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Retnoningrum DS, Yoshida H, Pajatiwi I, Muliadi R, Utami RA, Artarini A, Ismaya WT. Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04347-7. [PMID: 36701098 DOI: 10.1007/s12010-023-04347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
Manganese superoxide dismutase from Staphylococcus equorum (MnSODSeq) maintains its activity upon treatments like a wide range of pH, addition of detergent and denaturing agent, exposure to ultraviolet light, and heating up to 50 °C. The enzyme dimer dissociates at 52-55 °C, while its monomer unfolds at 63-67 °C. MnSOD dimeric form is indispensable for the enzyme activity; therefore, strengthening the interactions between the monomers is the most preferred strategy to improve the enzyme stability. However, to date, modification of MnSODSeq at the dimer interface has been unfruitful despite excluding the inner and outer sphere regions that are important to the enzyme activity. Here, a new strategy was developed and K38R-A121E/Y double substitutions were proposed. These mutants displayed similar enzyme activity to the wild type. K38R-A121E dimer was thermally more stable and its monomer stability was similar to the wild type. The thermal stability of K38R-A121Y dimer was similar to the wild type but its monomer was thermally less stable. In addition, the structure of the previously reported L169W mutant was also elucidated. The L169W mutant structure showed that intramolecular modification can decrease flexibility of the MnSODSeq monomer and leads to a less stable enzyme with similar activity to the wild type. Thus, while the enzyme activity depends on arrangement of residues in the dimer interface, the stability appears to depend more on its monomeric architecture. Furthermore, in the L169W structure in complex with azide, which is a specific inhibitor for MnSOD, one of the azide molecules was present in the dimer interface region that previously has been identified to involve in the enzymatic reaction. Nevertheless, the present results show that an MnSODSeq mutant with better thermal stability has been obtained.
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Affiliation(s)
- Debbie S Retnoningrum
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Hiromi Yoshida
- Department of Basic Life Science, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-Cho, Kita-Gun, Kagawa, 761-0793, Japan
| | - Ismiana Pajatiwi
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Rahmat Muliadi
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Ratna A Utami
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Anita Artarini
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia.
| | - Wangsa T Ismaya
- Dexa Laboratories of Biomolecular Sciences, Dexa Medica, Industri Selatan V Blok PP-7, Cikarang, 17750, West Java, Indonesia
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2
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The Intestinal Redox System and Its Significance in Chemotherapy-Induced Intestinal Mucositis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7255497. [PMID: 35585883 PMCID: PMC9110227 DOI: 10.1155/2022/7255497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/12/2022]
Abstract
Chemotherapy-induced intestinal mucositis (CIM) is a significant dose-limiting adverse reaction brought on by the cancer treatment. Multiple studies reported that reactive oxygen species (ROS) is rapidly produced during the initial stages of chemotherapy, when the drugs elicit direct damage to intestinal mucosal cells, which, in turn, results in necrosis, mitochondrial dysfunction, and ROS production. However, the mechanism behind the intestinal redox system-based induction of intestinal mucosal injury and necrosis of CIM is still undetermined. In this article, we summarized relevant information regarding the intestinal redox system, including the composition and regulation of redox enzymes, ROS generation, and its regulation in the intestine. We innovatively proposed the intestinal redox “Tai Chi” theory and revealed its significance in the pathogenesis of CIM. We also conducted an extensive review of the English language-based literatures involving oxidative stress (OS) and its involvement in the pathological mechanisms of CIM. From the date of inception till July 31, 2021, 51 related articles were selected. Based on our analysis of these articles, only five chemotherapeutic drugs, namely, MTX, 5-FU, cisplatin, CPT-11, and oxaliplatin were shown to trigger the ROS-based pathological mechanisms of CIM. We also discussed the redox system-mediated modulation of CIM pathogenesis via elaboration of the relationship between chemotherapeutic drugs and the redox system. It is our belief that this overview of the intestinal redox system and its role in CIM pathogenesis will greatly enhance research direction and improve CIM management in the future.
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3
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MnSOD functions as a thermoreceptor activated by low temperature. J Inorg Biochem 2022; 229:111745. [DOI: 10.1016/j.jinorgbio.2022.111745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/22/2022] [Accepted: 01/22/2022] [Indexed: 11/20/2022]
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4
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Kumar R, Pandey B, Singh A, Rajaraman G. Mechanistic Insights into the Oxygen Atom Transfer Reactions by Nonheme Manganese Complex: A Computational Case Study on the Comparative Oxidative Ability of Manganese-Hydroperoxo vs High-Valent Mn IV═O and Mn IV-OH Intermediates. Inorg Chem 2021; 60:12085-12099. [PMID: 34293860 DOI: 10.1021/acs.inorgchem.1c01306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the comparative oxidative abilities of high-valent metal-oxo/hydroxo/hydroperoxo species holds the key to robust biomimic catalysts that perform desired organic transformations with very high selectivity and efficiency. The comparative oxidative abilities of popular high-valent iron-oxo and manganese-oxo species are often counterintuitive, for example, oxygen atom transfer (OAT) reaction by [(Me2EBC)MnIV-OOH]3+, [(Me2EBC)MnIV-OH]3+, and [(Me2EBC)MnIV═O]2+ (Me2EBC = 4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane) shows extremely high reactivity for MnIV-OOH species and no reactivity for MnIV-OH and MnIV═O species toward alkyl/aromatic sulfides. Using a combination of density functional theory (DFT) and ab initio domain-based local pair natural orbital coupled-cluster with single, double, and perturbative triples excitation (DLPNO-CCSD(T)) and complete-active space self-consistent field/N-electron valence perturbation theory second order (CASSCF/NEVPT2) calculations, here, we have explored the electronic structures and sulfoxidation mechanism of these species. Our calculations unveil that MnIV-OOH reacts through distal oxygen atom with the substrate via electron transfer (ET) mechanism with a very small kinetic barrier (16.5 kJ/mol), placing this species at the top among the best-known catalysts for such transformations. The MnIV-OH and MnIV═O species have a much larger barrier. The mechanism has also been found to switch from ET in the former to concerted in the latter, rendering both unreactive under the tested experimental conditions. Intrinsic differences in the electronic structures, such as the presence and absence of the multiconfigurational character coupled with the steric effects, are responsible for such variations observed. This comparative oxidative ability that runs contrary to the popular iron-oxo/hydroperoxo reactivity will have larger mechanistic implications in understanding the reactivity of biomimic catalysts and the underlying mechanisms in PSII.
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Affiliation(s)
- Ravi Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Bhawana Pandey
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Akta Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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5
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Nagibina GS, Melnik TN, Glukhova KA, Uversky VN, Melnik BS. Intrinsic disorder-based design of stable globular proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:157-186. [PMID: 32828465 DOI: 10.1016/bs.pmbts.2020.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Directed stabilization of globular proteins via substitution of a minimal number of amino acid residues is one of the most complicated experimental tasks. In this work, we have successfully used algorithms for the evaluation of intrinsic disorder predisposition (such as PONDR® FIT and IsUnstruct) as tools for searching for the weakened regions in structured globular proteins. We have shown that the weakened regions found by these programs as regions with highest levels of predicted intrinsic disorder predisposition are a suitable target for introduction of stabilizing mutations.
