1
|
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.
Collapse
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
| |
Collapse
|
2
|
Song LC, Wang YP, Dong YX, Yang XY. Functionalized nickel(II)-iron(II) dithiolates as biomimetic models of [NiFe]-H 2ases. Dalton Trans 2023; 52:3755-3768. [PMID: 36857705 DOI: 10.1039/d3dt00039g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
To develop the structural and functional modeling chemistry of [NiFe]-H2ases, a series of new biomimetics for the active site of [NiFe]-H2ases have been prepared by various synthetic methods. Treatment of the mononuclear Ni complex (pnp)NiCl2 (pnp = (Ph2PCH2)2NPh) with (dppv)Fe(CO)2(pdt) (dppv = 1,2-(Ph2P)2C2H2, pdt = 1,3-propanedithiolate) and KPF6 gave the dicarbonyl complex [(pnp)Ni(pdt)Fe(CO)2(dppv)](PF6)2 ([1](PF6)2). Further treatment of [1](PF6)2 and [(dppe)Ni(pdt)Fe(CO)2(dppv)](BF4)2 (dppe = 1,2-(Ph2P)2C2H4) with the decarbonylation agent Me3NO and pyridine afforded the novel sp3 C-Fe bond-containing complexes [(pnp)Ni(SCH2CH2CHS)Fe(CO)(dppv)]PF6 ([2]PF6) and [(dppe)Ni(SCH2CH2CHS)Fe(CO)(dppv)]BF4 ([3]BF4). More interestingly, the first t-carboxylato complexes [(pnp)Ni(pdt)Fe(CO)(t-O2CR)(dppv)]PF6 ([4]PF6, R = H; [5]PF6, R = Me; [6]PF6, R = Ph) could be prepared by reactions of [1]PF6 with the corresponding carboxylic acids RCO2H in the presence of Me3NO, whereas further reactions of [4]PF6-[6]PF6 with aqueous HPF6 and 1.5 MPa H2 gave rise to the μ-hydride complex [(pnp)Ni(pdt)Fe(CO)(μ-H)(dppv)]PF6 ([7]PF6). Except for H2 activation by t-carboxylato complexes [4]PF6-[6]PF6 to give a μ-hydride complex ([7]PF6), the sp3 C-Fe bond-containing complex [2]PF6 was found to be a catalyst for proton reduction to H2 under CV conditions. Furthermore, the chemical reactivity of the μ-hydride complex [7]PF6 displayed in the e- transfer reaction with FcPF6 in the presence of CO, the H2 evolution reaction with the protonic acid HCl, and the H- transfer reaction with N-methylacridinium hexafluorophosphate ([NMA]PF6) was systematically studied. As a result, a series of the expected products such as H2, ferrocene, the dicarbonyl complex [1](PF6)2, the μ-chloro complex [(pnp)Ni(pdt)Fe(CO)(μ-Cl)(dppv)]PF6 ([8]PF6), the t-MeCN-coordinated complex [(pnp)Ni(pdt)Fe(CO)(t-MeCN)(dppv)](PF6)2 ([9](PF6)2) and the H- transfer product AcrH2 were produced. While all the newly prepared model complexes were structurally characterized by spectroscopic methods, the molecular structures of some of their representatives were confirmed by X-ray crystallography.
Collapse
Affiliation(s)
- Li-Cheng Song
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Yin-Peng Wang
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Yi-Xiong Dong
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Xi-Yue Yang
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| |
Collapse
|
3
|
Understanding 2D-IR Spectra of Hydrogenases: A Descriptive and Predictive Computational Study. Catalysts 2022. [DOI: 10.3390/catal12090988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to the presence of CO and ligands at this cofactor, infrared (IR) spectroscopy represents an ideal technique for studying these aspects, but molecular information from linear IR absorption experiments is limited. More detailed insights can be obtained from ultrafast nonlinear IR techniques like IRpump−IRprobe and two-dimensional (2D-)IR spectroscopy. However, fully exploiting these advanced techniques requires an in-depth understanding of experimental observables and the encoded molecular information. To address this challenge, we present a descriptive and predictive computational approach for the simulation and analysis of static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. Accurate reproduction of experimental spectra from a first-coordination-sphere model suggests a decisive role of the [NiFe] core in shaping the enzymatic potential energy surface. We also reveal spectrally encoded molecular information that is not accessible by experiments, thereby helping to understand the catalytic role of the diatomic ligands, structural differences between [NiFe] intermediates, and possible energy transfer mechanisms. Our studies demonstrate the feasibility and benefits of computational spectroscopy in the 2D-IR investigation of hydrogenases, thereby further strengthening the potential of this nonlinear IR technique as a powerful research tool for the investigation of complex bioinorganic molecules.
