1
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Fasano A, Fourmond V, Léger C. Outer-sphere effects on the O 2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases. Chem Sci 2024; 15:5418-5433. [PMID: 38638217 PMCID: PMC11023054 DOI: 10.1039/d4sc00691g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
The comparison of homologous metalloenzymes, in which the same inorganic active site is surrounded by a variable protein matrix, has demonstrated that residues that are remote from the active site may have a great influence on catalytic properties. In this review, we summarise recent findings on the diverse molecular mechanisms by which the protein matrix may define the oxygen tolerance, catalytic directionality and catalytic reversibility of hydrogenases, enzymes that catalyse the oxidation and evolution of H2. These mechanisms involve residues in the second coordination sphere of the active site metal ion, more distant residues affecting protein flexibility through their side chains, residues lining the gas channel and even accessory subunits. Such long-distance effects, which contribute to making enzymes efficient, robust and different from one another, are a source of wonder for biochemists and a challenge for synthetic bioinorganic chemists.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
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2
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Aldinio-Colbachini A, Grossi A, Duarte AG, Daurelle JV, Fourmond V. Combining a Commercial Mixer with a Wall-Tube Electrode Allows the Arbitrary Control of Concentrations in Protein Film Electrochemistry. Anal Chem 2024; 96:4868-4875. [PMID: 38466774 DOI: 10.1021/acs.analchem.3c05293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Protein film electrochemistry is a technique in which an enzyme is immobilized on an electrode in a configuration that allows following the changes in turnover frequency as a response to changes in the experimental conditions. Insights into the reactivity of the enzyme can be obtained by quantitatively modeling such responses. As a consequence, the more the technique allows flexibility in changing conditions, the more useful it becomes. The most commonly used setup, based on the rotating disc electrode, allows easy stepwise increases in the concentration of nongaseous substrates, or exposure to constant concentration of dissolved gas, but does not permit to easily decrease the concentration of nongaseous substrates, or to change the concentration of dissolved gas in a stepwise fashion. To overcome the limitation by mass transport of the substrate toward the electrode when working with fast enzymes, we have designed another kind of electrochemical cell based on the wall-tube electrode (WTE). We demonstrate here that by using a system combining two syringe pumps, a commercial mixer, and the WTE, it is possible to change the concentration of species in a stepwise fashion in all directions, opening new possibilities to study redox enzymes. As a proof of concept, this device was applied to the study of the electrochemical response of the cytochrome c nitrite reductase of Desulfovibrio desulfuricans.
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Affiliation(s)
- Anna Aldinio-Colbachini
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
- Laboratoire IUSTI (UMR AMU-CNRS 7343) Polytech Marseille, Dpt Mécanique Energétique (ME), Technopôle de Château Gombert, 5 rue Enrico Fermi, Marseille cedex 13 13453, France
| | - Alain Grossi
- Aix-Marseille Université, CNRS, IMM FR3479, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Jean-Vincent Daurelle
- Laboratoire IUSTI (UMR AMU-CNRS 7343) Polytech Marseille, Dpt Mécanique Energétique (ME), Technopôle de Château Gombert, 5 rue Enrico Fermi, Marseille cedex 13 13453, France
| | - Vincent Fourmond
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
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3
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Duan J, Veliju A, Lampret O, Liu L, Yadav S, Apfel UP, Armstrong FA, Hemschemeier A, Hofmann E. Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases. J Am Chem Soc 2023; 145:26068-26074. [PMID: 37983562 DOI: 10.1021/jacs.3c07800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
[FeFe]-hydrogenases are efficient H2 converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor's amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules.