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Affiliation(s)
- Galina S Nagibina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Tatiana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Ksenia A Glukhova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia.
| | - Bogdan S Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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6
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Hou Z, Zhao L, Wang Y, Liao X. Purification and Characterization of Superoxide Dismutases from Sea Buckthorn and Chestnut Rose. J Food Sci 2019; 84:746-753. [PMID: 30861132 DOI: 10.1111/1750-3841.14441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 11/29/2022]
Abstract
Superoxide dismutases (SODs) were purified from sea buckthorn and chestnut rose by ammonium sulfate precipitation and anion-exchange chromatography, and the detection methods of water-soluble tetrazolium-1 (WST-1), nitrobluetetrazolium (NBT) and pyrogallol autoxidation (PA) for SOD activity were compared. WST-1 method was selected due to its coefficient of variation (CV) <6% in this study. Two SODs exhibited similar characteristics. Their molecular mass and isoelectric point were about 30 kDa and 4.8 to 5.0 estimated by electrophoresis, and the Km was 0.05 to 0.08 mmol/L, respectively. Dynamic light scattering analysis suggested their hydrodynamic radius distributes from 60 to 1500 nm. The activity of two SODs was unchanged at <80 °C or pH 2 to 9 or in simulated human gastric fluid. Their circular dichroism spectra suggested a main β-sheet structure, the fluorescence spectra reflected that the tryptophan residues of two SODs is partially exposed, these structures were rather stable at pH 2 to 9 or 50 to 90 °C. PRACTICAL APPLICATION: Superoxide dismutase (SOD) is an important antioxidant enzyme. SODs from sea buckthorn and chestnut rose were stable at high temperature or low pH or simulated gastric fluid. This result can provide a new approach for the potential application of SOD in the food and pharmaceutical fields.
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Affiliation(s)
- Zhiqiang Hou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Coll. of Food Science and Nutritional Engineering, China Agricultural Univ., Beijing, 100083, China.,Key Lab of Fruit and Vegetable Processing of Ministry of Agriculture, China Agricultural Univ., Beijing, 100083, China.,Beijing Key Laboratory for Food Non-thermal Processing, China Agricultural Univ., Beijing, 100083, China
| | - Liang Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Coll. of Food Science and Nutritional Engineering, China Agricultural Univ., Beijing, 100083, China.,Key Lab of Fruit and Vegetable Processing of Ministry of Agriculture, China Agricultural Univ., Beijing, 100083, China.,Beijing Key Laboratory for Food Non-thermal Processing, China Agricultural Univ., Beijing, 100083, China
| | - Yongtao Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Coll. of Food Science and Nutritional Engineering, China Agricultural Univ., Beijing, 100083, China.,Key Lab of Fruit and Vegetable Processing of Ministry of Agriculture, China Agricultural Univ., Beijing, 100083, China.,Beijing Key Laboratory for Food Non-thermal Processing, China Agricultural Univ., Beijing, 100083, China
| | - Xiaojun Liao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Coll. of Food Science and Nutritional Engineering, China Agricultural Univ., Beijing, 100083, China.,Key Lab of Fruit and Vegetable Processing of Ministry of Agriculture, China Agricultural Univ., Beijing, 100083, China.,Beijing Key Laboratory for Food Non-thermal Processing, China Agricultural Univ., Beijing, 100083, China
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7
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Costa RO, Ferreira SS, Pereira CA, Harmer JR, Noble CJ, Schenk G, Franco RWA, Resende JALC, Comba P, Roberts AE, Fernandes C, Horn A. A New Mixed-Valence Mn(II)Mn(III) Compound With Catalase and Superoxide Dismutase Activities. Front Chem 2018; 6:491. [PMID: 30456211 PMCID: PMC6231112 DOI: 10.3389/fchem.2018.00491] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/26/2018] [Indexed: 12/17/2022] Open
Abstract
The synthesis, X-ray molecular structure, physico-chemical characterization and dual antioxidant activity (catalase and superoxide dismutase) of a new polymeric mixed valence Mn(III)Mn(II) complex, containing the ligand H2BPClNOL (N-(2-hydroxybenzyl)-N-(2-pyridylmethyl)[(3-chloro)(2-hydroxy)] propylamine) is described. The monomeric unit is composed of a dinuclear Mn(II)Mn(III) moiety, [Mn(III)(μ-HBPClNOL)(μ-BPClNOL)Mn(II)(Cl)](ClO4)·2H2O, 1, in which the Mn ions are connected by two different bridging groups provided by two molecules of the ligand H2BPClNOL, a phenoxide and an alkoxide group. In the solid state, this mixed valence dinuclear unit is connected to its neighbors through chloro bridges. Magnetic measurements indicated the presence of ferromagnetic [J = +0.076(13) cm−1] and antiferromagnetic [J = −5.224(13) cm−1] interactions. The compound promotes O2•- dismutation in aqueous solution (IC50 = 0.370 μmol dm−3, kcat = 3.6x106 M−1 s−1). EPR studies revealed that a high-valent Mn(III)-O-Mn(IV) species is involved in the superoxide dismutation catalytic cycle. Complex 1 shows catalase activity only in the presence of a base, e.g., piperazine or triethylamine. Kinetic studies were carried out in the presence of piperazine and employing two different methods, resulting in kcat values of 0.58 ± 0.03 s−1 (detection of O2 production employing a Clark electrode) and 2.59 ± 0.12 s−1 (H2O2 consuption recorded via UV-Vis). EPR and ESI-(+)-MS studies indicate that piperazine induces the oxidation of 1, resulting in the formation of the catalytically active Mn(III)-O-Mn(IV) species.
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Affiliation(s)
- Rafael O Costa
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | | | - Crystiane A Pereira
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane, QLD, Australia
| | - Christopher J Noble
- Centre for Advanced Imaging, University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Roberto W A Franco
- Laboratório de Ciências Físicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Jackson A L C Resende
- Instituto de Ciências Exatas e da Terra, Campus Universitário do Araguaia, Universidade Federal do Mato Grosso, Barra do Garças, Brazil
| | - Peter Comba
- Anorganisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany.,Interdisziplinäres Zentrum für Wissenschaftliches Rechnen, Heidelberg, Germany
| | - Asha E Roberts
- Anorganisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany.,Interdisziplinäres Zentrum für Wissenschaftliches Rechnen, Heidelberg, Germany
| | - Christiane Fernandes
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Adolfo Horn
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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8
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Rashid GMM, Zhang X, Wilkinson RC, Fülöp V, Cottyn B, Baumberger S, Bugg TDH. Sphingobacterium sp. T2 Manganese Superoxide Dismutase Catalyzes the Oxidative Demethylation of Polymeric Lignin via Generation of Hydroxyl Radical. ACS Chem Biol 2018; 13:2920-2929. [PMID: 30247873 DOI: 10.1021/acschembio.8b00557] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sphingobacterium sp. T2 contains two extracellular manganese superoxide dismutase enzymes which exhibit unprecedented activity for lignin oxidation but via an unknown mechanism. Enzymatic treatment of lignin model compounds gave products whose structures were indicative of aryl-Cα oxidative cleavage and demethylation, as well as alkene dihydroxylation and alcohol oxidation. 18O labeling studies on the SpMnSOD-catalyzed oxidation of lignin model compound guiaiacylglycerol-β-guaiacyl ether indicated that the an oxygen atom inserted by the enzyme is derived from superoxide or peroxide. Analysis of an alkali lignin treated by SpMnSOD1 by quantitative 31P NMR spectroscopy demonstrated 20-40% increases in phenolic and aliphatic OH content, consistent with lignin demethylation and some internal oxidative cleavage reactions. Assay for hydroxyl radical generation using a fluorometric hydroxyphenylfluorescein assay revealed the release of 4.1 molar equivalents of hydroxyl radical by SpMnSOD1. Four amino acid replacements in SpMnSOD1 were investigated, and A31H or Y27H site-directed mutant enzymes were found to show no lignin demethylation activity according to 31P NMR analysis. Structure determination of the A31H and Y27H mutant enzymes reveals the repositioning of an N-terminal protein loop, leading to widening of a solvent channel at the dimer interface, which would provide increased solvent access to the Mn center for hydroxyl radical generation.
