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Carpentier P, van der Linden P, Mueller-Dieckmann C. The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF. Acta Crystallogr D Struct Biol 2024; 80:80-92. [PMID: 38265873 PMCID: PMC10836400 DOI: 10.1107/s2059798323010707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Important scientific applications of high pressure to macromolecules at the HPMX include noble-gas derivatization of crystals to detect and map the internal architecture of proteins (pockets, tunnels and channels) that allows the storage and diffusion of ligands or substrates/products, the investigation of the catalytic mechanisms of gas-employing enzymes (using oxygen, carbon dioxide or methane as substrates) to possibly decipher intermediates, and studies of the conformational fluctuations or structure modifications that are necessary for proteins to function. Additionally, cryo-cooling protein crystals under high pressure (helium or argon at 2000 bar) enables the addition of cryo-protectant to be avoided and noble gases can be employed to produce derivatives for structure resolution. The high-pressure systems are designed to process crystals along a well defined pathway in the phase diagram (pressure-temperature) of the gas to cryo-cool the samples according to the three-step `soak-and-freeze method'. Firstly, crystals are soaked in a pressurized pure gas atmosphere (at 294 K) to introduce the gas and facilitate its interactions within the macromolecules. Samples are then flash-cooled (at 100 K) while still under pressure to cryo-trap macromolecule-gas complexation states or pressure-induced protein modifications. Finally, the samples are recovered after depressurization at cryo-temperatures. The final section of this publication presents a selection of different typical high-pressure experiments carried out at the HPMX, showing that this technique has already answered a wide range of scientific questions. It is shown that the use of different gases and pressure conditions can be used to probe various effects, such as mapping the functional internal architectures of enzymes (tunnels in the haloalkane dehalogenase DhaA) and allosteric sites on membrane-protein surfaces, the interaction of non-inert gases with proteins (oxygen in the hydrogenase ReMBH) and pressure-induced structural changes of proteins (tetramer dissociation in urate oxidase). The technique is versatile and the provision of pressure cells and their application at the HPMX is gradually being extended to address new scientific questions.
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Affiliation(s)
- Philippe Carpentier
- Université Grenoble Alpes CEA CNRS, IRIG–LCBM UMR 5249, 17 Avenue des Martyrs, 38000 Grenoble, France
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Peter van der Linden
- ESRF, PSCM (Partnership for Soft Condensed Matter), 71 Avenue des Martyrs, 38000 Grenoble, France
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Mohammadpour P, Safaei E, Mazarei E, Zeinalipour-Yazdi CD. TEMPO and a co-reductant mediated aerobic epoxidation of olefins using a new magnetically recoverable iron(III) bis(phenol)diamine complex: experimental and computational studies. Phys Chem Chem Phys 2023; 25:26588-26603. [PMID: 37753780 DOI: 10.1039/d3cp02254d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
A magnetically recoverable catalyst of an iron(III) bis(phenol) diamine complex immobilized onto amine functionalized silica-coated magnetic nanoparticles has been synthesized. The catalyst was characterized using FESEM, TEM and XRD which confirmed the nano structure of the catalyst. The physicochemical techniques of ICP, FT-IR, XPS, EDS and TGA proved the loading of the ligand and metal complex on silica-coated magnetic nanoparticles. Using the prepared heterogeneous catalyst, aerobic epoxidation reactions of different alkenes have been investigated in the presence of SO32- as a reducing agent. Moreover, using TEMPO (2,2,6,6-tetramethyl-1-piperidinyloxy) to discover the mechanism of the aerobic epoxidation of olefins, a new TEMPO-assisted route has been explored. Both of the reaction pathways led to a moderate to high percentage yield of epoxides in water at room temperature. For further understanding mechanistic aspects, density functional theory (DFT) computational studies have been performed. The DFT calculations confirm the suggested mechanism for the title reaction and show the electron density in the vicinity of Fe(II) in the presence of TEMPO as a co-catalyst was more than that in the presence of SO32-.
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Affiliation(s)
- Pegah Mohammadpour
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz, 7194684795, Iran.
| | - Elham Safaei
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz, 7194684795, Iran.
| | - Elham Mazarei
- Theoretical Chemistry, Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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Dedushko MA, Pikul JH, Kovacs JA. Superoxide Oxidation by a Thiolate-Ligated Iron Complex and Anion Inhibition. Inorg Chem 2021; 60:7250-7261. [PMID: 33900756 DOI: 10.1021/acs.inorgchem.1c00336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Superoxide (O2•-) is a toxic radical, generated via the adventitious reduction of dioxygen (O2), which has been implicated in a number of human disease states. Nonheme iron enzymes, superoxide reductase (SOR) and superoxide dismutase (SOD), detoxify O2•- via reduction to afford H2O2 and disproportionation to afford O2 and H2O2, respectively. The former contains a thiolate in the coordination sphere, which has been proposed to prevent O2•- oxidation to O2. The work described herein shows that, in contrast to this, oxidized thiolate-ligated [FeIII(SMe2N4(tren)(THF)]2+ (1ox-THF) is capable of oxidizing O2•- to O2. Coordinating anions, Cl- and OAc-, are shown to inhibit dioxygen evolution, implicating an inner-sphere mechanism. Previously we showed that the reduced thiolate-ligated [FeII(SMe2N4(tren))]+ (1) is capable of reducing O2•- via a proton-dependent inner-sphere mechanism involving a transient Fe(III)-OOH intermediate. A transient ferric-superoxo intermediate, [FeIII(SMe2N4(tren))(O2)]+ (3), is detected by electronic absorption spectroscopy at -130 °C in the reaction between 1ox-THF and KO2 and shown to evolve O2 upon slight warming to -115 °C. The DFT calculated O-O (1.306 Å) and Fe-O (1.943 Å) bond lengths of 3 are typical of ferric-superoxo complexes, and the time-dependent DFT calculated electronic absorption spectrum of 3 reproduces the experimental spectrum. The electronic structure of 3 is shown to consist of two antiferromagnetically coupled (Jcalc = -180 cm-1) unpaired electrons, one in a superoxo π*(O-O) orbital and the other in an antibonding π*(Fe(dyz)-S(py)) orbital.
