcellular compartments are more oxidizing (such as lysosomes or peroxisomes) whereas others are more reducing (mitochondria, nuclei). Moreover, although more reducing, mitochondria are especially susceptible to oxidation, most likely due to the high number of exposed thiols present in that compartment. Recent advances in the development of redox probes allow specific measurement of defined ROS in different cellular compartments in intact living cells or organisms. The availability of these tools now allows simultaneous spatio-temporal measurements and correlation between ROS generation and organelle and/or cellular function. The study of ROS compartmentalization and microdomains will help elucidate their role in physiology and disease. Here we will examine redox probes currently available and how ROS generation may vary between subcellular compartments. Furthermore, we will discuss ROS compartmentalization in physiological and pathological conditions focusing our attention on mitochondria, since their vulnerability to oxidative stress is likely at the basis of several diseases.
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Affiliation(s)
- Nina Kaludercic
- Neuroscience Institute, National Research Council of Italy (CNR) Padova, Italy
| | - Soni Deshwal
- Department of Biomedical Sciences, University of Padova Padova, Italy
| | - Fabio Di Lisa
- Neuroscience Institute, National Research Council of Italy (CNR) Padova, Italy ; Department of Biomedical Sciences, University of Padova Padova, Italy
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32
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Kabil O, Motl N, Banerjee R. H2S and its role in redox signaling. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1844:1355-66. [PMID: 24418393 PMCID: PMC4048824 DOI: 10.1016/j.bbapap.2014.01.002] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/19/2013] [Accepted: 01/02/2014] [Indexed: 02/08/2023]
Abstract
Hydrogen sulfide (H2S) has emerged as an important gaseous signaling molecule that is produced endogenously by enzymes in the sulfur metabolic network. H2S exerts its effects on multiple physiological processes important under both normal and pathological conditions. These functions include neuromodulation, regulation of blood pressure and cardiac function, inflammation, cellular energetics and apoptosis. Despite the recognition of its biological importance and its beneficial effects, the mechanism of H2S action and the regulation of its tissue levels remain unclear in part owing to its chemical and physical properties that render handling and analysis challenging. Furthermore, the multitude of potential H2S effects has made it difficult to dissect its signaling mechanism and to identify specific targets. In this review, we focus on H2S metabolism and provide an overview of the recent literature that sheds some light on its mechanism of action in cellular redox signaling in health and disease. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.
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Affiliation(s)
- Omer Kabil
- University of Michigan Medical School, Ann Arbor, MI 48109-0600, USA
| | - Nicole Motl
- University of Michigan Medical School, Ann Arbor, MI 48109-0600, USA
| | - Ruma Banerjee
- University of Michigan Medical School, Ann Arbor, MI 48109-0600, USA.
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33
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Reisz JA, Bansal N, Qian J, Zhao W, Furdui CM. Effects of ionizing radiation on biological molecules--mechanisms of damage and emerging methods of detection. Antioxid Redox Signal 2014; 21:260-92. [PMID: 24382094 PMCID: PMC4060780 DOI: 10.1089/ars.2013.5489] [Citation(s) in RCA: 414] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 12/07/2013] [Accepted: 01/01/2014] [Indexed: 12/13/2022]
Abstract
SIGNIFICANCE The detrimental effects of ionizing radiation (IR) involve a highly orchestrated series of events that are amplified by endogenous signaling and culminating in oxidative damage to DNA, lipids, proteins, and many metabolites. Despite the global impact of IR, the molecular mechanisms underlying tissue damage reveal that many biomolecules are chemoselectively modified by IR. RECENT ADVANCES The development of high-throughput "omics" technologies for mapping DNA and protein modifications have revolutionized the study of IR effects on biological systems. Studies in cells, tissues, and biological fluids are used to identify molecular features or biomarkers of IR exposure and response and the molecular mechanisms that regulate their expression or synthesis. CRITICAL ISSUES In this review, chemical mechanisms are described for IR-induced modifications of biomolecules along with methods for their detection. Included with the detection methods are crucial experimental considerations and caveats for their use. Additional factors critical to the cellular response to radiation, including alterations in protein expression, metabolomics, and epigenetic factors, are also discussed. FUTURE DIRECTIONS Throughout the review, the synergy of combined "omics" technologies such as genomics and epigenomics, proteomics, and metabolomics is highlighted. These are anticipated to lead to new hypotheses to understand IR effects on biological systems and improve IR-based therapies.
