1
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Sirohiwal A, Gamiz-Hernandez AP, Kaila VRI. Mechanistic Principles of Hydrogen Evolution in the Membrane-Bound Hydrogenase. J Am Chem Soc 2024; 146:18019-18031. [PMID: 38888987 PMCID: PMC11228991 DOI: 10.1021/jacs.4c04476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
The membrane-bound hydrogenase (Mbh) from Pyrococcus furiosus is an archaeal member of the Complex I superfamily. It catalyzes the reduction of protons to H2 gas powered by a [NiFe] active site and transduces the free energy into proton pumping and Na+/H+ exchange across the membrane. Despite recent structural advances, the mechanistic principles of H2 catalysis and ion transport in Mbh remain elusive. Here, we probe how the redox chemistry drives the reduction of the proton to H2 and how the catalysis couples to conformational dynamics in the membrane domain of Mbh. By combining large-scale quantum chemical density functional theory (DFT) and correlated ab initio wave function methods with atomistic molecular dynamics simulations, we show that the proton transfer reactions required for the catalysis are gated by electric field effects that direct the protons by water-mediated reactions from Glu21L toward the [NiFe] site, or alternatively along the nearby His75L pathway that also becomes energetically feasible in certain reaction steps. These local proton-coupled electron transfer (PCET) reactions induce conformational changes around the active site that provide a key coupling element via conserved loop structures to the ion transport activity. We find that H2 forms in a heterolytic proton reduction step, with spin crossovers tuning the energetics along key reaction steps. On a general level, our work showcases the role of electric fields in enzyme catalysis and how these effects are employed by the [NiFe] active site of Mbh to drive PCET reactions and ion transport.
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Affiliation(s)
- Abhishek Sirohiwal
- Department of Biochemistry
and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ana P. Gamiz-Hernandez
- Department of Biochemistry
and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ville R. I. Kaila
- Department of Biochemistry
and Biophysics, Stockholm University, Stockholm 10691, Sweden
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2
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Evans R, Krahn N, Weiss J, Vincent KA, Söll D, Armstrong FA. Replacing a Cysteine Ligand by Selenocysteine in a [NiFe]-Hydrogenase Unlocks Hydrogen Production Activity and Addresses the Role of Concerted Proton-Coupled Electron Transfer in Electrocatalytic Reversibility. J Am Chem Soc 2024; 146:16971-16976. [PMID: 38747098 PMCID: PMC11212049 DOI: 10.1021/jacs.4c03489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/27/2024]
Abstract
Hydrogenases catalyze hydrogen/proton interconversion that is normally electrochemically reversible (having minimal overpotential requirement), a special property otherwise almost exclusive to platinum metals. The mechanism of [NiFe]-hydrogenases includes a long-range proton-coupled electron-transfer process involving a specific Ni-coordinated cysteine and the carboxylate of a nearby glutamate. A variant in which this cysteine has been exchanged for selenocysteine displays two distinct changes in electrocatalytic properties, as determined by protein film voltammetry. First, proton reduction, even in the presence of H2 (a strong product inhibitor), is greatly enhanced relative to H2 oxidation: this result parallels a characteristic of natural [NiFeSe]-hydrogenases which are superior H2 production catalysts. Second, an inflection (an S-shaped "twist" in the trace) appears around the formal potential, the small overpotentials introduced in each direction (oxidation and reduction) signaling a departure from electrocatalytic reversibility. Concerted proton-electron transfer offers a lower energy pathway compared to stepwise transfers. Given the much lower proton affinity of Se compared to that of S, the inflection provides compelling evidence that concerted proton-electron transfer is important in determining why [NiFe]-hydrogenases are reversible electrocatalysts.
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Affiliation(s)
- Rhiannon
M. Evans
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Natalie Krahn
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United
States
| | - Joshua Weiss
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United
States
| | - Kylie A. Vincent
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Dieter Söll
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Fraser A. Armstrong
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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3
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T Waffo AF, Lorent C, Katz S, Schoknecht J, Lenz O, Zebger I, Caserta G. Structural Determinants of the Catalytic Ni a-L Intermediate of [NiFe]-Hydrogenase. J Am Chem Soc 2023. [PMID: 37328284 DOI: 10.1021/jacs.3c01625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
[NiFe]-hydrogenases catalyze the reversible cleavage of H2 into two protons and two electrons at the inorganic heterobimetallic NiFe center of the enzyme. Their catalytic cycle involves at least four intermediates, some of which are still under debate. While the core reaction, including H2/H- binding, takes place at the inorganic cofactor, a major challenge lies in identifying those amino acid residues that contribute to the reactivity and how they stabilize (short-lived) intermediate states. Using cryogenic infrared and electron paramagnetic resonance spectroscopy on the regulatory [NiFe]-hydrogenase from Cupriavidus necator, a model enzyme for the analysis of catalytic intermediates, we deciphered the structural basis of the hitherto elusive Nia-L intermediates. We unveiled the protonation states of a proton-accepting glutamate and a Ni-bound cysteine residue in the Nia-L1, Nia-L2, and the hydride-binding Nia-C intermediates as well as previously unknown conformational changes of amino acid residues in proximity of the bimetallic active site. As such, this study unravels the complexity of the Nia-L intermediate and reveals the importance of the protein scaffold in fine-tuning proton and electron dynamics in [NiFe]-hydrogenase.
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Affiliation(s)
- Armel F T Waffo
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, 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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Hong YH, Lee YM, Nam W, Fukuzumi S. Reaction Intermediates in Artificial Photosynthesis with Molecular Catalysts. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Young Hyun Hong
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul03760, Korea
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul03760, Korea
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6
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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: 50] [Impact Index Per Article: 25.0] [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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7
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Burgstaller H, Wang Y, Caliebe J, Hueren V, Appel J, Boehm M, Leitzke S, Theune M, King PW, Gutekunst K. Synechocystis sp. PCC 6803 Requires the Bidirectional Hydrogenase to Metabolize Glucose and Arginine Under Oxic Conditions. Front Microbiol 2022; 13:896190. [PMID: 35711753 PMCID: PMC9195167 DOI: 10.3389/fmicb.2022.896190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
The cyanobacterium Synechocystis sp.PCC 6803 possesses a bidirectional NiFe-hydrogenase, HoxEFUYH. It functions to produce hydrogen under dark, fermentative conditions and photoproduces hydrogen when dark-adapted cells are illuminated. Unexpectedly, we found that the deletion of the large subunit of the hydrogenase (HoxH) in Synechocystis leads to an inability to grow on arginine and glucose under continuous light in the presence of oxygen. This is surprising, as the hydrogenase is an oxygen-sensitive enzyme. In wild-type (WT) cells, thylakoid membranes largely disappeared, cyanophycin accumulated, and the plastoquinone (PQ) pool was highly reduced, whereas ΔhoxH cells entered a dormant-like state and neither consumed glucose nor arginine at comparable rates to the WT. Hydrogen production was not traceable in the WT under these conditions. We tested and could show that the hydrogenase does not work as an oxidase on arginine and glucose but has an impact on the redox states of photosynthetic complexes in the presence of oxygen. It acts as an electron valve as an immediate response to the supply of arginine and glucose but supports the input of electrons from arginine and glucose oxidation into the photosynthetic electron chain in the long run, possibly via the NDH-1 complex. Despite the data presented in this study, the latter scenario requires further proof. The exact role of the hydrogenase in the presence of arginine and glucose remains unresolved. In addition, a unique feature of the hydrogenase is its ability to shift electrons between NAD(H), NADP(H), ferredoxin, and flavodoxin, which was recently shown in vitro and might be required for fine-tuning. Taken together, our data show that Synechocystis depends on the hydrogenase to metabolize organic carbon and nitrogen in the presence of oxygen, which might be an explanation for its prevalence in aerobic cyanobacteria.