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Affiliation(s)
- Maksym A Dedushko
- The Department of Chemistry, University of Washington: Box 351700, Seattle, Washington 98195-1700, United States
| | - Jessica H Pikul
- The Department of Chemistry, University of Washington: Box 351700, Seattle, Washington 98195-1700, United States
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington: Box 351700, Seattle, Washington 98195-1700, United States
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4
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Desbois A, Valton J, Moreau Y, Torelli S, Nivière V. Conformational H-bonding modulation of the iron active site cysteine ligand of superoxide reductase: absorption and resonance Raman studies. Phys Chem Chem Phys 2021; 23:4636-4645. [PMID: 33527107 DOI: 10.1039/d0cp03898a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Superoxide reductases (SORs) are mononuclear non-heme iron enzymes involved in superoxide radical detoxification in some microorganisms. Their atypical active site is made of an iron atom pentacoordinated by four equatorial nitrogen atoms from histidine residues and one axial sulfur atom from a cysteinate residue, which plays a central role in catalysis. In most SORs, the residue immediately following the cysteinate ligand is an asparagine, which belongs to the second coordination sphere and is expected to have a critical influence on the properties of the active site. In this work, in order to investigate the role of this asparagine residue in the Desulfoarculus baarsii enzyme (Asn117), we carried out, in comparison with the wild-type enzyme, absorption and resonance Raman (RR) studies on a SOR mutant in which Asn117 was changed into an alanine. RR analysis was developed in order to assign the different bands using excitation in the (Cys116)-S-→ Fe3+ charge transfer band. By investigating the correlation between the (Cys116)-S-→ Fe3+ charge transfer band maximum with the frequency of each RR band in different SOR forms, we assessed the contribution of the ν(Fe-S) vibration among the different RR bands. The data showed that Asn117, by making hydrogen bond interactions with Lys74 and Tyr76, allows a rigidification of the backbone of the Cys116 ligand, as well as that of the neighboring residues Ile118 and His119. Such a structural role of Asn117 has a deep impact on the S-Fe bond. It results in a tight control of the H-bond distance between the Ile118 and His119 NH peptidic moiety with the cysteine sulfur ligand, which in turn enables fine-tuning of the S-Fe bond strength, an essential property for the SOR active site. This study illustrates the intricate roles of second coordination sphere residues to adjust the ligand to metal bond properties in the active site of metalloenzymes.
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Affiliation(s)
- Alain Desbois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette Cedex, France
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5
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Role of Superoxide Reductase FA796 in Oxidative Stress Resistance in Filifactor alocis. Sci Rep 2020; 10:9178. [PMID: 32513978 PMCID: PMC7280497 DOI: 10.1038/s41598-020-65806-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022] Open
Abstract
Filifactor alocis, a Gram-positive anaerobic bacterium, is now a proposed diagnostic indicator of periodontal disease. Because the stress response of this bacterium to the oxidative environment of the periodontal pocket may impact its pathogenicity, an understanding of its oxidative stress resistance strategy is vital. Interrogation of the F. alocis genome identified the HMPREF0389_00796 gene that encodes for a putative superoxide reductase (SOR) enzyme. SORs are non-heme, iron-containing enzymes that can catalyze the reduction of superoxide radicals to hydrogen peroxide and are important in the protection against oxidative stress. In this study, we have functionally characterized the putative SOR (FA796) from F. alocis ATCC 35896. The recombinant FA796 protein, which is predicted to be a homotetramer of the 1Fe-SOR class, can reduce superoxide radicals. F. alocis FLL141 (∆FA796::ermF) was significantly more sensitive to oxygen/air exposure compared to the parent strain. Sensitivity correlated with the level of intracellular superoxide radicals. Additionally, the FA796-defective mutant had increased sensitivity to hydrogen peroxide-induced stress, was inhibited in its ability to form biofilm and had reduced survival in epithelial cells. Collectively, these results suggest that the F. alocis SOR protein is a key enzymatic scavenger of superoxide radicals and protects the bacterium from oxidative stress conditions.
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Martins MC, Romão CV, Folgosa F, Borges PT, Frazão C, Teixeira M. How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes. Free Radic Biol Med 2019; 140:36-60. [PMID: 30735841 DOI: 10.1016/j.freeradbiomed.2019.01.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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Horch M. Rational redox tuning of transition metal sites: learning from superoxide reductase. Chem Commun (Camb) 2019; 55:9148-9151. [PMID: 31304493 DOI: 10.1039/c9cc04004h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using superoxide reductase as a model system, a computational approach reveals how histidine tautomerism tunes the redox properties of metalloenzymes to enable their catalytic function. Inspired by these experimentally inaccessible insights, non-canonical histidine congeners are introduced as new versatile tools for the rational engineering of biological transition metal sites.
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Affiliation(s)
- Marius Horch
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK.
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8
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Gordon JB, Vilbert AC, Siegler MA, Lancaster KM, Moënne-Loccoz P, Goldberg DP. A Nonheme Thiolate-Ligated Cobalt Superoxo Complex: Synthesis and Spectroscopic Characterization, Computational Studies, and Hydrogen Atom Abstraction Reactivity. J Am Chem Soc 2019; 141:3641-3653. [PMID: 30776222 DOI: 10.1021/jacs.8b13134] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The synthesis and characterization of a Co(II) dithiolato complex Co(Me3TACN)(S2SiMe2) (1) are reported. Reaction of 1 with O2 generates a rare thiolate-ligated cobalt-superoxo species Co(O2)(Me3TACN)(S2SiMe2) (2) that was characterized spectroscopically and structurally by resonance Raman, EPR, and X-ray absorption spectroscopies as well as density functional theory. Metal-superoxo species are proposed to S-oxygenate metal-bound thiolate donors in nonheme thiol dioxygenases, but 2 does not lead to S-oxygenation of the intramolecular thiolate donors and does not react with exogenous sulfur donors. However, complex 2 is capable of oxidizing the O-H bonds of 2,2,6,6-tetramethylpiperidin-1-ol derivatives via H atom abstraction. Complementary proton-coupled electron-transfer reactivity is seen for 2 with separated proton/reductant pairs. The reactivity studies indicate that 2 can abstract H atoms from weak X-H bonds with bond dissociation free energy (BDFE) ≤ 70 kcal mol-1. DFT calculations predict that the putative Co(OOH) product has an O-H BDFE = 67 kcal mol-1, which matches the observed pattern of reactivity seen for 2. These data provide new information regarding the selectivity of S-oxygenation versus H atom abstraction in thiolate-ligated nonheme metalloenzymes that react with O2.