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Affiliation(s)
- Julie A Reisz
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
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Stinson CA, Xia Y. Reactions of hydroxyalkyl radicals with cysteinyl peptides in a nanoESI plume. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1192-1201. [PMID: 24793576 DOI: 10.1007/s13361-014-0898-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/20/2014] [Accepted: 03/20/2014] [Indexed: 06/03/2023]
Abstract
In biological systems, carbon-centered small molecule radicals are primarily formed via external radiation or internal radical reactions. These radical species can react with a variety of biomolecules, most notably nucleic acids, the consequence of which has possible links to gene mutation and cancer. Sulfur-containing peptides and proteins are reactive toward a variety of radical species and many of them behave as radical scavengers. In this study, the reactions between alkyl alcohol carbon-centered radicals (e.g., •CH2OH for methanol) and cysteinyl peptides within a nanoelectrospray ionization (nanoESI) plume were explored. The reaction system involved ultraviolet (UV) irradiation of a nanoESI plume using a low pressure mercury lamp consisting of 185 and 254 nm emission bands. The alkyl alcohol was added as solvent into the nanoESI solution and served as the precursor of hydroxyalkyl radicals upon UV irradiation. The hydroxyalkyl radicals subsequently reacted with cysteinyl peptides either containing a disulfide linkage or free thiol, which led to the formation of peptide-S-hydroxyalkyl product. This radical reaction coupled with subsequent MS/MS was shown to have analytical potential by cleaving intrachain disulfide linked peptides prior to CID to enhance sequence information. Tandem mass spectrometry via collision-induced dissociation (CID), stable isotope labeling, and accurate mass measurement were employed to verify the identities of the reaction products.
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Affiliation(s)
- Craig A Stinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
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35
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Singh B, Das RS, Banerjee R, Mukhopadhyay S. Uncatalyzed and copper(II) catalyzed oxidation of glutathione by Co(III)2 bound superoxide complex. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Höhn A, Jung T, Grune T. Pathophysiological importance of aggregated damaged proteins. Free Radic Biol Med 2014; 71:70-89. [PMID: 24632383 DOI: 10.1016/j.freeradbiomed.2014.02.028] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/28/2014] [Accepted: 02/28/2014] [Indexed: 02/06/2023]
Abstract
Reactive oxygen species (ROS) are formed continuously in the organism even under physiological conditions. If the level of ROS in cells exceeds the cellular defense capacity, components such as RNA/DNA, lipids, and proteins are damaged and modified, thus affecting the functionality of organelles as well. Proteins are especially prominent targets of various modifications such as oxidation, glycation, or conjugation with products of lipid peroxidation, leading to the alteration of their biological function, nonspecific interactions, and the production of high-molecular-weight protein aggregates. To ensure the maintenance of cellular functions, two proteolytic systems are responsible for the removal of oxidized and modified proteins, especially the proteasome and organelles, mainly the autophagy-lysosomal systems. Furthermore, increased protein oxidation and oxidation-dependent impairment of proteolytic systems lead to an accumulation of oxidized proteins and finally to the formation of nondegradable protein aggregates. Accordingly, the cellular homeostasis cannot be maintained and the cellular metabolism is negatively affected. Here we address the current knowledge of protein aggregation during oxidative stress, aging, and disease.
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Affiliation(s)
- Annika Höhn
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Tobias Jung
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Tilman Grune
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller-University Jena, 07743 Jena, Germany.
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37
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Hobbs GA, Zhou B, Cox AD, Campbell SL. Rho GTPases, oxidation, and cell redox control. Small GTPases 2014; 5:e28579. [PMID: 24809833 DOI: 10.4161/sgtp.28579] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
While numerous studies support regulation of Ras GTPases by reactive oxygen and nitrogen species, the Rho subfamily has received considerably less attention. Over the last few years, increasing evidence is emerging that supports the redox sensitivity of Rho GTPases. Moreover, as Rho GTPases regulate the cellular redox state by controlling enzymes that generate and convert reactive oxygen and nitrogen species, redox feedback loops likely exist. Here, we provide an overview of cellular oxidants, Rho GTPases, and their inter-dependence.