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Ash PA, Kendall-Price SET, Evans RM, Carr SB, Brasnett AR, Morra S, Rowbotham JS, Hidalgo R, Healy AJ, Cinque G, Frogley MD, Armstrong FA, Vincent KA. The crystalline state as a dynamic system: IR microspectroscopy under electrochemical control for a [NiFe] hydrogenase. Chem Sci 2021; 12:12959-12970. [PMID: 34745526 PMCID: PMC8514002 DOI: 10.1039/d1sc01734a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/03/2021] [Indexed: 12/24/2022] Open
Abstract
Controlled formation of catalytically-relevant states within crystals of complex metalloenzymes represents a significant challenge to structure-function studies. Here we show how electrochemical control over single crystals of [NiFe] hydrogenase 1 (Hyd1) from Escherichia coli makes it possible to navigate through the full array of active site states previously observed in solution. Electrochemical control is combined with synchrotron infrared microspectroscopy, which enables us to measure high signal-to-noise IR spectra in situ from a small area of crystal. The output reports on active site speciation via the vibrational stretching band positions of the endogenous CO and CN- ligands at the hydrogenase active site. Variation of pH further demonstrates how equilibria between catalytically-relevant protonation states can be deliberately perturbed in the crystals, generating a map of electrochemical potential and pH conditions which lead to enrichment of specific states. Comparison of in crystallo redox titrations with measurements in solution or of electrode-immobilised Hyd1 confirms the integrity of the proton transfer and redox environment around the active site of the enzyme in crystals. Slowed proton-transfer equilibria in the hydrogenase in crystallo reveals transitions which are only usually observable by ultrafast methods in solution. This study therefore demonstrates the possibilities of electrochemical control over single metalloenzyme crystals in stabilising specific states for further study, and extends mechanistic understanding of proton transfer during the [NiFe] hydrogenase catalytic cycle.
Collapse
Affiliation(s)
- Philip A Ash
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- School of Chemistry, University of Leicester Leicester LE1 7RH UK
- Leicester Institute of Structural and Chemical Biology, University of Leicester LE1 7RH UK
| | - Sophie E T Kendall-Price
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Rhiannon M Evans
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Stephen B Carr
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus Didcot UK
| | - Amelia R Brasnett
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Simone Morra
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Jack S Rowbotham
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Ricardo Hidalgo
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Adam J Healy
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Gianfelice Cinque
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Department of Engineering Sciences, University of Oxford Parks Road Oxford OX1 3PJ UK
| | - Mark D Frogley
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0QX UK
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| |
Collapse
|
6
|
Song LC, Feng L, Lu Y, Yang XY. Synthesis, Structures, and Reactivity of [NiFe]-H 2ase Mimics Containing One Square-Planar N 2S 2 Ligand Bridged between Their Ni/Fe Centers through One or Two S Atoms. Organometallics 2021. [DOI: 10.1021/acs.organomet.0c00778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li-Cheng Song
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Li Feng
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu Lu
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xi-Yue Yang
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| |
Collapse
|
7
|
Abstract
Hydrogenases are metalloenzymes that catalyze proton reduction and H2 oxidation with outstanding efficiency. They are model systems for bioinorganic chemistry, including low-valent transition metals, hydride chemistry, and proton-coupled electron transfer. In this Account, we describe how photochemistry and infrared difference spectroscopy can be used to identify the dynamic hydrogen-bonding changes that facilitate proton transfer in [NiFe]- and [FeFe]-hydrogenase.[NiFe]-hydrogenase binds a heterobimetallic nickel/iron site embedded in the protein by four cysteine ligands. [FeFe]-hydrogenase carries a homobimetallic iron/iron site attached to the protein by only a single cysteine. Carbon monoxide and cyanide ligands in the active site facilitate detailed investigations of hydrogenase catalysis by infrared spectroscopy because of their strong signals and redox-dependent frequency shifts. We found that specific redox-state transitions in [NiFe]- and [FeFe]-hydrogenase can be triggered by visible light to record extremely sensitive "light-minus-dark" infrared difference spectra monitoring key amino acid residues. As these transitions are coupled to protonation changes, our data allowed investigation of dynamic hydrogen-bonding changes that go well beyond the resolution of protein crystallography.In [NiFe]-hydrogenase, photolysis of the bridging hydride ligand in the Ni-C state was followed by infrared difference spectroscopy. Our data clearly indicate the formation of a protonated cysteine residue as well as hydrogen-bonding changes involving a glutamic acid residue and a "dangling water" molecule. These findings are in excellent agreement with crystallographic analyses of [NiFe]-hydrogenase. In [FeFe]-hydrogenase, an external redox dye was used to accumulate the Hred state. Infrared difference spectra indicate hydrogen-bonding changes involving two glutamic acid residues and a conserved arginine residue. While crystallographic analyses of [FeFe]-hydrogenase in the oxidized state failed to explain the rapid proton transfer because of a breach in the succession of residues, our findings facilitated a precise molecular model of discontinued proton transfer.Comparing both systems, our data emphasize the role of the outer coordination sphere in bimetallic hydrogenases: we suggest that protonation of a nickel-ligating cysteine in [NiFe]-hydrogenase causes the notable preference toward H2 oxidation. On the contrary, proton transfer in [FeFe]-hydrogenase involves an adjacent cysteine as a relay group, promoting both H2 oxidation and proton reduction. These observations may guide the design of organometallic compounds that mimic the catalytic properties of hydrogenases.