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Affiliation(s)
- Jesse B Gordon
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Avery C Vilbert
- Department of Chemistry and Chemical Biology, Baker Laboratory , Cornell University , Ithaca , New York 14853 , United States
| | - Maxime A Siegler
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory , Cornell University , Ithaca , New York 14853 , United States
| | - Pierre Moënne-Loccoz
- Department of Biochemistry & Molecular Biology , Oregon Health & Science University , Portland , Oregon 97239-3098 , United States
| | - David P Goldberg
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
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9
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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10
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Romão CV, Matias PM, Sousa CM, Pinho FG, Pinto AF, Teixeira M, Bandeiras TM. Insights into the Structures of Superoxide Reductases from the Symbionts Ignicoccus hospitalis and Nanoarchaeum equitans. Biochemistry 2018; 57:5271-5281. [PMID: 29939726 DOI: 10.1021/acs.biochem.8b00334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Superoxide reductases (SORs) are enzymes that detoxify the superoxide anion through its reduction to hydrogen peroxide and exist in both prokaryotes and eukaryotes. The substrate is transformed at an iron catalytic center, pentacoordinated in the ferrous state by four histidines and one cysteine. SORs have a highly conserved motif, (E)(K)HxP-, in which the glutamate is associated with a redox-driven structural change, completing the octahedral coordination of the iron in the ferric state, whereas the lysine may be responsible for stabilization and donation of a proton to catalytic intermediates. We aimed to understand at the structural level the role of these two residues, by determining the X-ray structures of the SORs from the hyperthermophilic archaea Ignicoccus hospitalis and Nanoarchaeum equitans that lack the quasi-conserved lysine and glutamate, respectively, but have catalytic rate constants similar to those of the canonical enzymes, as we previously demonstrated. Furthermore, we have determined the crystal structure of the E23A mutant of I. hospitalis SOR, which mimics several enzymes that lack both residues. The structures revealed distinct structural arrangements of the catalytic center that simulate several catalytic cycle intermediates, namely, the reduced and the oxidized forms, and the glutamate-free and deprotonated ferric forms. Moreover, the structure of the I. hospitalis SOR provides evidence for the presence of an alternative lysine close to the iron center in the reduced state that may be a functional substitute for the "canonical" lysine.
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Affiliation(s)
- Célia V Romão
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal
| | - Pedro M Matias
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal.,iBET , Instituto de Biologia Experimental e Tecnológica , Apartado 12 , 2781-901 Oeiras , Portugal
| | - Cristiana M Sousa
- iBET , Instituto de Biologia Experimental e Tecnológica , Apartado 12 , 2781-901 Oeiras , Portugal
| | - Filipa G Pinho
- iBET , Instituto de Biologia Experimental e Tecnológica , Apartado 12 , 2781-901 Oeiras , Portugal
| | - Ana F Pinto
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal
| | - Miguel Teixeira
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal
| | - Tiago M Bandeiras
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal.,iBET , Instituto de Biologia Experimental e Tecnológica , Apartado 12 , 2781-901 Oeiras , Portugal
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Vergara A, Caterino M, Merlino A. Raman-markers of X-ray radiation damage of proteins. Int J Biol Macromol 2018; 111:1194-1205. [PMID: 29374529 DOI: 10.1016/j.ijbiomac.2018.01.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 12/25/2022]
Abstract
Despite their high relevance, the mechanisms of X-ray radiation damage on protein structure yet have to be completely established. Here, we used Raman microspectrophotometry to follow X-ray-induced chemical modifications on the structure of the model protein bovine pancreatic ribonuclease (RNase A). The combination of dose-dependent Raman spectra and ultrahigh resolution (eight structures solved using data collected between 0.85 and 1.17 Å resolution on the same single crystal) allowed direct observation of several radiation damage events, including covalent bond breakages and formation of radicals. Our results are relevant for analytical photodamage detection and provide implications for a detailed understanding of the mechanisms of photoproduct formation.
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Affiliation(s)
- Alessandro Vergara
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy; CEINGE Biotecnologie Avanzate Scarl, Via G. Salvatore, Napoli, Italy
| | - Marco Caterino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy.
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von Stetten D, Giraud T, Bui S, Steiner RA, Fihman F, de Sanctis D, Royant A. Online Raman spectroscopy for structural biology on beamline ID29 of the ESRF. J Struct Biol 2017; 200:124-127. [DOI: 10.1016/j.jsb.2017.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/11/2017] [Accepted: 10/13/2017] [Indexed: 10/18/2022]
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13
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Li J, Banerjee A, Hasse TA, Loloee R, Biros SM, Staples RJ, Chavez FA. Synthesis and reactivity of a 4His enzyme model complex. RSC Adv 2017; 7:50713-50719. [PMID: 29147561 PMCID: PMC5683714 DOI: 10.1039/c7ra09456f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new iron(II) complex has been prepared and characterized. [Fe(TrIm)4(OTf)2] (1, TrIm = 1-Tritylimidazole). The solid state structure of 1 has been determined by X-ray crystallography. Compound 1 crystallizes in triclinic space group P1̄, with a = 13.342(7) Å, b = 13.5131(7) Å and c = 13.7025(7) Å. The iron center resides in distorted octahedral geometry coordinated to four equatorial imidazole groups and two axial triflate oxygens groups. The complex is high spin between 20 K and 300 K as indicated by variable field variable temperature magnetic measurements. A fit of the magnetic data yielded g = 2.24 and D = -0.80 cm-1. A large HOMO-LUMO gap energy (3.89 eV) exists for 1 indicating high stability. Addition of H2O2 or t BuOOH to 1 results in formation of an oxygenated intermediate which upon decomposition results in oxidation of the trityl substituent on the imidazole ligand.