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Affiliation(s)
- Jifu Duan
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Astrit Veliju
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Oliver Lampret
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lingling Liu
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Shanika Yadav
- Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Energy, Electrosynthesis Group, Fraunhofer UMSICHT, 46047 Oberhausen, Germany
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Anja Hemschemeier
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
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4
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Corrigan PS, Majer SH, Silakov A. Evidence of Atypical Structural Flexibility of the Active Site Surrounding of an [FeFe] Hydrogenase from Clostridium beijerinkii. J Am Chem Soc 2023; 145:11033-11044. [PMID: 37163727 DOI: 10.1021/jacs.2c13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
[FeFe] hydrogenase from Clostridium beijerinkii (CbHydA1) is an unusual hydrogenase in that it can withstand prolonged exposure to O2 by reversibly converting into an O2-protected, inactive state (Hinact). It has been indicated in the past that an atypical conformation of the "SC367CP" loop near the [2Fe]H portion of the six-iron active site (H-cluster) allows the Cys367 residue to adopt an "off-H+-pathway" orientation, promoting a facile transition of the cofactor to Hinact. Here, we investigated the electronic structure of the H-cluster in the oxidized state (Hox) that directly converts to Hinact under oxidizing conditions and the related CO-inhibited state (Hox-CO). We demonstrate that both states exhibit two distinct forms in electron paramagnetic resonance (EPR) spectroscopy. The ratio between the two forms is pH-dependent but also sensitive to the buffer choice. Our IR and EPR analyses illustrate that the spectral heterogeneity is due to a perturbation of the coordination environment of the H-cluster's [4Fe4S]H subcluster without affecting the [2Fe]H subcluster. Overall, we conclude that the observation of two spectral components per state is evidence of heterogeneity of the environment of the H-cluster likely associated with conformational mobility of the SCCP loop. Such flexibility may allow Cys367 to switch rapidly between off- and on-H+-pathway rotamers. Consequently, we believe such structural mobility may be the key to maintaining high enzymatic activity while allowing a facile transition to the O2-protected state.
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Affiliation(s)
- Patrick S Corrigan
- Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Sean H Majer
- Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
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5
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Sidabras JW, Stripp ST. A personal account on 25 years of scientific literature on [FeFe]-hydrogenase. J Biol Inorg Chem 2023; 28:355-378. [PMID: 36856864 DOI: 10.1007/s00775-023-01992-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/25/2023] [Indexed: 03/02/2023]
Abstract
[FeFe]-hydrogenases are gas-processing metalloenzymes that catalyze H2 oxidation and proton reduction (H2 release) in microorganisms. Their high turnover frequencies and lack of electrical overpotential in the hydrogen conversion reaction has inspired generations of biologists, chemists, and physicists to explore the inner workings of [FeFe]-hydrogenase. Here, we revisit 25 years of scientific literature on [FeFe]-hydrogenase and propose a personal account on 'must-read' research papers and review article that will allow interested scientists to follow the recent discussions on catalytic mechanism, O2 sensitivity, and the in vivo synthesis of the active site cofactor with its biologically uncommon ligands carbon monoxide and cyanide. Focused on-but not restricted to-structural biology and molecular biophysics, we highlight future directions that may inspire young investigators to pursue a career in the exciting and competitive field of [FeFe]-hydrogenase research.
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Affiliation(s)
- Jason W Sidabras
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI, USA, 53226.
| | - Sven T Stripp
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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6
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Man HM, Mazurenko I, Le Guenno H, Bouffier L, Lojou E, de Poulpiquet A. Local pH Modulation during Electro-Enzymatic O 2 Reduction: Characterization of the Influence of Ionic Strength by In Situ Fluorescence Microscopy. Anal Chem 2022; 94:15604-15612. [DOI: 10.1021/acs.analchem.2c02135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiu Mun Man
- Laboratory of Bioenergetics and Protein Engineering, Mediterranean Institute of Microbiology, Aix-Marseille Univ., CNRS, UMR, 7281Marseille, France
| | - Ievgen Mazurenko
- Laboratory of Bioenergetics and Protein Engineering, Mediterranean Institute of Microbiology, Aix-Marseille Univ., CNRS, UMR, 7281Marseille, France
| | - Hugo Le Guenno
- Mediterranean Institute of Microbiology, CNRS, Microscopy Facility, FR 3479Marseille, France
| | - Laurent Bouffier
- Institute of Molecular Sciences, Univ. Bordeaux, CNRS, Bordeaux INP, UMR 5255, F-33400Talence, France