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Affiliation(s)
| | | | | | | | - Betty Cottyn
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS,
Université Paris-Saclay, 78000 Versailles, France
| | - Stéphanie Baumberger
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS,
Université Paris-Saclay, 78000 Versailles, France
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9
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Azadmanesh J, Borgstahl GEO. A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase. Antioxidants (Basel) 2018; 7:antiox7020025. [PMID: 29385710 PMCID: PMC5836015 DOI: 10.3390/antiox7020025] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/13/2018] [Accepted: 01/26/2018] [Indexed: 12/15/2022] Open
Abstract
Superoxide dismutases (SODs) are necessary antioxidant enzymes that protect cells from reactive oxygen species (ROS). Decreased levels of SODs or mutations that affect their catalytic activity have serious phenotypic consequences. SODs perform their bio-protective role by converting superoxide into oxygen and hydrogen peroxide by cyclic oxidation and reduction reactions with the active site metal. Mutations of SODs can cause cancer of the lung, colon, and lymphatic system, as well as neurodegenerative diseases such as Parkinson's disease and amyotrophic lateral sclerosis. While SODs have proven to be of significant biological importance since their discovery in 1968, the mechanistic nature of their catalytic function remains elusive. Extensive investigations with a multitude of approaches have tried to unveil the catalytic workings of SODs, but experimental limitations have impeded direct observations of the mechanism. Here, we focus on human MnSOD, the most significant enzyme in protecting against ROS in the human body. Human MnSOD resides in the mitochondrial matrix, the location of up to 90% of cellular ROS generation. We review the current knowledge of the MnSOD enzymatic mechanism and ongoing studies into solving the remaining mysteries.
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Affiliation(s)
- Jahaun Azadmanesh
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA.
| | - Gloria E O Borgstahl
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA.
- Eppley Institute for Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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10
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Demicheli V, Moreno DM, Radi R. Human Mn-superoxide dismutase inactivation by peroxynitrite: a paradigm of metal-catalyzed tyrosine nitration in vitro and in vivo. Metallomics 2018; 10:679-695. [DOI: 10.1039/c7mt00348j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nitration of human MnSOD at active site Tyr34 represents a biologically-relevant oxidative post-translational modification that causes enzyme inactivation.
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Affiliation(s)
- Verónica Demicheli
- Departmento de Bioquimica
- Facultad de Medicina
- Center for Free Radical and Biomedical Research
- Universidad de la República
- Montevideo
| | - Diego M. Moreno
- Instituto de Química Rosario (IQUIR, CONICET-UNR)
- Área Química General e Inorgánica
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Argentina
| | - Rafael Radi
- Departmento de Bioquimica
- Facultad de Medicina
- Center for Free Radical and Biomedical Research
- Universidad de la República
- Montevideo
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11
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Jing C, Haodong Z. Crystal structure of dinitrato-κ O-bis(tris((1 H-benzo[ d]imidazol-2-yl)methyl)amine-κ 4
N, N′, N′′, N′′′)-(μ 2-cyclohexane-1,4-dicarboxylato-κ 4
O, O′: O′′, O′′′)dimanganese(II) – methanol – water (1/6/2), C 62H 80Mn 2N 16O 18. Z KRIST-NEW CRYST ST 2017. [DOI: 10.1515/ncrs-2017-0029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C62H80Mn2N16O18, triclinic, P1̅ (no. 2), a = 11.3232(10) Å, b = 12.879(2) Å, c = 13.035(2) Å, α = 84.854(17)°, β = 69.317(16)°, γ = 73.929(13)°, V = 1708.8(4) Å3, Z = 1, R
gt(F) = 0.0320, wR
ref(F
2) = 0.0860, T = 113 K.
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Affiliation(s)
- Chen Jing
- Department of Chemistry, School of Science , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
| | - Zhang Haodong
- Department of Chemistry, School of Science , Tianjin University of Science and Technology , Tianjin 300457 , P. R. China
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12
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Ranawat P, Rawat S. Radiation resistance in thermophiles: mechanisms and applications. World J Microbiol Biotechnol 2017; 33:112. [DOI: 10.1007/s11274-017-2279-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/28/2022]
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13
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Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase. J Struct Biol 2017; 199:68-75. [PMID: 28461152 DOI: 10.1016/j.jsb.2017.04.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/10/2017] [Accepted: 04/27/2017] [Indexed: 01/22/2023]
Abstract
Superoxide dismutases (SODs) are enzymes that play a key role in protecting cells from toxic oxygen metabolites by disproportionation of two molecules of superoxide into molecular oxygen and hydrogen peroxide via cyclic reduction and oxidation at the active site metal. The azide anion is a potent competitive inhibitor that binds directly to the metal and is used as a substrate analog to superoxide in studies of SOD. The crystal structure of human MnSOD-azide complex was solved and shows the putative binding position of superoxide, providing a model for binding to the active site. Azide is bound end-on at the sixth coordinate position of the manganese ion. Tetrameric electrostatic surfaces were calculated incorporating accurate partial charges for the active site in three states, including a state with superoxide coordinated to the metal using the position of azide as a model. These show facilitation of the anionic ligand to the active site pit via a 'valley' of positively-charged surface patches. Surrounding ridges of negative charge help guide the superoxide anion. Within the active site pit, Arg173 and Glu162 further guide and align superoxide for efficient catalysis. Superoxide coordination at the sixth position causes the electrostatic surface of the active site pit to become nearly neutral. A model for electrostatic-mediated diffusion, and efficient binding of superoxide for catalysis is presented.
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14
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Fujikawa M, Kobayashi K, Tsutsui Y, Tanaka T, Kozawa T. Rational Tuning of Superoxide Sensitivity in SoxR, the [2Fe-2S] Transcription Factor: Implications of Species-Specific Lysine Residues. Biochemistry 2017; 56:403-410. [DOI: 10.1021/acs.biochem.6b01096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mayu Fujikawa
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Kazuo Kobayashi
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Yuko Tsutsui
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Takahiro Tanaka
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Takahiro Kozawa
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
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15
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Sensing the active site properties of enzymes as a function of the size of an effective peptidic environment using DFT reactivity parameters. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1980-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Demicheli V, Moreno DM, Jara GE, Lima A, Carballal S, Ríos N, Batthyany C, Ferrer-Sueta G, Quijano C, Estrı́n DA, Martí MA, Radi R. Mechanism of the Reaction of Human Manganese Superoxide Dismutase with Peroxynitrite: Nitration of Critical Tyrosine 34. Biochemistry 2016; 55:3403-17. [PMID: 27227512 DOI: 10.1021/acs.biochem.6b00045] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human Mn-containing superoxide dismutase (hMnSOD) is a mitochondrial enzyme that metabolizes superoxide radical (O2(•-)). O2(•-) reacts at diffusional rates with nitric oxide to yield a potent nitrating species, peroxynitrite anion (ONOO(-)). MnSOD is nitrated and inactivated in vivo, with active site Tyr34 as the key oxidatively modified residue. We previously reported a k of ∼1.0 × 10(5) M(-1) s(-1) for the reaction of hMnSOD with ONOO(-) by direct stopped-flow spectroscopy and the critical role of Mn in the nitration process. In this study, we further established the mechanism of the reaction of hMnSOD with ONOO(-), including the necessary re-examination of the second-order rate constant by an independent method and the delineation of the microscopic steps that lead to the regio-specific nitration of Tyr34. The redetermination of k was performed by competition kinetics utilizing coumarin boronic acid, which reacts with ONOO(-) at a rate of ∼1 × 10(6) M(-1) s(-1) to yield the fluorescence product, 7-hydroxycoumarin. Time-resolved fluorescence studies in the presence of increasing concentrations of hMnSOD provided a k of ∼1.0 × 10(5) M(-1) s(-1), fully consistent with the direct method. Proteomic analysis indicated that ONOO(-), but not other nitrating agents, mediates the selective modification of active site Tyr34. Hybrid quantum-classical (quantum mechanics/molecular mechanics) simulations supported a series of steps that involve the initial reaction of ONOO(-) with Mn(III) to yield Mn(IV) and intermediates that ultimately culminate in 3-nitroTyr34. The data reported herein provide a kinetic and mechanistic basis for rationalizing how MnSOD constitutes an intramitochondrial target for ONOO(-) and the microscopic events, with atomic level resolution, that lead to selective and efficient nitration of critical Tyr34.