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Affiliation(s)
- Jia Li
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA, , Ph: (248) 370-4092
| | - Atanu Banerjee
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA, , Ph: (248) 370-4092
| | - Timothy A Hasse
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA, , Ph: (248) 370-4092
| | - Reza Loloee
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Shannon M Biros
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Richard J Staples
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ferman A Chavez
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA, , Ph: (248) 370-4092
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David R, Jamet H, Nivière V, Moreau Y, Milet A. Iron Hydroperoxide Intermediate in Superoxide Reductase: Protonation or Dissociation First? MM Dynamics and QM/MM Metadynamics Study. J Chem Theory Comput 2017; 13:2987-3004. [DOI: 10.1021/acs.jctc.7b00126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rolf David
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/MCT, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Hélène Jamet
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
| | - Vincent Nivière
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/BioCat, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Yohann Moreau
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/MCT, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Anne Milet
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
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15
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Fujikawa M, Kobayashi K, Tsutsui Y, Tanaka T, Kozawa T. Rational Tuning of Superoxide Sensitivity in SoxR, the [2Fe-2S] Transcription Factor: Implications of Species-Specific Lysine Residues. Biochemistry 2017; 56:403-410. [DOI: 10.1021/acs.biochem.6b01096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mayu Fujikawa
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Kazuo Kobayashi
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Yuko Tsutsui
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Takahiro Tanaka
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Takahiro Kozawa
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
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16
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Attia AAA, Cioloboc D, Lupan A, Silaghi-Dumitrescu R. Multiconfigurational and DFT analyses of the electromeric formulation and UV-vis absorption spectra of the superoxide adduct of ferrous superoxide reductase. J Inorg Biochem 2016; 165:49-53. [PMID: 27768962 DOI: 10.1016/j.jinorgbio.2016.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 09/14/2016] [Accepted: 09/29/2016] [Indexed: 11/29/2022]
Abstract
The putative initial adduct of ferrous superoxide reductase (SOR) with superoxide has been alternatively formulated as ferric-peroxo or ferrous-superoxo. The ~600-nm UV-vis absorption band proposed to be assigned to this adduct (either as sole intermediate in the SOR catalytic cycle, or as one of the two intermediates) has recently been interpreted as due to a ligand-to-metal charge transfer, involving thiolate and superoxide in a ferrous complex, contrary to an alternative assignment as a predominantly cysteine thiolate-to-ferric charge transfer in a ferric-peroxo electromer. In an attempt to clarify the electromeric formulation of this adduct, we report a computational study using a multiconfigurational complete active space self-consistent field (MC-CASSCF) wave function approach as well as modelling the UV-vis absorption spectra with time-dependent density functional theory (TD-DFT). The MC-CASSCF calculations disclose a weak interaction between iron and the dioxygenic ligand and a dominant configuration with an essentially ferrous-superoxo character. The computed UV-vis absorption spectra reveal a marked dependence on the choice of density functional - both in terms of location of bands and in terms of orbital contributors. For the main band in the visible region, besides the recently reported thiolate-to-superoxide charge transfer, a more salient, and less functional-dependent, feature is a thiolate-to-ferric iron charge transfer, consistent with a ferric-peroxo electromer. By contrast, the computed UV-vis spectra of a ferric-hydroperoxo SOR model match distinctly better (and with no qualitative dependence on the DFT methodology) the 600-nm band as due to a mainly thiolate-to-ferric character - supporting the assignment of the SOR "600-nm intermediate" as a S=5/2 ferric-hydroperoxo species.
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Affiliation(s)
- Amr A A Attia
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Daniela Cioloboc
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, United States
| | - Alexandru Lupan
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.
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17
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Nakano S, Yasukawa K, Tokiwa T, Ishikawa T, Ishitsubo E, Matsuo N, Ito S, Tokiwa H, Asano Y. Origin of Stereoselectivity and Substrate/Ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase. J Phys Chem B 2016; 120:10736-10743. [DOI: 10.1021/acs.jpcb.6b09328] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shogo Nakano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kazuyuki Yasukawa
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takaki Tokiwa
- Department
of Chemistry, Graduate School of Science, Tohoku University, Aramaki,
Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takeshi Ishikawa
- Department
of Molecular Microbiology and Immunology, Graduate School of Biomedical
Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Erika Ishitsubo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Naoya Matsuo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Sohei Ito
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
- Research
Center of Smart Molecules, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuhisa Asano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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18
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Antioxidant defence systems in the protozoan pathogen Giardia intestinalis. Mol Biochem Parasitol 2016; 206:56-66. [DOI: 10.1016/j.molbiopara.2015.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 01/03/2023]
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19
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Horch M, Utesch T, Hildebrandt P, Mroginski MA, Zebger I. Domain motions and electron transfer dynamics in 2Fe-superoxide reductase. Phys Chem Chem Phys 2016; 18:23053-66. [DOI: 10.1039/c6cp03666j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical studies on 2Fe-superoxide reductase provide mechanistic insights into structural dynamics and electron transfer efficiencies.