| | - Elisabeth Lojou
- Laboratory of Bioenergetics and Protein Engineering, Mediterranean Institute of Microbiology, Aix-Marseille Univ., CNRS, UMR, 7281Marseille, France
| | - Anne de Poulpiquet
- Laboratory of Bioenergetics and Protein Engineering, Mediterranean Institute of Microbiology, Aix-Marseille Univ., CNRS, UMR, 7281Marseille, France
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7
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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8
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Chatelain L, Breton JB, Arrigoni F, Schollhammer P, Zampella G. Geometrical influence on the non-biomimetic heterolytic splitting of H 2 by bio-inspired [FeFe]-hydrogenase complexes: a rare example of inverted frustrated Lewis pair based reactivity. Chem Sci 2022; 13:4863-4873. [PMID: 35655865 PMCID: PMC9067592 DOI: 10.1039/d1sc06975f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/13/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the high levels of interest in the synthesis of bio-inspired [FeFe]-hydrogenase complexes, H2 oxidation, which is one specific aspect of hydrogenase enzymatic activity, is not observed for most reported complexes. To attempt H-H bond cleavage, two disubstituted diiron dithiolate complexes in the form of [Fe2(μ-pdt)L2(CO)4] (L: PMe3, dmpe) have been used to play the non-biomimetic role of a Lewis base, with frustrated Lewis pairs (FLPs) formed in the presence of B(C6F5)3 Lewis acid. These unprecedented FLPs, based on the bimetallic Lewis base partner, allow the heterolytic splitting of the H2 molecule, forming a protonated diiron cation and hydrido-borate anion. The substitution, symmetrical or asymmetrical, of two phosphine ligands at the diiron dithiolate core induces a strong difference in the H2 bond cleavage abilities, with the FLP based on the first complex being more efficient than the second. DFT investigations examined the different mechanistic pathways involving each accessible isomer and rationalized the experimental findings. One of the main DFT results highlights that the iron site acting as a Lewis base for the asymmetrical complex is the {Fe(CO)3} subunit, which is less electron-rich than the {FeL(CO)2} site of the symmetrical complex, diminishing the reactivity towards H2. Calculations relating to the different mechanistic pathways revealed the presence of a terminal hydride intermediate at the apical site of a rotated {Fe(CO)3} site, which is experimentally observed, and a semi-bridging hydride intermediate from H2 activation at the Fe-Fe site; these are responsible for a favourable back-reaction, reducing the conversion yield observed in the case of the asymmetrical complex. The use of two equivalents of Lewis acid allows for more complete and faster H2 bond cleavage due to the encapsulation of the hydrido-borate species by a second borane, favouring the reactivity of each FLP, in agreement with DFT calculations.
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Affiliation(s)
- Lucile Chatelain
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Jean-Baptiste Breton
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Federica Arrigoni
- Department of Biotechnology and Bioscience, University of Milano-Bicocca Piazza della Scienza 2 20126 Milan Italy
| | - Philippe Schollhammer
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Giuseppe Zampella
- Department of Biotechnology and Bioscience, University of Milano-Bicocca Piazza della Scienza 2 20126 Milan Italy
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9
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Senger M, Kernmayr T, Lorenzi M, Redman HJ, Berggren G. Hydride state accumulation in native [FeFe]-hydrogenase with the physiological reductant H2 supports its catalytic relevance. Chem Commun (Camb) 2022; 58:7184-7187. [PMID: 35670542 PMCID: PMC9219605 DOI: 10.1039/d2cc00671e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecules in solution may interfere with mechanistic investigations, as they can affect the stability of catalytic states and produce off-cycle states that can be mistaken for catalytically relevant species. Here we show that the hydride state (Hhyd), a proposed central intermediate in the catalytic cycle of [FeFe]-hydrogenase, can be formed in wild-type [FeFe]-hydrogenases treated with H2 in absence of other, non-biological, reductants. Moreover, we reveal a new state with unclear role in catalysis induced by common low pH buffers. Studies of enzymatic catalysis often rely on non-biological reagents, which may affect catalytic intermediates and produce off-cycle states. Here the influence of buffer and reductant on key intermediates of [FeFe]-hydrogenase are explored.![]()
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Affiliation(s)
- Moritz Senger
- Department of Chemistry, Physical Chemistry, Uppsala University, 75120 Uppsala, Sweden.
| | - Tobias Kernmayr
- Department of Chemistry, Molecular Biomimetics, Uppsala University, 75120 Uppsala, Sweden.
| | - Marco Lorenzi
- Department of Chemistry, Molecular Biomimetics, Uppsala University, 75120 Uppsala, Sweden.
| | - Holly J Redman
- Department of Chemistry, Molecular Biomimetics, Uppsala University, 75120 Uppsala, Sweden.
| | - Gustav Berggren
- Department of Chemistry, Molecular Biomimetics, Uppsala University, 75120 Uppsala, Sweden.