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Affiliation(s)
- Heinrich Burgstaller
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany
| | - Yingying Wang
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany
| | - Johanna Caliebe
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Vanessa Hueren
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany
| | - Jens Appel
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Marko Boehm
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Sinje Leitzke
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany
| | - Marius Theune
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Kirstin Gutekunst
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
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8
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Imanishi T, Nishikawa K, Taketa M, Higuchi K, Tai H, Hirota S, Hojo H, Kawakami T, Hataguchi K, Matsumoto K, Ogata H, Higuchi Y. Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-77. Acta Crystallogr F Struct Biol Commun 2022; 78:66-74. [PMID: 35102895 PMCID: PMC8805213 DOI: 10.1107/s2053230x22000188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/05/2022] [Indexed: 02/03/2023] Open
Abstract
Hydrogenases catalyze the reversible oxidation of H2. Carbon monoxide (CO) is known to be a competitive inhibitor of O2-sensitive [NiFe]-hydrogenases. Although the activities of some O2-tolerant [NiFe]-hydrogenases are unaffected by CO, the partially O2-tolerant [NiFe]-hydrogenase from Citrobacter sp. S-77 (S77-HYB) is inhibited by CO. In this work, the CO-bound state of S77-HYB was characterized by activity assays, spectroscopic techniques and X-ray crystallography. Electron paramagnetic resonance spectroscopy showed a diamagnetic Ni2+ state, and Fourier-transform infrared spectroscopy revealed the stretching vibration of the exogenous CO ligand. The crystal structure determined at 1.77 Å resolution revealed that CO binds weakly to the nickel ion in the Ni-Fe active site of S77-HYB. These results suggest a positive correlation between O2 and CO tolerance in [NiFe]-hydrogenases.
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Affiliation(s)
- Takahiro Imanishi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Koji Nishikawa
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Midori Taketa
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Katsuhiro Higuchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hulin Tai
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Department of Chemistry, Yanbian University, Yanji 133002, Jilin, People’s Republic of China
| | - Shun Hirota
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Toru Kawakami
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Kiriko Hataguchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kayoko Matsumoto
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hideaki Ogata
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan
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9
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Isegawa M, Matsumoto T, Ogo S. Hydrogen evolution, electron-transfer, and hydride-transfer reactions in a nickel-iron hydrogenase model complex: a theoretical study of the distinctive reactivities for the conformational isomers of nickel-iron hydride. Dalton Trans 2021; 51:312-323. [PMID: 34897337 DOI: 10.1039/d1dt03582g] [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
Hydrogen fuel is a promising alternative to fossil fuel. Therefore, efficient hydrogen production is crucial to elucidate the distinctive reactivities of metal hydride species, the intermediates formed during hydrogen activation/evolution in the presence of organometallic catalysts. This study uses density functional theory (DFT) to investigate the isomerizations and reactivities of three nickel-iron (NiFe) hydride isomers synthesized by mimicking the active center of NiFe hydrogenase. Hydride transfer within these complexes, rather than a chemical reaction between the complexes, converts the three hydrides internally. Their reactivities, including their electron-transfer, hydride-transfer and proton-transfer reactions, are investigated. The bridging hydride complex exhibits a higher energy level for the highest occupied molecular orbital (HOMO) than the terminal hydride during the electron-transfer reaction. This energy level indicates that the bridging hydride is more easily oxidized and is more susceptible to electron transfer than the terminal hydride. Regarding the hydride-transfer reaction between the NiFe hydride complex and methylene blue, the terminal hydrides exhibit larger hydricity and lower reaction barriers than the bridging hydride complexes. The results of energy decomposition analysis indicate that the structural deformation energy of the terminal hydride in the transition state is smaller than that of the bridging hydride complex, which lowers the reaction barrier of hydride transfer in the terminal hydride. To produce hydrogen, the rate-determining step is represented by the protonation of the hydride, and the terminal hydrides are thermodynamically and kinetically superior to the bridging ones. The differences in the reactivities of the hydride isomers ensure the precise control of hydrogen, and the theoretical calculations can be applied to design catalysts for hydrogen activation/production.
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Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
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10
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Isegawa M, Matsumoto T, Ogo S. H 2 activation by hydrogenase-inspired NiFe catalyst using frustrated Lewis pair: effect of buffer and halide ion in the heterolytic H-H bond cleavage. RSC Adv 2021; 11:28420-28432. [PMID: 35480737 PMCID: PMC9038005 DOI: 10.1039/d1ra05928a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Hydrogen is a clean fuel alternative to fossil fuels, and it is vital to develop catalysts for its efficient activation and production. We investigate the reaction mechanism of H2 activation in an aqueous solution by the recently developed NiFe complex (Ogo et al. Sci. Adv. 2020, 6, eaaz8181) using density functional theory (DFT) calculation. Our computational results showed that H2 is activated using frustrated Lewis pair. That is, H2 binds to the Fe site of the NiFe complex, acting as a Lewis acid, while the added buffer, acting as Lewis base, abstracts protons to form a hydride complex. Furthermore, the higher basicity in the proton abstraction reaction characterises reaction more exergonic and lowers the reaction barrier. In addition, in the proton abstraction by the water molecule, the reaction barrier was lowered when anion such as Cl− is in the vicinity of the water. Understanding the chemical species that contribute to the catalytic process in cooperation with the metal catalyst at the atomic level should help to maximise the function of the catalyst. Hydrogen is a clean fuel alternative to fossil fuels, and it is vital to develop catalysts for its efficient activation and production.![]()
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Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
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11
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Caserta G, Pelmenschikov V, Lorent C, Tadjoung Waffo AF, Katz S, Lauterbach L, Schoknecht J, Wang H, Yoda Y, Tamasaku K, Kaupp M, Hildebrandt P, Lenz O, Cramer SP, Zebger I. Hydroxy-bridged resting states of a [NiFe]-hydrogenase unraveled by cryogenic vibrational spectroscopy and DFT computations. Chem Sci 2020; 12:2189-2197. [PMID: 34163984 PMCID: PMC8179317 DOI: 10.1039/d0sc05022a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The catalytic mechanism of [NiFe]-hydrogenases is a subject of extensive research. Apart from at least four reaction intermediates of H2/H+ cycling, there are also a number of resting states, which are formed under oxidizing conditions. Although not directly involved in the catalytic cycle, the knowledge of their molecular structures and reactivity is important, because these states usually accumulate in the course of hydrogenase purification and may also play a role in vivo during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit (HoxC) of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure resting redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, 57Fe-labeled HoxC provided an unprecedented insight into the [NiFe] site modes, revealing their contributions in a spectral range otherwise superimposed by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data provide structural descriptions of the previously uncharacterized hydroxy- and water-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site. Active site vibrations of a [NiFe]-hydrogenase catalytic subunit are selectively probed by IR and NRV spectroscopy in two NiIIFeII and NiIIIFeII resting states, contributing in combination with DFT modeling to rationalized structural candidates.![]()
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Affiliation(s)
- Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Armel F Tadjoung Waffo
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Lars Lauterbach
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Hongxin Wang
