1
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Borgstahl G, Azadmanesh J, Slobodnik K, Struble L, Lutz W, Coates L, Weiss K, Myles D, Kroll T. Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. RESEARCH SQUARE 2024:rs.3.rs-3880128. [PMID: 38405788 PMCID: PMC10889052 DOI: 10.21203/rs.3.rs-3880128/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ∙ - to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.
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2
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Azadmanesh J, Slobodnik K, Struble LR, Lutz WE, Coates L, Weiss KL, Myles DAA, Kroll T, Borgstahl GEO. Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577433. [PMID: 38328249 PMCID: PMC10849630 DOI: 10.1101/2024.01.26.577433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ●- to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.
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3
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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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4
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The structure-function relationships and physiological roles of MnSOD mutants. Biosci Rep 2022; 42:231385. [PMID: 35662317 PMCID: PMC9208312 DOI: 10.1042/bsr20220202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/10/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
In this review, we focus on understanding the structure–function relationships of numerous manganese superoxide dismutase (MnSOD) mutants to investigate the role that various amino acids play to maintain enzyme quaternary structure or the active site structure, catalytic potential and metal homeostasis in MnSOD, which is essential to maintain enzyme activity. We also observe how polymorphisms of MnSOD are linked to pathologies and how post-translational modifications affect the antioxidant properties of MnSOD. Understanding how modified forms of MnSOD may act as tumor promoters or suppressors by altering the redox status in the body, ultimately aid in generating novel therapies that exploit the therapeutic potential of mutant MnSODs or pave the way for the development of synthetic SOD mimics.
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5
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Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase. Nat Commun 2021; 12:2079. [PMID: 33824320 PMCID: PMC8024262 DOI: 10.1038/s41467-021-22290-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/26/2021] [Indexed: 11/30/2022] Open
Abstract
Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O2•−. The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn3+ and Mn2+ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pKas, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn3+ and Mn2+ redox states. Human manganese superoxide dismutase (MnSOD) is an oxidoreductase that uses concerted proton and electron transfers to reduce the levels of superoxide radicals in mitochondria, but mechanistic insights into this process are limited. Here, the authors report neutron crystal structures of Mn3+SOD and Mn2+SOD, revealing changes in the protonation states of key residues in the enzyme active site during the redox cycle.
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6
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Retnoningrum DS, Yoshida H, Razani MD, Meidianto VF, Hartanto A, Artarini A, Ismaya WT. Unprecedented Role of the N73-F124 Pair in the Staphylococcus equorum MnSOD Activity. ACTA ACUST UNITED AC 2021. [DOI: 10.2174/1573408016999201027212952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Bacterial manganese superoxide dismutase (MnSOD) occurs as a dimer,
which is responsible for its activity and stability. Therefore, increasing the dimeric strength would increase
the stability of the enzyme while maintaining its activity.
Objective:
An N73F substitution was introduced to strengthen interactions between the monomers at
the dimer interface. This substitution would introduce a π-stacking interaction between F73 of one
monomer to F124 from the other monomers.
Methods:
Site-directed mutagenesis was carried out to substitute N73 with phenylalanine. The activity
of the mutant was qualitative- and quantitatively checked while the stability was evaluated with a fluorescence-
based thermal-shift assay. Finally, the structure of the mutant was elucidated by means of Xray
crystallography.
Results:
The N73F mutant activity was only ~40% of the wild type. The N73F mutant showed one TM
at 60+1°C while the wild type has two (at 52-55°C and 63-67°C). The crystal structure of the mutant
showed the interactions between F73 from one monomer to F124 from the other monomer. The N73F
structure presents an enigma because of no change in the enzyme structure including the active site.
Furthermore, N73 and F124 position and interaction are conserved in human MnSOD but with a different
location in the amino acid sequence. N73 has a role in the enzyme activity, likely related to its interaction
with F124, which resides in the active site region but has not been considered to participate in
the reaction.
Conclusion:
The N73F substitution has revealed the unprecedented role of the N73-F124 pair in the
enzyme activity.