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Affiliation(s)
- Verónica Demicheli
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Diego M Moreno
- Instituto de Química de Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Suipacha 531, S2002LRK Rosario, Argentina
| | - Gabriel E Jara
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Analía Lima
- Unidad Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Sebastián Carballal
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Natalia Ríos
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Departamento de Química Orgánica, Facultad de Química, Universidad de la República , Avda. General Flores 2124, Montevideo, Uruguay
| | - Carlos Batthyany
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Unidad Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Gerardo Ferrer-Sueta
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la Repúbica , Igua 4225, Montevideo, Uruguay
| | - Celia Quijano
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Darío A Estrı́n
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
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17
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Engineering a thermostable iron superoxide dismutase based on manganese superoxide dismutase from Thermus thermophilus. Process Biochem 2016. [DOI: 10.1016/j.procbio.2015.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Varga G, Csendes Z, Bajnóczi ÉG, Carlson S, Sipos P, Pálinkó I. Fe-amino acid complexes immobilized on silica gel as active and highly selective catalysts in cyclohexene epoxidation. RESEARCH ON CHEMICAL INTERMEDIATES 2015. [DOI: 10.1007/s11164-015-1920-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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RAO AR, DASH MANOSWINI, SAHU TANMAYAKUMAR, BEHERA BK, MOHAPATRA T. Detection of novel key residues of MnSOD enzyme and its role in salinity management across species. J Genet 2015. [DOI: 10.1007/s12041-014-0333-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Hunter GJ, Trinh CH, Bonetta R, Stewart EE, Cabelli DE, Hunter T. The structure of the Caenorhabditis elegans manganese superoxide dismutase MnSOD-3-azide complex. Protein Sci 2015; 24:1777-88. [PMID: 26257399 PMCID: PMC4622211 DOI: 10.1002/pro.2768] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 08/03/2015] [Indexed: 01/18/2023]
Abstract
C. elegans MnSOD-3 has been implicated in the longevity pathway and its mechanism of catalysis is relevant to the aging process and carcinogenesis. The structures of MnSOD-3 provide unique crystallographic evidence of a dynamic region of the tetrameric interface (residues 41-54). We have determined the structure of the MnSOD-3-azide complex to 1.77-Å resolution. Analysis of this complex shows that the substrate analog, azide, binds end-on to the manganese center as a sixth ligand and that it ligates directly to a third and new solvent molecule also positioned within interacting distance to the His30 and Tyr34 residues of the substrate access funnel. This is the first structure of a eukaryotic MnSOD-azide complex that demonstrates the extended, uninterrupted hydrogen-bonded network that forms a proton relay incorporating three outer sphere solvent molecules, the substrate analog, the gateway residues, Gln142, and the solvent ligand. This configuration supports the formation and release of the hydrogen peroxide product in agreement with the 5-6-5 catalytic mechanism for MnSOD. The high product dissociation constant k4 of MnSOD-3 reflects low product inhibition making this enzyme efficient even at high levels of superoxide.
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Affiliation(s)
- Gary J Hunter
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of MaltaMsida, Malta
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of LeedsLeeds, United Kingdom
| | - Rosalin Bonetta
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of MaltaMsida, Malta
| | - Emma E Stewart
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of LeedsLeeds, United Kingdom
| | - Diane E Cabelli
- Chemistry Department, Brookhaven National LaboratoryUpton, New York
| | - Therese Hunter
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of MaltaMsida, Malta
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21
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Rashid GMM, Taylor CR, Liu Y, Zhang X, Rea D, Fülöp V, Bugg TDH. Identification of Manganese Superoxide Dismutase from Sphingobacterium sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation. ACS Chem Biol 2015. [PMID: 26198187 DOI: 10.1021/acschembio.5b00298] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The valorization of aromatic heteropolymer lignin is an important unsolved problem in the development of a biomass-based biorefinery, for which novel high-activity biocatalysts are needed. Sequencing of the genomic DNA of lignin-degrading bacterial strain Sphingobacterium sp. T2 revealed no matches to known lignin-degrading genes. Proteomic matches for two manganese superoxide dismutase proteins were found in partially purified extracellular fractions. Recombinant MnSOD1 and MnSOD2 were both found to show high activity for oxidation of Organosolv and Kraft lignin, and lignin model compounds, generating multiple oxidation products. Structure determination revealed that the products result from aryl-Cα and Cα-Cβ bond oxidative cleavage and O-demethylation. The crystal structure of MnSOD1 was determined to 1.35 Å resolution, revealing a typical MnSOD homodimer harboring a five-coordinate trigonal bipyramidal Mn(II) center ligated by three His, one Asp, and a water/hydroxide in each active site. We propose that the lignin oxidation reactivity of these enzymes is due to the production of a hydroxyl radical, a highly reactive oxidant. This is the first demonstration that MnSOD is a microbial lignin-oxidizing enzyme.
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Affiliation(s)
- Goran M. M. Rashid
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Charles R. Taylor
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Yangqingxue Liu
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Xiaoyang Zhang
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Dean Rea
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vilmos Fülöp
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Timothy D. H. Bugg
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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22
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Jung M, Rentschler E. Magnetic and Spectroscopic Study on a New Asymmetric Mixed-valence Mn 2(II,III) Coordination Compound. Z Anorg Allg Chem 2015. [DOI: 10.1002/zaac.201500551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Chakraborty D, Taly A, Sterpone F. Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins. J Phys Chem B 2015; 119:12760-70. [PMID: 26335353 DOI: 10.1021/acs.jpcb.5b05791] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a systematic computational investigation of the internal hydration of a set of homologous proteins of different stability content and molecular complexities. The goal of the study is to verify whether structural water can be part of the molecular mechanisms ensuring enhanced stability in thermophilic enzymes. Our free-energy calculations show that internal hydration in the thermophilic variants is generally more favorable, and that the cumulated effect of wetting multiple sites results in a meaningful contribution to stability. Moreover, thanks to a more effective capability to retain internal water, some thermophilic proteins benefit by a systematic gain from internal wetting up to their optimal working temperature. Our work supports the idea that internal wetting can be viewed as an alternative molecular variable to be tuned for increasing protein stability.
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Affiliation(s)
- Debashree Chakraborty
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
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24
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Ribeiro TP, Fernandes C, Melo KV, Ferreira SS, Lessa JA, Franco RWA, Schenk G, Pereira MD, Horn A. Iron, copper, and manganese complexes with in vitro superoxide dismutase and/or catalase activities that keep Saccharomyces cerevisiae cells alive under severe oxidative stress. Free Radic Biol Med 2015; 80:67-76. [PMID: 25511255 DOI: 10.1016/j.freeradbiomed.2014.12.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 11/24/2014] [Accepted: 12/01/2014] [Indexed: 12/31/2022]
Abstract
Due to their aerobic lifestyle, eukaryotic organisms have evolved different strategies to overcome oxidative stress. The recruitment of some specific metalloenzymes such as superoxide dismutases (SODs) and catalases (CATs) is of great importance for eliminating harmful reactive oxygen species (hydrogen peroxide and superoxide anion). Using the ligand HPClNOL {1-[bis(pyridin-2-ylmethyl)amino]-3-chloropropan-2-ol}, we have synthesized three coordination compounds containing iron(III), copper(II), and manganese(II) ions, which are also present in the active site of the above-noted metalloenzymes. These compounds were evaluated as SOD and CAT mimetics. The manganese and iron compounds showed both SOD and CAT activities, while copper showed only SOD activity. The copper and manganese in vitro SOD activities are very similar (IC50~0.4 μmol dm(-3)) and about 70-fold higher than those of iron. The manganese compound showed CAT activity higher than that of the iron species. Analyzing their capacity to protect Saccharomyces cerevisiae cells against oxidative stress (H2O2 and the O2(•-) radical), we observed that all compounds act as antioxidants, increasing the resistance of yeast cells mainly due to a reduction of lipid oxidation. Especially for the iron compound, the data indicate complete protection when wild-type cells were exposed to H2O2 or O2(•-) species. Interestingly, these compounds also compensate for both superoxide dismutase and catalase deficiencies; their antioxidant activity is metal ion dependent, in the order iron(III)>copper(II)>manganese(II). The protection mechanism employed by the complexes proved to be independent of the activation of transcription factors (such as Yap1, Hsf1, Msn2/Msn4) and protein synthesis. There is no direct relation between the in vitro and the in vivo antioxidant activities.