- SETI Institute 189 Bernardo Avenue Mountain View CA 94043 USA
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute (JASRI) SPring-8, 1-1-1 Kouto, Sayo-gun Hyogo 679-5198 Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo-cho, Sayo-gun Hyogo 679-5148 Japan
| | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
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12
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Caserta G, Lorent C, Ciaccafava A, Keck M, Breglia R, Greco C, Limberg C, Hildebrandt P, Cramer SP, Zebger I, Lenz O. The large subunit of the regulatory [NiFe]-hydrogenase from Ralstonia eutropha - a minimal hydrogenase? Chem Sci 2020; 11:5453-5465. [PMID: 34094072 PMCID: PMC8159394 DOI: 10.1039/d0sc01369b] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Chemically synthesized compounds that are capable of facilitating the reversible splitting of dihydrogen into protons and electrons are rare in chemists' portfolio. The corresponding biocatalysts – hydrogenases – are, however, abundant in the microbial world. [NiFe]-hydrogenases represent a major subclass and display a bipartite architecture, composed of a large subunit, hosting the catalytic NiFe(CO)(CN)2 cofactor, and a small subunit whose iron–sulfur clusters are responsible for electron transfer. To analyze in detail the catalytic competence of the large subunit without its smaller counterpart, we purified the large subunit HoxC of the regulatory [NiFe]-hydrogenase of the model H2 oxidizer Ralstonia eutropha to homogeneity. Metal determination and infrared spectroscopy revealed a stoichiometric loading of the metal cofactor. This enabled for the first time the determination of the UV-visible extinction coefficient of the NiFe(CO)(CN)2 cofactor. Moreover, the absence of disturbing iron–sulfur clusters allowed an unbiased look into the low-spin Fe2+ of the active site by Mössbauer spectroscopy. Isolated HoxC was active in catalytic hydrogen–deuterium exchange, demonstrating its capacity to activate H2. Its catalytic activity was drastically lower than that of the bipartite holoenzyme. This was consistent with infrared and electron paramagnetic resonance spectroscopic observations, suggesting that the bridging position between the active site nickel and iron ions is predominantly occupied by water-derived ligands, even under reducing conditions. In fact, the presence of water-derived ligands bound to low-spin Ni2+ was reflected by the absorption bands occurring in the corresponding UV-vis spectra, as revealed by time-dependent density functional theory calculations conducted on appropriate in silico models. Thus, the isolated large subunits indeed represent simple [NiFe]-hydrogenase models, which could serve as blueprints for chemically synthesized mimics. Furthermore, our data point to a fundamental role of the small subunit in preventing water access to the catalytic center, which significantly increases the H2 splitting capacity of the enzyme. Spectroscopic investigation of an isolated [NiFe]-hydrogenase large subunit enables a unique view of the NiFe(CO)(CN)2 cofactor.![]()
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Affiliation(s)
- Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Alexandre Ciaccafava
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Matthias Keck
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Raffaella Breglia
- Department of Earth and Environmental Sciences, Milano-Bicocca University Piazza della Scienza 1 20126 Milan Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, Milano-Bicocca University Piazza della Scienza 1 20126 Milan Italy
| | - Christian Limberg
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
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13
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Nishikawa K, Ogata H, Higuchi Y. Structural Basis of the Function of [NiFe]-hydrogenases. CHEM LETT 2020. [DOI: 10.1246/cl.190814] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Nishikawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hideaki Ogata
- Institute of Low Temperature Science, Hokkaido University, Kita19Nishi8, Kita-ku, Sapporo, Hokkaido 060-0819, Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
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14
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Popescu CV, Ding S, Ghosh P, Hall MB, Cohara M. Mössbauer Spectroscopy and Theoretical Studies of Iron Bimetallic Complexes Showing Electrocatalytic Hydrogen Evolution. Inorg Chem 2019; 58:7069-7077. [PMID: 31059245 DOI: 10.1021/acs.inorgchem.9b00746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mössbauer spectroscopy and density functional theory (DFT) calculations are reported for the mononuclear Fe-nitrosyl complex [Fe( N, N'-bis(2-mercaptoethyl)-1,4-diazacycloheptane)NO] {[Fe(bme-dach)(NO)] (1)} and the series of dithiolate-bridged dinuclear complexes M-Fe(CO)Cp [M = Fe(bme-dach)(NO) (1-A), Ni(bme-dach) (2-A), and Co(bme-dach)(NO) (3-A)], in which M is a metallo-ligand to Fe(CO)Cp+ (Fe'Cp). The latter is an organometallic fragment in which Fe is coordinated by one CO and one cyclopentadienyl ligand. Complexes 1-A and 2-A were previously shown to have electrocatalytic hydrogen evolution activity. Mononuclear {Fe-NO}7 complex 1, with overall spin of 1/2, has an isomer shift of 0.23(2) mm/s [Δ EQ = 1.37(2) mm/s] and magnetic hyperfine couplings of {-38 T, -26.8 T, 8.6 T}. In complexes 2-A and 3-A, Fe'(CO)Cp+ has a diamagnetic ground state and δ = 0.33(2) mm/s (Δ EQ ≈ 1.78 mm/s), consistent with a low-spin FeII site. In contrast, in complex 1-A, M = Fe(bme-dach)(NO) (i.e., complex 1) the magnetic hyperfine interactions of both metallo-ligand, M, and low-spin Fe'Cp are perturbed and Fe'Cp exhibits small magnetic hyperfine interactions, although its isomer shift and quadrupole splittings are largely unaltered. The DFT calculations for 1-A are in agreement with the paramagnetism observed for the Fe'(CO)Cp+ iron site.
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Affiliation(s)
- Codrina V Popescu
- Department of Chemistry , University of St. Thomas , St. Paul , Minnesota 55105 , United States
| | - Shengda Ding
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Pokhraj Ghosh
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Michael B Hall
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Morgan Cohara
- Department of Chemistry , Colgate University , Hamilton , New York 13346 , United States
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15
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Yang X, Gianetti TL, Wörle MD, van Leest NP, de Bruin B, Grützmacher H. A low-valent dinuclear ruthenium diazadiene complex catalyzes the oxidation of dihydrogen and reversible hydrogenation of quinones. Chem Sci 2019; 10:1117-1125. [PMID: 30774909 PMCID: PMC6346631 DOI: 10.1039/c8sc02864h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/01/2018] [Indexed: 12/27/2022] Open
Abstract
The dinuclear ruthenium complex [Ru2H(μ-H)(Me2dad)(dbcot)2] contains a 1,4-dimethyl-diazabuta-1,3-diene (Me2dad) as a non-innocent bridging ligand between the metal centers to give a [Ru2(Me2dad)] core. In addition, each ruthenium is bound to one dibenzo[a,e]cyclooctatetraene (dbcot) ligand. This Ru dimer converts H2 to protons and electrons. It also catalyzes reversibly under mild conditions the selective hydrogenation of vitamins K2 and K3 to their corresponding hydroquinone equivalents without affecting the C[double bond, length as m-dash]C double bonds. Mechanistic studies suggest that the [Ru2(Me2dad)] moiety, like hydrogenases, reacts with H2 and releases electrons and protons stepwise.
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Affiliation(s)
- Xiuxiu Yang
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 1 , 8093 Zürich , Switzerland .
| | - Thomas L Gianetti
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 1 , 8093 Zürich , Switzerland . .,Department of Chemistry and Biochemistry , The University of Arizona , Tucson , Arizona 85721 , USA .
| | - Michael D Wörle
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 1 , 8093 Zürich , Switzerland .
| | - Nicolaas P van Leest
- Van't Hoff Institute for Molecular Sciences (HIMS) , University of Amsterdam (UvA) , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Bas de Bruin
- Van't Hoff Institute for Molecular Sciences (HIMS) , University of Amsterdam (UvA) , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Hansjörg Grützmacher
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 1 , 8093 Zürich , Switzerland .
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16
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Abstract
Hydrogenases catalyze the simple yet important interconversion between H2 and protons and electrons. Found throughout prokaryotes, lower eukaryotes, and archaea, hydrogenases are used for a variety of redox and signaling purposes and are found in many different forms. This diverse group of metalloenzymes is divided into [NiFe], [FeFe], and [Fe] variants, based on the transition metal contents of their active sites. A wide array of biochemical and spectroscopic methods has been used to elucidate hydrogenases, and this along with a general description of the main enzyme types and catalytic mechanisms is discussed in this chapter.
