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Azadmanesh J, Slobodnik K, Struble LR, Cone EA, Dasgupta M, Lutz WE, Kumar S, Natarajan A, Coates L, Weiss KL, Myles DAA, Kroll T, Borgstahl GEO. The role of Tyr34 in proton-coupled electron transfer of human manganese superoxide dismutase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596464. [PMID: 38853997 PMCID: PMC11160768 DOI: 10.1101/2024.05.29.596464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O 2 •- ) to molecular oxygen (O 2 ) and hydrogen peroxide (H 2 O 2 ) with proton-coupled electron transfers (PCETs). The reactivity of human MnSOD is determined by the state of a key catalytic residue, Tyr34, that becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. We previously reported that Tyr34 has an unusual pK a due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. To shed light on the role of Tyr34 MnSOD catalysis, we performed neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations of Tyr34Phe MnSOD in various enzymatic states. The data identifies the contributions of Tyr34 in MnSOD activity that support mitochondrial function and presents a thorough characterization of how a single tyrosine modulates PCET catalysis.
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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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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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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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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: 24] [Impact Index Per Article: 8.0] [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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Reddy KK, Bandal H, Satyanarayana M, Goud KY, Gobi KV, Jayaramudu T, Amalraj J, Kim H. Recent Trends in Electrochemical Sensors for Vital Biomedical Markers Using Hybrid Nanostructured Materials. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902980. [PMID: 32670744 PMCID: PMC7341105 DOI: 10.1002/advs.201902980] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/12/2020] [Indexed: 05/09/2023]
Abstract
This work provides a succinct insight into the recent developments in electrochemical quantification of vital biomedical markers using hybrid metallic composite nanostructures. After a brief introduction to the biomarkers, five types of crucial biomarkers, which require timely and periodical monitoring, are shortlisted, namely, cancer, cardiac, inflammatory, diabetic and renal biomarkers. This review emphasizes the usage and advantages of hybrid nanostructured materials as the recognition matrices toward the detection of vital biomarkers. Different transduction methods (fluorescence, electrophoresis, chemiluminescence, electrochemiluminescence, surface plasmon resonance, surface-enhanced Raman spectroscopy) reported for the biomarkers are discussed comprehensively to present an overview of the current research works. Recent advancements in the electrochemical (amperometric, voltammetric, and impedimetric) sensor systems constructed with metal nanoparticle-derived hybrid composite nanostructures toward the selective detection of chosen vital biomarkers are specifically analyzed. It describes the challenges involved and the strategies reported for the development of selective, sensitive, and disposable electrochemical biosensors with the details of fabrication, functionalization, and applications of hybrid metallic composite nanostructures.
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Affiliation(s)
- K. Koteshwara Reddy
- Smart Living Innovation Technology CentreDepartment of Energy Science and TechnologyMyongji UniversityYonginGyeonggi‐do17058Republic of Korea
- Laboratory of Materials ScienceInstituto de Química de Recursos NaturalesUniversidad de TalcaP.O. Box 747Talca3460000Chile
| | - Harshad Bandal
- Smart Living Innovation Technology CentreDepartment of Energy Science and TechnologyMyongji UniversityYonginGyeonggi‐do17058Republic of Korea
| | - Moru Satyanarayana
- Department of ChemistryNational Institute of Technology WarangalWarangalTelangana506004India
| | - Kotagiri Yugender Goud
- Department of ChemistryNational Institute of Technology WarangalWarangalTelangana506004India
| | | | - Tippabattini Jayaramudu
- Laboratory of Materials ScienceInstituto de Química de Recursos NaturalesUniversidad de TalcaP.O. Box 747Talca3460000Chile
| | - John Amalraj
- Laboratory of Materials ScienceInstituto de Química de Recursos NaturalesUniversidad de TalcaP.O. Box 747Talca3460000Chile
| | - Hern Kim
- Smart Living Innovation Technology CentreDepartment of Energy Science and TechnologyMyongji UniversityYonginGyeonggi‐do17058Republic of Korea
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Dao O, Asaithambi K, Na BK, Lee KH. Crystal structure of an iron superoxide dismutase from the pathogenic amoeba Acanthamoeba castellanii. Acta Crystallogr F Struct Biol Commun 2019; 75:480-488. [PMID: 31282867 PMCID: PMC6613442 DOI: 10.1107/s2053230x19008112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/05/2019] [Indexed: 11/10/2022] Open
Abstract
The iron superoxide dismutase found in the pathogenic amoeba Acanthamoeba castellanii (AcFeSOD) may play essential roles in the survival of the parasite, not only by protecting it from endogenous oxidative stress but also by detoxifying oxidative killing of the parasite by host immune effector cells. The AcFeSOD protein was expressed in a stable form using an Escherichia coli expression system and was crystallized by the microbatch and hanging-drop vapour-diffusion methods. The structure was determined to 2.33 Å resolution from a single AcFeSOD crystal. The crystal belonged to the hexagonal space group P61 and contained 12 molecules forming three tetramers in the asymmetric unit, with an iron ion bound in each molecule. Structural comparisons and sequence alignment of AcFeSOD with other FeSODs showed a well conserved overall fold and conserved active-site residues with subtle differences.
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Affiliation(s)
- Oanh Dao
- Department of Convergence Medical Science, Gyeongsang National University College of Medicine, Jinju, Gyeongsangnam, Republic of Korea
| | - Killivalavan Asaithambi
- Department of Convergence Medical Science, Gyeongsang National University College of Medicine, Jinju, Gyeongsangnam, Republic of Korea
| | - Byeong Kuk Na
- Department of Convergence Medical Science, Gyeongsang National University College of Medicine, Jinju, Gyeongsangnam, Republic of Korea
- Department of Parasitology and Tropical Medicine and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Gyeongsangnam, Republic of Korea
| | - Kon Ho Lee
- Department of Convergence Medical Science, Gyeongsang National University College of Medicine, Jinju, Gyeongsangnam, Republic of Korea
- Department of Microbiology, Gyeongsang National University College of Medicine, Jinju, Gyeongsangnam, Republic of Korea
- PMBBRC, Gyeongsang National University, Jinju, Gyeongsangnam, Republic of Korea
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Verma D, Lakhanpal N, Singh K. Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa. BMC Genomics 2019; 20:227. [PMID: 30890148 PMCID: PMC6425617 DOI: 10.1186/s12864-019-5593-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/11/2019] [Indexed: 12/20/2022] Open
Abstract
Background Abiotic stresses like drought, heat, cold and salinity cause major productivity loss in the rapeseed-mustard crops (Brassica). Major efforts have been made in the past to identify genes that provide resistance against such stresses. Superoxide dismutase (SOD) proteins, member of the metallo-enzyme family play vital role in protecting plants against abiotic stresses. In the present study, genome-wide analysis of abiotic stress responsive SOD gene family has been done in B. juncea and B. rapa. Results A total of 29 and 18 SOD genes were identified in B. juncea and B. rapa respectively and chromosome location mapping indicated their wide distribution across genome. On the basis of domain composition, the SODs were phylogenetically classified into sub-groups which was also substantiated by the gene structure and sub-cellular locations of SOD proteins. Functional annotation of SODs was also done by Gene Ontology (GO) mapping and the result was corroborated by the identified cis-regulatory elements in the promoter region of SOD genes. Based on FPKM analysis of SRA data available for drought, heat and salt stress, we identified 14 and 10 abiotic stress responsive SOD genes in B. rapa and B. juncea respectively. The differential expression analysis under drought and heat stress of identified abiotic-stress responsive SOD genes was done through quantitative Real Time PCR. Conclusion We identified abiotic-stress responsive genes that could help in improving the plant tolerance against abiotic stresses. This was the first study to describe the genome-wide analysis of SOD gene family in B. rapa and B. juncea, and the results will help in laying basic ground for future work of cloning and functional validation of SOD genes during abiotic stresses leading to Brassica crop improvement. Electronic supplementary material The online version of this article (10.1186/s12864-019-5593-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deepika Verma
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Panjab University, Chandigarh, 160014, India
| | - Neha Lakhanpal
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Panjab University, Chandigarh, 160014, India
| | - Kashmir Singh
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Panjab University, Chandigarh, 160014, India.