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Affiliation(s)
- Thales P Ribeiro
- Laboratório de Citotoxicidade e Genotoxicidade, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-909, RJ, Brazil
| | - Christiane Fernandes
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro - Campos dos Goytacazes, 28013-602, RJ, Brazil
| | - Karen V Melo
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro - Campos dos Goytacazes, 28013-602, RJ, Brazil
| | - Sarah S Ferreira
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro - Campos dos Goytacazes, 28013-602, RJ, Brazil
| | - Josane A Lessa
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro - Campos dos Goytacazes, 28013-602, RJ, Brazil
| | - Roberto W A Franco
- Laboratório de Ciência Físicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro - Campos dos Goytacazes, 28013-602, RJ, Brazil
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Marcos D Pereira
- Laboratório de Citotoxicidade e Genotoxicidade, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-909, RJ, Brazil.
| | - Adolfo Horn
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro - Campos dos Goytacazes, 28013-602, RJ, Brazil.
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25
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Manganese superoxide dismutase from human pathogen Clostridium difficile. Amino Acids 2015; 47:987-95. [PMID: 25655385 DOI: 10.1007/s00726-015-1927-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/21/2015] [Indexed: 01/05/2023]
Abstract
Clostridium difficile is a human pathogen that causes severe antibiotic-associated Clostridium difficile infection (CDI). Herein the MnSODcd from C. difficile was cloned, expressed in Escherichia Coli,and characterized by X-ray crystallography, UV/Vis and EPR spectroscopy, and activity assay, et al. The crystal structure of MnSODcd (2.32 Å) reveals a manganese coordination geometry of distorted trigonal bipyramidal, with His111, His197 and Asp193 providing the equatorial ligands and with His56 and a hydroxide or water forming the axial ligands. The catalytic activity of MnSODcd (8,600 U/mg) can be effectively inhibited by 2-methoxyestradiol with an IC50 of 75 μM. The affinity investigation between 2-methoxyestradiol and MnSODcd by ITC indicated a binding constant of 8.6 μM with enthalpy changes (ΔH = -4.08 ± 0.03 kcal/mol, ΔS = 9.53 ± 0.02 cal/mol/deg). An inhibitory mechanism of MnSODcd by 2-methoxyestradiol was probed and proposed based on molecular docking models and gel filtration analysis. The 2-methoxyestradiol may bind MnSODcd to interfere with the cross-linking between the two active sites of the dimer enzyme, compromising the SOD activity. These results provide valuable insight into the rational design of MnSODcd inhibitors for potential therapeutics for CDI.
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26
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Sheng Y, Abreu IA, Cabelli DE, Maroney MJ, Miller AF, Teixeira M, Valentine JS. Superoxide dismutases and superoxide reductases. Chem Rev 2014; 114:3854-918. [PMID: 24684599 PMCID: PMC4317059 DOI: 10.1021/cr4005296] [Citation(s) in RCA: 587] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Yuewei Sheng
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
| | - Isabel A. Abreu
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- Instituto
de Biologia Experimental e Tecnológica, Av. da República,
Qta. do Marquês, Estação Agronómica Nacional,
Edificio IBET/ITQB, 2780-157, Oeiras, Portugal
| | - Diane E. Cabelli
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Michael J. Maroney
- Department
of Chemistry, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Anne-Frances Miller
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Miguel Teixeira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Joan Selverstone Valentine
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
- Department
of Bioinspired Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
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27
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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28
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Merlino A, Russo Krauss I, Castellano I, Ruocco MR, Capasso A, De Vendittis E, Rossi B, Sica F. Structural and denaturation studies of two mutants of a cold adapted superoxide dismutase point to the importance of electrostatic interactions in protein stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:632-40. [DOI: 10.1016/j.bbapap.2014.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 01/07/2014] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
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29
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Haikarainen T, Frioux C, Zhnag LQ, Li DC, Papageorgiou AC. Crystal structure and biochemical characterization of a manganese superoxide dismutase from Chaetomium thermophilum. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:422-9. [PMID: 24316252 DOI: 10.1016/j.bbapap.2013.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 11/20/2013] [Accepted: 11/23/2013] [Indexed: 10/25/2022]
Abstract
A manganese superoxide dismutase from the thermophilic fungus Chaetomium thermophilum (CtMnSOD) was expressed in Pichia pastoris and purified to homogeneity. Its optimal temperature was 60°C with approximately 75% of its activity retained after incubation at 70°C for 60min. Recombinant yeast cells carrying C. thermophilum mnsod gene exhibited higher stress resistance to salt and oxidative stress-inducing agents than control yeast cells. In an effort to provide structural insights, CtMnSOD was crystallized and its structure was determined at 2.0Å resolution. The overall architecture of CtMnSOD was found similar to other MnSODs with highest structural similarities obtained against a MnSOD from the thermotolerant fungus Aspergillus fumigatus. In order to explain its thermostability, structural and sequence analysis of CtMnSOD with other MnSODs was carried out. An increased number of charged residues and an increase in the number of intersubunit salt bridges and the Thr:Ser ratio were identified as potential reasons for the thermostability of CtMnSOD.
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Affiliation(s)
- Teemu Haikarainen
- Turku Centre for Biotechnology, University of Turku, BioCity, Turku 20521, Finland; Åbo Akademi University, BioCity, Turku 20521, Finland
| | - Clémence Frioux
- Turku Centre for Biotechnology, University of Turku, BioCity, Turku 20521, Finland; Åbo Akademi University, BioCity, Turku 20521, Finland
| | - Li-Qing Zhnag
- Department of Environmental Biology, Shandong Agricultural University, Taian, Shandong 271018, China; Department of Chemistry and Chemical Engineering, Taishan Medical College, Taian, Shandong 271016, China
| | - Duo-Chuan Li
- Department of Environmental Biology, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Anastassios C Papageorgiou
- Turku Centre for Biotechnology, University of Turku, BioCity, Turku 20521, Finland; Åbo Akademi University, BioCity, Turku 20521, Finland.
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30
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Raghavan PS, Rajaram H, Apte SK. N-terminal processing of membrane-targeted MnSOD and formation of multiple active superoxide dismutase dimers in the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC7120. FEBS J 2013; 280:4827-38. [PMID: 23895424 DOI: 10.1111/febs.12455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/24/2013] [Indexed: 11/30/2022]
Abstract
Anabaena sp. strain PCC7120 expresses a 30 kDa manganese-dependent superoxide dismutase (MnSOD) comprising a hydrophobic region (signal peptide + linker peptide) attached to a catalytic unit. Bioinformatics predicted cleavage of the signal peptide at (25)CQPQ by signal peptidase and of the linker peptide by an Arg-C-like protease at the Arg52/Arg59 residue. The three predicted forms of MnSOD were immunodetected in Anabaena, with the 30 kDa MnSOD found exclusively in the membrane and the shorter 27 and 24 kDa forms found both in the membrane and soluble fractions. The corresponding sodA gene was truncated for (a) the first eight residues, or, (b) the signal peptide, or (c) the entire hydrophobic region, or (d) the Arg52/Arg59 residues were modified to serine. Overexpression of these MnSOD variants in recombinant Anabaena strains revealed that (a) the 30 kDa membrane-targeted MnSOD was cleaved by membrane-localized signal peptidase either during or after its transport through the membrane to release the 27 kDa form, either in the cytosol or in the periplasmic/thylakoid lumen, (b) the 27 kDa form was further cleaved to the 24 kDa form by Arg-C-like protease, both in the cytosol and in the periplasmic/thylakoid lumen, (c) deletion of signal peptide localized the MnSOD forms in the cytosol, and (d) alteration of the signal/linker peptide cleavage sites interfered with MnSOD localization and processing. Homo/heterodimerization of the 24 and 27 kDa forms of MnSOD and the cytosolic iron-dependent SOD results in multiple SOD activities, from a single MnSOD gene (sodA), in different cellular compartments of Anabaena.