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Affiliation(s)
- Debbie S. Retnoningrum
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Muthia D. Razani
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | | | - Andrian Hartanto
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Anita Artarini
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Wangsa T. Ismaya
- Dexa Laboratories of Biomolecular Sciences, Dexa Medica, Cikarang, Indonesia
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7
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Cabrejos DAL, Alexandrino AV, Pereira CM, Mendonça DC, Pereira HD, Novo-Mansur MTM, Garratt RC, Goto LS. Structural characterization of a pathogenicity-related superoxide dismutase codified by a probably essential gene in Xanthomonas citri subsp. citri. PLoS One 2019; 14:e0209988. [PMID: 30615696 PMCID: PMC6322740 DOI: 10.1371/journal.pone.0209988] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 12/14/2018] [Indexed: 11/24/2022] Open
Abstract
Citrus canker is a plant disease caused by the bacteria Xanthomonas citri subsp. citri that affects all domestic varieties of citrus. Some annotated genes from the X. citri subsp. citri genome are assigned to an interesting class named "pathogenicity, virulence and adaptation". Amongst these is sodM, which encodes for the gene product XcSOD, one of four superoxide dismutase homologs predicted from the genome. SODs are widespread enzymes that play roles in the oxidative stress response, catalyzing the degradation of the deleterious superoxide radical. In Xanthomonas, SOD has been associated with pathogenesis as a counter measure against the plant defense response. In this work we initially present the 1.8 Å crystal structure of XcSOD, a manganese containing superoxide dismutase from Xanthomonas citri subsp. citri. The structure bears all the hallmarks of a dimeric member of the MnSOD family, including the conserved hydrogen-bonding network residues. Despite the apparent gene redundancy, several attempts to obtain a sodM deletion mutant were unsuccessful, suggesting the encoded protein to be essential for bacterial survival. This intriguing observation led us to extend our structural studies to the remaining three SOD homologs, for which comparative models were built. The models imply that X. citri subsp. citri produces an iron-containing SOD which is unlikely to be catalytically active along with two conventional Cu,ZnSODs. Although the latter are expected to possess catalytic activity, we propose they may not be able to replace XcSOD for reasons such as distinct subcellular compartmentalization or differential gene expression in pathogenicity-inducing conditions.
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Affiliation(s)
- Diego Antonio Leonardo Cabrejos
- Laboratório de Biologia Estrutural, Grupo de Cristalografia, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - André Vessoni Alexandrino
- Laboratório de Bioquímica e Biologia Molecular Aplicada—LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Camila Malvessi Pereira
- Laboratório de Bioquímica e Biologia Molecular Aplicada—LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Deborah Cezar Mendonça
- Laboratório de Biologia Estrutural, Grupo de Cristalografia, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Humberto D'Muniz Pereira
- Laboratório de Biologia Estrutural, Grupo de Cristalografia, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Maria Teresa Marques Novo-Mansur
- Laboratório de Bioquímica e Biologia Molecular Aplicada—LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Richard Charles Garratt
- Laboratório de Biologia Estrutural, Grupo de Cristalografia, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Leandro Seiji Goto
- Laboratório de Bioquímica e Biologia Molecular Aplicada—LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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8
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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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9
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Azadmanesh J, Trickel SR, Weiss KL, Coates L, Borgstahl GEO. Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals. Acta Crystallogr F Struct Biol Commun 2017; 73:235-240. [PMID: 28368283 PMCID: PMC5379174 DOI: 10.1107/s2053230x17003508] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/04/2017] [Indexed: 11/10/2022] Open
Abstract
Superoxide dismutases (SODs) are enzymes that protect against oxidative stress by dismutation of superoxide into oxygen and hydrogen peroxide through cyclic reduction and oxidation of the active-site metal. The complete enzymatic mechanisms of SODs are unknown since data on the positions of hydrogen are limited. Here, methods are presented for large crystal growth and neutron data collection of human manganese SOD (MnSOD) using perdeuteration and the MaNDi beamline at Oak Ridge National Laboratory. The crystal from which the human MnSOD data set was obtained is the crystal with the largest unit-cell edge (240 Å) from which data have been collected via neutron diffraction to sufficient resolution (2.30 Å) where hydrogen positions can be observed.
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Affiliation(s)
- Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Scott R. Trickel
- Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
| | - Kevin L. Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA
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10
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Kim HS, Eom D, Koo YM, Yingling YG. The effect of imidazolium cations on the structure and activity of the Candida antarctica Lipase B enzyme in ionic liquids. Phys Chem Chem Phys 2016; 18:22062-9. [DOI: 10.1039/c6cp02355j] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To understand how cations affect the enzyme structure and activity of Candida antarctica Lipase B, we performed MD simulations of CALB in four types of ionic liquids with varying sizes of cations and correlated the results with the experimental data.