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Azadmanesh J, Lutz WE, Weiss KL, Coates L, Borgstahl GEO. Redox manipulation of the manganese metal in human manganese superoxide dismutase for neutron diffraction. Acta Crystallogr F Struct Biol Commun 2018; 74:677-687. [PMID: 30279321 PMCID: PMC6168772 DOI: 10.1107/s2053230x18011299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022] Open
Abstract
Human manganese superoxide dismutase (MnSOD) is one of the most significant enzymes in preventing mitochondrial dysfunction and related diseases by combating reactive oxygen species (ROS) in the mitochondrial matrix. Mitochondria are the source of up to 90% of cellular ROS generation, and MnSOD performs its necessary bioprotective role by converting superoxide into oxygen and hydrogen peroxide. This vital catalytic function is conducted via cyclic redox reactions between the substrate and the active-site manganese using proton-coupled electron transfers. Owing to protons being difficult to detect experimentally, the series of proton transfers that compose the catalytic mechanism of MnSOD are unknown. Here, methods are described to discern the proton-based mechanism using chemical treatments to control the redox state of large perdeuterated MnSOD crystals and subsequent neutron diffraction. These methods could be applicable to other crystal systems in which proton information on the molecule in question in specific chemical states is desired.
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Affiliation(s)
- Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - William E. Lutz
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, 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, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
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Amin M, Mohamed Z, El-Sayed M, Samy A, Sultan A, Bassuoni M, Alkordi MH. Combined QM/MM and Monte Carlo study for redox leveling in Mn and Fe superoxide dismutase. J Biol Inorg Chem 2017; 23:285-293. [PMID: 29282552 DOI: 10.1007/s00775-017-1530-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/19/2017] [Indexed: 12/22/2022]
Abstract
Superoxide dismutases (SOD) are vital enzymes for disproportionation of superoxide molecules in mammals. Despite the high similarity between the Mn-SOD and Fe-SOD, they are inactive if the metals in the active sites are exchanged. Here, we use DFT, QM/MM and Monte Carlo sampling to optimize the crystal structure and to calculate the mid-point potential for the native and substituted Mn/Fe-SOD. The optimized DFT and QM/MM structures of the Mn-SOD show a major conformational change for the conserved TYR34 compared to the X-ray structure. These changes reduce the distance between TYR34 and Mn ion to 2.59 Å, which yields a lower reduction potential for the Mn. On contrary, there is no significant difference between optimized and crystal structures in the Fe-SOD. The calculated E m values starting from the DFT structures of the active sites show similar pattern, in good agreement with those observed experimentally. However, the calculated E m values starting with the QM/MM structures that include the whole protein are significantly higher due to the desolvation penalty. In addition, the pK a values for the water ligand in the reduced state Mn(II) and Fe(II) were calculated. The water pK a in Mn-SOD is higher than that in Fe-SOD by 3.5 pH units, which is similar to the shift measured experimentally. Finally, we investigated the role of HIS30 and the effect of its protonation state on the E m values.
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Affiliation(s)
- Muhamed Amin
- Department of Physics, City College of New York, New York, NY, 10031, USA.
- Center for Materials Science, Zewail City of Science and Technology, Ahmed Zewail Road, 6th of October City, Giza, 12578, Egypt.
| | - Zainab Mohamed
- Center for Materials Science, Zewail City of Science and Technology, Ahmed Zewail Road, 6th of October City, Giza, 12578, Egypt
| | - Mohamed El-Sayed
- Center for Materials Science, Zewail City of Science and Technology, Ahmed Zewail Road, 6th of October City, Giza, 12578, Egypt
| | - Asmaa Samy
- Center for Materials Science, Zewail City of Science and Technology, Ahmed Zewail Road, 6th of October City, Giza, 12578, Egypt
| | - Afnan Sultan
- Center for Materials Science, Zewail City of Science and Technology, Ahmed Zewail Road, 6th of October City, Giza, 12578, Egypt
| | - Mahmoud Bassuoni
- Center for Materials Science, Zewail City of Science and Technology, Ahmed Zewail Road, 6th of October City, Giza, 12578, Egypt
| | - Mohamed H Alkordi
- Center for Materials Science, Zewail City of Science and Technology, Ahmed Zewail Road, 6th of October City, Giza, 12578, Egypt
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Soldatova AV, Tao L, Romano CA, Stich TA, Casey WH, Britt RD, Tebo BM, Spiro TG. Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Binuclear Activation Mechanism. J Am Chem Soc 2017; 139:11369-11380. [PMID: 28712284 DOI: 10.1021/jacs.7b02771] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterial protein complex Mnx contains a multicopper oxidase (MCO) MnxG that, unusually, catalyzes the two-electron oxidation of Mn(II) to MnO2 biomineral, via a Mn(III) intermediate. Although Mn(III)/Mn(II) and Mn(IV)/Mn(III) reduction potentials are expected to be high, we find a low reduction potential, 0.38 V (vs Normal Hydrogen Electrode, pH 7.8), for the MnxG type 1 Cu2+, the electron acceptor. Indeed the type 1 Cu2+ is not reduced by Mn(II) in the absence of molecular oxygen, indicating that substrate oxidation requires an activation step. We have investigated the enzyme mechanism via electronic absorption spectroscopy, using chemometric analysis to separate enzyme-catalyzed MnO2 formation from MnO2 nanoparticle aging. The nanoparticle aging time course is characteristic of nucleation and particle growth; rates for these processes followed expected dependencies on Mn(II) concentration and temperature, but exhibited different pH optima. The enzymatic time course is sigmoidal, signaling an activation step, prior to turnover. The Mn(II) concentration and pH dependence of a preceding lag phase indicates weak Mn(II) binding. The activation step is enabled by a pKa > 8.6 deprotonation, which is assigned to Mn(II)-bound H2O; it induces a conformation change (consistent with a high activation energy, 106 kJ/mol) that increases Mn(II) affinity. Mnx activation is proposed to decrease the Mn(III/II) reduction potential below that of type 1 Cu(II/I) by formation of a hydroxide-bridged binuclear complex, Mn(II)(μ-OH)Mn(II), at the substrate site. Turnover is found to depend cooperatively on two Mn(II) and is enabled by a pKa 7.6 double deprotonation. It is proposed that turnover produces a Mn(III)(μ-OH)2Mn(III) intermediate that proceeds to the enzyme product, likely Mn(IV)(μ-O)2Mn(IV) or an oligomer, which subsequently nucleates MnO2 nanoparticles. We conclude that Mnx exploits manganese polynuclear chemistry in order to facilitate an otherwise difficult oxidation reaction, as well as biomineralization. The mechanism of the Mn(III/IV) conversion step is elucidated in an accompanying paper .