Collapse
Affiliation(s)
- Hulin Tai
- Department of Chemistry, National Demonstration Centre for Experimental Chemistry Education, Yanbian University, Yanji, Jilin 133002, China
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Sven T. Stripp
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|
8
|
Caserta G, Lorent C, Pelmenschikov V, Schoknecht J, Yoda Y, Hildebrandt P, Cramer SP, Zebger I, Lenz O. In Vitro Assembly as a Tool to Investigate Catalytic Intermediates of [NiFe]-Hydrogenase. ACS Catal 2020; 10:13890-13894. [PMID: 33680535 PMCID: PMC7932190 DOI: 10.1021/acscatal.0c04079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[NiFe]-hydrogenases catalyze the reversible reaction H2 ⇄ 2H+ + 2e-. Their basic module consists of a large subunit, coordinating the NiFe(CO)(CN)2 center, and a small subunit that carries electron-transferring iron-sulfur clusters. Here, we report the in vitro assembly of fully functional [NiFe]-hydrogenase starting from the isolated large and small subunits. Activity assays complemented by spectroscopic measurements revealed a native-like hydrogenase. This approach was used to label exclusively the NiFe(CO)(CN)2 center with 57Fe, enabling a clear view of the catalytic site by means of nuclear resonance vibrational spectroscopy. This strategy paves the way for in-depth studies of [NiFe]-hydrogenase catalytic intermediates.
Collapse
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
| | - Vladimir Pelmenschikov
- 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
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, RIKEN SPring-8, Hyogo 679-5198, Japan
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Stephen P. Cramer
- SETI Institute, 189 Bernardo Avenue, Mountain View, CA 94043, United States
| | - 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
| |
Collapse
|
9
|
Guo JT, Chen XD. Templated syntheses of heterometal tungsten-cobalt-sulfur clusters with different nuclearities. Dalton Trans 2020; 49:5523-5530. [PMID: 32267264 DOI: 10.1039/d0dt00765j] [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
A series of new W-Co-S clusters have been synthesized utilizing the complex [Et4N][(Tp*)WS3] (Tp* = hydridotris(3,5-dimethylpyrazol-1-yl)borate(1-)) as the synthetic template, by rational control of the stoichiometry of reactants and by employment of a reductant or precipitant as an auxiliary reagent. By solubility control or addition of a precipitant to avoid the involvement of Cl- in the reaction, the cluster [(Tp*)WS3]2Co (2) could be obtained. With different ratios of the Co source to the template, together with the use of an appropriate amount of reducing reagent, clusters [{(Tp*)WS3}2Co]1- (3) and [{(Tp*)WS3}2Co2Cl]1- (4) could be synthesized as their Et4N+ salts, and [{(Tp*)WS3}2Co4Cl2(DMF)]1- (5) could be isolated as its [Co(DMF)6]2+ salt. A common structural feature of these clusters is that they all have a pair of [(Tp*)WS3] templates chelating different numbers of Co atoms to form W-Co-S clusters with distinct nuclearities. The clusters [(Tp*)WS3]2Co (2) and [{(Tp*)WS3}2Co]1- (3) both have one Co atom chelated by two [(Tp*)WS3] templates, and the difference lies in not only the oxidation states but also the fact that the Co atom in 2 adopts an octahedral coordination environment while that in 3 bears a tetrahedral coordination sphere, which means that the [(Tp*)WS3] template is tri-dentate in 2 and bi-dentate in 3. The cluster [{(Tp*)WS3}2Co2Cl]1- (4) has two Co atoms chelated by a pair of [(Tp*)WS3] templates, in which one of the Co atoms is also terminally bound by a Cl- ligand. There are four Co atoms chelated by two [(Tp*)WS3] templates in the cluster [{(Tp*)WS3}2Co4Cl2(DMF)]1- (5), two of which are bound terminally by the Cl- ligands. Studies of redox properties by cyclic voltammetry indicate the existence of two reversible redox pairs related to clusters 2 and 3, respectively.