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Affiliation(s)
- Ho Shin Kim
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
| | - Doyoung Eom
- Department of Biological Engineering
- Inha University
- Incheon
- Republic of Korea
| | - Yoon-Mo Koo
- Department of Biological Engineering
- Inha University
- Incheon
- Republic of Korea
| | - Yaroslava G. Yingling
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
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11
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Abstract
UNLABELLED Superoxide dismutases (SODs) are metalloproteins that protect organisms from toxic reactive oxygen species by catalyzing the conversion of superoxide anion to hydrogen peroxide and molecular oxygen. Chlorovirus PBCV-1 encodes a 187-amino-acid protein that resembles a Cu-Zn SOD with all of the conserved amino acid residues for binding copper and zinc (named cvSOD). cvSOD has an internal Met that results in a 165-amino-acid protein (named tcvSOD). Both cvSOD and tcvSOD recombinant proteins inhibited nitroblue tetrazolium reduction of superoxide anion generated in a xanthine-xanthine oxidase system in solution. tcvSOD was chosen for further characterization because it was easier to produce. Recombinant tcvSOD also inhibited a riboflavin photochemical reduction system in a polyacrylamide gel assay, which was blocked by the Cu-Zn SOD inhibitor cyanide but not by azide, which inhibits Fe and Mn SODs. A k(cat)/K(m) value for cvSOD was determined by stop-flow spectrophotometry as 1.28 × 10(8) M(-1) s(-1), suggesting that cvSOD-catalyzed O2 (-) dismutation was not a diffusion controlled encounter. The cvsod gene was expressed as a late gene, and cvSOD activity was detected in purified virions. Superoxide accumulated rapidly during virus infection, and circumstantial evidence indicates that cvSOD aids its decomposition to benefit virus replication. Cu-Zn SOD homologs have been described to occur in 3 other families of large DNA viruses, poxviruses, baculoviruses, and mimiviruses, which group as a clade. Interestingly, cvSOD does not group in the same clade as the other virus SODs but instead groups in an expanded clade that includes Cu-Zn SODs from many cellular organisms. IMPORTANCE Virus infection often leads to an increase in toxic reactive oxygen species in the host, which can be detrimental to virus replication. Viruses have developed various ways to overcome this barrier. As reported in this article, the chloroviruses often encode and package a functional Cu-Zn superoxide dismutase in the virion that presumably lowers the concentration of reactive oxygen induced early during virus infection.
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12
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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: 569] [Impact Index Per Article: 56.9] [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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13
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14
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Brophy MB, Nakashige TG, Gaillard A, Nolan EM. Contributions of the S100A9 C-terminal tail to high-affinity Mn(II) chelation by the host-defense protein human calprotectin. J Am Chem Soc 2013; 135:17804-17. [PMID: 24245608 PMCID: PMC3892207 DOI: 10.1021/ja407147d] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Human calprotectin (CP) is an antimicrobial protein that coordinates Mn(II) with high affinity in a Ca(II)-dependent manner at an unusual histidine-rich site (site 2) formed at the S100A8/S100A9 dimer interface. We present a 16-member CP mutant family where mutations in the S100A9 C-terminal tail (residues 96-114) are employed to evaluate the contributions of this region, which houses three histidines and four acidic residues, to Mn(II) coordination at site 2. The results from analytical size-exclusion chromatography, Mn(II) competition titrations, and electron paramagnetic resonance spectroscopy establish that the C-terminal tail is essential for high-affinity Mn(II) coordination by CP in solution. The studies indicate that His103 and His105 (HXH motif) of the tail complete the Mn(II) coordination sphere in solution, affording an unprecedented biological His6 site. These solution studies are in agreement with a Mn(II)-CP crystal structure reported recently (Damo, S. M.; et al. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 3841). Remarkably high-affinity Mn(II) binding is retained when either H103 or H105 are mutated to Ala, when the HXH motif is shifted from positions 103-105 to 104-106, and when the human tail is substituted by the C-terminal tail of murine S100A9. Nevertheless, antibacterial activity assays employing human CP mutants reveal that the native disposition of His residues is important for conferring growth inhibition against Escherichia coli and Staphylococcus aureus. Within the S100 family, the S100A8/S100A9 heterooligomer is essential for providing high-affinity Mn(II) binding; the S100A7, S100A9(C3S), S100A12, and S100B homodimers do not exhibit such Mn(II)-binding capacity.