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Affiliation(s)
- Marius Horch
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Tillmann Utesch
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Peter Hildebrandt
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | | | - Ingo Zebger
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
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20
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Sousa CM, Carpentier P, Matias PM, Testa F, Pinho F, Sarti P, Giuffrè A, Bandeiras TM, Romão CV. Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction. ACTA ACUST UNITED AC 2015; 71:2236-47. [PMID: 26527141 DOI: 10.1107/s1399004715015825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/24/2015] [Indexed: 11/11/2022]
Abstract
Superoxide reductase (SOR), which is commonly found in prokaryotic organisms, affords protection from oxidative stress by reducing the superoxide anion to hydrogen peroxide. The reaction is catalyzed at the iron centre, which is highly conserved among the prokaryotic SORs structurally characterized to date. Reported here is the first structure of an SOR from a eukaryotic organism, the protozoan parasite Giardia intestinalis (GiSOR), which was solved at 2.0 Å resolution. By collecting several diffraction data sets at 100 K from the same flash-cooled protein crystal using synchrotron X-ray radiation, photoreduction of the iron centre was observed. Reduction was monitored using an online UV-visible microspectrophotometer, following the decay of the 647 nm absorption band characteristic of the iron site in the glutamate-bound, oxidized state. Similarly to other 1Fe-SORs structurally characterized to date, the enzyme displays a tetrameric quaternary-structure arrangement. As a distinctive feature, the N-terminal loop of the protein, containing the characteristic EKHxP motif, revealed an unusually high flexibility regardless of the iron redox state. At variance with previous evidence collected by X-ray crystallography and Fourier transform infrared spectroscopy of prokaryotic SORs, iron reduction did not lead to dissociation of glutamate from the catalytic metal or other structural changes; however, the glutamate ligand underwent X-ray-induced chemical changes, revealing high sensitivity of the GiSOR active site to X-ray radiation damage.
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Affiliation(s)
- Cristiana M Sousa
- Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Philippe Carpentier
- Structural Biology Group, ESRF - The European Synchrotron, CS40220, 38043 Grenoble CEDEX 9, France
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Fabrizio Testa
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Filipa Pinho
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Paolo Sarti
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Tiago M Bandeiras
- Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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21
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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22
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Rettenmeier CA, Wadepohl H, Gade LH. Structural Characterization of a Hydroperoxo Nickel Complex and Its Autoxidation: Mechanism of Interconversion between Peroxo, Superoxo, and Hydroperoxo Species. Angew Chem Int Ed Engl 2015; 54:4880-4. [DOI: 10.1002/anie.201500141] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 11/06/2022]
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23
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Rettenmeier CA, Wadepohl H, Gade LH. Structural Characterization of a Hydroperoxo Nickel Complex and Its Autoxidation: Mechanism of Interconversion between Peroxo, Superoxo, and Hydroperoxo Species. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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von Stetten D, Giraud T, Carpentier P, Sever F, Terrien M, Dobias F, Juers DH, Flot D, Mueller-Dieckmann C, Leonard GA, de Sanctis D, Royant A. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:15-26. [PMID: 25615856 PMCID: PMC4304682 DOI: 10.1107/s139900471401517x] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/27/2014] [Indexed: 01/04/2023]
Abstract
The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for `spectroscopy'). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.
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Affiliation(s)
| | - Thierry Giraud
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | - Franc Sever
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Maxime Terrien
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Douglas H. Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, USA
| | - David Flot
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | | | | | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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25
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Pinto AF, Romão CV, Pinto LC, Huber H, Saraiva LM, Todorovic S, Cabelli D, Teixeira M. Superoxide reduction by a superoxide reductase lacking the highly conserved lysine residue. J Biol Inorg Chem 2015; 20:155-164. [PMID: 25476860 DOI: 10.1007/s00775-014-1222-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/26/2014] [Indexed: 01/12/2023]
Abstract
Superoxide reductases (SORs) are the most recently identified superoxide detoxification systems, being found in microorganisms from the three domains of life. These enzymes are characterized by a catalytic mononuclear iron site, with one cysteine and four histidine ligands of the ferrous active form. A lysine residue in the -EKHVP- motif, located close to the active site, has been considered to be essential for the enzyme function, by contributing to the positive surface patch that attracts the superoxide anion and by controlling the chemistry of the catalytic mechanism through a hydrogen bond network. However, we show here that this residue is substituted by non-equivalent amino acids in several putative SORs from Archaea and unicellular Eukarya. In this work, we focus on mechanistic and spectroscopic studies of one of these less common enzymes, the SOR from the hyperthermophilic Crenarchaeon Ignicoccus hospitalis. We employ pulse radiolysis fast kinetics and spectroscopic approaches to study the wild-type enzyme (-E23T24HVP-), and two mutants, T24K and E23A, the later mimicking enzymes lacking both the lysine and glutamate (a ferric ion ligand) of the motif. The efficiency of the wild-type protein and mutants in reducing superoxide is comparable to other SORs, revealing the robustness of these enzymes to single mutations.
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Affiliation(s)
- Ana F Pinto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177, Stockholm, Sweden
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Liliana C Pinto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Harald Huber
- Lehrstuhl fuer Mikrobiologie, Universität Regensburg, 93053, Regensburg, Germany
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Diane Cabelli
- Chemistry Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal.
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26
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Microbial biosynthesis of medium-chain 1-alkenes by a nonheme iron oxidase. Proc Natl Acad Sci U S A 2014; 111:18237-42. [PMID: 25489112 DOI: 10.1073/pnas.1419701112] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Aliphatic medium-chain 1-alkenes (MCAEs, ∼10 carbons) are "drop-in" compatible next-generation fuels and precursors to commodity chemicals. Mass production of MCAEs from renewable resources holds promise for mitigating dependence on fossil hydrocarbons. An MCAE, such as 1-undecene, is naturally produced by Pseudomonas as a semivolatile metabolite through an unknown biosynthetic pathway. We describe here the discovery of a single gene conserved in Pseudomonas responsible for 1-undecene biosynthesis. The encoded enzyme is able to convert medium-chain fatty acids (C10-C14) into their corresponding terminal olefins using an oxygen-activating, nonheme iron-dependent mechanism. Both biochemical and X-ray crystal structural analyses suggest an unusual mechanism of β-hydrogen abstraction during fatty acid substrate activation. Our discovery unveils previously unidentified chemistry in the nonheme Fe(II) enzyme family, provides an opportunity to explore the biology of 1-undecene in Pseudomonas, and paves the way for tailored bioconversion of renewable raw materials to MCAE-based biofuels and chemical commodities.