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10
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Fasano A, Land H, Fourmond V, Berggren G, Léger C. Reversible or Irreversible Catalysis of H +/H 2 Conversion by FeFe Hydrogenases. J Am Chem Soc 2021; 143:20320-20325. [PMID: 34813699 DOI: 10.1021/jacs.1c09554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies of molecular catalysts traditionally aim at understanding how a certain mechanism allows the reaction to be fast. A distinct question, which has only recently received attention in the case of bidirectional molecular catalysts, is how much thermodynamic driving force is required to achieve fast catalysis in either direction of the reaction. "Reversible" catalysts are bidirectional catalysts that work either way in response to even a small departure from equilibrium and thus do not waste input free energy as heat; conversely, "irreversible" catalysts require a large driving force to proceed at an appreciable rate [Fourmond et al. Nat. Rev. Chem. 2021, 5, 348-360]. Numerous mechanistic rationales for these contrasting behaviors have been proposed. To understand the determinants of catalytic (ir)reversibility, we examined the steady-state, direct electron transfer voltammetry of a particular FeFe hydrogenase, from Thermoanaerobacter mathranii, which is very unusual in that it irreversibly catalyzes H2 oxidation and production: a large overpotential is required for the reaction to proceed in either direction [Land et al. Chem. Sci. 2020, 11, 12789-12801]. In contrast to previous hypotheses, we demonstrate that in this particular enzyme catalytic irreversibility can be explained without invoking slow interfacial electron transfer or variations in the mechanism: the observed kinetics is fully consistent with the same catalytic pathway being used in both directions of the reaction.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
| | - Henrik Land
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Box-523, Uppsala 751 20, Sweden
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Box-523, Uppsala 751 20, Sweden
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
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11
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Felbek C, Arrigoni F, de Sancho D, Jacq-Bailly A, Best RB, Fourmond V, Bertini L, Léger C. Mechanism of Hydrogen Sulfide-Dependent Inhibition of FeFe Hydrogenase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christina Felbek
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille Cedex 20 13402, France
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - David de Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20080 Donostia-San Sebastián, Spain
| | - Aurore Jacq-Bailly
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille Cedex 20 13402, France
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, Maryland 20892-0520, United States
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille Cedex 20 13402, France
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille Cedex 20 13402, France
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12
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Birrell JA, Rodríguez-Maciá P, Reijerse EJ, Martini MA, Lubitz W. The catalytic cycle of [FeFe] hydrogenase: A tale of two sites. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214191] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Abstract
Efficient electrocatalytic energy conversion requires the devices to function reversibly, i.e. deliver a significant current at minimal overpotential. Redox-active films can effectively embed and stabilise molecular electrocatalysts, but mediated electron transfer through the film typically makes the catalytic response irreversible. Here, we describe a redox-active film for bidirectional (oxidation or reduction) and reversible hydrogen conversion, consisting of [FeFe] hydrogenase embedded in a low-potential, 2,2’-viologen modified hydrogel. When this catalytic film served as the anode material in a H2/O2 biofuel cell, an open circuit voltage of 1.16 V was obtained - a benchmark value near the thermodynamic limit. The same film also acted as a highly energy efficient cathode material for H2 evolution. We explained the catalytic properties using a kinetic model, which shows that reversibility can be achieved despite intermolecular electron transfer being slower than catalysis. This understanding of reversibility simplifies the design principles of highly efficient and stable bioelectrocatalytic films, advancing their implementation in energy conversion.
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Abstract
[FeFe]-hydrogenases are efficient H2-catalysts, yet upon contact with dioxygen their catalytic cofactor (H-cluster) is irreversibly inactivated. Here, we combine X-ray crystallography, rational protein design, direct electrochemistry, and Fourier-transform infrared spectroscopy to describe a protein morphing mechanism that controls the reversible transition between the catalytic Hox-state and the inactive but oxygen-resistant Hinact-state in [FeFe]-hydrogenase CbA5H of Clostridium beijerinckii. The X-ray structure of air-exposed CbA5H reveals that a conserved cysteine residue in the local environment of the active site (H-cluster) directly coordinates the substrate-binding site, providing a safety cap that prevents O2-binding and consequently, cofactor degradation. This protection mechanism depends on three non-conserved amino acids situated approximately 13 Å away from the H-cluster, demonstrating that the 1st coordination sphere chemistry of the H-cluster can be remote-controlled by distant residues.