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Affiliation(s)
- Megan Brunjes Brophy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Toshiki G. Nakashige
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Aleth Gaillard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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15
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Sheng Y, Durazo A, Schumacher M, Gralla EB, Cascio D, Cabelli DE, Valentine JS. Tetramerization reinforces the dimer interface of MnSOD. PLoS One 2013; 8:e62446. [PMID: 23667478 PMCID: PMC3646814 DOI: 10.1371/journal.pone.0062446] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/21/2013] [Indexed: 11/19/2022] Open
Abstract
Two yeast manganese superoxide dismutases (MnSOD), one from Saccharomyces cerevisiae mitochondria (ScMnSOD) and the other from Candida albicans cytosol (CaMnSODc), have most biochemical and biophysical properties in common, yet ScMnSOD is a tetramer and CaMnSODc is a dimer or "loose tetramer" in solution. Although CaMnSODc was found to crystallize as a tetramer, there is no indication from the solution properties that the functionality of CaMnSODc in vivo depends upon the formation of the tetrameric structure. To elucidate further the functional significance of MnSOD quaternary structure, wild-type and mutant forms of ScMnSOD (K182R, A183P mutant) and CaMnSODc (K184R, L185P mutant) with the substitutions at dimer interfaces were analyzed with respect to their oligomeric states and resistance to pH, heat, and denaturant. Dimeric CaMnSODc was found to be significantly more subject to thermal or denaturant-induced unfolding than tetrameric ScMnSOD. The residue substitutions at dimer interfaces caused dimeric CaMnSODc but not tetrameric ScMnSOD to dissociate into monomers. We conclude that the tetrameric assembly strongly reinforces the dimer interface, which is critical for MnSOD activity.
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Affiliation(s)
- Yuewei Sheng
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Armando Durazo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Chemical and Environmental Engineering, University of Arizona, Tuscon, Arizona, United States of America
| | - Mikhail Schumacher
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Edith Butler Gralla
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Duilio Cascio
- Department of Energy-Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Diane E. Cabelli
- Chemistry Department, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Joan Selverstone Valentine
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Bioinspired Science, Ewha Womans University, Seoul, Korea
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16
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Celotto AM, Liu Z, VanDemark AP, Palladino MJ. A novel Drosophila SOD2 mutant demonstrates a role for mitochondrial ROS in neurodevelopment and disease. Brain Behav 2012; 2:424-34. [PMID: 22950046 PMCID: PMC3432965 DOI: 10.1002/brb3.73] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 05/17/2012] [Accepted: 05/19/2012] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) play essential roles in cell signaling, survival, and homeostasis. Aberrant ROS lead to disease and contribute to the aging process. Numerous enzymes and vigilant antioxidant pathways are required to regulate ROS for normal cellular health. Mitochondria are a major source of ROS, and mechanisms to prevent elevated ROS during oxidative phosphorylation require super oxide dismutase (SOD) activity. SOD2, also known as MnSOD, is targeted to mitochondria and is instrumental in regulating ROS by conversion of superoxides to hydrogen peroxide, which is further broken down into H(2)O and oxygen. Here, we describe the identification of a novel mutation within the mitochondrial SOD2 enzyme in Drosophila that results in adults with an extremely shortened life span, sensitivity to hyperoxia, and neuropathology. Additional studies demonstrate that this novel mutant, SOD2(bewildered), exhibits abnormal brain morphology, suggesting a critical role for this protein in neurodevelopment. We investigated the basis of this neurodevelopmental defect and discovered an increase in aberrant axonal that could underlie the aberrant neurodevelopment and brain morphology defects. This novel allele, SOD2(bewildered), provides a unique opportunity to study the effects of increased mitochondrial ROS on neural development, axonal targeting, and neural cell degeneration in vivo.
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Affiliation(s)
- Alicia M. Celotto
- Department of Pharmacology and Chemical Biology University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
- Pittsburgh Institute for Neurodegenerative Diseases University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
| | - Zhaohui Liu
- Department of Pharmacology and Chemical Biology University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
- Pittsburgh Institute for Neurodegenerative Diseases University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
| | - Andrew P. VanDemark
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania 15260
| | - Michael J. Palladino
- Department of Pharmacology and Chemical Biology University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
- Pittsburgh Institute for Neurodegenerative Diseases University of Pittsburgh School of Medicine Pittsburgh Pennsylvania 15261
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17
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Clares MP, Blasco S, Inclán M, del Castillo Agudo L, Verdejo B, Soriano C, Doménech A, Latorre J, García-España E. Manganese(II) complexes of scorpiand-like azamacrocycles as MnSOD mimics. Chem Commun (Camb) 2011; 47:5988-90. [PMID: 21537499 DOI: 10.1039/c1cc10526d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mn(II) complexes of scorpiand-type azamacrocycles constituted by a tretrazapyridinophane core appended with an ethylamino tail including 2- or 4-quinoline functionalities show very appealing in vitro SOD activity. The observed behaviour is related to structural and electrochemical parameters.