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27
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Liu J, Meier KK, Tian S, Zhang JL, Guo H, Schulz CE, Robinson H, Nilges MJ, Münck E, Lu Y. Redesigning the blue copper azurin into a redox-active mononuclear nonheme iron protein: preparation and study of Fe(II)-M121E azurin. J Am Chem Soc 2014; 136:12337-44. [PMID: 25082811 DOI: 10.1021/ja505410u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Much progress has been made in designing heme and dinuclear nonheme iron enzymes. In contrast, engineering mononuclear nonheme iron enzymes is lagging, even though these enzymes belong to a large class that catalyzes quite diverse reactions. Herein we report spectroscopic and X-ray crystallographic studies of Fe(II)-M121E azurin (Az), by replacing the axial Met121 and Cu(II) in wild-type azurin (wtAz) with Glu and Fe(II), respectively. In contrast to the redox inactive Fe(II)-wtAz, the Fe(II)-M121EAz mutant can be readily oxidized by Na2IrCl6, and interestingly, the protein exhibits superoxide scavenging activity. Mössbauer and EPR spectroscopies, along with X-ray structural comparisons, revealed similarities and differences between Fe(II)-M121EAz, Fe(II)-wtAz, and superoxide reductase (SOR) and allowed design of the second generation mutant, Fe(II)-M121EM44KAz, that exhibits increased superoxide scavenging activity by 2 orders of magnitude. This finding demonstrates the importance of noncovalent secondary coordination sphere interactions in fine-tuning enzymatic activity.
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Affiliation(s)
- Jing Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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28
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Reeves KG, Kanai Y. Theoretical oxidation state analysis of Ru-(bpy)3: influence of water solvation and Hubbard correction in first-principles calculations. J Chem Phys 2014; 141:024305. [PMID: 25028017 DOI: 10.1063/1.4886406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oxidation state is a powerful concept that is widely used in chemistry and materials physics, although the concept itself is arguably ill-defined quantum mechanically. In this work, we present impartial comparison of four, well-recognized theoretical approaches based on Lowdin atomic orbital projection, Bader decomposition, maximally localized Wannier function, and occupation matrix diagonalization, for assessing how well transition metal oxidation states can be characterized. Here, we study a representative molecular complex, tris(bipyridine)ruthenium. We also consider the influence of water solvation through first-principles molecular dynamics as well as the improved electronic structure description for strongly correlated d-electrons by including Hubbard correction in density functional theory calculations.
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Affiliation(s)
- Kyle G Reeves
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina 27599-3290, USA
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina 27599-3290, USA
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29
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Bonnot F, Tremey E, von Stetten D, Rat S, Duval S, Carpentier P, Clemancey M, Desbois A, Nivière V. Formation of High-Valent Iron-Oxo Species in Superoxide Reductase: Characterization by Resonance Raman Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Kekilli D, Dworkowski FSN, Pompidor G, Fuchs MR, Andrew CR, Antonyuk S, Strange RW, Eady RR, Hasnain SS, Hough MA. Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy. ACTA ACUST UNITED AC 2014; 70:1289-96. [PMID: 24816098 DOI: 10.1107/s1399004714004039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 02/20/2014] [Indexed: 11/10/2022]
Abstract
It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.
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Affiliation(s)
- Demet Kekilli
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | | | - Guillaume Pompidor
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Martin R Fuchs
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Colin R Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, OR 97850-2899, USA
| | - Svetlana Antonyuk
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Richard W Strange
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Robert R Eady
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - S Samar Hasnain
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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31
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Bonnot F, Tremey E, von Stetten D, Rat S, Duval S, Carpentier P, Clemancey M, Desbois A, Nivière V. Formation of High-Valent Iron-Oxo Species in Superoxide Reductase: Characterization by Resonance Raman Spectroscopy. Angew Chem Int Ed Engl 2014; 53:5926-30. [DOI: 10.1002/anie.201400356] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/13/2014] [Indexed: 11/11/2022]
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32
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Sheng Y, Abreu IA, Cabelli DE, Maroney MJ, Miller AF, Teixeira M, Valentine JS. Superoxide dismutases and superoxide reductases. Chem Rev 2014; 114:3854-918. [PMID: 24684599 PMCID: PMC4317059 DOI: 10.1021/cr4005296] [Citation(s) in RCA: 569] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Yuewei Sheng
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
| | - Isabel A. Abreu
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- Instituto
de Biologia Experimental e Tecnológica, Av. da República,
Qta. do Marquês, Estação Agronómica Nacional,
Edificio IBET/ITQB, 2780-157, Oeiras, Portugal
| | - Diane E. Cabelli
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Michael J. Maroney
- Department
of Chemistry, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Anne-Frances Miller
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Miguel Teixeira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Joan Selverstone Valentine
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
- Department
of Bioinspired Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
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Chishiro T, Kon Y, Nakashima T, Goto M, Sato K. Practical Iron-Catalyzed Hydrogen Peroxide Epoxidation of Aromatic Olefins using a Combination of Two Kinds of Simple Picolinate Ligands under Halide-Free Reaction Conditions. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300774] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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34
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Rat S, Ménage S, Thomas F, Nivière V. Non-heme iron hydroperoxo species in superoxide reductase as a catalyst for oxidation reactions. Chem Commun (Camb) 2014; 50:14213-6. [DOI: 10.1039/c4cc06114d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The non-heme high-spin ferric iron hydroperoxo species formed in superoxide reductase can act both as a nucleophile and as an electrophile to catalyze oxidation reactions.