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Affiliation(s)
- G Aaron Hobbs
- Department of Biochemistry and Biophysics; University of North Carolina; Chapel Hill, NC USA
| | - Bingying Zhou
- Department of Pharmacology; University of North Carolina; Chapel Hill, NC USA
| | - Adrienne D Cox
- Department of Pharmacology; University of North Carolina; Chapel Hill, NC USA; Department of Radiation Oncology, University of North Carolina; Chapel Hill, NC USA; Lineberger Comprehensive Cancer Center; University of North Carolina; Chapel Hill, NC USA
| | - Sharon L Campbell
- Department of Biochemistry and Biophysics; University of North Carolina; Chapel Hill, NC USA; Lineberger Comprehensive Cancer Center; University of North Carolina; Chapel Hill, NC USA
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38
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Kranner I, Grill D. Significance of Thiol-Disulfide Exchange in Resting Stages of Plant Development. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1996.tb00864.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Carballal S, Bartesaghi S, Radi R. Kinetic and mechanistic considerations to assess the biological fate of peroxynitrite. Biochim Biophys Acta Gen Subj 2013; 1840:768-80. [PMID: 23872352 DOI: 10.1016/j.bbagen.2013.07.005] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/25/2013] [Accepted: 07/04/2013] [Indexed: 01/21/2023]
Abstract
BACKGROUND Peroxynitrite, the product of the reaction between superoxide radicals and nitric oxide, is an elusive oxidant with a short half-life and a low steady-state concentration in biological systems; it promotes nitroxidative damage. SCOPE OF REVIEW We will consider kinetic and mechanistic aspects that allow rationalizing the biological fate of peroxynitrite from data obtained by a combination of methods that include fast kinetic techniques, electron paramagnetic resonance and kinetic simulations. In addition, we provide a quantitative analysis of peroxynitrite production rates and conceivable steady-state levels in living systems. MAJOR CONCLUSIONS The preferential reactions of peroxynitrite in vivo include those with carbon dioxide, thiols and metalloproteins; its homolysis represents only <1% of its fate. To note, carbon dioxide accounts for a significant fraction of peroxynitrite consumption leading to the formation of strong one-electron oxidants, carbonate radicals and nitrogen dioxide. On the other hand, peroxynitrite is rapidly reduced by peroxiredoxins, which represent efficient thiol-based peroxynitrite detoxification systems. Glutathione, present at mM concentration in cells and frequently considered a direct scavenger of peroxynitrite, does not react sufficiently fast with it in vivo; glutathione mainly inhibits peroxynitrite-dependent processes by reactions with secondary radicals. The detection of protein 3-nitrotyrosine, a molecular footprint, can demonstrate peroxynitrite formation in vivo. Basal peroxynitrite formation rates in cells can be estimated in the order of 0.1 to 0.5μMs(-1) and its steady-state concentration at ~1nM. GENERAL SIGNIFICANCE The analysis provides a handle to predict the preferential fate and steady-state levels of peroxynitrite in living systems. This is useful to understand pathophysiological aspects and pharmacological prospects connected to peroxynitrite. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.
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Affiliation(s)
- Sebastián Carballal
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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40
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Paulsen C, Carroll KS. Cysteine-mediated redox signaling: chemistry, biology, and tools for discovery. Chem Rev 2013; 113:4633-79. [PMID: 23514336 PMCID: PMC4303468 DOI: 10.1021/cr300163e] [Citation(s) in RCA: 815] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Candice
E. Paulsen
- Department of Chemistry, The Scripps Research
Institute, Jupiter, Florida, 33458, United States
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research
Institute, Jupiter, Florida, 33458, United States
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41
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Gupta V, Carroll KS. Sulfenic acid chemistry, detection and cellular lifetime. Biochim Biophys Acta Gen Subj 2013; 1840:847-75. [PMID: 23748139 DOI: 10.1016/j.bbagen.2013.05.040] [Citation(s) in RCA: 302] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/24/2013] [Accepted: 05/26/2013] [Indexed: 02/03/2023]
Abstract
BACKGROUND Reactive oxygen species-mediated cysteine sulfenic acid modification has emerged as an important regulatory mechanism in cell signaling. The stability of sulfenic acid in proteins is dictated by the local microenvironment and ability of antioxidants to reduce this modification. Several techniques for detecting this cysteine modification have been developed, including direct and in situ methods. SCOPE OF REVIEW This review presents a historical discussion of sulfenic acid chemistry and highlights key examples of this modification in proteins. A comprehensive survey of available detection techniques with advantages and limitations is discussed. Finally, issues pertaining to rates of sulfenic acid formation, reduction, and chemical trapping methods are also covered. MAJOR CONCLUSIONS Early chemical models of sulfenic acid yielded important insights into the unique reactivity of this species. Subsequent pioneering studies led to the characterization of sulfenic acid formation in proteins. In parallel, the discovery of oxidant-mediated cell signaling pathways and pathological oxidative stress has led to significant interest in methods to detect these modifications. Advanced methods allow for direct chemical trapping of protein sulfenic acids directly in cells and tissues. At the same time, many sulfenic acids are short-lived and the reactivity of current probes must be improved to sample these species, while at the same time, preserving their chemical selectivity. Inhibitors with binding scaffolds can be rationally designed to target sulfenic acid modifications in specific proteins. GENERAL SIGNIFICANCE Ever increasing roles for protein sulfenic acids have been uncovered in physiology and pathology. A more complete understanding of sulfenic acid-mediated regulatory mechanisms will continue to require rigorous and new chemical insights. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.