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Mandelli F, Franco Cairo J, Citadini A, Büchli F, Alvarez T, Oliveira R, Leite V, Paes Leme A, Mercadante A, Squina F. The characterization of a thermostable and cambialistic superoxide dismutase from Thermus filiformis. Lett Appl Microbiol 2013; 57:40-6. [DOI: 10.1111/lam.12071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/15/2013] [Accepted: 03/15/2013] [Indexed: 01/06/2023]
Affiliation(s)
- F. Mandelli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas Brazil
- Departamento de Ciência de Alimentos da Faculdade de Engenharia de Alimentos; UNICAMP; Campinas Brazil
| | - J.P.L. Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas Brazil
| | - A.P.S. Citadini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas Brazil
| | - F. Büchli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas Brazil
| | - T.M. Alvarez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas Brazil
| | - R.J. Oliveira
- Departamento de Física; Instituto de Biociências, Letras e Ciências Exatas; Universidade Estadual Paulista; São José do Rio Preto Brazil
| | - V.B.P. Leite
- Departamento de Física; Instituto de Biociências, Letras e Ciências Exatas; Universidade Estadual Paulista; São José do Rio Preto Brazil
| | - A.F. Paes Leme
- Laboratório Nacional de Biociências (LNBio); do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas Brazil
| | - A.Z. Mercadante
- Departamento de Ciência de Alimentos da Faculdade de Engenharia de Alimentos; UNICAMP; Campinas Brazil
| | - F.M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE); do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM); Campinas Brazil
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Jackson TA, Gutman CT, Maliekal J, Miller AF, Brunold TC. Geometric and electronic structures of manganese-substituted iron superoxide dismutase. Inorg Chem 2013; 52:3356-67. [PMID: 23461587 PMCID: PMC3974275 DOI: 10.1021/ic302867y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The active-site structures of the oxidized and reduced forms of manganese-substituted iron superoxide dismutase (Mn(Fe)SOD) are examined, for the first time, using a combination of spectroscopic and computational methods. On the basis of electronic absorption, circular dichroism (CD), magnetic CD (MCD), and variable-temperature variable-field MCD data obtained for oxidized Mn(Fe)SOD, we propose that the active site of this species is virtually identical to that of wild-type manganese SOD (MnSOD), with both containing a metal ion that resides in a trigonal bipyramidal ligand environment. This proposal is corroborated by quantum mechanical/molecular mechanical (QM/MM) computations performed on complete protein models of Mn(Fe)SOD in both its oxidized and reduced states and, for comparison, wild-type (WT) MnSOD. The major differences between the QM/MM optimized active sites of WT MnSOD and Mn(Fe)SOD are a smaller (His)N-Mn-N(His) equatorial angle and a longer (Gln146(69))NH···O(sol) H-bond distance in the metal-substituted protein. Importantly, these modest geometric differences are consistent with our spectroscopic data obtained for the oxidized proteins and high-field electron paramagnetic resonance spectra reported previously for reduced Mn(Fe)SOD and MnSOD. As Mn(Fe)SOD exhibits a reduction midpoint potential (E(m)) almost 700 mV higher than that of MnSOD, which has been shown to be sufficient for explaining the lack of SOD activity displayed by the metal-subtituted species (Vance, C. K.; Miller, A. F. Biochemistry 2001, 40, 13079-13087), E(m)'s were computed for our experimentally validated QM/MM optimized models of Mn(Fe)SOD and MnSOD. These computations properly reproduce the experimental trend and reveal that the drastically elevated E(m) of the metal substituted protein stems from a larger separation between the second-sphere Gln residue and the coordinated solvent in Mn(Fe)SOD relative to MnSOD, which causes a weakening of the corresponding H-bond interaction in the oxidized state and alleviates steric crowding in the reduced state.
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Affiliation(s)
| | | | - James Maliekal
- Department of Chemistry, University of Kentucky, Lexington, KY 40506
| | | | - Thomas C. Brunold
- To whom correspondence should be addressed: 1101 University Ave., Madison, WI 53706, phone: (608) 265-9056, fax: (608) 262-6143,
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Dhar SK, St Clair DK. Manganese superoxide dismutase regulation and cancer. Free Radic Biol Med 2012; 52:2209-22. [PMID: 22561706 DOI: 10.1016/j.freeradbiomed.2012.03.009] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 03/06/2012] [Accepted: 03/06/2012] [Indexed: 01/03/2023]
Abstract
Mitochondria are the power plants of the eukaryotic cell and the integrators of many metabolic activities and signaling pathways important for the life and death of a cell. Normal aerobic cells use oxidative phosphorylation to generate ATP, which supplies energy for metabolism. To drive ATP production, electrons are passed along the electron transport chain, with some leaking as superoxide during the process. It is estimated that, during normal respiration, intramitochondrial superoxide concentrations can reach 10⁻¹² M. This extremely high level of endogenous superoxide production dictates that mitochondria are equipped with antioxidant systems that prevent consequential oxidative injury to mitochondria and maintain normal mitochondrial functions. The major antioxidant enzyme that scavenges superoxide anion radical in mitochondria is manganese superoxide dismutase (MnSOD). Extensive studies on MnSOD have demonstrated that MnSOD plays a critical role in the development and progression of cancer. Many human cancer cells harbor low levels of MnSOD proteins and enzymatic activity, whereas some cancer cells possess high levels of MnSOD expression and activity. This apparent variation in MnSOD level among cancer cells suggests that differential regulation of MnSOD exists in cancer cells and that this regulation may be linked to the type and stage of cancer development. This review summarizes current knowledge of the relationship between MnSOD levels and cancer with a focus on the mechanisms regulating MnSOD expression.
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Affiliation(s)
- Sanjit Kumar Dhar
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY 40536, USA
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Isobe K, Kataoka M, Ogawa J, Hasegawa J, Shimizu S. Microbial oxidases catalyzing conversion of glycolaldehyde into glyoxal. N Biotechnol 2011; 29:177-82. [PMID: 21820089 DOI: 10.1016/j.nbt.2011.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 04/26/2011] [Accepted: 05/10/2011] [Indexed: 10/18/2022]
Abstract
The present paper reviews oxidases catalyzing conversion of glycolaldehyde into glyoxal. The enzymatic oxidation of glycolaldehyde into glyoxal was first reported in alcohol oxidases (AODs) from methylotrophic yeasts such as Candida and Pichia, and glycerol oxidase (GLOD) from Aspergillus japonicus, although it had been reported that these enzymes are specific to short-chain linear aliphatic alcohols and glycerol, respectively. These enzymes continuously oxidized ethylene glycol into glyoxal via glycolaldehyde. The AODs produced by Aspergillus ochraceus and Penicillium purpurescens also oxidized glycolaldehyde. A new enzyme exhibiting oxidase activity for glycolaldehyde was reported from a newly isolated bacterium, Paenibacillus sp. AIU 311. The Paenibacillus enzyme exhibited high activity for aldehyde alcohols such as glycolaldehyde and glyceraldehyde, but not for methanol, ethanol, ethylene glycol or glycerol. The deduced amino acid sequence of the Paenibacillus AOD was similar to that of superoxide dismutases (SODs), but not to that of methylotrophic yeast AODs. Then, it was demonstrated that SODs had oxidase activity for aldehyde alcohols including glycolaldehyde. The present paper describes characteristics of glycolaldehyde oxidation by those enzymes produced by different microorganisms.
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Affiliation(s)
- Kimiyasu Isobe
- Department of Biological Chemistry and Food Science, Iwate University, Ueda-3, Morioka 020-8550, Japan.
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35
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The characterization of Thermotoga maritima ferritin reveals an unusual subunit dissociation behavior and efficient DNA protection from iron-mediated oxidative stress. Extremophiles 2011; 15:431-9. [DOI: 10.1007/s00792-011-0374-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 03/31/2011] [Indexed: 11/26/2022]
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Abstract
The calcium ion (Ca(2+)) is the main second messenger that helps to transmit depolarization status and synaptic activity to the biochemical machinery of a neuron. These features make Ca(2+) regulation a critical process in neurons, which have developed extensive and intricate Ca(2+) signaling pathways. High intensity Ca(2+) signaling necessitates high ATP consumption to restore basal (low) intracellular Ca(2+) levels after Ca(2+) influx through plasma membrane receptor and voltage-dependent ion channels. Ca(2+) influx may also lead to increased generation of mitochondrial reactive oxygen species (ROS). Impaired abilities of neurons to maintain cellular energy levels and to suppress ROS may impact Ca(2+) signaling during aging and in neurodegenerative disease processes. This review focuses on mitochondrial and endoplasmic reticulum Ca(2+) homeostasis and how they relate to synaptic Ca(2+) signaling processes, neuronal energy metabolism, and ROS generation. Also, the contribution of altered Ca(2+) signaling to neurodegeneration during aging will be considered. Advances in understanding the molecular regulation of Ca(2+) homeostasis and how it is perturbed in neurological disorders may lead to therapeutic strategies that modulate neuronal Ca(2+) signaling to enhance function and counteract disease processes.