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Affiliation(s)
- Ma Paz Clares
- Instituto de Ciencia Molecular, Departamento de Química Inorgánica, Universidad de Valencia, C/Catedrático José Beltrán 2, 46980, Paterna (Valencia), Spain
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18
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Baek KH, Skinner DZ. Molecular Cloning and Expression of Sequence Variants of Manganese Superoxide Dismutase Genes from Wheat. ACTA ACUST UNITED AC 2010. [DOI: 10.5338/kjea.2010.29.1.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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19
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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: 313] [Impact Index Per Article: 22.4] [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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20
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Abreu IA, Cabelli DE. Superoxide dismutases-a review of the metal-associated mechanistic variations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:263-74. [PMID: 19914406 DOI: 10.1016/j.bbapap.2009.11.005] [Citation(s) in RCA: 316] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
Superoxide dismutases are enzymes that function to catalytically convert superoxide radical to oxygen and hydrogen peroxide. These enzymes carry out catalysis at near diffusion controlled rate constants via a general mechanism that involves the sequential reduction and oxidation of the metal center, with the concomitant oxidation and reduction of superoxide radicals. That the catalytically active metal can be copper, iron, manganese or, recently, nickel is one of the fascinating features of this class of enzymes. In this review, we describe these enzymes in terms of the details of their catalytic properties, with an emphasis on the mechanistic differences between the enzymes. The focus here will be concentrated mainly on two of these enzymes, copper, zinc superoxide dismutase and manganese superoxide dismutase, and some relatively subtle variations in the mechanisms by which they function.
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Affiliation(s)
- Isabel A Abreu
- Plant Genetic Engineering Group, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal
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21
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Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis. Biochemistry 2009; 48:3417-24. [PMID: 19265433 PMCID: PMC2756076 DOI: 10.1021/bi8023288] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Superoxide dismutase (SOD) enzymes are critical in controlling levels of reactive oxygen species (ROS) that are linked to aging, cancer, and neurodegenerative disease. Superoxide (O(2)(*-)) produced during respiration is removed by the product of the SOD2 gene, the homotetrameric manganese superoxide dismutase (MnSOD). Here, we examine the structural and catalytic roles of the highly conserved active-site residue Tyr34, based upon structure-function studies of MnSOD enzymes with mutations at this site. Substitution of Tyr34 with five different amino acids retained the active-site protein structure and assembly but caused a substantial decrease in the catalytic rate constant for the reduction of superoxide. The rate constant for formation of the product inhibition complex also decreases but to a much lesser extent, resulting in a net increase in the level of product inhibited form of the mutant enzymes. Comparisons of crystal structures and catalytic rates also suggest that one mutation, Y34V, interrupts the hydrogen-bonded network, which is associated with a rapid dissociation of the product-inhibited complex. Notably, with three of the Tyr34 mutants, we also observe an intermediate in catalysis, which has not been reported previously. Thus, these mutants establish a means of trapping a catalytic intermediate that promises to help elucidate the mechanism of catalysis.