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Affiliation(s)
- Vinayak Gupta
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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42
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Nagy P. Kinetics and mechanisms of thiol-disulfide exchange covering direct substitution and thiol oxidation-mediated pathways. Antioxid Redox Signal 2013; 18:1623-41. [PMID: 23075118 PMCID: PMC3613173 DOI: 10.1089/ars.2012.4973] [Citation(s) in RCA: 280] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
SIGNIFICANCE Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol-disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. CRITICAL ISSUES This review is focused on the kinetics and mechanisms of thiol-disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. RECENT ADVANCES AND FUTURE DIRECTIONS Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery.
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Affiliation(s)
- Péter Nagy
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary.
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43
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Collins Y, Chouchani ET, James AM, Menger KE, Cochemé HM, Murphy MP. Mitochondrial redox signalling at a glance. J Cell Sci 2013; 125:801-6. [PMID: 22448036 DOI: 10.1242/jcs.098475] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Yvonne Collins
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 0XY, UK
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44
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Chung HS, Wang SB, Venkatraman V, Murray CI, Van Eyk JE. Cysteine oxidative posttranslational modifications: emerging regulation in the cardiovascular system. Circ Res 2013; 112:382-92. [PMID: 23329793 PMCID: PMC4340704 DOI: 10.1161/circresaha.112.268680] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 10/05/2012] [Indexed: 12/22/2022]
Abstract
In the cardiovascular system, changes in oxidative balance can affect many aspects of cellular physiology through redox-signaling. Depending on the magnitude, fluctuations in the cell's production of reactive oxygen and nitrogen species can regulate normal metabolic processes, activate protective mechanisms, or be cytotoxic. Reactive oxygen and nitrogen species can have many effects including the posttranslational modification of proteins at critical cysteine thiols. A subset can act as redox-switches, which elicit functional effects in response to changes in oxidative state. Although the general concepts of redox-signaling have been established, the identity and function of many regulatory switches remains unclear. Characterizing the effects of individual modifications is the key to understand how the cell interprets oxidative signals under physiological and pathological conditions. Here, we review the various cysteine oxidative posttranslational modifications and their ability to function as redox-switches that regulate the cell's response to oxidative stimuli. In addition, we discuss how these modifications have the potential to influence other posttranslational modifications' signaling pathways though cross-talk. Finally, we review the increasing number of tools being developed to identify and quantify the various cysteine oxidative posttranslational modifications and how this will advance our understanding of redox-regulation.
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Affiliation(s)
- Heaseung S Chung
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21224, USA
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45
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Zhang W, Xiao S, Ahn DU. Protein Oxidation: Basic Principles and Implications for Meat Quality. Crit Rev Food Sci Nutr 2013; 53:1191-201. [DOI: 10.1080/10408398.2011.577540] [Citation(s) in RCA: 334] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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46
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Madrasi K, Joshi MS, Gadkari T, Kavallieratos K, Tsoukias NM. Glutathiyl radical as an intermediate in glutathione nitrosation. Free Radic Biol Med 2012; 53:1968-76. [PMID: 22951977 PMCID: PMC3494776 DOI: 10.1016/j.freeradbiomed.2012.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 06/26/2012] [Accepted: 08/09/2012] [Indexed: 11/30/2022]
Abstract
Nitrosation of thiols is thought to be mediated by dinitrogen trioxide (N(2)O(3)) or by nitrogen dioxide radical (()NO(2)). A kinetic study of glutathione (GSH) nitrosation by NO donors in aerated buffered solutions was undertaken. S-nitrosoglutathione (GSNO) formation was assessed spectrophotometrically and by chemiluminescence. The results suggest an increase in the rate of GSNO formation with an increase in GSH with a half-maximum constant EC(50) that depends on NO concentration. Our observed increase in EC(50) with NO concentration suggests a significant contribution of ()NO(2)-mediated nitrosation with the glutathiyl radical as an intermediate in the production of GSNO.