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Affiliation(s)
- Alexandra V Soldatova
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | | | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | | | | | | | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
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Miller AF, Wang T. A Single Outer-Sphere Mutation Stabilizes apo-Mn Superoxide Dismutase by 35 °C and Disfavors Mn Binding. Biochemistry 2017; 56:3787-3799. [PMID: 28704037 PMCID: PMC6010041 DOI: 10.1021/acs.biochem.7b00175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The catalytic active site of Mn-specific superoxide dismutase (MnSOD) is organized around a redox-active Mn ion. The most highly conserved difference between MnSODs and the homologous FeSODs is the origin of a Gln in the second coordination sphere. In MnSODs it derives from the C-terminal domain whereas in FeSODs it derives from the N-terminal domain, yet its side chain occupies almost superimposable positions in the active sites of these two types of SODs. Mutation of this Gln69 to Glu in Escherichia coli FeSOD increased the Fe3+/2+ reduction midpoint potential by >0.6 V without disrupting the structure or Fe binding [ Yikilmaz, E., Rodgers, D. W., and Miller, A.-F. ( 2006 ) Biochemistry 45 ( 4 ), 1151 - 1161 ]. We now describe the analogous Q146E mutant of MnSOD, explaining its low Mn content in terms increased stability of the apo-Mn protein. In 0.8 M guanidinium HCl, Q146E-apoMnSOD displays an apparent melting midpoint temperature (Tm) 35 °C higher that of wild-type (WT) apoMnSOD, whereas the Tm of WT-holoMnSOD is only 20 °C higher than that of WT-apoMnSOD. In contrast, the Tm attributed to Q146E-holoMnSOD is 40 °C lower than that of Q146E-apoMnSOD. Thus, our data refute the notion that the WT residues optimize the structural stability of the protein and instead are consistent with conservation on the basis of enzyme function and therefore ability to bind metal ion. We propose that the WT-MnSOD protein conserves a destabilizing amino acid at position 146 as part of a strategy to favor metal ion binding.
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Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, Lexington Kentucky, 40506, United States
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 S. Limestone Street, Lexington, KY. 40536-0509
| | - Ting Wang
- Department of Chemistry, University of Kentucky, Lexington Kentucky, 40506, United States
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13
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Singh O, Tyagi N, Olmstead MM, Ghosh K. The design of synthetic superoxide dismutase mimetics: seven-coordinate water soluble manganese(ii) and iron(ii) complexes and their superoxide dismutase-like activity studies. Dalton Trans 2017; 46:14186-14191. [DOI: 10.1039/c7dt03278a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Manganese(ii) and iron(ii) complexes derived from a pentadentate ligand have been characterized and these were utilized for superoxide dismutase-like activity studies.
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Affiliation(s)
- Ovender Singh
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee 247667
- India
| | - Nidhi Tyagi
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee 247667
- India
| | | | - Kaushik Ghosh
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee 247667
- India
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14
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Oszajca M, Brindell M, Orzeł Ł, Dąbrowski JM, Śpiewak K, Łabuz P, Pacia M, Stochel-Gaudyn A, Macyk W, van Eldik R, Stochel G. Mechanistic studies on versatile metal-assisted hydrogen peroxide activation processes for biomedical and environmental incentives. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.05.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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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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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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Mukherjee S, Bandyopadhyay S, Chatterjee S, Dey A. Electrocatalytic O2reduction by a monolayer of hemin: the role of pKaof distal and proximal oxygen of a FeIII–OOH species in determining reactivity. Chem Commun (Camb) 2014; 50:12304-7. [DOI: 10.1039/c4cc03886j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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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: 580] [Impact Index Per Article: 58.0] [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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19
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Li W, Wang H, Wang Q, Tan X. Structural, spectroscopic and functional investigation into Fe-substituted MnSOD from human pathogen Clostridium difficile. Metallomics 2014; 6:1540-8. [DOI: 10.1039/c4mt00090k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SODcd could modulate the Fe and Mn dependent activity through its active site microenvironment.
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Affiliation(s)
- Wei Li
- Department of Chemistry & Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433, China
| | - Hongfei Wang
- Institute of Molecular Science
- Shanxi University
- Taiyuan 030006, China
| | - Qingli Wang
- College of Chemistry
- Chemical Engineering and Materials Science
- Shandong Normal University
- Jinan 250014, China
| | - Xiangshi Tan
- Department of Chemistry & Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433, China
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20
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Cotruvo JA, Stubbe J. Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study. Metallomics 2012; 4:1020-36. [PMID: 22991063 PMCID: PMC3488304 DOI: 10.1039/c2mt20142a] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
How cells ensure correct metallation of a given protein and whether a degree of promiscuity in metal binding has evolved are largely unanswered questions. In a classic case, iron- and manganese-dependent superoxide dismutases (SODs) catalyze the disproportionation of superoxide using highly similar protein scaffolds and nearly identical active sites. However, most of these enzymes are active with only one metal, although both metals can bind in vitro and in vivo. Iron(ii) and manganese(ii) bind weakly to most proteins and possess similar coordination preferences. Their distinct redox properties suggest that they are unlikely to be interchangeable in biological systems except when they function in Lewis acid catalytic roles, yet recent work suggests this is not always the case. This review summarizes the diversity of ways in which iron and manganese are substituted in similar or identical protein frameworks. As models, we discuss (1) enzymes, such as epimerases, thought to use Fe(II) as a Lewis acid under normal growth conditions but which switch to Mn(II) under oxidative stress; (2) extradiol dioxygenases, which have been found to use both Fe(II) and Mn(II), the redox role of which in catalysis remains to be elucidated; (3) SODs, which use redox chemistry and are generally metal-specific; and (4) the class I ribonucleotide reductases (RNRs), which have evolved unique biosynthetic pathways to control metallation. The primary focus is the class Ib RNRs, which can catalyze formation of a stable radical on a tyrosine residue in their β2 subunits using either a di-iron or a recently characterized dimanganese cofactor. The physiological roles of enzymes that can switch between iron and manganese cofactors are discussed, as are insights obtained from the studies of many groups regarding iron and manganese homeostasis and the divergent and convergent strategies organisms use for control of protein metallation. We propose that, in many of the systems discussed, "discrimination" between metals is not performed by the protein itself, but it is instead determined by the environment in which the protein is expressed.
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Affiliation(s)
- Joseph A. Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.; Fax: +1 617 324-0505; Tel: +1 617 253-1814
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.; Fax: +1 617 324-0505; Tel: +1 617 253-1814
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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21
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Six-coordinate manganese(3+) in catalysis by yeast manganese superoxide dismutase. Proc Natl Acad Sci U S A 2012; 109:14314-9. [PMID: 22908245 DOI: 10.1073/pnas.1212367109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reduction of superoxide (O2-) by manganese-containing superoxide dismutase occurs through either a "prompt protonation" pathway, or an "inner-sphere" pathway, with the latter leading to formation of an observable Mn-peroxo complex. We recently reported that wild-type (WT) manganese superoxide dismutases (MnSODs) from Saccharomyces cerevisiae and Candida albicans are more gated toward the "prompt protonation" pathway than human and bacterial MnSODs and suggested that this could result from small structural changes in the second coordination sphere of manganese. We report here that substitution of a second-sphere residue, Tyr34, by phenylalanine (Y34F) causes the MnSOD from S. cerevisiae to react exclusively through the "inner-sphere" pathway. At neutral pH, we have a surprising observation that protonation of the Mn-peroxo complex in the mutant yeast enzyme occurs through a fast pathway, leading to a putative six-coordinate Mn(3+) species, which actively oxidizes O2- in the catalytic cycle. Upon increasing pH, the fast pathway is gradually replaced by a slow proton-transfer pathway, leading to the well-characterized five-coordinate Mn(3+). We here propose and compare two hypothetical mechanisms for the mutant yeast enzyme, differing in the structure of the Mn-peroxo complex yet both involving formation of the active six-coordinate Mn(3+) and proton transfer from a second-sphere water molecule, which has substituted for the -OH of Tyr34, to the Mn-peroxo complex. Because WT and the mutant yeast MnSOD both rest in the 2+ state and become six-coordinate when oxidized up from Mn(2+), six-coordinate Mn(3+) species could also actively function in the mechanism of WT yeast MnSODs.