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Affiliation(s)
- Marc Gleichmann
- Laboratory of Neurosciences, National Institute on Aging, Baltimore, Maryland, USA.
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Nakamura T, Torikai K, Uegaki K, Morita J, Machida K, Suzuki A, Kawata Y. Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 - insights into the enzyme mechanism and stability. FEBS J 2010; 278:598-609. [DOI: 10.1111/j.1742-4658.2010.07977.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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38
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Exploring the molecular basis of human manganese superoxide dismutase inactivation mediated by tyrosine 34 nitration. Arch Biochem Biophys 2010; 507:304-9. [PMID: 21167124 DOI: 10.1016/j.abb.2010.12.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 11/17/2010] [Accepted: 12/09/2010] [Indexed: 11/23/2022]
Abstract
Manganese Superoxide Dismutase (MnSOD) is an essential mitochondrial antioxidant enzyme that protects organisms against oxidative damage, dismutating superoxide radical (O₂(.)⁻) into H₂O₂ and O₂. The active site of the protein presents a Mn ion in a distorted trigonal-bipyramidal environment, coordinated by H26, H74, H163, D159 and one ⁻OH ion or H₂O molecule. The catalytic cycle of the enzyme is a "ping-pong" mechanism involving Mn³+/Mn²+. It is known that nitration of Y34 is responsible for enzyme inactivation, and that this protein oxidative modification is found in tissues undergoing inflammatory and degenerative processes. However, the molecular basis about MnSOD tyrosine nitration affects the protein catalytic function is mostly unknown. In this work we strongly suggest, using computer simulation tools, that Y34 nitration affects protein function by restricting ligand access to the active site. In particular, deprotonation of 3-nitrotyrosine increases drastically the energetic barrier for ligand entry due to the absence of the proton. Our results for the WT and selected mutant proteins confirm that the phenolic moiety of Y34 plays a key role in assisting superoxide migration.
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Agari Y, Kuramitsu S, Shinkai A. Identification of novel genes regulated by the oxidative stress-responsive transcriptional activator SdrP in Thermus thermophilus HB8. FEMS Microbiol Lett 2010; 313:127-34. [PMID: 21054499 DOI: 10.1111/j.1574-6968.2010.02133.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The stationary phase-dependent regulatory protein (SdrP) from the extremely thermophilic bacterium, Thermus thermophilus HB8, a CRP/FNR family protein, is a transcription activator, whose expression increases in the stationary phase of growth. SdrP positively regulates the expression of several genes involved in nutrient and energy supply, redox control, and nucleic acid metabolism. We found that sdrP mRNA showed an increased response to various environmental or chemical stresses in the logarithmic growth phase, the most effective stress being oxidative stress. From genome-wide expression pattern analysis using 306 DNA microarray datasets from 117 experimental conditions, eight new SdrP-regulated genes were identified among the genes whose expression was highly correlated with that of sdrP. The gene products included manganese superoxide dismutase, catalase, and excinuclease ABC subunit B (UvrB), which plays a central role in the nucleotide excision repair of damaged DNA. Expression of these genes also tended to increase upon entry into stationary phase, as in the case of the previously identified SdrP-regulated genes. These results indicate that the main function of SdrP is in the oxidative stress response.
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Porta J, Vahedi-Faridi A, Borgstahl GE. Structural Analysis of Peroxide-Soaked MnSOD Crystals Reveals Side-On Binding of Peroxide to Active-Site Manganese. J Mol Biol 2010; 399:377-84. [DOI: 10.1016/j.jmb.2010.04.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/24/2010] [Accepted: 04/18/2010] [Indexed: 10/19/2022]
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Osawa M, Yamakura F, Mihara M, Okubo Y, Yamada K, Hiraoka BY. Conversion of the metal-specific activity of Escherichia coli Mn-SOD by site-directed mutagenesis of Gly165Thr. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1775-9. [PMID: 20451673 DOI: 10.1016/j.bbapap.2010.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2009] [Revised: 04/03/2010] [Accepted: 04/26/2010] [Indexed: 11/27/2022]
Abstract
Glycine 165, which is located near the active site metal, is mostly conserved in aligned amino acid sequences of manganese-containing superoxide dismutase (Mn-SOD) proteins, but is substituted to threonine in most iron-containing SODs (Fe-SODs). Because threonine 165 is located between Trp128 and Trp130, and Trp128 is one of the metal-surrounding aromatic amino acids, the conversion of this amino acid may affect the metal-specific activity of Escherichia coli Mn-SOD. In order to clarify this possibility, we prepared a mutant of E. coli Mn-SOD with the replacement of Gly165 by Thr. The ratio of the specific activities of Mn- to Fe-reconstituted enzyme increased from 0.006 in the wild-type to 0.044 in the mutant SOD; therefore, the metal-specific SOD was converted to a metal-tolerant SOD. The visible absorption spectra of the Fe- and Mn-reconstituted mutant SODs indicated the loss of Mn-SOD character. It was concluded that Gly at position 165 plays a catalytic role in maintaining the integrity of the metal specificity of Mn-SOD.
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Affiliation(s)
- Masaki Osawa
- Department of Hard Tissue Research, Graduate School of Oral Medicine, Matsumoto Dental University, Shiojiri 3990781, Japan
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42
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Moreno D, Daier V, Palopoli C, Tuchagues JP, Signorella S. Synthesis, characterization and antioxidant activity of water soluble MnIII complexes of sulphonato-substituted Schiff base ligands. J Inorg Biochem 2010; 104:496-502. [DOI: 10.1016/j.jinorgbio.2009.12.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 11/24/2022]
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43
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Sasaki Y, Kataoka M, Urano N, Ogawa J, Iwasaki A, Hasegawa J, Isobe K, Shimizu S. Cloning, sequencing and expression analysis of a gene encoding alcohol oxidase in Paenibacillus sp. AIU 311. J Biosci Bioeng 2010; 110:147-51. [PMID: 20547358 DOI: 10.1016/j.jbiosc.2010.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/23/2010] [Accepted: 01/25/2010] [Indexed: 11/19/2022]
Abstract
We have cloned a gene encoding an alcohol oxidase (AOD) specific to aldehyde alcohols from Paenibacillus sp. AIU 311. The AOD gene contains an open reading frame consisting of 618 nucleotides corresponding to 205 amino acid residues. The deduced amino acid sequence exhibits a high similarity to that of manganese superoxide dismutases (SODs). We expressed the cloned gene as an active product in Escherichia coli BL21 cells. The productivity (total units per culture broth volume) of the recombinant AOD expressed in E. coli BL21 is 26,000-fold higher than that of AOD in Paenibacillus sp. AIU 311. The recombinant AOD also exhibits aldehyde alcohol oxidase activity and SOD activity. The recombinant cells described in this study have utility for the production of glyoxal from glycolaldehyde.