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17
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Breglia R, Greco C, Fantucci P, De Gioia L, Bruschi M. Reactivation of the Ready and Unready Oxidized States of [NiFe]-Hydrogenases: Mechanistic Insights from DFT Calculations. Inorg Chem 2018; 58:279-293. [PMID: 30576127 DOI: 10.1021/acs.inorgchem.8b02348] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The apparently simple dihydrogen formation from protons and electrons (2H+ + 2e- ⇄ H2) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H2 as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni-B and Ni-A states of the [NiFe]-hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni-B and Ni-A. However, this process is sufficient to activate only the Ni-B state. H2 binding to the active site is required to convert Ni-A to the active Ni-SIa state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni-SIr and Ni-SU species, formed respectively from the one-electron reduction of Ni-B and Ni-A. Ni-SIr, depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni-SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni-A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H2O and H2 binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni-B and Ni-A states.
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18
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Dong G, Phung QM, Pierloot K, Ryde U. Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods. Inorg Chem 2018; 57:15289-15298. [PMID: 30500163 DOI: 10.1021/acs.inorgchem.8b02590] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
[NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular mechanics (QM/MM) calculations. To get more accurate energies and obtain a detailed account of the surroundings, we performed big-QM calculations with 819 atoms in the QM region. Moreover, QM/MM thermodynamic cycle perturbation calculations were performed to obtain free energies. Finally, density matrix renormalisation group complete active space self-consistent field calculations were carried out to study the electronic structures of the various states in the reaction mechanism. Our calculations indicate that the Ni-L state is not involved in the reaction mechanism. Instead, the Ni-C state is reduced by one electron and then the bridging hydride ion is transferred to the sulfur atom of Cys546 as a proton and the two electrons transfer to the Ni ion. This step turned out to be rate-determining with an energy barrier of 58 kJ/mol, which is consistent with the experimental rate of 750 ± 90 s-1 (corresponding to ∼52 kJ/mol). The cleavage of the H-H bond is facile with an energy barrier of 33 kJ/mol, according to our calculations. We also find that the reaction energies are sensitive to the size of the QM system, the basis set, and the density functional theory method, in agreement with previous studies.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Chemical Centre , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
- Department of Biochemistry and Molecular Biology , Shantou University Medical College , Shantou 514041 , Guangdong , PR China
| | - Quan Manh Phung
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Leuven , Belgium
| | - Kristine Pierloot
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Leuven , Belgium
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
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19
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Szczesny J, Marković N, Conzuelo F, Zacarias S, Pereira IAC, Lubitz W, Plumeré N, Schuhmann W, Ruff A. A gas breathing hydrogen/air biofuel cell comprising a redox polymer/hydrogenase-based bioanode. Nat Commun 2018; 9:4715. [PMID: 30413708 PMCID: PMC6226449 DOI: 10.1038/s41467-018-07137-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/17/2018] [Indexed: 11/21/2022] Open
Abstract
Hydrogen is one of the most promising alternatives for fossil fuels. However, the power output of hydrogen/oxygen fuel cells is often restricted by mass transport limitations of the substrate. Here, we present a dual-gas breathing H2/air biofuel cell that overcomes these limitations. The cell is equipped with a hydrogen-oxidizing redox polymer/hydrogenase gas-breathing bioanode and an oxygen-reducing bilirubin oxidase gas-breathing biocathode (operated in a direct electron transfer regime). The bioanode consists of a two layer system with a redox polymer-based adhesion layer and an active, redox polymer/hydrogenase top layer. The redox polymers protect the biocatalyst from high potentials and oxygen damage. The bioanodes show remarkable current densities of up to 8 mA cm-2. A maximum power density of 3.6 mW cm-2 at 0.7 V and an open circuit voltage of up to 1.13 V were achieved in biofuel cell tests, representing outstanding values for a device that is based on a redox polymer-based hydrogenase bioanode.
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Affiliation(s)
- Julian Szczesny
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Nikola Marković
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Felipe Conzuelo
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Nicolas Plumeré
- Center for Electrochemical Sciences (CES) - Molecular Nanostructures, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Wolfgang Schuhmann
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany.
| | - Adrian Ruff
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany.
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20
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Infrared Characterization of the Bidirectional Oxygen-Sensitive [NiFe]-Hydrogenase from E. coli. Catalysts 2018. [DOI: 10.3390/catal8110530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
[NiFe]-hydrogenases are gas-processing metalloenzymes that catalyze the conversion of dihydrogen (H2) to protons and electrons in a broad range of microorganisms. Within the framework of green chemistry, the molecular proceedings of biological hydrogen turnover inspired the design of novel catalytic compounds for H2 generation. The bidirectional “O2-sensitive” [NiFe]-hydrogenase from Escherichia coli HYD-2 has recently been crystallized; however, a systematic infrared characterization in the presence of natural reactants is not available yet. In this study, we analyze HYD-2 from E. coli by in situ attenuated total reflection Fourier-transform infrared spectroscopy (ATR FTIR) under quantitative gas control. We provide an experimental assignment of all catalytically relevant redox intermediates alongside the O2- and CO-inhibited cofactor species. Furthermore, the reactivity and mutual competition between H2, O2, and CO was probed in real time, which lays the foundation for a comparison with other enzymes, e.g., “O2-tolerant” [NiFe]-hydrogenases. Surprisingly, only Ni-B was observed in the presence of O2 with no indications for the “unready” Ni-A state. The presented work proves the capabilities of in situ ATR FTIR spectroscopy as an efficient and powerful technique for the analysis of biological macromolecules and enzymatic small molecule catalysis.
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21
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Brazzolotto D, Wang L, Tang H, Gennari M, Queyriaux N, Philouze C, Demeshko S, Meyer F, Orio M, Artero V, Hall MB, Duboc C. Tuning Reactivity of Bioinspired [NiFe]-Hydrogenase Models by Ligand Design and Modeling the CO Inhibition Process. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02830] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Deborah Brazzolotto
- Université Grenoble Alpes, UMR CNRS 5250, Département de Chimie Moléculaire, F-38000 Grenoble, France
- Université Grenoble Alpes, UMR CNRS 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Lianke Wang
- Université Grenoble Alpes, UMR CNRS 5250, Département de Chimie Moléculaire, F-38000 Grenoble, France
| | - Hao Tang
- Department of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - Marcello Gennari
- Université Grenoble Alpes, UMR CNRS 5250, Département de Chimie Moléculaire, F-38000 Grenoble, France
| | - Nicolas Queyriaux
- Université Grenoble Alpes, UMR CNRS 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Christian Philouze
- Université Grenoble Alpes, UMR CNRS 5250, Département de Chimie Moléculaire, F-38000 Grenoble, France
| | - Serhiy Demeshko
- University of Göttingen, Insitute für Anorganische Chemie, Tammannstrasse 4, D- 37077 Göttingen, Germany
| | - Franc Meyer
- University of Göttingen, Insitute für Anorganische Chemie, Tammannstrasse 4, D- 37077 Göttingen, Germany
| | - Maylis Orio
- Institut des Sciences Moléculaires de Marseille, Aix Marseille Université, CNRS, Centrale Marseille, ISM2 UMR 7313, 13397 Marseille, France
| | - Vincent Artero
- Université Grenoble Alpes, UMR CNRS 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Michael B. Hall
- Department of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - Carole Duboc
- Université Grenoble Alpes, UMR CNRS 5250, Département de Chimie Moléculaire, F-38000 Grenoble, France
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22
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Isegawa M, Sharma AK, Ogo S, Morokuma K. Electron and Hydride Transfer in a Redox-Active NiFe Hydride Complex: A DFT Study. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02368] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Akhilesh K. Sharma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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23
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Ruff A, Szczesny J, Marković N, Conzuelo F, Zacarias S, Pereira IAC, Lubitz W, Schuhmann W. A fully protected hydrogenase/polymer-based bioanode for high-performance hydrogen/glucose biofuel cells. Nat Commun 2018; 9:3675. [PMID: 30202006 PMCID: PMC6131248 DOI: 10.1038/s41467-018-06106-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/15/2018] [Indexed: 12/03/2022] Open
Abstract
Hydrogenases with Ni- and/or Fe-based active sites are highly active hydrogen oxidation catalysts with activities similar to those of noble metal catalysts. However, the activity is connected to a sensitivity towards high-potential deactivation and oxygen damage. Here we report a fully protected polymer multilayer/hydrogenase-based bioanode in which the sensitive hydrogen oxidation catalyst is protected from high-potential deactivation and from oxygen damage by using a polymer multilayer architecture. The active catalyst is embedded in a low-potential polymer (protection from high-potential deactivation) and covered with a polymer-supported bienzymatic oxygen removal system. In contrast to previously reported polymer-based protection systems, the proposed strategy fully decouples the hydrogenase reaction form the protection process. Incorporation of the bioanode into a hydrogen/glucose biofuel cell provides a benchmark open circuit voltage of 1.15 V and power densities of up to 530 µW cm-2 at 0.85 V.