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Affiliation(s)
- S. Rat
- Univ. Grenoble Alpes
- iRTSV-LCBM
- F-38000 Grenoble, France
- CNRS
- iRTSV-LCBM
| | - S. Ménage
- Univ. Grenoble Alpes
- iRTSV-LCBM
- F-38000 Grenoble, France
- CNRS
- iRTSV-LCBM
| | - F. Thomas
- Département de Chimie Moléculaire – Chimie Inorganique Redox Biomimétique (CIRE) – UMR CNRS 5250
- Univ. Grenoble Alpes
- 38041 Grenoble cedex 9, France
| | - V. Nivière
- Univ. Grenoble Alpes
- iRTSV-LCBM
- F-38000 Grenoble, France
- CNRS
- iRTSV-LCBM
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Horch M, Pinto AF, Mroginski MA, Teixeira M, Hildebrandt P, Zebger I. Metal-induced histidine deprotonation in biocatalysis? Experimental and theoretical insights into superoxide reductase. RSC Adv 2014. [DOI: 10.1039/c4ra11976b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An experimental and theoretical case study on superoxide reductase explores the protonation states of iron-bound histidines and their relevance for metalloenzyme catalysis.
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Affiliation(s)
- Marius Horch
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - Ana Filipa Pinto
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- P-2780-157 Oeiras, Portugal
| | | | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- P-2780-157 Oeiras, Portugal
| | - Peter Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - Ingo Zebger
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
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36
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Horch M, Pinto AF, Utesch T, Mroginski MA, Romão CV, Teixeira M, Hildebrandt P, Zebger I. Reductive activation and structural rearrangement in superoxide reductase: a combined infrared spectroscopic and computational study. Phys Chem Chem Phys 2014; 16:14220-30. [DOI: 10.1039/c4cp00884g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Local and global structural changes that enable reductive activation of superoxide reductase are revealed by a combined approach of infrared difference spectroscopy and computational methods.
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Affiliation(s)
- M. Horch
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - A. F. Pinto
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - T. Utesch
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - M. A. Mroginski
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - C. V. Romão
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - M. Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - P. Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - I. Zebger
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
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37
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Frankaer CG, Mossin S, Ståhl K, Harris P. Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T(6) bovine insulin derivatives. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:110-22. [PMID: 24419384 PMCID: PMC3919263 DOI: 10.1107/s1399004713029040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/22/2013] [Indexed: 11/21/2022]
Abstract
Using synchrotron radiation (SR), the crystal structures of T6 bovine insulin complexed with Ni(2+) and Cu(2+) were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni(2+) with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu(2+) as a result of the Jahn-Teller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01 Å. The insulin derivative containing Cu(2+) is sensitive towards photoreduction when exposed to SR. During the reduction of Cu(2+) to Cu(+), the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of structural changes around the Cu atoms after exposure to different radiation doses was studied by crystallography using a laboratory diffractometer. Protection against photoreduction and subsequent radiation damage was carried out by solid embedment of Cu insulin in a saccharose matrix. At 100 K the photoreduction was suppressed by ∼15%, and it was suppressed by a further ∼30% on cooling the samples to 20 K.
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Affiliation(s)
| | - Susanne Mossin
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs. Lyngby, Denmark
| | - Kenny Ståhl
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs. Lyngby, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs. Lyngby, Denmark
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38
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Reaction of Hg2+ Insertion into Cysteine Pairs Within Bovine Insulin Crystals Followed via Raman Spectroscopy. J SOLUTION CHEM 2013. [DOI: 10.1007/s10953-013-0066-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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39
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Pompidor G, Dworkowski FSN, Thominet V, Schulze-Briese C, Fuchs MR. A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:765-76. [PMID: 23955041 PMCID: PMC3747950 DOI: 10.1107/s0909049513016063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/10/2013] [Indexed: 05/08/2023]
Abstract
The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years.
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Affiliation(s)
| | | | | | | | - Martin R. Fuchs
- Paul Scherrer Institut, CH-5232 Villigen, Switzerland
- Correspondence e-mail:
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40
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Tremey E, Bonnot F, Moreau Y, Berthomieu C, Desbois A, Favaudon V, Blondin G, Houée-Levin C, Nivière V. Hydrogen bonding to the cysteine ligand of superoxide reductase: acid–base control of the reaction intermediates. J Biol Inorg Chem 2013; 18:815-30. [DOI: 10.1007/s00775-013-1025-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/15/2013] [Indexed: 12/26/2022]
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41
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Lee YM, Bang S, Kim YM, Cho J, Hong S, Nomura T, Ogura T, Troeppner O, Ivanović-Burmazović I, Sarangi R, Fukuzumi S, Nam W. A Mononuclear Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Metal Ions. Chem Sci 2013; 4:3917-3923. [PMID: 25426288 PMCID: PMC4241270 DOI: 10.1039/c3sc51864g] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Redox-inactive metal ions that function as Lewis acids play pivotal roles in modulating reactivities of oxygen-containing metal complexes in a variety of biological and biomimetic reactions, including dioxygen activation/formation and functionalization of organic substrates. Mononuclear nonheme iron(III)-peroxo species are invoked as active oxygen intermediates in the catalytic cycles of dioxygen activation by nonheme iron enzymes and their biomimetic compounds. Here, we report mononuclear nonheme iron(III)-peroxo complexes binding redox-inactive metal ions, [(TMC)FeIII(O2)]+-M3+ (M3+ = Sc3+ and Y3+; TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), which are characterized spectroscopically as a 'side-on' iron(III)-peroxo complex binding a redox-inactive metal ion, (TMC)FeIII-(μ,η2:η2-O2)-M3+ (2-M). While an iron(III)-peroxo complex, [(TMC)FeIII(O2)]+, does not react with electron donors (e.g., ferrocene), one-electron reduction of the iron(III)-peroxo complexes binding redox-inactive metal ions occurs readily upon addition of electron donors, resulting in the generation of an iron(IV)-oxo complex, [(TMC)FeIV(O)]2+ (4), via heterolytic O-O bond cleavage of the peroxide ligand. The rates of the conversion of 2-M to 4 are found to depend on the Lewis acidity of the redox-inactive metal ions and the oxidation potential of the electron donors. We have also determined the fundamental electron-transfer properties of 2-M, such as the reduction potential and the reorganization energy in electron-transfer reaction. Based on the results presented herein, we have proposed a mechanism for the reactions of 2-M and electron donors; the reduction of 2-M to the reduced species, (TMC)FeII-(O2)-M3+ (2'-M), is the rate-determining step, followed by heterolytic O-O bond cleavage of the reduced species to form 4. The present results provide a biomimetic example demonstrating that redox-inactive metal ions bound to an iron(III)-peroxo intermediate play a significant role in activating the peroxide O-O bond to form a high-valent iron(IV)-oxo species.