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22
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Sheng Y, Stich TA, Barnese K, Gralla EB, Cascio D, Britt RD, Cabelli DE, Valentine JS. Comparison of two yeast MnSODs: mitochondrial Saccharomyces cerevisiae versus cytosolic Candida albicans. J Am Chem Soc 2011; 133:20878-89. [PMID: 22077216 PMCID: PMC3268005 DOI: 10.1021/ja2077476] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human MnSOD is significantly more product-inhibited than bacterial MnSODs at high concentrations of superoxide (O(2)(-)). This behavior limits the amount of H(2)O(2) produced at high [O(2)(-)]; its desirability can be explained by the multiple roles of H(2)O(2) in mammalian cells, particularly its role in signaling. To investigate the mechanism of product inhibition in MnSOD, two yeast MnSODs, one from Saccharomyces cerevisiae mitochondria (ScMnSOD) and the other from Candida albicans cytosol (CaMnSODc), were isolated and characterized. ScMnSOD and CaMnSODc are similar in catalytic kinetics, spectroscopy, and redox chemistry, and they both rest predominantly in the reduced state (unlike most other MnSODs). At high [O(2)(-)], the dismutation efficiencies of the yeast MnSODs surpass those of human and bacterial MnSODs, due to very low level of product inhibition. Optical and parallel-mode electron paramagnetic resonance (EPR) spectra suggest the presence of two Mn(3+) species in yeast Mn(3+)SODs, including the well-characterized 5-coordinate Mn(3+) species and a 6-coordinate L-Mn(3+) species with hydroxide as the putative sixth ligand (L). The first and second coordination spheres of ScMnSOD are more similar to bacterial than to human MnSOD. Gln154, an H-bond donor to the Mn-coordinated solvent molecule, is slightly further away from Mn in yeast MnSODs, which may result in their unusual resting state. Mechanistically, the high efficiency of yeast MnSODs could be ascribed to putative translocation of an outer-sphere solvent molecule, which could destabilize the inhibited complex and enhance proton transfer from protein to peroxide. Our studies on yeast MnSODs indicate the unique nature of human MnSOD in that it predominantly undergoes the inhibited pathway at high [O(2)(-)].
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Affiliation(s)
- Yuewei Sheng
- Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, USA
| | - Troy A. Stich
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, USA
| | - Kevin Barnese
- Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, USA
| | - Edith B. Gralla
- Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, USA
| | - Duilio Cascio
- Department of Energy-Institute for Genomics and Proteomics, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, USA
| | - R. David Britt
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, USA
| | - Diane E. Cabelli
- Chemistry Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Joan Selverstone Valentine
- Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, USA
- Department of Bioinspired Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
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23
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Lee WZ, Chiang CW, Lin TH, Kuo TS. A Discrete Five-Coordinate NiIII Complex Resembling the Active Site of the Oxidized Form of Nickel Superoxide Dismutase. Chemistry 2011; 18:50-3. [DOI: 10.1002/chem.201102690] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/20/2011] [Indexed: 11/08/2022]
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24
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Miller AF. Superoxide dismutases: ancient enzymes and new insights. FEBS Lett 2011; 586:585-95. [PMID: 22079668 DOI: 10.1016/j.febslet.2011.10.048] [Citation(s) in RCA: 340] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 10/27/2011] [Accepted: 10/30/2011] [Indexed: 11/25/2022]
Abstract
Superoxide dismutases (SODs) catalyze the de toxification of superoxide. SODs therefore acquired great importance as O(2) became prevalent following the evolution of oxygenic photosynthesis. Thus the three forms of SOD provide intriguing insights into the evolution of the organisms and organelles that carry them today. Although ancient organisms employed Fe-dependent SODs, oxidation of the environment made Fe less bio-available, and more dangerous. Indeed, modern lineages make greater use of homologous Mn-dependent SODs. Our studies on the Fe-substituted MnSOD of Escherichia coli, as well as redox tuning in the FeSOD of E. coli shed light on how evolution accommodated differences between Fe and Mn that would affect SOD performance, in SOD proteins whose activity is specific to one or other metal ion.
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Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA.
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25
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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: 321] [Impact Index Per Article: 22.9] [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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26
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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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27
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Groni S, Hureau C, Guillot R, Blondin G, Blain G, Anxolabéhère-Mallart E. Characterizations of chloro and aqua Mn(II) mononuclear complexes with amino-pyridine ligands. Comparison of their electrochemical properties with those of Fe(II) counterparts. Inorg Chem 2009; 47:11783-97. [PMID: 19007154 DOI: 10.1021/ic8015172] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution behavior of mononuclear Mn(II) complexes, namely, [(L(5)(2))MnCl](+) (1), [(L(5)(3))MnCl](+) (2), [(L(5)(2))Mn(OH(2))](2+) (3), [(L(5)(3))Mn(OH(2))](2+) (4), and [(L(6)(2))Mn(OH(2))](2+) (6), with L(5)(2/3) and L(6)(2) being penta- and hexadentate amino-pyridine ligands, is investigated in MeCN using EPR, UV-vis spectroscopies, and electrochemistry. The addition of one chloride ion onto species 6 leads to the formation of the complex [(L(6)(2))MnCl](+) (5) that is X-ray characterized. EPR and UV-vis spectra indicate that structure and redox states of complexes 1-6 are maintained in MeCN solution. Chloro complexes 1, 2, and 5 show reversible Mn(II)/Mn(III) process at 0.95, 1.02, and 1.05 V vs SCE, respectively, whereas solvated complexes 3, 4, and 6 show an irreversible anodic peak around 1.5 V vs SCE. Electrochemical oxidations of 1 and 5 leading to the Mn(III) complexes [(L(5)(2))MnCl](2+) (7) and [(L(6)(2))MnCl](2+) (8) are successful. The UV-vis signatures of 7 and 8 show features associated with chloro to Mn(III) LMCT and d-d transitions. The X-ray characterization of the heptacoordinated Mn(III) species 8 is also reported. The analogous electrochemical generation of the corresponding Mn(III) complex was not possible when starting from 2. The new mixed-valence di-mu-oxo [(L(5)(2))Mn(muO)(2)Mn(L(5)(2))](3+) species (9) can be obtained from 3, whereas the sister [(L(5)(3))Mn(muO)(2)Mn(L(5)(3))](3+) species can not be generated from 4. Such different responses upon oxidations are commented on with the help of comparison with related Mn/Fe complexes and are discussed in relation with the size of the metallacycle formed between the diamino bridge and the metal center (5- vs 6-membered). Lastly, a comparison between redox potentials of the studied Mn(II) complexes with those of Fe(II) analogues is drawn and completed with previously reported data on Mn/Fe isostructural systems. This gives us the opportunity to get some indirect insights into the metal specificity encountered in enzymes among which superoxide dismutase is the archetypal model.