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22
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Grove LE, Brunold TC. SECOND-SPHERE TUNING OF THE METAL ION REDUCTION POTENTIALS IN IRON AND MANGANESE SUPEROXIDE DISMUTASES. COMMENT INORG CHEM 2008. [DOI: 10.1080/02603590802429529] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Grove LE, Xie J, Yikilmaz E, Miller AF, Brunold TC. Spectroscopic and computational investigation of second-sphere contributions to redox tuning in Escherichia coli iron superoxide dismutase. Inorg Chem 2008; 47:3978-92. [PMID: 18433120 DOI: 10.1021/ic702412y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In Fe- and Mn-dependent superoxide dismutases (SODs), second-sphere residues have been implicated in precisely tuning the metal ion reduction potential to maximize catalytic activity (Vance, C. K.; Miller, A.-F. J. Am. Chem. Soc. 1998, 120, 461-467). In the present study, spectroscopic and computational methods were used to characterize three distinct Fe-bound SOD species that possess different second-coordination spheres and, consequently, Fe(3+/2+)reduction potentials that vary by approximately 1 V, namely, FeSOD, Fe-substituted MnSOD (Fe(Mn)SOD), and the Q69E FeSOD mutant. Despite having markedly different metal ion reduction potentials, FeSOD, Fe(Mn)SOD, and Q69E FeSOD exhibit virtually identical electronic absorption, circular dichroism, and magnetic circular dichroism (MCD) spectra in both their oxidized and reduced states. Likewise, variable-temperature, variable-field MCD data obtained for the oxidized and reduced species do not reveal any significant electronic, and thus geometric, variations within the Fe ligand environment. To gain insight into the mechanism of metal ion redox tuning, complete enzyme models for the oxidized and reduced states of all three Fe-bound SOD species were generated using combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations. Consistent with our spectroscopic data, density functional theory computations performed on the corresponding active-site models predict that the three SOD species share similar active-site electronic structures in both their oxidized and reduced states. By using the QM/MM-optimized active-site models in conjunction with the conductor-like screening model to calculate the proton-coupled Fe(3+/2+) reduction potentials, we found that different hydrogen-bonding interactions with the conserved second-sphere Gln (changed to Glu in Q69E FeSOD) greatly perturb the p K of the Fe-bound solvent ligand and, thus, drastically affect the proton-coupled metal ion reduction potential.
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Affiliation(s)
- Laurie E Grove
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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24
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Grove LE, Xie J, Yikilmaz E, Karapetyan A, Miller AF, Brunold TC. Spectroscopic and computational insights into second-sphere amino-acid tuning of substrate analogue/active-site interactions in iron(III) superoxide dismutase. Inorg Chem 2008; 47:3993-4004. [PMID: 18433119 DOI: 10.1021/ic702414m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, the mechanism by which second-sphere residues modulate the structural and electronic properties of substrate-analogue complexes of the Fe-dependent superoxide dismutase (FeSOD) has been explored. Both spectroscopic and computational methods were used to investigate the azide (N3(-)) adducts of Fe(3+)SOD (N3-Fe(3+)SOD) and its Q69E mutant, as well as Fe(3+)-substituted MnSOD (N3-Fe(3+)(Mn)SOD) and its Y34F mutant. Electronic absorption, circular dichroism, and magnetic circular dichroism spectroscopic data reveal that the energy of the dominant N3(-)-->Fe(3+) ligand-to-metal charge transfer (LMCT) transition decreases in the order N3-Fe(3+)(Mn)SOD>N3-Fe(3+)SOD>Q69E N3-Fe(3+)SOD. Intriguingly, the LMCT transition energies correlate almost linearly with the Fe(3+/2+) reduction potentials of the corresponding Fe(3+)-bound SOD species in the absence of azide, which span a range of approximately 1 V (see the preceding paper). To explore the origin of this correlation, combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations were performed on complete enzyme models. The INDO/S-CI computed electronic transition energies satisfactorily reproduce the experimental trend in LMCT transition energies, indicating that the QM/MM optimized active-site models are reasonable. Density functional theory calculations on these experimentally validated active-site models reveal that the differences in spectral and electronic properties among the four N 3(-) adducts arise primarily from differences in the hydrogen-bond network involving the conserved second-sphere Gln (mutated to Glu in Q69E FeSOD) and the solvent ligand. The implications of our findings with respect to the mechanism by which the second-coordination sphere modulates substrate-analogue binding as well as the catalytic properties of FeSOD are discussed.