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Affiliation(s)
- Kumpal Madrasi
- Department of Biomedical Engineering, Florida International University, Miami, FL 33174
| | - Mahesh S. Joshi
- Department of Biomedical Engineering, Florida International University, Miami, FL 33174
- Correspondence to: Mahesh S. Joshi, Ph.D. Department of Biomedical Engineering, 10555 W. Flagler Street, Florida International University, Miami, FL 33174. Tel: 305-348-7292. Fax: 305-348-6954.
| | - Tushar Gadkari
- Department of Biomedical Engineering, Florida International University, Miami, FL 33174
| | | | - Nikolaos M. Tsoukias
- Department of Biomedical Engineering, Florida International University, Miami, FL 33174
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47
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Buchert F, Schober Y, Römpp A, Richter ML, Forreiter C. Reactive oxygen species affect ATP hydrolysis by targeting a highly conserved amino acid cluster in the thylakoid ATP synthase γ subunit. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:2038-48. [PMID: 22727877 DOI: 10.1016/j.bbabio.2012.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/08/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
Abstract
The vast majority of organisms produce ATP by a membrane-bound rotating protein complex, termed F-ATP synthase. In chloroplasts, the corresponding enzyme generates ATP by using a transmembrane proton gradient generated during photosynthesis, a process releasing high amounts of molecular oxygen as a natural byproduct. Due to its chemical properties, oxygen can be reduced incompletely which generates several highly reactive oxygen species (ROS) that are able to oxidize a broad range of biomolecules. In extension to previous studies it could be shown that ROS dramatically decreased ATP synthesis in situ and affected the CF1 portion in vitro. A conserved cluster of three methionines and a cysteine on the chloroplast γ subunit could be identified by mass spectrometry to be oxidized by ROS. Analysis of amino acid substitutions in a hybrid F1 assembly system indicated that these residues were exclusive catalytic targets for hydrogen peroxide and singlet oxygen, although it could be deduced that additional unknown amino acid targets might be involved in the latter reaction. The cluster was tightly integrated in catalytic turnover since mutants varied in MgATPase rates, stimulation by sulfite and chloroplast-specific γ subunit redox-modulation. Some partial disruptions of the cluster by mutagenesis were dominant over others regarding their effects on catalysis and response to ROS.
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Affiliation(s)
- Felix Buchert
- Department of Plant Physiology, Justus-Liebig-University Giessen, Germany
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48
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Takashima M, Shichiri M, Hagihara Y, Yoshida Y, Niki E. Reactivity toward oxygen radicals and antioxidant action of thiol compounds. Biofactors 2012; 38:240-8. [PMID: 22488889 DOI: 10.1002/biof.1014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 03/08/2012] [Indexed: 01/15/2023]
Abstract
Thiol compounds exert diverse functions in the defense network against oxidative stress in vivo. Above all, the role of glutathione in the enzymatic removal of hydrogen peroxide and lipid hydroperoxides has been well established. The scavenging of reactive free radicals is one of the many functions. In this study, the reactivities of several thiol compounds toward oxygen- and nitrogen-centered radicals were measured from their reaction with galvinoxyl and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals and also from their sparing effects on the decay of fluorescein, pyrogallol red, and BODIPY induced by peroxyl radicals. Furthermore, the antioxidant capacity against lipid peroxidation was assessed in the oxidation of methyl linoleate induced by free radicals in micelle systems. Cysteine, homocysteine, and glutathione exhibited considerable reactivity toward galvinoxyl, DPPH, and peroxyl radicals in this order but methionine did not. Bovine serum albumin (BSA) was less reactive toward these radicals than cysteine on molar base. Cysteine, homocysteine, and glutathione suppressed the oxidation of methyl linoleate in micelle systems, but methionine did not. The reactivity toward free radicals and antioxidant capacity of these thiol compounds were less than that of ascorbic acid, but higher than that of uric acid.