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Affiliation(s)
- Sihem Groni
- Equipe de Chimie Inorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Sud 11, UMR 8182 CNRS, Orsay F-91405, France
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28
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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: 46] [Impact Index Per Article: 3.1] [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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29
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Herbst RW, Guce A, Bryngelson PA, Higgins KA, Ryan KC, Cabelli DE, Garman SC, Maroney MJ. Role of conserved tyrosine residues in NiSOD catalysis: a case of convergent evolution. Biochemistry 2009; 48:3354-69. [PMID: 19183068 PMCID: PMC3690555 DOI: 10.1021/bi802029t] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Superoxide dismutases rely on protein structural elements to adjust the redox potential of the metallocenter to an optimum value near 300 mV (vs NHE), to provide a source of protons for catalysis, and to control the access of anions to the active site. These aspects of the catalytic mechanism are examined herein for recombinant preparations of the nickel-dependent SOD (NiSOD) from Streptomyces coelicolor and for a series of mutants that affect a key tyrosine residue, Tyr9 (Y9F-, Y62F-, Y9F/Y62F-, and D3A-NiSOD). Structural aspects of the nickel sites are examined by a combination of EPR and X-ray absorption spectroscopies, and by single-crystal X-ray diffraction at approximately 1.9 A resolution in the case of Y9F- and D3A-NiSODs. The functional effects of the mutations are examined by kinetic studies employing pulse radiolytic generation of O2- and by redox titrations. These studies reveal that although the structure of the nickel center in NiSOD is unique, the ligand environment is designed to optimize the redox potential at 290 mV and results in the oxidation of 50% of the nickel centers in the oxidized hexamer. Kinetic investigations show that all of the mutant proteins have considerable activity. In the case of Y9F-NiSOD, the enzyme exhibits saturation behavior that is not observed in wild-type (WT) NiSOD and suggests that release of peroxide is inhibited. The crystal structure of Y9F-NiSOD reveals an anion binding site that is occupied by either Cl- or Br- and is located close to but not within bonding distance of the nickel center. The structure of D3A-NiSOD reveals that in addition to affecting the interaction between subunits, this mutation repositions Tyr9 and leads to altered chemistry with peroxide. Comparisons with Mn(SOD) and Fe(SOD) reveal that although different strategies for adjusting the redox potential and supply of protons are employed, NiSOD has evolved a similar strategy for controlling the access of anions to the active site.
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Affiliation(s)
- Robert W. Herbst
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Abigail Guce
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Peter A. Bryngelson
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Khadine A. Higgins
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Kelly C. Ryan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Diane E. Cabelli
- Department of Chemistry. Brookhaven National Laboratory, Upton, New York 11973
| | - Scott C. Garman
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003,
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003,
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30
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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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31
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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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Miller AF. Redox tuning over almost 1 V in a structurally conserved active site: lessons from Fe-containing superoxide dismutase. Acc Chem Res 2008; 41:501-10. [PMID: 18376853 DOI: 10.1021/ar700237u] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metalloenzymes catalyze some of the most demanding reactions in biochemistry, thereby enabling organisms to extract energy from redox reactions and utilize inorganic starting materials such as N 2 and CH 4. Bound metal ions bring to enzymes greater chemical versatility and reactivity than would be possible from amino acids alone. However the host proteins must control this broad reactivity, activating the metal for the intended reaction while excluding the rest of its chemical repertoire. To this end, metalloproteins must control the metal ion reduction midpoint potential ( E m), because the E m determines what redox reactions are possible. We have documented potent redox tuning in Fe- and Mn-containing superoxide dismutases (FeSODs and MnSODs), and manipulated it to generate FeSOD variants with E ms spanning 900 mV (21 kcal/mol or 87 kJ/mol) with retention of overall structure. This achievement demonstrates possibilities and strategies with great promise for efforts to design or modify catalytic metal sites. FeSODs and MnSODs oxidize and reduce superoxide in alternating reactions that are coupled to proton transfer, wherein the metal site is believed to cycle between M3+ x OH- and M2+ x OH2 (M = Fe or Mn). Thus the E m reflects the ease both of reducing the metal ion and of protonating the coordinated solvent molecule. Moreover similar E ms are achieved by Fe-specific and Mn-specific SODs despite the very different intrinsic E(m)s of high-spin Fe3+/2+ and Mn3+/2+. We provide evidence that E(m) depression by some 300 mV can be achieved via a key enforced H-bond that appears able to disfavor proton acquisition by coordinated solvent. Based on 15N-nuclear magnetic resonance (NMR), stronger H-bond donation to coordinated solvent can explain the greater redox depression achieved by the Mn-specific SOD protein compared with the Fe-specific protein. Furthermore, by manipulating the strength and polarity of this one H-bond, with comparatively minor perturbation to active site atomic and electronic structure, we succeeded in raising the E m of FeSOD by more than 660 mV, apparently by a combination of promoting protonation of coordinated solvent and providing an energetically favorable source of a redox-coupled proton. These studies have combined the use of electron paramagnetic resonance (EPR), NMR, magnetic circular dichroism (MCD), and optical spectrophotometry to characterize the electronic structures of the various metal sites, with complementary density functional theoretical (DFT) calculations, NMR spectroscopy, and X-ray crystallography to define the protein structures and protonation states. Overall, we have generated structurally homologous Fe sites that span some 900 mV, and have demonstrated the enormous redox tuning accessible via the energies associated with proton transfer coupled to electron transfer. In this regard, we note the possible significance of coordinated solvent molecules in numerous biological redox-active metal sites besides that of SOD.