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Affiliation(s)
- Adrian Ruff
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstr. 150, Bochum, D-44780, Germany.
| | - Julian Szczesny
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstr. 150, Bochum, D-44780, Germany
| | - Nikola Marković
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstr. 150, Bochum, D-44780, Germany
| | - Felipe Conzuelo
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstr. 150, Bochum, D-44780, Germany
| | - Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, Mülheim an der Ruhr, 45470, Germany
| | - Wolfgang Schuhmann
- Analytical Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstr. 150, Bochum, D-44780, Germany.
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24
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A [4Fe-4S]-Fe(CO)(CN)-L-cysteine intermediate is the first organometallic precursor in [FeFe] hydrogenase H-cluster bioassembly. Nat Chem 2018; 10:555-560. [PMID: 29632334 PMCID: PMC6380689 DOI: 10.1038/s41557-018-0026-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/14/2018] [Indexed: 12/27/2022]
Abstract
Biosynthesis of the [FeFe] hydrogenase active site (the 'H-cluster') requires the interplay of multiple proteins and small molecules. Among them, the radical S-adenosylmethionine enzyme HydG, a tyrosine lyase, has been proposed to generate a complex that contains an Fe(CO)2(CN) moiety that is eventually incorporated into the H-cluster. Here we describe the characterization of an intermediate in the HydG reaction: a [4Fe-4S][(Cys)Fe(CO)(CN)] species, 'Complex A', in which a CO, a CN- and a cysteine (Cys) molecule bind to the unique 'dangler' Fe site of the auxiliary [5Fe-4S] cluster of HydG. The identification of this intermediate-the first organometallic precursor to the H-cluster-validates the previously hypothesized HydG reaction cycle and provides a basis for elucidating the biosynthetic origin of other moieties of the H-cluster.
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25
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Qiu S, Olsen S, MacFarlane DR, Sun C. The oxygen reduction reaction on [NiFe] hydrogenases. Phys Chem Chem Phys 2018; 20:23528-23534. [DOI: 10.1039/c8cp04160a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Oxygen tolerance capacity is critical for hydrogen oxidation/evolution catalysts.
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Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute
- Dongguan University of Technology
- Dongguan
- China
- School of Chemistry
| | - Seth Olsen
- School of Chemistry
- Faculty of Science
- Monash University
- Clayton
- VIC 3800
| | | | - Chenghua Sun
- Science & Technology Innovation Institute
- Dongguan University of Technology
- Dongguan
- China
- Department of Chemistry and Biotechnology
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26
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Breglia R, Greco C, Fantucci P, De Gioia L, Bruschi M. Theoretical investigation of aerobic and anaerobic oxidative inactivation of the [NiFe]-hydrogenase active site. Phys Chem Chem Phys 2018; 20:1693-1706. [DOI: 10.1039/c7cp06228a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The extraordinary capability of [NiFe]-hydrogenases to catalyse the reversible interconversion of protons and electrons into dihydrogen (H2) has stimulated numerous experimental and theoretical studies addressing the direct utilization of these enzymes in H2 production processes.
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Affiliation(s)
- Raffaella Breglia
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Claudio Greco
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Maurizio Bruschi
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
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27
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Kure B, Sano M, Watanabe N, Nakajima T, Tanase T. Synthesis and Reactivity of Thiolate‐Bridged Ni
II
M
I
Heterodinuclear Complexes (M = Rh, Ir) with an S‐Bidentate NiP
2
S
2
Metalloligand. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bunsho Kure
- Department of Chemistry Faculty of Science Nara Women's University Kitauoya‐nishi‐machi 630‐8506 Nara Japan
| | - Mikie Sano
- Department of Chemistry Faculty of Science Nara Women's University Kitauoya‐nishi‐machi 630‐8506 Nara Japan
| | - Natsuki Watanabe
- Department of Chemistry Faculty of Science Nara Women's University Kitauoya‐nishi‐machi 630‐8506 Nara Japan
| | - Takayuki Nakajima
- Department of Chemistry Faculty of Science Nara Women's University Kitauoya‐nishi‐machi 630‐8506 Nara Japan
| | - Tomoaki Tanase
- Department of Chemistry Faculty of Science Nara Women's University Kitauoya‐nishi‐machi 630‐8506 Nara Japan
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28
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Ash PA, Hidalgo R, Vincent KA. Proton Transfer in the Catalytic Cycle of [NiFe] Hydrogenases: Insight from Vibrational Spectroscopy. ACS Catal 2017; 7:2471-2485. [PMID: 28413691 PMCID: PMC5387674 DOI: 10.1021/acscatal.6b03182] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/30/2017] [Indexed: 12/11/2022]
Abstract
![]()
Catalysis
of H2 production and oxidation reactions is
critical in renewable energy systems based around H2 as
a clean fuel, but the present reliance on platinum-based catalysts
is not sustainable. In nature, H2 is oxidized at minimal
overpotential and high turnover frequencies at [NiFe] catalytic sites
in hydrogenase enzymes. Although an outline mechanism has been established
for the [NiFe] hydrogenases involving heterolytic cleavage of H2 followed by a first and then second transfer of a proton
and electron away from the active site, details remain vague concerning
how the proton transfers are facilitated by the protein environment
close to the active site. Furthermore, although [NiFe] hydrogenases
from different organisms or cellular environments share a common active
site, they exhibit a broad range of catalytic characteristics indicating
the importance of subtle changes in the surrounding protein in controlling
their behavior. Here we review recent time-resolved infrared (IR)
spectroscopic studies and IR spectroelectrochemical studies carried
out in situ during electrocatalytic turnover. Additionally, we re-evaluate
the significant body of IR spectroscopic data on hydrogenase active
site states determined through more conventional solution studies,
in order to highlight mechanistic steps that seem to apply generally
across the [NiFe] hydrogenases, as well as steps which so far seem
limited to specific groups of these enzymes. This analysis is intended
to help focus attention on the key open questions where further work
is needed to assess important aspects of proton and electron transfer
in the mechanism of [NiFe] hydrogenases.
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Affiliation(s)
- Philip A. Ash
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ricardo Hidalgo
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kylie A. Vincent
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
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29
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Slater JW, Marguet SC, Cirino SL, Maugeri PT, Shafaat HS. Experimental and DFT Investigations Reveal the Influence of the Outer Coordination Sphere on the Vibrational Spectra of Nickel-Substituted Rubredoxin, a Model Hydrogenase Enzyme. Inorg Chem 2017; 56:3926-3938. [PMID: 28323426 DOI: 10.1021/acs.inorgchem.6b02934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nickel-substituted rubredoxin (NiRd) is a functional enzyme mimic of hydrogenase, highly active for electrocatalytic and solution-phase hydrogen generation. Spectroscopic methods can provide valuable insight into the catalytic mechanism, provided the appropriate technique is used. In this study, we have employed multiwavelength resonance Raman spectroscopy coupled with DFT calculations on an extended active-site model of NiRd to probe the electronic and geometric structures of the resting state of this system. Excellent agreement between experiment and theory is observed, allowing normal mode assignments to be made on the basis of frequency and intensity analyses. Both metal-ligand and ligand-centered vibrational modes are enhanced in the resonance Raman spectra. The latter provide information about the hydrogen bonding network and structural distortions due to perturbations in the secondary coordination sphere. To reproduce the resonance enhancement patterns seen for high-frequency vibrational modes, the secondary coordination sphere must be included in the computational model. The structure and reduction potential of the NiIIIRd state have also been investigated both experimentally and computationally. This work begins to establish a foundation for computational resonance Raman spectroscopy to serve in a predictive fashion for investigating catalytic intermediates of NiRd.