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15
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Jacq-Bailly A, Benvenuti M, Payne N, Kpebe A, Felbek C, Fourmond V, Léger C, Brugna M, Baffert C. Electrochemical Characterization of a Complex FeFe Hydrogenase, the Electron-Bifurcating Hnd From Desulfovibrio fructosovorans. Front Chem 2021; 8:573305. [PMID: 33490032 PMCID: PMC7820892 DOI: 10.3389/fchem.2020.573305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/10/2020] [Indexed: 12/02/2022] Open
Abstract
Hnd, an FeFe hydrogenase from Desulfovibrio fructosovorans, is a tetrameric enzyme that can perform flavin-based electron bifurcation. It couples the oxidation of H2 to both the exergonic reduction of NAD+ and the endergonic reduction of a ferredoxin. We previously showed that Hnd retains activity even when purified aerobically unlike other electron-bifurcating hydrogenases. In this study, we describe the purification of the enzyme under O2-free atmosphere and its biochemical and electrochemical characterization. Despite its complexity due to its multimeric composition, Hnd can catalytically and directly exchange electrons with an electrode. We characterized the catalytic and inhibition properties of this electron-bifurcating hydrogenase using protein film electrochemistry of Hnd by purifying Hnd aerobically or anaerobically, then comparing the electrochemical properties of the enzyme purified under the two conditions via protein film electrochemistry. Hydrogenases are usually inactivated under oxidizing conditions in the absence of dioxygen and can then be reactivated, to some extent, under reducing conditions. We demonstrate that the kinetics of this high potential inactivation/reactivation for Hnd show original properties: it depends on the enzyme purification conditions and varies with time, suggesting the coexistence and the interconversion of two forms of the enzyme. We also show that Hnd catalytic properties (Km for H2, diffusion and reaction at the active site of CO and O2) are comparable to those of standard hydrogenases (those which cannot catalyze electron bifurcation). These results suggest that the presence of the additional subunits, needed for electron bifurcation, changes neither the catalytic behavior at the active site, nor the gas diffusion kinetics but induces unusual rates of high potential inactivation/reactivation.
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Affiliation(s)
| | | | - Natalie Payne
- CNRS, Aix Marseille University, BIP, Marseille, France
| | - Arlette Kpebe
- CNRS, Aix Marseille University, BIP, Marseille, France
| | | | | | | | - Myriam Brugna
- CNRS, Aix Marseille University, BIP, Marseille, France
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16
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Rodríguez‐Maciá P, Galle LM, Bjornsson R, Lorent C, Zebger I, Yoda Y, Cramer SP, DeBeer S, Span I, Birrell JA. Caught in the H inact : Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O 2 -stable State of [FeFe] Hydrogenase. Angew Chem Int Ed Engl 2020; 59:16786-16794. [PMID: 32488975 PMCID: PMC7540559 DOI: 10.1002/anie.202005208] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/01/2020] [Indexed: 01/25/2023]
Abstract
[FeFe] hydrogenases are the most active H2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O2 -stable state called Hinact . To date, the structure and mechanism of formation of Hinact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in-depth spectroscopic characterization by X-ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O2 -stable hydrogenases and molecular catalysts.