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Affiliation(s)
- Yasutaka Sasaki
- The United Graduate School of Agricultural Sciences, Iwate University, 18-8, Ueda 3-chome, Morioka 020-8550, Japan
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44
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Perry J, Shin D, Getzoff E, Tainer J. The structural biochemistry of the superoxide dismutases. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:245-62. [PMID: 19914407 PMCID: PMC3098211 DOI: 10.1016/j.bbapap.2009.11.004] [Citation(s) in RCA: 322] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 01/11/2023]
Abstract
The discovery of superoxide dismutases (SODs), which convert superoxide radicals to molecular oxygen and hydrogen peroxide, has been termed the most important discovery of modern biology never to win a Nobel Prize. Here, we review the reasons this discovery has been underappreciated, as well as discuss the robust results supporting its premier biological importance and utility for current research. We highlight our understanding of SOD function gained through structural biology analyses, which reveal important hydrogen-bonding schemes and metal-binding motifs. These structural features create remarkable enzymes that promote catalysis at faster than diffusion-limited rates by using electrostatic guidance. These architectures additionally alter the redox potential of the active site metal center to a range suitable for the superoxide disproportionation reaction and protect against inhibition of catalysis by molecules such as phosphate. SOD structures may also control their enzymatic activity through product inhibition; manipulation of these product inhibition levels has the potential to generate therapeutic forms of SOD. Markedly, structural destabilization of the SOD architecture can lead to disease, as mutations in Cu,ZnSOD may result in familial amyotrophic lateral sclerosis, a relatively common, rapidly progressing and fatal neurodegenerative disorder. We describe our current understanding of how these Cu,ZnSOD mutations may lead to aggregation/fibril formation, as a detailed understanding of these mechanisms provides new avenues for the development of therapeutics against this so far untreatable neurodegenerative pathology.
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Affiliation(s)
- J.J.P. Perry
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The School of Biotechnology, Amrita University, Kollam, Kerala 690525, India
| | - D.S. Shin
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - E.D. Getzoff
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J.A. Tainer
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Yeguas V, Campomanes P, López R. Reactivity of a rhenium hydroxo–carbonyl complex toward carbon disulfide: insights from theory. Dalton Trans 2010; 39:874-82. [DOI: 10.1039/b915766b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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46
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Tabares LC, Gätjens J, Un S. Understanding the influence of the protein environment on the Mn(II) centers in Superoxide Dismutases using High-Field Electron Paramagnetic Resonance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:308-17. [PMID: 19818880 DOI: 10.1016/j.bbapap.2009.09.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 09/16/2009] [Accepted: 09/23/2009] [Indexed: 01/20/2023]
Abstract
One of the most puzzling questions of manganese and iron superoxide dismutases (SODs) is what is the basis for their metal-specificity. This review summarizes our findings on the Mn(II) electronic structure of SODs and related synthetic models using high-field high-frequency electron paramagnetic resonance (HFEPR), a technique that is able to achieve a very detailed and quantitative information about the electronic structure of the Mn(II) ions. We have used HFEPR to compare eight different SODs, including iron, manganese and cambialistic proteins. This comparative approach has shown that in spite of their high structural homology each of these groups have specific spectroscopic and biochemical characteristics. This has allowed us to develop a model about how protein and metal interactions influence protein pK, inhibitor binding and the electronic structure of the manganese center. To better appreciate the thermodynamic prerequisites required for metal discriminatory SOD activity and their relationship to HFEPR spectroscopy, we review the work on synthetic model systems that functionally mimic Mn-and FeSOD. Using a single ligand framework, it was possible to obtain metal-discriminatory "activity" as well as variations in the HFEPR spectra that parallel those found in the proteins. Our results give new insights into protein-metal interactions from the perspective of the Mn(II) and new steps towards solving the puzzle of metal-specificity in SODs.
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Affiliation(s)
- Leandro C Tabares
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
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47
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Whittaker MM, Whittaker JW. In vitro metal uptake by recombinant human manganese superoxide dismutase. Arch Biochem Biophys 2009; 491:69-74. [PMID: 19755112 DOI: 10.1016/j.abb.2009.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 09/05/2009] [Accepted: 09/09/2009] [Indexed: 01/18/2023]
Abstract
Metal uptake by the antioxidant defense metalloenzyme manganese superoxide dismutase (MnSOD) is an essential step in the functional maturation of the protein that is just beginning to be investigated in detail. We have extended earlier in vitro studies on metal binding by the dimeric Escherichia coli apo-MnSOD to investigate the mechanism of metal uptake by tetrameric human and Thermus thermophilus apo-MnSODs. Like the E. coli apo-MnSOD, these proteins also bind metal ions in vitro in a thermally activated, pH-sensitive process. However, metal uptake by the tetrameric apo-MnSODs exhibits a number of important differences. In particular, there is no indication of conformational gating requirement for metal binding for these proteins, and the reaction is first-order in metal ion. The high concentration of metal ion that is required to achieve physiologically relevant metallation rates for tetrameric human apo-MnSOD in vitro suggests the possibility that co-translational metal binding or chaperone interactions may be required in vivo.
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Affiliation(s)
- Mei M Whittaker
- Department of Science and Engineering, Division of Environmental and Biomolecular Systems, School of Medicine, Oregon Health and Science University, Beaverton, OR 97006-8921, USA
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48
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Lee HI, Lee JW, Yang TC, Kang SO, Hoffman BM. ENDOR and ESEEM investigation of the Ni-containing superoxide dismutase. J Biol Inorg Chem 2009; 15:175-82. [DOI: 10.1007/s00775-009-0581-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 08/14/2009] [Indexed: 11/28/2022]
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49
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Wang T, Qiu A, Meng F, Zhou H. Changing the metal binding specificity of superoxide dismutase from Thermus thermophilus HB-27 by a single mutation. Mol Biotechnol 2009; 42:146-53. [PMID: 19191037 DOI: 10.1007/s12033-009-9149-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 01/20/2009] [Indexed: 11/24/2022]
Abstract
Metal binding of superoxide dismutase from Thermus thermophilus HB27 was analyzed by comparing the related structures and sequences from different origins. Mutants (Ile166Leu, Asp167Glu, and Ile166Leu-Asp167Glu) were prepared and characterized. The mutants Asp167Glu and Ile166Leu-Asp167Glu changed their binding specificities from manganese to iron, which were manifested by the differences in color of the enzyme solutions and by flame atomic absorption analysis. Specific activities of the three mutants were 112, 52, and 62% of that of the wild-type enzyme, respectively. Asp167Glu and Ile166Leu-Asp167Glu only retained 6.8 and 6.1%, respectively, of the original activities after dialysis against 1 mM EDTA. Tryptophan fluorescence measurement and native gel electrophoresis implied that the three mutants could fold into a less condensed structure. Their folding and changes in the ion binding sites of the modeled structures might be the reason for their low affinities to metal ions. These findings increased our understanding of metal binding specificity of superoxide dismutase.
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Affiliation(s)
- Tianwen Wang
- Jiangnan University, Wuxi, Jiangsu, People's Republic of China.
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50
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Trinh CH, Hunter T, Stewart EE, Phillips SEV, Hunter GJ. Purification, crystallization and X-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:1110-4. [PMID: 19052361 PMCID: PMC2593702 DOI: 10.1107/s1744309108037056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 11/10/2008] [Indexed: 11/29/2022]
Abstract
Caenorhabditis elegans expresses two manganese superoxide dismutase enzymes (MnSOD-2 and MnSOD-3) that are targeted to the mitochondrion. MnSOD-2 is constitutively expressed, while synthesis of MnSOD-3 is inducible. The structures of these two mononuclear metalloenzymes have been determined to 1.8 and 1.7 A resolution, respectively. Pink crystals formed in space group P4(1)2(1)2 for each, with unit-cell parameters a = b = 81.0, c = 137.4 A for MnSOD-2 and a = b = 81.8, c = 136.0 A for MnSOD-3. The final structure of MnSOD-3 was refined to R = 21.6% and R(free) = 26.2% at 293 K, and R = 18.9% and R(free) = 22.6% at 100 K, while that of MnSOD-2 was refined to R = 16.9% and R(free) = 20.1% at 100 K. The asymmetric unit cell is comprised of two subunits. The resulting structures are very similar to that of human MnSOD and form a tetramer corresponding to a dimer of dimers. The subunit interface between dimers is comprised of two four-helix bundles that stabilize the biologically significant homotetramer.
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Affiliation(s)
- Chi H. Trinh
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Thérèse Hunter
- Department of Physiology and Biochemistry, University of Malta, Msida, MSD 2080, Malta
| | - Emma E. Stewart
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Simon E. V. Phillips
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Gary J. Hunter
- Department of Physiology and Biochemistry, University of Malta, Msida, MSD 2080, Malta
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