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Affiliation(s)
- Jeffrey W Slater
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sean C Marguet
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sabrina L Cirino
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Pearson T Maugeri
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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30
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Breglia R, Ruiz-Rodriguez MA, Vitriolo A, Gonzàlez-Laredo RF, De Gioia L, Greco C, Bruschi M. Theoretical insights into [NiFe]-hydrogenases oxidation resulting in a slowly reactivating inactive state. J Biol Inorg Chem 2016; 22:137-151. [DOI: 10.1007/s00775-016-1416-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/09/2016] [Indexed: 11/28/2022]
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31
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Ogata H, Lubitz W, Higuchi Y. Structure and function of [NiFe] hydrogenases. J Biochem 2016; 160:251-258. [PMID: 27493211 DOI: 10.1093/jb/mvw048] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/06/2016] [Indexed: 12/22/2022] Open
Abstract
Hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons via a heterolytic splitting mechanism. The active sites of [NiFe] hydrogenases comprise a dinuclear Ni-Fe center carrying CO and CN- ligands. The catalytic activity of the standard (O2-sensitive) [NiFe] hydrogenases vanishes under aerobic conditions. The O2-tolerant [NiFe] hydrogenases can sustain H2 oxidation activity under atmospheric conditions. These hydrogenases have very similar active site structures that change the ligand sphere during the activation/catalytic process. An important structural difference between these hydrogenases has been found for the proximal iron-sulphur cluster located in the vicinity of the active site. This unprecedented [4Fe-3S]-6Cys cluster can supply two electrons, which lead to rapid recovery of the O2 inactivation, to the [NiFe] active site.
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Affiliation(s)
- Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, Mülheim an der Ruhr 45470, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, Mülheim an der Ruhr 45470, Germany
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan .,RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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32
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Brazzolotto D, Gennari M, Queyriaux N, Simmons TR, Pécaut J, Demeshko S, Meyer F, Orio M, Artero V, Duboc C. Nickel-centred proton reduction catalysis in a model of [NiFe] hydrogenase. Nat Chem 2016; 8:1054-1060. [PMID: 27768098 DOI: 10.1038/nchem.2575] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 06/13/2016] [Indexed: 02/07/2023]
Abstract
Hydrogen production through water splitting is one of the most promising solutions for the storage of renewable energy. [NiFe] hydrogenases are organometallic enzymes containing nickel and iron centres that catalyse hydrogen evolution with performances that rival those of platinum. These enzymes provide inspiration for the design of new molecular catalysts that do not require precious metals. However, all heterodinuclear NiFe models reported so far do not reproduce the Ni-centred reactivity found at the active site of [NiFe] hydrogenases. Here, we report a structural and functional NiFe mimic that displays reactivity at the Ni site. This is shown by the detection of two catalytic intermediates that reproduce structural and electronic features of the Ni-L and Ni-R states of the enzyme during catalytic turnover. Under electrocatalytic conditions, this mimic displays high rates for H2 evolution (second-order rate constant of 2.5 × 104 M-1 s-1; turnover frequency of 250 s-1 at 10 mM H+ concentration) from mildly acidic solutions.
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Affiliation(s)
- Deborah Brazzolotto
- Univ. Grenoble Alpes, CNRS UMR 5250, DCM, F-38000 Grenoble, France.,Univ. Grenoble Alpes, CNRS UMR 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Marcello Gennari
- Univ. Grenoble Alpes, CNRS UMR 5250, DCM, F-38000 Grenoble, France
| | - Nicolas Queyriaux
- Univ. Grenoble Alpes, CNRS UMR 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Trevor R Simmons
- Univ. Grenoble Alpes, CNRS UMR 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Jacques Pécaut
- Univ. Grenoble Alpes, INAC-LCIB, F-38000 Grenoble, France.,CEA, DRF-INAC-SyMMES, Reconnaissance Ionique et Chimie de Coordination, F-38000 Grenoble, France
| | - Serhiy Demeshko
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Franc Meyer
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.,International Center for Advanced Studies of Energy Conversion (ICASEC), Georg-August-University, D-37077 Göttingen, Germany
| | - Maylis Orio
- Institut des Sciences Moléculaires de Marseille, Aix Marseille Université, CNRS, Centrale Marseille, ISM2 UMR 7313, 13397, Marseille, France
| | - Vincent Artero
- Univ. Grenoble Alpes, CNRS UMR 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Carole Duboc
- Univ. Grenoble Alpes, CNRS UMR 5250, DCM, F-38000 Grenoble, France
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33
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Boll M, Einsle O, Ermler U, Kroneck PMH, Ullmann GM. Structure and Function of the Unusual Tungsten Enzymes Acetylene Hydratase and Class II Benzoyl-Coenzyme A Reductase. J Mol Microbiol Biotechnol 2016; 26:119-37. [PMID: 26959374 DOI: 10.1159/000440805] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In biology, tungsten (W) is exclusively found in microbial enzymes bound to a bis-pyranopterin cofactor (bis-WPT). Previously known W enzymes catalyze redox oxo/hydroxyl transfer reactions by directly coordinating their substrates or products to the metal. They comprise the W-containing formate/formylmethanofuran dehydrogenases belonging to the dimethyl sulfoxide reductase (DMSOR) family and the aldehyde:ferredoxin oxidoreductase (AOR) families, which form a separate enzyme family within the Mo/W enzymes. In the last decade, initial insights into the structure and function of two unprecedented W enzymes were obtained: the acetaldehyde forming acetylene hydratase (ACH) belongs to the DMSOR and the class II benzoyl-coenzyme A (CoA) reductase (BCR) to the AOR family. The latter catalyzes the reductive dearomatization of benzoyl-CoA to a cyclic diene. Both are key enzymes in the degradation of acetylene (ACH) or aromatic compounds (BCR) in strictly anaerobic bacteria. They are unusual in either catalyzing a nonredox reaction (ACH) or a redox reaction without coordinating the substrate or product to the metal (BCR). In organic chemical synthesis, analogous reactions require totally nonphysiological conditions depending on Hg2+ (acetylene hydration) or alkali metals (benzene ring reduction). The structural insights obtained pave the way for biological or biomimetic approaches to basic reactions in organic chemistry.
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Affiliation(s)
- Matthias Boll
- Fakultx00E4;t fx00FC;r Biologie/Mikrobiologie, Institut fx00FC;r Biochemie, Albert-Ludwigs-Universitx00E4;t Freiburg, Freiburg, Germany
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34
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Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods. J Biol Inorg Chem 2016; 21:383-94. [DOI: 10.1007/s00775-016-1348-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/23/2016] [Indexed: 10/22/2022]
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35
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Yang H, Gandhi H, Cornish AJ, Moran JJ, Kreuzer HW, Ostrom NE, Hegg EL. Isotopic fractionation associated with [NiFe]- and [FeFe]-hydrogenases. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:285-292. [PMID: 27071219 DOI: 10.1002/rcm.7432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RATIONALE Hydrogenases catalyze the reversible formation of H2 from electrons and protons with high efficiency. Understanding the relationships between H2 production, H2 uptake, and H2-H2O exchange can provide insight into the metabolism of microbial communities in which H2 is an essential component in energy cycling. METHODS We used stable H isotopes (1H and 2H) to probe the isotope effects associated with three [FeFe]-hydrogenases and three [NiFe]-hydrogenases. RESULTS All six hydrogenases displayed fractionation factors for H2 formation that were significantly less than 1, producing H2 that was severely depleted in 2H relative to the substrate, water. Consistent with differences in their active site structure, the fractionation factors for each class appear to cluster, with the three [NiFe]-hydrogenases (α = 0.27–0.40) generally having smaller values than the three [FeFe]-hydrogenases (α = 0.41–0.55). We also obtained isotopic fractionation factors associated with H2 uptake and H2-H2O exchange under conditions similar to those utilized for H2 production, providing a more complete picture of the reactions catalyzed by hydrogenases. CONCLUSIONS The fractionation factors determined in our studies can be used as signatures for different hydrogenases to probe their activity under different growth conditions and to ascertain which hydrogenases are most responsible for H2 production and/or uptake in complex microbial communities.