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Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, and Departments of Chemistry and Biophysics, The Johns Hopkins University, Baltimore, Maryland 21218
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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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Abreu IA, Hearn A, An H, Nick HS, Silverman DN, Cabelli DE. The Kinetic Mechanism of Manganese-Containing Superoxide Dismutase from Deinococcus radiodurans: A Specialized Enzyme for the Elimination of High Superoxide Concentrations. Biochemistry 2008; 47:2350-6. [DOI: 10.1021/bi7016206] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Isabel A. Abreu
- Chemistry Department, Brookhaven National Laboratory, Building 555, Upton, New York 11973-5000, and Department of Pharmacology, University of Florida, Gainesville, Florida 32610
| | - Amy Hearn
- Chemistry Department, Brookhaven National Laboratory, Building 555, Upton, New York 11973-5000, and Department of Pharmacology, University of Florida, Gainesville, Florida 32610
| | - Haiqain An
- Chemistry Department, Brookhaven National Laboratory, Building 555, Upton, New York 11973-5000, and Department of Pharmacology, University of Florida, Gainesville, Florida 32610
| | - Harry S. Nick
- Chemistry Department, Brookhaven National Laboratory, Building 555, Upton, New York 11973-5000, and Department of Pharmacology, University of Florida, Gainesville, Florida 32610
| | - David N. Silverman
- Chemistry Department, Brookhaven National Laboratory, Building 555, Upton, New York 11973-5000, and Department of Pharmacology, University of Florida, Gainesville, Florida 32610
| | - Diane E. Cabelli
- Chemistry Department, Brookhaven National Laboratory, Building 555, Upton, New York 11973-5000, and Department of Pharmacology, University of Florida, Gainesville, Florida 32610
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35
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Zheng J, Domsic JF, Cabelli D, McKenna R, Silverman DN. Structural and Kinetic Study of Differences between Human and Escherichia coli Manganese Superoxide Dismutases. Biochemistry 2007; 46:14830-7. [DOI: 10.1021/bi7014103] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiayin Zheng
- 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 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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36
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Affiliation(s)
- My Hang V Huynh
- DE-1: High Explosive Science and Technology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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37
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Carrasco R, Morgenstern-Badarau I, Cano J. Two proton-one electron coupled transfer in iron and manganese superoxide dismutases: A density functional study. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2006.07.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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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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39
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Ren X, Tu C, Bhatt D, Perry JJP, Tainer JA, Cabelli DE, Silverman DN. Kinetic and structural characterization of human manganese superoxide dismutase containing 3-fluorotyrosines. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.10.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Tabares LC, Cortez N, Hiraoka BY, Yamakura F, Un S. Effects of Substrate Analogues and pH on Manganese Superoxide Dismutases. Biochemistry 2006; 45:1919-29. [PMID: 16460038 DOI: 10.1021/bi051947m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of the substrate analogues azide and fluoride on the manganese(II) zero-field interactions of different manganese-containing superoxide dismutases (SOD) was measured using high-field electron paramagnetic resonance spectroscopy. Two cambialistic types, proteins that are active with manganese or iron, were studied along with two that were only active with iron and another that was only active with manganese. It was found that azide was able to coordinate directly to the pentacoordinated Mn(II) site of only the MnSOD from Escherichia coli and the cambialistic SOD from Rhodobacter capsulatus. The formation of a hexacoordinate azide-bound center was characterized by a large reduction in the Mn(II) zero-field interaction. In contrast, all five SODs were affected by fluoride, but no evidence for hexacoordinate Mn(II) formation was detected. For both azide and fluoride, the extent of binding was no more than 50%, implying either that a second binding site was present or that binding was self-limiting. Only the Mn(II) zero-field interactions of the two SODs that had little or no activity with manganese were found to be significantly affected by pH, the manganese-substituted iron superoxide dismutase from E. coli and the Gly155Thr mutant of the cambialistic SOD from Porphyromonas gingivalis. A model for anion binding and the observed pK involving tyrosine-34 is presented.
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Affiliation(s)
- Leandro C Tabares
- Service de Bioénergétique, DBJC, CNRS URA 2096, CEA Saclay, 91191 Gif-sur-Yvette, France
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41
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Abreu IA, Rodriguez JA, Cabelli DE. Theoretical Studies of Manganese and Iron Superoxide Dismutases: Superoxide Binding and Superoxide Oxidation. J Phys Chem B 2005; 109:24502-9. [PMID: 16375454 DOI: 10.1021/jp052368u] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density-functional calculations indicate that the second sphere of coordination around the metal centers of manganese and iron superoxide dismutases (MnSODs and FeSODs) plays an important role in the binding of O2(-). In these systems, O2(-) prefers to bind to Mn or Fe in end-on configurations. For human and E. coli MnSODs, the bound O2(-) forms hydrogen bonds with the tyrosine and glutamine amino acid residues in the second sphere of coordination. In the cases of E. coli and T. elongates FeSODs, hydrogen bonding occurs between the bound O2(-) and the tyrosine amino acid only because the glutamine is too far away for an effective bonding interaction. The manner in which the O2(-) binds to the metal center in MnSODs and FeSODs can affect the rate of subsequent protonation and determine the mechanism for the formation of H2O2. Both Mn- and Fe-containing superoxide dismutases contain a metal-bound solvent molecule that has been suggested to be involved in the uptake of a H+ upon reduction of the metal center [Bull, C.; Fee, J. A. J. Am. Chem. Soc. 1985, 107, 3295; Miller, A.-F.; Padmakumar, K.; Sorkin, D. L.; Karapetian, A.; Vance, C. K. J. Inorg. Biochem. 2003, 93, 71]. Using density-functional theory, we confirm this suggestion and show the involvement of the second sphere of coordination in the process. We show that the oxidation of superoxide by Mn- or Fe-containing superoxide dismutases is facilitated by a cooperative effect between superoxide binding, protonation of the OH- bound to the metal, and electron transfer from the superoxide molecule to the oxidized metal. In particular, proton transfer through tyrosine-34 on the absence of a bound superoxide is uphill while, once superoxide is bound, the energetic barrier is lowered. It is this barrier that likely keeps the resting state (Mn(III)SOD) of the enzyme with a bound hydroxide, instead of a water. This work provides a model for the mechanism of reaction of superoxide with the oxidized form of the metal within Mn- and FeSODs.
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Affiliation(s)
- Isabel A Abreu
- Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973, USA
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42
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Ayala I, Perry JJP, Szczepanski J, Tainer JA, Vala MT, Nick HS, Silverman DN. Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine. Biophys J 2005; 89:4171-9. [PMID: 16150974 PMCID: PMC1366982 DOI: 10.1529/biophysj.105.060616] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Incorporation of 3-fluorotyrosine and site-specific mutagenesis has been utilized with Fourier transform infrared (FTIR) spectroscopy and x-ray crystallography to elucidate active-site structure and the role of an active-site residue Tyr34 in human manganese superoxide dismutase (MnSOD). Calculated harmonic frequencies at the B3LYP/6-31G** level of theory for L-tyrosine and its 3-fluorine substituted analog are compared to experimental frequencies for vibrational mode assignments. Each of the nine tyrosine residues in each of the four subunits of the homotetramer of human MnSOD was replaced with 3-fluorotyrosine. The crystal structures of the unfluorinated and fluorinated wild-type MnSOD are nearly superimposable with the root mean-square deviation for 198 alpha-carbon atoms at 0.3 A. The FTIR data show distinct vibrational modes arising from 3-fluorotyrosine in MnSOD. Comparison of spectra for wild-type and Y34F MnSOD showed that the phenolic hydroxyl of Tyr34 is hydrogen bonded, acting as a proton donor in the active site. Comparison with crystal structures demonstrates that the hydroxyl of Tyr34 is a hydrogen bond donor to an adjacent water molecule; this confirms the participation of Tyr34 in a network of residues and water molecules that extends from the active site to the adjacent subunit.