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Affiliation(s)
- Laurie E Grove
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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25
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Neuba A, Herres-Pawlis S, Flörke U, Henkel G. Synthese und Strukturen der ersten mehrkernigen Mangan-Guanidin-Komplexe und der ersten Mangan-Komplexe mit mono-protonierten Bis-Guanidinliganden. Z Anorg Allg Chem 2008. [DOI: 10.1002/zaac.200700531] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Quint PS, Domsic JF, Cabelli DE, McKenna R, Silverman DN. Role of a Glutamate Bridge Spanning the Dimeric Interface of Human Manganese Superoxide Dismutase,. Biochemistry 2008; 47:4621-8. [DOI: 10.1021/bi7024518] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick S. Quint
- Department of Pharmacology and Therapeutics and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
| | - John F. Domsic
- Department of Pharmacology and Therapeutics and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
| | - Diane E. Cabelli
- Department of Pharmacology and Therapeutics and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
| | - Robert McKenna
- Department of Pharmacology and Therapeutics and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
| | - David N. Silverman
- Department of Pharmacology and Therapeutics and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
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27
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Wintjens R, Gilis D, Rooman M. Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence. Proteins 2007; 70:1564-77. [PMID: 17912757 DOI: 10.1002/prot.21650] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fe- and Mn-containing superoxide dismutase (sod) enzymes are closely related and similar in both amino acid sequence and structure, but differ in their mode of oligomerization and in their specificity for the Fe or Mn cofactor. The goal of the present work is to identify and analyze the sequence and structure characteristics that ensure the cofactor specificities and the oligomerization modes. For that purpose, 374 sod sequences and 17 sod crystal structures were collected and aligned. These alignments were searched for residues and inter-residue interactions that are conserved within the whole sod family, or alternatively, that are specific to a given sod subfamily sharing common characteristics. This led us to define key residues and inter-residue interaction fingerprints in each subfamily. The comparison of these fingerprints allows, on a rational basis, the design of mutants likely to modulate the activity and/or specificity of the target sod, in good agreement with the available experimental results on known mutants. The key residues and interaction fingerprints are furthermore used to predict if a novel sequence corresponds to a sod enzyme, and if so, what type of sod it is. The predictions of this fingerprint method reach much higher scores and present much more discriminative power than the commonly used method that uses pairwise sequence comparisons.
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Affiliation(s)
- René Wintjens
- Service de Chimie générale, Institut de Pharmacie, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
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28
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Perry JJP, Fan L, Tainer JA. Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair. Neuroscience 2006; 145:1280-99. [PMID: 17174478 PMCID: PMC1904427 DOI: 10.1016/j.neuroscience.2006.10.045] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 10/15/2006] [Accepted: 10/17/2006] [Indexed: 12/11/2022]
Abstract
This review is focused on proteins with key roles in pathways controlling either reactive oxygen species or DNA damage responses, both of which are essential for preserving the nervous system. An imbalance of reactive oxygen species or inappropriate DNA damage response likely causes mutational or cytotoxic outcomes, which may lead to cancer and/or aging phenotypes. Moreover, individuals with hereditary disorders in proteins of these cellular pathways have significant neurological abnormalities. Mutations in a superoxide dismutase, which removes oxygen free radicals, may cause the neurodegenerative disease amyotrophic lateral sclerosis. Additionally, DNA repair disorders that affect the brain to various extents include ataxia-telangiectasia-like disorder, Cockayne syndrome or Werner syndrome. Here, we highlight recent advances gained through structural biochemistry studies on enzymes linked to these disorders and other related enzymes acting within the same cellular pathways. We describe the current understanding of how these vital proteins coordinate chemical steps and integrate cellular signaling and response events. Significantly, these structural studies may provide a set of master keys to developing a unified understanding of the survival mechanisms utilized after insults by reactive oxygen species and genotoxic agents, and also provide a basis for developing an informed intervention in brain tumor and neurodegenerative disease progression.
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Affiliation(s)
- J J P Perry
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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29
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Chockalingam K, Luba J, Nick HS, Silverman DN, Zhao H. Engineering and characterization of human manganese superoxide dismutase mutants with high activity and low product inhibition. FEBS J 2006; 273:4853-61. [PMID: 16999822 DOI: 10.1111/j.1742-4658.2006.05484.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human manganese superoxide dismutase is a mitochondrial metalloenzyme that is involved in protecting aerobic organisms against superoxide toxicity, and has been implicated in slowing tumor growth. Unfortunately, this enzyme exhibits strong product inhibition, which limits its potential biomedical applications. Previous efforts to alleviate human manganese superoxide dismutase product inhibition utilized rational protein design and site-directed mutagenesis. These efforts led to variants of human manganese superoxide dismutase at residue 143 with dramatically reduced product inhibition, but also reduced catalytic activity and efficiency. Here, we report the use of a directed evolution approach to engineer two variants of the Q143A human manganese superoxide dismutase mutant enzyme with improved catalytic activity and efficiency. Two separate activity-restoring mutations were found--C140S and N73S--that increase the catalytic efficiency of the parent Q143A human manganese superoxide dismutase enzyme by up to five-fold while maintaining low product inhibition. Interestingly, C140S is a context-dependent mutation, and the C140S-Q143A human manganese superoxide dismutase did not follow Michaelis-Menten kinetics. The re-engineered human manganese superoxide dismutase mutants should be useful for biomedical applications, and our kinetic and structural studies also provide new insights into the structure-function relationships of human manganese superoxide dismutase.