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Affiliation(s)
- Patricia Rodríguez‐Maciá
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstraße 34–3645470Mülheim an der RuhrGermany
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Lisa M. Galle
- Physikalische BiologieHeinrich-Heine-Universität DüsseldorfUniversitätsstraße 140225DüsseldorfGermany
| | - Ragnar Bjornsson
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstraße 34–3645470Mülheim an der RuhrGermany
| | - Christian Lorent
- Physikalische Chemie/ Biophysikalische ChemieInstitut für ChemieTechnische Universität BerlinStraße des 17. Juni 13510623BerlinGermany
| | - Ingo Zebger
- Physikalische Chemie/ Biophysikalische ChemieInstitut für ChemieTechnische Universität BerlinStraße des 17. Juni 13510623BerlinGermany
| | - Yoshitaka Yoda
- Japanese Synchrotron Radiation Institute, Spring-81-1-1 Kouto, Mikazuki-choSayo-gunHyogo679-5198Japan
| | | | - Serena DeBeer
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstraße 34–3645470Mülheim an der RuhrGermany
| | - Ingrid Span
- Physikalische BiologieHeinrich-Heine-Universität DüsseldorfUniversitätsstraße 140225DüsseldorfGermany
| | - James A. Birrell
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstraße 34–3645470Mülheim an der RuhrGermany
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17
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Rodríguez‐Maciá P, Galle LM, Bjornsson R, Lorent C, Zebger I, Yoda Y, Cramer SP, DeBeer S, Span I, Birrell JA. Kristallstruktur und Spektroskopie offenbaren einen Schwefel‐Liganden am aktiven Zentrum einer O
2
‐stabilen [FeFe]‐Hydrogenase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Patricia Rodríguez‐Maciá
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy Conversion Stiftstraße 34–36 45470 Mülheim an der Ruhr Deutschland
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QR UK
| | - Lisa M. Galle
- Physikalische BiologieHeinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Deutschland
| | - Ragnar Bjornsson
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy Conversion Stiftstraße 34–36 45470 Mülheim an der Ruhr Deutschland
| | - Christian Lorent
- Physikalische Chemie/ Biophysikalische ChemieInstitut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Ingo Zebger
- Physikalische Chemie/ Biophysikalische ChemieInstitut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Yoshitaka Yoda
- Japanese Synchrotron Radiation Institute, Spring-8 1-1-1 Kouto, Mikazuki-cho Sayo-gun Hyogo 679-5198 Japan
| | - Stephen P. Cramer
- SETI Institute 189 Bernardo Avenue Mountain View California 94043 USA
| | - Serena DeBeer
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy Conversion Stiftstraße 34–36 45470 Mülheim an der Ruhr Deutschland
| | - Ingrid Span
- Physikalische BiologieHeinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Deutschland
| | - James A. Birrell
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy Conversion Stiftstraße 34–36 45470 Mülheim an der Ruhr Deutschland
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18
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Barrio M, Fourmond V. Redox (In)activations of Metalloenzymes: A Protein Film Voltammetry Approach. ChemElectroChem 2019. [DOI: 10.1002/celc.201901028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Melisa Barrio
- CNRSAix-Marseille Université, BIP UMR 7281 31 chemin J. Aiguier F-13402 Marseille cedex 20 France
| | - Vincent Fourmond
- CNRSAix-Marseille Université, BIP UMR 7281 31 chemin J. Aiguier F-13402 Marseille cedex 20 France
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19
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Fourmond V, Wiedner ES, Shaw WJ, Léger C. Understanding and Design of Bidirectional and Reversible Catalysts of Multielectron, Multistep Reactions. J Am Chem Soc 2019; 141:11269-11285. [PMID: 31283209 DOI: 10.1021/jacs.9b04854] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some enzymes, including those that are involved in the activation of small molecules such as H2 or CO2, can be wired to electrodes and function in either direction of the reaction depending on the electrochemical driving force and display a significant rate at very small deviations from the equilibrium potential. We call the former property "bidirectionality" and the latter "reversibility". This performance sets very high standards for chemists who aim at designing synthetic electrocatalysts. Only recently, in the particular case of the hydrogen production/evolution reaction, has it been possible to produce inorganic catalysts that function bidirectionally, with an even smaller number that also function reversibly. This raises the question of how to engineer such desirable properties in other synthetic catalysts. Here we introduce the kinetic modeling of bidirectional two-electron-redox reactions in the case of molecular catalysts and enzymes that are either attached to an electrode or diffusing in solution in the vicinity of an electrode. We emphasize that trying to discuss bidirectionality and reversibility in relation to a single redox potential leads to an impasse: the catalyst undergoes two redox transitions, and therefore two catalytic potentials must be defined, which may depart from the two potentials measured in the absence of catalysis. The difference between the two catalytic potentials defines the reversibility; the difference between their average value and the equilibrium potential defines the directionality (also called "preference", or "bias"). We describe how the sequence of events in the bidirectional catalytic cycle can be elucidated on the basis of the voltammetric responses. Further, we discuss the design principles of bidirectionality and reversibility in terms of thermodynamics and kinetics and conclude that neither bidirectionality nor reversibility requires that the catalytic energy landscape be flat. These theoretical findings are illustrated by previous results obtained with nickel diphosphine molecular catalysts and hydrogenases. In particular, analysis of the nickel catalysts highlights the fact that reversible catalysis can be achieved by catalysts that follow complex mechanisms with branched reaction pathways.