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Affiliation(s)
- Idelisa Ayala
- Department of Pharmacology, University of Florida, Gainesville, Florida 32610, USA
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43
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Goldsmith CR, Cole AP, Stack TDP. C−H Activation by a Mononuclear Manganese(III) Hydroxide Complex: Synthesis and Characterization of a Manganese-Lipoxygenase Mimic? J Am Chem Soc 2005; 127:9904-12. [PMID: 15998097 DOI: 10.1021/ja039283w] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipoxygenases are mononuclear non-heme metalloenzymes that regio- and stereospecifically convert 1,4-pentadiene subunit-containing fatty acids into alkyl peroxides. The rate-determining step is generally accepted to be hydrogen atom abstraction from the pentadiene subunit of the substrate by an active metal(III)-hydroxide species to give a metal(II)-water species and an organic radical. All known plant and animal lipoxygenases contain iron as the active metal; recently, however, manganese was found to be the active metal in a fungal lipoxygenase. Reported here are the synthesis and characterization of a mononuclear Mn(III) complex, [Mn(III)(PY5)(OH)](CF(3)SO(3))(2) (PY5 = 2,6-bis(bis(2-pyridyl)methoxymethane)pyridine), that reacts with hydrocarbon substrates in a manner most consistent with hydrogen atom abstraction and provides chemical precedence for the proposed reaction mechanism. The neutral penta-pyridyl ligation of PY5 endows a strong Lewis acidic character to the metal center allowing the Mn(III) compound to perform this oxidation chemistry. Thermodynamic analysis of [Mn(III)(PY5)(OH)](2+) and the reduced product, [Mn(II)(PY5)(H(2)O)](2+), estimates the strength of the O-H bond in the metal-bound water in the Mn(II) complex to be 82 (+/-2) kcal mol(-)(1), slightly less than that of the O-H bond in the related reduced iron complex, [Fe(II)(PY5)(MeOH)](2+). [Mn(III)(PY5)(OH)](2+) reacts with hydrocarbon substrates at rates comparable to those of the analogous [Fe(III)(PY5)(OMe)](2+) at 323 K. The crystal structure of [Mn(III)(PY5)(OH)](2+) displays Jahn-Teller distortions that are absent in [Mn(II)(PY5)(H(2)O)](2+), notably a compression along the Mn(III)-OH axis. Consequently, a large internal structural reorganization is anticipated for hydrogen atom transfer, which may be correlated to the lessened dependence of the rate of substrate oxidation on the substrate bond dissociation energy as compared to other metal complexes. The results presented here suggest that manganese is a viable metal for lipoxygenase activity and that, with similar coordination spheres, iron and manganese can oxidize substrates through a similar mechanism.
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Miller AF, Sorkin DL, Padmakumar K. Anion Binding Properties of Reduced and Oxidized Iron-Containing Superoxide Dismutase Reveal No Requirement for Tyrosine 34. Biochemistry 2005; 44:5969-81. [PMID: 15835886 DOI: 10.1021/bi0476331] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first spectroscopic observation of substrate analogue binding to the reduced state of iron superoxide dismutase from Escherichia coli (Fe(2+)SOD) and demonstrate that the pH dependence reflects inhibition of anion binding by ionized Tyr34, not loss of a positive contribution on the part of Tyr34's labile proton. This can also explain the pH dependence of the K(M) of Fe(2+)SOD. Thus, it appears that substrate binding to Fe(2+)SOD occurs in the second sphere and is not strongly coupled to hydrogen bond donation. Parallel investigations of substrate analogue binding to the oxidized state (Fe(3+)SOD) confirm formation of a six-coordinate complex and resolve the apparent conflict with earlier nuclear magnetic relaxation dispersion (NMRD) results. Thus, we propose that two F(-) ions can bind to the oxidized Fe(3+)SOD active site, either displacing the coordinated solvent or lowering its exchange rate with bulk solvent. We show that neutral Tyr34's unfavorable effect on binding of the substrate analogue N(3)(-) can be ascribed to steric interference, as it does not apply to the smaller substrate analogues F(-) and OH(-). Finally, we report the first demonstration that HS(-) can act as a substrate analogue with regard both to redox reactivity with FeSOD and to ability to coordinate to the active site Fe(3+). Indeed, it forms a novel green complex. Thus, we have begun to evaluate the relative importance of different contributions that Tyr34 may make to substrate binding, and we have identified a novel, redox active substrate analogue that offers new possibilities for elucidating the mechanism of FeSOD.
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Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
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45
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Muñoz IG, Moran JF, Becana M, Montoya G. The crystal structure of an eukaryotic iron superoxide dismutase suggests intersubunit cooperation during catalysis. Protein Sci 2005; 14:387-94. [PMID: 15659371 PMCID: PMC2253407 DOI: 10.1110/ps.04979505] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Revised: 09/30/2004] [Accepted: 09/30/2004] [Indexed: 10/25/2022]
Abstract
Superoxide dismutases (SODs) are a family of metalloenzymes that catalyze the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. Iron superoxide dismutases (FeSODs) are only expressed in some prokaryotes and plants. A new and highly active FeSOD with an unusual subcellular localization has recently been isolated from the plant Vigna unguiculata (cowpea). This protein functions as a homodimer and, in contrast to the other members of the SOD family, is localized to the cytosol. The crystal structure of the recombinant enzyme has been solved and the model refined to 1.97 A resolution. The superoxide anion binding site is located in a cleft close to the dimer interface. The coordination geometry of the Fe site is a distorted trigonal bipyramidal arrangement, whose axial ligands are His43 and a solvent molecule, and whose in-plane ligands are His95, Asp195, and His199. A comparison of the structural features of cowpea FeSOD with those of homologous SODs reveals subtle differences in regard to the metal-protein interactions, and confirms the existence of two regions that may control the traffic of substrate and product: one located near the Fe binding site, and another in the dimer interface. The evolutionary conservation of reciprocal interactions of both monomers in neighboring active sites suggests possible subunit cooperation during catalysis.
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Affiliation(s)
- Inés G Muñoz
- Structural Biology and Biocomputing Program, Spanish National Cancer Center (CNIO), Macromolecular Crystallography Group, c/o Melchor Fernández Almagro 3, 28029 Madrid, Spain
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46
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Jackson TA, Karapetian A, Miller AF, Brunold TC. Probing the Geometric and Electronic Structures of the Low-Temperature Azide Adduct and the Product-Inhibited Form of Oxidized Manganese Superoxide Dismutase. Biochemistry 2005; 44:1504-20. [PMID: 15683235 DOI: 10.1021/bi048639t] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The geometric and electronic structures of the six-coordinate azide adduct of oxidized manganese superoxide dismutase (Mn3+ SOD) that is formed at low temperatures, LT N3-Mn3+ SOD, has been examined in detail through a combined spectroscopic/computational approach. Electronic absorption, circular dichroism (CD), magnetic CD (MCD) and variable-temperature, variable-field (VTVH) MCD spectroscopies were used to determine electronic transition energies and to obtain an estimate of zero-field splitting parameters for LT N3-Mn3+ SOD. These experimental data were utilized in conjunction with semiempirical intermediate neglect of differential overlap/spectroscopic parametrization-configuration interaction (INDO/S-CI) and time-dependent density functional theory (TD-DFT) computations to evaluate hypothetical active-site models of LT N3-Mn3+ SOD generated by constrained DFT geometry optimizations. Collectively, our spectroscopic/computational results indicate that N3- binding to Mn3+ SOD at low temperatures promotes neither protonation of the axial solvent ligand nor reorientation of the redox-active molecular orbital, both of which had been previously suggested. Using the same experimentally validated computational approach, models of the product-inhibited form of MnSOD were also developed and evaluated by their relative energies and TD-DFT-computed absorption spectra. On the basis of our computational results as well as previously published kinetic data, we propose that the product-inhibited form of MnSOD is best described as a side-on peroxo-Mn3+ adduct possessing an axial H2O ligand. Notably, attempts to generate a stable hydroperoxo-Mn3+ SOD species by protonation of the proximal O atom of the hydroperoxo ligand resulted in dissociation of HOO- and eventual H+ transfer from Tyr34 to HOO-, generating deprotonated Tyr34 and H2O2. The implications of these results with respect to the mechanism of O2*- dismutation by MnSOD are discussed.