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Affiliation(s)
- Karuppiah Chockalingam
- Department of Chemical Engineering and Biomolecular Engineering, Institute for Genomic Biology, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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30
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Scarpellini M, Wu AJ, Kampf JW, Pecoraro VL. Corroborative models of the cobalt(II) inhibited Fe/Mn superoxide dismutases. Inorg Chem 2005; 44:5001-10. [PMID: 15998028 DOI: 10.1021/ic050281h] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Attempting to model superoxide dismutase (SOD) enzymes, we designed two new N3O-donor ligands to provide the same set of donor atoms observed in the active site of these enzymes: K(i)Pr2TCMA (potassium 1,4-diisopropyl-1,4,7-triazacyclononane-N-acetate) and KBPZG (potassium N,N-bis(3,5-dimethylpyrazolylmethyl) glycinate). Five new Co(II) complexes (1-5) were obtained and characterized by X-ray crystallography, mass spectrometry, electrochemistry, magnetochemistry, UV-vis, and electron paramagnetic resonance (EPR) spectroscopies. The crystal structures of 1 and 3-5 revealed five-coordinate complexes, whereas complex 2 is six-coordinate. The EPR data of complexes 3 and 4 agree with those of the Co(II)-substituted SOD, which strongly support the proposition that the active site of the enzyme structurally resembles these models. The redox behavior of complexes 1-5 clearly demonstrates the stabilization of the Co(II) state in the ligand field provided by these ligands. The irreversibility displayed by all of the complexes is probably related to an electron-transfer process followed by a rearrangement of the geometry around the metal center for complexes 1 and 3-5 that probably changes from a trigonal bipyramidal (high spin, d7) to octahedral (low spin, d6) as Co(II) is oxidized to Co(III), which is also expected to be accompanied by a spin-state conversion. As the redox potentials to convert the Co(II) to Co(III) are high, it can be inferred that the redox potential of the Co(II)-substituted SOD may be outside the range required to convert the superoxide radical (O2*-) to hydrogen peroxide, and this is sufficient to explain the inactivity of the enzyme. Finally, the complexes reported here are the first corroborative structural models of the Co(II)-substituted SOD.
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Affiliation(s)
- Marciela Scarpellini
- Willard H. Dow Laboratories, Department of Chemistry, University of Michigan, 930 North University, Ann Arbor, Michigan 48108, USA
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31
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Landis GN, Tower J. Superoxide dismutase evolution and life span regulation. Mech Ageing Dev 2005; 126:365-79. [PMID: 15664623 DOI: 10.1016/j.mad.2004.08.012] [Citation(s) in RCA: 300] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Revised: 08/30/2004] [Accepted: 08/30/2004] [Indexed: 02/02/2023]
Abstract
Superoxide is among the most abundant reactive oxygen species (ROS) produced by the mitochondria, and is involved in cellular signaling pathways. Superoxide and other ROS can damage cellular macromolecules and levels of oxidative damage products are positively correlated with aging. Superoxide dismutase (SOD) enzymes catalyze the breakdown of superoxide into hydrogen peroxide and water and are therefore central regulators of ROS levels. Genetic and transgenic manipulation of SOD activities in model systems such as S. cereviseae, mouse and Drosophila are consistent with a central role for SOD enzymes in regulating oxidative stress resistance. Over-expression of SOD in S. cereviseae and Drosophila can reduce oxidative damage and extend life span, but the mechanism(s) are not yet clear. A phylogenetic analysis of publicly available SOD protein sequences suggests several additional conserved gene families. For example, in addition to the well-characterized soluble Cu/Zn enzyme (Sod) and mitochondrial manganese-containing form (Sod2), Drosophila melanogaster is found to contain a putative copper chaperone (CCS), an extracellular Cu/Zn enzyme (Sod3), and an extracellular protein distantly related to the Cu/Zn forms (Sodq). C. elegans and blue crab are unusual in having two Mn-containing SODs, and A. gambiae contains an unusual internally repeated SOD. The most parsimonius conclusion from the analysis of the extracellular SODs is that they evolved independently multiple times by addition of a signal peptide to cytoplasmic SOD.
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Affiliation(s)
- Gary N Landis
- Molecular and Computational Biology Program, Department of Biological Sciences, SHS172, University of Southern California, Los Angeles, CA 90089-1340, USA
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