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36
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Das R, Neese F, van Gastel M. Hydrogen evolution in [NiFe] hydrogenases and related biomimetic systems: similarities and differences. Phys Chem Chem Phys 2016; 18:24681-92. [DOI: 10.1039/c6cp03672d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Schematic overview of the orbitals that play a role in the cycle of reversible hydrogen oxidation in [NiFe] hydrogenases.
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Affiliation(s)
- Ranjita Das
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Maurice van Gastel
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
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37
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Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy. Nat Commun 2015; 6:7890. [PMID: 26259066 PMCID: PMC4531378 DOI: 10.1038/ncomms8890] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/18/2015] [Indexed: 11/28/2022] Open
Abstract
The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging' mode involving H− motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H− binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts. Understanding the catalytic mechanism of redox-active hydrogenases is a key to efficient hydrogen production and consumption. Here, the authors use nuclear resonance vibrational spectroscopy to study [NiFe]-hydrogenase, and observe a bridging hydride structure in an EPR silent intermediate.
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38
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Weinert T, Huwiler SG, Kung JW, Weidenweber S, Hellwig P, Stärk HJ, Biskup T, Weber S, Cotelesage JJH, George GN, Ermler U, Boll M. Structural basis of enzymatic benzene ring reduction. Nat Chem Biol 2015; 11:586-91. [PMID: 26120796 DOI: 10.1038/nchembio.1849] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/15/2015] [Indexed: 12/19/2022]
Abstract
In chemical synthesis, the widely used Birch reduction of aromatic compounds to cyclic dienes requires alkali metals in ammonia as extremely low-potential electron donors. An analogous reaction is catalyzed by benzoyl-coenzyme A reductases (BCRs) that have a key role in the globally important bacterial degradation of aromatic compounds at anoxic sites. Because of the lack of structural information, the catalytic mechanism of enzymatic benzene ring reduction remained obscure. Here, we present the structural characterization of a dearomatizing BCR containing an unprecedented tungsten cofactor that transfers electrons to the benzene ring in an aprotic cavity. Substrate binding induces proton transfer from the bulk solvent to the active site by expelling a Zn(2+) that is crucial for active site encapsulation. Our results shed light on the structural basis of an electron transfer process at the negative redox potential limit in biology. They open the door for biological or biomimetic alternatives to a basic chemical synthetic tool.
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Affiliation(s)
| | - Simona G Huwiler
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Johannes W Kung
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Hans-Joachim Stärk
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
| | - Till Biskup
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Julien J H Cotelesage
- 1] Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada. [2] Canadian Light Source, Saskatoon, Saskatchewan, Canada
| | - Graham N George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ulrich Ermler
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Matthias Boll
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
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39
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Murphy BJ, Hidalgo R, Roessler MM, Evans RM, Ash PA, Myers WK, Vincent KA, Armstrong FA. Discovery of Dark pH-Dependent H(+) Migration in a [NiFe]-Hydrogenase and Its Mechanistic Relevance: Mobilizing the Hydrido Ligand of the Ni-C Intermediate. J Am Chem Soc 2015; 137:8484-9. [PMID: 26103582 PMCID: PMC4500644 DOI: 10.1021/jacs.5b03182] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Despite extensive studies on [NiFe]-hydrogenases,
the mechanism
by which these enzymes produce and activate H2 so efficiently
remains unclear. A well-known EPR-active state produced under H2 and known as Ni-C is assigned as a NiIII–FeII species with a hydrido ligand in the bridging position between
the two metals. It has long been known that low-temperature photolysis
of Ni-C yields distinctive EPR-active states, collectively termed
Ni-L, that are attributed to migration of the bridging-H species as
a proton; however, Ni-L has mainly been regarded as an artifact with
no mechanistic relevance. It is now demonstrated, based on EPR and
infrared spectroscopic studies, that the Ni-C to Ni-L interconversion
in Hydrogenase-1 (Hyd-1) from Escherichia coli is a pH-dependent process that proceeds readily in the dark—proton
migration from Ni-C being favored as the pH is increased. The persistence
of Ni-L in Hyd-1 must relate to unassigned differences in proton affinities
of metal and adjacent amino acid sites, although the unusually high
reduction potentials of the adjacent Fe–S centers in this O2-tolerant hydrogenase might also be a contributory factor,
impeding elementary electron transfer off the [NiFe] site after proton
departure. The results provide compelling evidence that Ni-L is a
true, albeit elusive, catalytic intermediate of [NiFe]-hydrogenases.
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Affiliation(s)
- Bonnie J Murphy
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Ricardo Hidalgo
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Maxie M Roessler
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Rhiannon M Evans
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Philip A Ash
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - William K Myers
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Kylie A Vincent
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
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40
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Cox N, Pantazis DA, Neese F, Lubitz W. Artificial photosynthesis: understanding water splitting in nature. Interface Focus 2015; 5:20150009. [PMID: 26052426 PMCID: PMC4410565 DOI: 10.1098/rsfs.2015.0009] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In the context of a global artificial photosynthesis (GAP) project, we review our current work on nature's water splitting catalyst. In a recent report (Cox et al. 2014 Science 345, 804-808 (doi:10.1126/science.1254910)), we showed that the catalyst-a Mn4O5Ca cofactor-converts into an 'activated' form immediately prior to the O-O bond formation step. This activated state, which represents an all Mn(IV) complex, is similar to the structure observed by X-ray crystallography but requires the coordination of an additional water molecule. Such a structure locates two oxygens, both derived from water, in close proximity, which probably come together to form the product O2 molecule. We speculate that formation of the activated catalyst state requires inherent structural flexibility. These features represent new design criteria for the development of biomimetic and bioinspired model systems for water splitting catalysts using first-row transition metals with the aim of delivering globally deployable artificial photosynthesis technologies.
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Affiliation(s)
- Nicholas Cox
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | | | | | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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41
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Barilone JL, Ogata H, Lubitz W, van Gastel M. Structural differences between the active sites of the Ni-A and Ni-B states of the [NiFe] hydrogenase: an approach by quantum chemistry and single crystal ENDOR spectroscopy. Phys Chem Chem Phys 2015; 17:16204-12. [PMID: 26035632 DOI: 10.1039/c5cp01322d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The two resting forms of the active site of [NiFe] hydrogenase, Ni-A and Ni-B, have significantly different activation kinetics, but reveal nearly identical spectroscopic features which suggest the two states exhibit subtle structural differences. Previous studies have indicated that the states differ by the identity of the bridging ligand between Ni and Fe; proposals include OH(-), OOH(-), H2O, O(2-), accompanied by modified cysteine residues. In this study, we use single crystal ENDOR spectroscopy and quantum chemical calculations within the framework of density functional theory (DFT) to calculate vibrational frequencies, (1)H and (17)O hyperfine coupling constants and g values with the aim to compare these data to experimental results obtained by crystallography, FTIR and EPR/ENDOR spectroscopy. We find that the Ni-A and Ni-B states are constitutional isomers that differ in their fine structural details. Calculated vibrational frequencies for the cyano and carbonyl ligands and (1)H and (17)O hyperfine coupling constants indicate that the bridging ligand in both Ni-A and Ni-B is indeed an OH(-) ligand. The difference in the isotropic hyperfine coupling constants of the β-CH2 protons of Cys-549 is sensitive to the orientation of Cys-549; a difference of 0.5 MHz is observed experimentally for Ni-A and 1.9 MHz for Ni-B, which results from a rotation of 7 degrees about the Cα-Cβ-Sγ-Ni dihedral angle. Likewise, the difference of the intermediate g value is correlated with a rotation of Cys-546 of about 10 degrees.