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Affiliation(s)
- Timothy A Jackson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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47
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Jackson TA, Karapetian A, Miller AF, Brunold TC. Spectroscopic and computational studies of the azide-adduct of manganese superoxide dismutase: definitive assignment of the ligand responsible for the low-temperature thermochromism. J Am Chem Soc 2004; 126:12477-91. [PMID: 15453782 DOI: 10.1021/ja0482583] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A variety of spectroscopic and computational techniques have been used to examine the thermochromic transition previously reported for the oxidized state of Mn-dependent superoxide dismutase from E. coli in the presence of substrate analog azide (N(3)-Mn(3+)SOD).[Whittaker, M. M.; Whittaker, J. W. Biochemistry 1996, 35, 6762-6770.] Although previous spectroscopic studies had shown that this thermochromic event corresponds to a change in coordination number of the active-site Mn(3+) ion from 6 to 5 as temperature is increased, the ligand that dissociates in this conversion had yet to be identified. Through the use of electronic absorption, circular dichroism (CD), and magnetic CD (MCD) spectroscopies, both d-->d and ligand-to-metal charge-transfer (LMCT) transition energies have been determined for native Mn(3+)SOD (possessing a five-coordinate Mn(3+) center) and Y34F N(3)-Mn(3+)SOD (forming a six-coordinate N(3)-Mn(3+) adduct at all temperatures). These two systems provide well-defined reference points from which to analyze the absorption and CD data obtained for N(3)-Mn(3+)SOD at room temperature (RT). Comparison of excited-state spectroscopic data reveals that Mn(3+)SOD and RT N(3)-Mn(3+)SOD exhibit virtually identical d-->d transition energies, suggesting that these two species possess similar geometric and electronic structures and, thus, that azide does not actually coordinate to the active-site Mn(3+) ion at RT. However, resonance Raman spectra of both N(3)-Mn(3+)SOD and Y34F N(3)-Mn(3+)SOD at 0 degrees C exhibit azide-related vibrations, indicating that azide does interact with the active site of the native enzyme at this temperature. To gain further insight into the nature of the azide/Mn(3+) interaction in RT N(3)-Mn(3+)SOD, several viable active-site models designed to promote either dissociation of coordinated solvent, Asp167, or azide were generated using DFT computations. By utilizing the time-dependent DFT method to predict absorption spectra for these models of RT N(3)-Mn(3+)SOD, we demonstrate that only azide dissociation is consistent with experimental data. Collectively, our spectroscopic and computational data provide evidence that the active site of N(3)-Mn(3+)SOD at RT exists in a dynamic equilibrium, with the azide molecule either hydrogen-bonded to the second-sphere Tyr34 residue or coordinated to the Mn(3+) ion. These results further highlight the role that second-sphere residues, especially Tyr34, play in tuning substrate (analog)/metal ion interactions.
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Affiliation(s)
- Timothy A Jackson
- Department of Chemistry, University of Wisconsin-Madison, 53706, USA
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48
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Jackson TA, Brunold TC. Combined spectroscopic/computational studies on Fe- and Mn-dependent superoxide dismutases: insights into second-sphere tuning of active site properties. Acc Chem Res 2004; 37:461-70. [PMID: 15260508 DOI: 10.1021/ar030272h] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Superoxide dismutases (SODs) are metalloenzymes that protect aerobic organisms from oxidative damage mediated by the superoxide radical. While the Fe- and Mn-dependent SODs from E. coli possess virtually identical protein folds and active-site geometries, they are strictly metal specific. To explore the origin of this extraordinary metal-ion specificity and to elucidate the mechanisms by which these enzymes tune the geometric and electronic properties, and thus the reactivity, of their active-site metal ions, we utilized a combination of spectroscopic and computational methods to study the native enzymes, their metal-substituted derivatives, and several mutant proteins. Results from our research described in this Account reveal that second-sphere residues are critically involved in controlling both thermodynamic and kinetic properties of the Fe- and MnSOD active sites.
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Affiliation(s)
- Timothy A Jackson
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Renger G. Coupling of electron and proton transfer in oxidative water cleavage in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:195-204. [PMID: 15100032 DOI: 10.1016/j.bbabio.2003.07.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2003] [Revised: 07/23/2003] [Accepted: 07/23/2003] [Indexed: 11/29/2022]
Abstract
This minireview addresses questions on the mechanism of oxidative water cleavage with special emphasis on the coupling of electron (ET) and proton transfer (PT) of each individual redox step of the reaction sequence and on the mode of O-O bond formation. The following topics are discussed: (1) the multiphasic kinetics of Y(Z)(ox) formation by P680(+*) originate from three different types of rate limitations: (i) nonadiabatic electron transfer for the "fast" ns reaction, (ii) local "dielectric" relaxation for the "slow" ns reaction, and (iii) "large-scale" proton shift for the micros kinetics; (2) the ET/PT-coupling mode of the individual redox transitions within the water oxidizing complex (WOC) driven by Y(Z)(ox) is assumed to depend on the redox state S(i): the oxidation steps of S(0) and S(1) comprise separate ET and PT pathways while those of S(2) and S(3) take place via proton-coupled electron transfer (PCET) analogous to Jerry Babcock's hydrogen atom abstractor model [Biochim. Biophys. Acta, 1458 (2000) 199]; (3) S(3) is postulated to be a multistate redox level of the WOC with fast dynamic equilibria of both redox isomerism and proton tautomerism. The primary event in the essential O-O bond formation is the population of a state S(3)(P) characterized by an electronic configuration and nuclear geometry that corresponds with a complexed hydrogen peroxide; (4) the peroxidic type S(3)(P) is the entatic state for formation of complexed molecular oxygen through S(3) oxidation by Y(Z)(ox); and (5) the protein matrix itself is proposed to exert catalytic activity by functioning as "PCET director". The WOC is envisaged as a supermolecule that is especially tailored for oxidative water cleavage and acts as a molecular machine.
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Affiliation(s)
- G Renger
- Max-Volmer-Laboratory of the Institute of Chemistry, Technical University Berlin, PC 14, Strasse des 17 Juni 135, D-10623 Berlin, Germany.
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Greenleaf WB, Perry JJP, Hearn AS, Cabelli DE, Lepock JR, Stroupe ME, Tainer JA, Nick HS, Silverman DN. Role of Hydrogen Bonding in the Active Site of Human Manganese Superoxide Dismutase†,‡. Biochemistry 2004; 43:7038-45. [PMID: 15170341 DOI: 10.1021/bi049888k] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The side chain of Gln143, a conserved residue in manganese superoxide dismutase (MnSOD), forms a hydrogen bond with the manganese-bound solvent and is critical in maintaining catalytic activity. The side chains of Tyr34 and Trp123 form hydrogen bonds with the carboxamide of Gln143. We have replaced Tyr34 and Trp123 with Phe in single and double mutants of human MnSOD and measured their catalytic activity by stopped-flow spectrophotometry and pulse radiolysis. The replacements of these side chains inhibited steps in the catalysis as much as 50-fold; in addition, they altered the gating between catalysis and formation of a peroxide complex to yield a more product-inhibited enzyme. The replacement of both Tyr34 and Trp123 in a double mutant showed that these two residues interact cooperatively in maintaining catalytic activity. The crystal structure of Y34F/W123F human MnSOD at 1.95 A resolution suggests that this effect is not related to a conformational change in the side chain of Gln143, which does not change orientation in Y34F/W123F, but rather to more subtle electronic effects due to the loss of hydrogen bonding to the carboxamide side chain of Gln143. Wild-type MnSOD containing Trp123 and Tyr34 has approximately the same thermal stability compared with mutants containing Phe at these positions, suggesting the hydrogen bonds formed by these residues have functional rather than structural roles.
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Affiliation(s)
- William B Greenleaf
- Departments of Pharmacology and Neuroscience, University of Florida, Gainesville, Florida 32610-0267, USA
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