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Affiliation(s)
- Yong-Min Lee
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Suhee Bang
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Yun Mi Kim
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeheung Cho
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea ; Department of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - Seungwoo Hong
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Takashi Nomura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Oliver Troeppner
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | | | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Shunichi Fukuzumi
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea ; Department of Material and Life Science, Graduate School of Engineering, ALCA, Japan Science and Technology Agency (JST), Osaka University, Suita, Osaka 565-0871, Japan
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
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42
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Li F, Van Heuvelen KM, Meier KK, Münck E, Que L. Sc3+-triggered oxoiron(IV) formation from O2 and its non-heme iron(II) precursor via a Sc3+-peroxo-Fe3+ intermediate. J Am Chem Soc 2013; 135:10198-201. [PMID: 23802702 PMCID: PMC3760346 DOI: 10.1021/ja402645y] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report that redox-inactive Sc(3+) can trigger O2 activation by the Fe(II)(TMC) center (TMC = tetramethylcyclam) to generate the corresponding oxoiron(IV) complex in the presence of BPh4(-) as an electron donor. To model a possible intermediate in the above reaction, we generated an unprecedented Sc(3+) adduct of [Fe(III)(η(2)-O2)(TMC)](+) by an alternative route, which was found to have an Fe(3+)-(μ-η(2):η(2)-peroxo)-Sc(3+) core and to convert to the oxoiron(IV) complex. These results have important implications for the role a Lewis acid can play in facilitating O-O bond cleavage during the course of O2 activation at non-heme iron centers.
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Affiliation(s)
- Feifei Li
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Katherine M. Van Heuvelen
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Katlyn K. Meier
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
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43
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part I. {Fe(SγCys)4} proteins. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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44
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Krauss IR, Merlino A, Vergara A, Sica F. An overview of biological macromolecule crystallization. Int J Mol Sci 2013; 14:11643-91. [PMID: 23727935 PMCID: PMC3709751 DOI: 10.3390/ijms140611643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/11/2022] Open
Abstract
The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-81-674-479; Fax: +39-81-674-090
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46
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Min D, Zhang X, He W, Zhang Y, Li P, Zhang M, Liu J, Liu S, Xu F, Du Y, Zhang Z. Direct immobilization of glucose oxidase in magnetic mesoporous bioactive glasses. J Mater Chem B 2013; 1:3295-3303. [DOI: 10.1039/c3tb20480d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Collado A, Gómez-Suárez A, Oonishi Y, Slawin AMZ, Nolan SP. Synthesis, characterisation, and oxygen atom transfer reactions involving the first gold(i)-alkylperoxo complexes. Chem Commun (Camb) 2013; 49:10745-7. [DOI: 10.1039/c3cc47030j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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48
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Fe–O versus O–O bond cleavage in reactive iron peroxide intermediates of superoxide reductase. J Biol Inorg Chem 2012; 18:95-101. [DOI: 10.1007/s00775-012-0954-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
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49
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Wahlgren WY, Omran H, von Stetten D, Royant A, van der Post S, Katona G. Structural characterization of bacterioferritin from Blastochloris viridis. PLoS One 2012; 7:e46992. [PMID: 23056552 PMCID: PMC3467274 DOI: 10.1371/journal.pone.0046992] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Accepted: 09/07/2012] [Indexed: 12/02/2022] Open
Abstract
Iron storage and elimination of toxic ferrous iron are the responsibility of bacterioferritins in bacterial species. Bacterioferritins are capable of oxidizing iron using molecular oxygen and import iron ions into the large central cavity of the protein, where they are stored in a mineralized form. We isolated, crystallized bacterioferritin from the microaerophilic/anaerobic, purple non-sulfur bacterium Blastochloris viridis and determined its amino acid sequence and X-ray structure. The structure and sequence revealed similarity to other purple bacterial species with substantial differences in the pore regions. Static 3- and 4-fold pores do not allow the passage of iron ions even though structural dynamics may assist the iron gating. On the other hand the B-pore is open to water and larger ions in its native state. In order to study the mechanism of iron import, multiple soaking experiments were performed. Upon Fe(II) and urea treatment the ferroxidase site undergoes reorganization as seen in bacterioferritin from Escherichia coli and Pseudomonas aeruginosa. When soaking with Fe(II) only, a closely bound small molecular ligand is observed close to Fe1 and the coordination of Glu94 to Fe2 changes from bidentate to monodentate. DFT calculations indicate that the bound ligand is most likely a water or a hydroxide molecule representing a product complex. On the other hand the different soaking treatments did not modify the conformation of other pore regions.
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Affiliation(s)
- Weixiao Y. Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Hadil Omran
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | | | - Antoine Royant
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale Jean-Pierre Ebel, CNRS CEA Université Joseph Fourier, Grenoble, France
| | | | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
- * E-mail:
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50
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McDonald AR, Van Heuvelen KM, Guo Y, Li F, Bominaar EL, Münck E, Que L. Characterization of a thiolato iron(III) Peroxy dianion complex. Angew Chem Int Ed Engl 2012; 51:9132-6. [PMID: 22888066 PMCID: PMC3448492 DOI: 10.1002/anie.201203602] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/19/2012] [Indexed: 11/09/2022]
Abstract
Nucleophilic oxidant: The reaction between a thiolato iron(II) complex 1 and superoxide in aprotic solvent at -90 °C yields a novel thiolato iron(III) peroxide intermediate 2, which exhibits unusually high nucleophilic reactivity. Compound 2 is an isomer of the thiolato iron(II) superoxide intermediate that is invoked in the reaction between superoxide reductase and superoxide.
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Affiliation(s)
- Aidan R. McDonald
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Katherine M. Van Heuvelen
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Feifei Li
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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