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Affiliation(s)
- Jessica L Barilone
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany.
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42
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Roncaroli F, Bill E, Friedrich B, Lenz O, Lubitz W, Pandelia ME. Cofactor composition and function of a H 2-sensing regulatory hydrogenase as revealed by Mössbauer and EPR spectroscopy. Chem Sci 2015; 6:4495-4507. [PMID: 29142700 PMCID: PMC5665086 DOI: 10.1039/c5sc01560j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/26/2015] [Indexed: 01/22/2023] Open
Abstract
The regulatory hydrogenase (RH) from Ralstonia eutropha H16 acts as a sensor for the detection of environmental H2 and regulates gene expression related to hydrogenase-mediated cellular metabolism. In marked contrast to prototypical energy-converting [NiFe] hydrogenases, the RH is apparently insensitive to inhibition by O2 and CO. While the physiological function of regulatory hydrogenases is well established, little is known about the redox cycling of the [NiFe] center and the nature of the iron-sulfur (FeS) clusters acting as electron relay. The absence of any FeS cluster signals in EPR had been attributed to their particular nature, whereas the observation of essentially only two active site redox states, namely Ni-SI and Ni-C, invoked a different operant mechanism. In the present work, we employ a combination of Mössbauer, FTIR and EPR spectroscopic techniques to study the RH, and the results are consistent with the presence of three [4Fe-4S] centers in the small subunit. In the as-isolated, oxidized RH all FeS clusters reside in the EPR-silent 2+ state. Incubation with H2 leads to reduction of two of the [4Fe-4S] clusters, whereas only strongly reducing agents lead to reduction of the third cluster, which is ascribed to be the [4Fe-4S] center in 'proximal' position to the [NiFe] center. In the two different active site redox states, the low-spin FeII exhibits distinct Mössbauer features attributed to changes in the electronic and geometric structure of the catalytic center. The results are discussed with regard to the spectral characteristics and physiological function of H2-sensing regulatory hydrogenases.
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Affiliation(s)
- Federico Roncaroli
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ; .,Department of Condensed Matter Physics , Centro Atómico Constituyentes , Comisión Nacional de Energía Atómica (CNEA) , Argentina
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Bärbel Friedrich
- Institut für Biologie/Mikrobiologie , Humboldt-Universität zu Berlin , Chausseestraße 117 , 10115 Berlin , Germany
| | - Oliver Lenz
- Institut für Biologie/Mikrobiologie , Humboldt-Universität zu Berlin , Chausseestraße 117 , 10115 Berlin , Germany.,Institut für Chemie , Technische Universität Berlin , Max-Volmer-Laboratorium , Straße des 17. Juni 135 , 10623 Berlin , Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Maria-Eirini Pandelia
- The Pennsylvania State University , Department of Chemistry , State College , PA 16802 , USA . .,Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
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43
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Greene BL, Wu CH, McTernan PM, Adams MWW, Dyer RB. Proton-coupled electron transfer dynamics in the catalytic mechanism of a [NiFe]-hydrogenase. J Am Chem Soc 2015; 137:4558-66. [PMID: 25790178 DOI: 10.1021/jacs.5b01791] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The movement of protons and electrons is common to the synthesis of all chemical fuels such as H2. Hydrogenases, which catalyze the reversible reduction of protons, necessitate transport and reactivity between protons and electrons, but a detailed mechanism has thus far been elusive. Here, we use a phototriggered chemical potential jump method to rapidly initiate the proton reduction activity of a [NiFe] hydrogenase. Coupling the photochemical initiation approach to nanosecond transient infrared and visible absorbance spectroscopy afforded direct observation of interfacial electron transfer and active site chemistry. Tuning of intramolecular proton transport by pH and isotopic substitution revealed distinct concerted and stepwise proton-coupled electron transfer mechanisms in catalysis. The observed heterogeneity in the two sequential proton-associated reduction processes suggests a highly engineered protein environment modulating catalysis and implicates three new reaction intermediates; Nia-I, Nia-D, and Nia-SR(-). The results establish an elementary mechanistic understanding of catalysis in a [NiFe] hydrogenase with implications in enzymatic proton-coupled electron transfer and biomimetic catalyst design.
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Affiliation(s)
- Brandon L Greene
- †Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
| | - Chang-Hao Wu
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Patrick M McTernan
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael W W Adams
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R Brian Dyer
- †Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
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44
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Structural differences of oxidized iron–sulfur and nickel–iron cofactors in O 2 -tolerant and O 2 -sensitive hydrogenases studied by X-ray absorption spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:162-170. [DOI: 10.1016/j.bbabio.2014.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/06/2014] [Accepted: 06/16/2014] [Indexed: 11/23/2022]
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45
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Kaliakin DS, Zaari RR, Varganov SA. Effect of H2 Binding on the Nonadiabatic Transition Probability between Singlet and Triplet States of the [NiFe]-Hydrogenase Active Site. J Phys Chem A 2015; 119:1066-73. [DOI: 10.1021/jp510522z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Danil S. Kaliakin
- Department
of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
- Department
of Chemistry, Siberian Federal University, 79 Svobodnyi Prospect, Krasnoyarsk, Krasnoyarskiy kray 660041, Russia
| | - Ryan R. Zaari
- Department
of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
| | - Sergey A. Varganov
- Department
of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
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46
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Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase. Nature 2015; 520:571-4. [DOI: 10.1038/nature14110] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/20/2014] [Indexed: 01/22/2023]
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47
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Gan L, Jennings D, Laureanti J, Jones AK. Biomimetic Complexes for Production of Dihydrogen and Reduction of CO2. TOP ORGANOMETAL CHEM 2015. [DOI: 10.1007/3418_2015_146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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48
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Cox N, Nalepa A, Pandelia ME, Lubitz W, Savitsky A. Pulse Double-Resonance EPR Techniques for the Study of Metallobiomolecules. Methods Enzymol 2015; 563:211-49. [DOI: 10.1016/bs.mie.2015.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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49
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Volbeda A, Martin L, Barbier E, Gutiérrez-Sanz O, De Lacey AL, Liebgott PP, Dementin S, Rousset M, Fontecilla-Camps JC. Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states. J Biol Inorg Chem 2015; 20:11-22. [PMID: 25315838 DOI: 10.1007/s00775-014-1203-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/01/2014] [Indexed: 01/12/2023]
Abstract
Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species.
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Affiliation(s)
- Anne Volbeda
- University Grenoble Alpes, IBS, 38044, Grenoble, France. .,CEA, IBS, 38044, Grenoble, France. .,CNRS, IBS, 38044, Grenoble, France.
| | - Lydie Martin
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France
| | - Elodie Barbier
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France.,CEA, MINATEC, 38044, Grenoble, France
| | | | | | - Pierre-Pol Liebgott
- Aix-Marseille Université, CNRS, IMM, 13402, Marseille, France.,Aix-Marseille Université, CNRS/INSU, MIO, 13288, Marseille, France
| | | | - Marc Rousset
- Aix-Marseille Université, CNRS, IMM, 13402, Marseille, France.,Consulate General of France, 205 N Michigan Ave, Chicago, IL, 60601, USA
| | - Juan C Fontecilla-Camps
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France
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50
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Sode O, Voth GA. Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase. J Chem Phys 2014; 141:22D527. [DOI: 10.1063/1.4902236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Olaseni Sode
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA and Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA and Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois 60439, USA
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