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Affiliation(s)
- Mizuki Takashima
- Health Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka, Japan
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49
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Meesat R, Sanguanmith S, Meesungnoen J, Lepage M, Khalil A, Jay-Gerin JP. Utilization of the ferrous sulfate (Fricke) dosimeter for evaluating the radioprotective potential of cystamine: experiment and Monte Carlo simulation. Radiat Res 2012; 177:813-26. [PMID: 22475011 DOI: 10.1667/rr2829.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cystamine, an organic disulfide (RSSR), is among the best of the known radiation-protective compounds and has been used to protect normal tissues in clinical radiation therapy. Recently, it has also proved to be beneficial in the treatment of disorders of the central nervous system in animal models. However, the underlying mechanism of its action at the chemical level is not yet well understood. The present study aims at using the ferrous sulfate (Fricke) dosimeter to quantitatively evaluate, both experimentally and theoretically, the radioprotective potential of this compound. The well-known radiolysis of the Fricke dosimeter by (60)Co γ rays or fast electrons, based on the oxidation of ferrous ions to ferric ions by the oxidizing species (•)OH, HO(2)(•), and H(2)O(2) produced in the radiolytic decomposition of water, forms the basis for our method. The presence of cystamine in Fricke dosimeter solutions during irradiation prevents the radiolytic oxidation of Fe(2+) and leads to decreased ferric yields (or G values). The observed decrease in G(Fe(3+)) increases upon increasing the concentration of the disulfide compound over the range 0-0.1 M under both aerated and deaerated conditions. To help assess the basic radiation-protective mechanism of this compound, a full Monte Carlo computer code is developed to simulate in complete detail the radiation-induced chemistry of the studied Fricke/cystamine solutions. Benefiting from the fact that cystamine is reasonably well characterized in terms of radiation chemistry, this computer model proposes reaction mechanisms and incorporates specific reactions describing the radiolysis of cystamine in aerated and deaerated Fricke solutions that lead to the observable quantitative chemical yields. Results clearly indicate that the protective effect of cystamine originates from its radical-capturing ability, which allows this compound to act by competing with the ferrous ions for the various free radicals--especially (•)OH radicals and H(•) atoms--formed during irradiation of the surrounding water. Most interestingly, our simulation modeling also shows that the predominant pathway in the oxidation of cystamine by (•)OH radicals involves an electron-transfer mechanism, yielding RSSR(•+) and OH(-). A very good agreement is found between calculated G(Fe(3+)) values and experiment. This study concludes that Monte Carlo simulations represent a very efficient method for understanding indirect radiation damage at the molecular level.
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Affiliation(s)
- Ridthee Meesat
- Département de Médecine Nucléaire et de Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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50
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Murphy MP. Mitochondrial thiols in antioxidant protection and redox signaling: distinct roles for glutathionylation and other thiol modifications. Antioxid Redox Signal 2012; 16:476-95. [PMID: 21954972 DOI: 10.1089/ars.2011.4289] [Citation(s) in RCA: 251] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE The mitochondrial matrix contains much of the machinery at the heart of metabolism. This compartment is also exposed to a high and continual flux of superoxide, hydrogen peroxide, and related reactive species. To protect mitochondria from these sources of oxidative damage, there is an integrated set of thiol systems within the matrix comprising the thioredoxin/peroxiredoxin/methionine sulfoxide reductase pathways and the glutathione/glutathione peroxidase/glutathione-S-transferase/glutaredoxin pathways that in conjunction with protein thiols prevent much of this oxidative damage. In addition, the changes in the redox state of many components of these mitochondrial thiol systems may transduce and relay redox signals within and through the mitochondrial matrix to modulate the activity of biochemical processes. RECENT ADVANCES Here, mitochondrial thiol systems are reviewed, and areas of uncertainty are pointed out, focusing on recent developments in our understanding of their roles. CRITICAL ISSUES The areas of particular focus are on the multiple, overlapping roles of mitochondrial thiols and on understanding how these thiols contribute to both antioxidant defenses and redox signaling. FUTURE DIRECTIONS Recent technical progress in the identification and quantification of thiol modifications by redox proteomics means that many of the questions raised about the multiple roles of mitochondrial thiols can now be addressed.
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