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Affiliation(s)
- Vincent Fourmond
- Aix Marseille Université , CNRS, BIP UMR 7281 , Marseille , France
| | - Eric S Wiedner
- Pacific Northwest National Laboratory , P.O. Box 999, K2-57, Richland , Washington 99352 , United States
| | - Wendy J Shaw
- Pacific Northwest National Laboratory , P.O. Box 999, K2-57, Richland , Washington 99352 , United States
| | - Christophe Léger
- Aix Marseille Université , CNRS, BIP UMR 7281 , Marseille , France
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20
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Rodríguez-Maciá P, Kertess L, Burnik J, Birrell JA, Hofmann E, Lubitz W, Happe T, Rüdiger O. His-Ligation to the [4Fe–4S] Subcluster Tunes the Catalytic Bias of [FeFe] Hydrogenase. J Am Chem Soc 2018; 141:472-481. [DOI: 10.1021/jacs.8b11149] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Patricia Rodríguez-Maciá
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Leonie Kertess
- Photobiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Jan Burnik
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - James A. Birrell
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Thomas Happe
- Photobiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
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21
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Oughli AA, Vélez M, Birrell JA, Schuhmann W, Lubitz W, Plumeré N, Rüdiger O. Viologen-modified electrodes for protection of hydrogenases from high potential inactivation while performing H 2 oxidation at low overpotential. Dalton Trans 2018; 47:10685-10691. [PMID: 29881850 PMCID: PMC6083823 DOI: 10.1039/c8dt00955d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this work we present a viologen-modified electrode providing protection for hydrogenases against high potential inactivation.
In this work we present a viologen-modified electrode providing protection for hydrogenases against high potential inactivation. Hydrogenases, including O2-tolerant classes, suffer from reversible inactivation upon applying high potentials, which limits their use in biofuel cells to certain conditions. Our previously reported protection strategy based on the integration of hydrogenase into redox matrices enabled the use of these biocatalysts in biofuel cells even under anode limiting conditions. However, mediated catalysis required application of an overpotential to drive the reaction, and this translates into a power loss in a biofuel cell. In the present work, the enzyme is adsorbed on top of a covalently-attached viologen layer which leads to mixed, direct and mediated, electron transfer processes; at low overpotentials, the direct electron transfer process generates a catalytic current, while the mediated electron transfer through the viologens at higher potentials generates a redox buffer that prevents oxidative inactivation of the enzyme. Consequently, the enzyme starts the catalysis at no overpotential with viologen self-activated protection at high potentials.
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Affiliation(s)
- Alaa A Oughli
- Max-Planck-Institut for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany.
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22
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Rodríguez-Maciá P, Reijerse EJ, van Gastel M, DeBeer S, Lubitz W, Rüdiger O, Birrell JA. Sulfide Protects [FeFe] Hydrogenases From O 2. J Am Chem Soc 2018; 140:9346-9350. [PMID: 30008217 DOI: 10.1021/jacs.8b04339] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe] hydrogenases catalyze proton reduction and hydrogen oxidation with high rates and efficiency under physiological conditions, but are highly oxygen sensitive. The [FeFe] hydrogenase from Desulfovibrio desulfuricans ( DdHydAB) can be purified under air in an oxygen stable inactive state Hoxair. The formation of the Hoxair state in vitro allows the handling of hydrogenases in air, making their implementation in biotechnological applications more feasible. Here, we report a simple and robust protocol for the formation of the Hoxair state in DdHydAB and the [FeFe] hydrogenase from Chlamydomonas reinhardtii, which is based on high potential inactivation in the presence of sulfide.
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Affiliation(s)
- Patricia Rodríguez-Maciá
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Edward J Reijerse
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Maurice van Gastel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
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