Collapse
Affiliation(s)
- Jia-Ting Guo
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, Jiangsu, China.
| | | |
Collapse
|
10
|
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.![]()
Collapse
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
| |
Collapse
|
11
|
Tai H, Hirota S. Mechanism and Application of the Catalytic Reaction of [NiFe] Hydrogenase: Recent Developments. Chembiochem 2020; 21:1573-1581. [DOI: 10.1002/cbic.202000058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/25/2020] [Indexed: 01/28/2023]
Affiliation(s)
- Hulin Tai
- MOE Key Laboratory of Natural Resources of the Changbai Mountain and Functional MoleculesDepartment of ChemistryYanbian University Park Road 977 Yanji 133002 Jilin China
| | - Shun Hirota
- Division of Materials ScienceGraduate School of Science and TechnologyNara Institute of Science and Technology 8916-5 Takayama Ikoma Nara 630-0192 Japan
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
Ash PA, Kendall-Price SET, Vincent KA. Unifying Activity, Structure, and Spectroscopy of [NiFe] Hydrogenases: Combining Techniques To Clarify Mechanistic Understanding. Acc Chem Res 2019; 52:3120-3131. [PMID: 31675209 DOI: 10.1021/acs.accounts.9b00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Achieving a unified understanding of the mechanism of a multicenter redox enzyme such as [NiFe] hydrogenase is complicated by difficulties in reconciling information obtained by using different techniques and on samples in different physical forms. Measurements of the activity of the enzyme, and of factors which perturb activity, are generally carried out using biochemical assays in solution or with electrode-immobilized enzymes using protein film electrochemistry (PFE). Conversely, spectroscopy aimed at reporting on features of the metalloclusters in the enzyme, such as electron paramagnetic resonance (EPR) or X-ray absorption spectroscopy (XAS), is often conducted on frozen samples and is thus difficult to relate to catalytically relevant states as information about turnover and activity has been lost. To complicate matters further, most of our knowledge of the atomic-level structure of metalloenzymes comes from X-ray diffraction studies in the solid, crystalline state, which are again difficult to link to turnover conditions. Taking [NiFe] hydrogenases as our case study, we show here how it is possible to apply infrared (IR) spectroscopic sampling approaches to unite direct spectroscopic study with catalytic turnover. Using a method we have named protein film IR electrochemistry (PFIRE), we reveal the steady-state distribution of intermediates during catalysis and identify catalytic "bottlenecks" introduced by site-directed mutagenesis. We also show that it is possible to study dynamic transitions between active site states of enzymes in single crystals, uniting solid state and solution spectroscopic information. In all of these cases, the spectroscopic data complement and enhance interpretation of purely activity-based measurements by providing direct chemical insight that is otherwise hidden. The [NiFe] hydrogenases possess a bimetallic [NiFe] active site, coordinated by CO and CN- ligands, linked to the protein via bridging and terminal cysteine sulfur ligands, as well as an electron relay chain of iron sulfur clusters. Infrared spectroscopy is ideal for probing hydrogenases because the CO and CN- ligands are strong IR absorbers, but the suite of IR-based approaches we describe here will be equally valuable in studying substrate- or intermediate-bound states of other metalloenzymes where key mechanistic questions remain open, such as nitrogenase, formate dehydrogenase, or carbon monoxide dehydrogenase. We therefore hope that this Account will encourage future studies which unify information from different techniques across bioinorganic chemistry.
Collapse
Affiliation(s)
- Philip A. Ash
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | | | - Kylie A. Vincent
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| |
Collapse
|
14
|
Tai H, Nishikawa K, Higuchi Y, Mao ZW, Hirota S. Cysteine SH and Glutamate COOH Contributions to [NiFe] Hydrogenase Proton Transfer Revealed by Highly Sensitive FTIR Spectroscopy. Angew Chem Int Ed Engl 2019; 58:13285-13290. [PMID: 31343102 DOI: 10.1002/anie.201904472] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/10/2019] [Indexed: 11/12/2022]
Abstract
A [NiFe] hydrogenase (H2 ase) is a proton-coupled electron transfer enzyme that catalyses reversible H2 oxidation; however, its fundamental proton transfer pathway remains unknown. Herein, we observed the protonation of Cys546-SH and Glu34-COOH near the Ni-Fe site with high-sensitivity infrared difference spectra by utilizing Ni-C-to-Ni-L and Ni-C-to-Ni-SIa photoconversions. Protonated Cys546-SH in the Ni-L state was verified by the observed SH stretching frequency (2505 cm-1 ), whereas Cys546 was deprotonated in the Ni-C and Ni-SIa states. Glu34-COOH was double H-bonded in the Ni-L state, as determined by the COOH stretching frequency (1700 cm-1 ), and single H-bonded in the Ni-C and Ni-SIa states. Additionally, a stretching mode of an ordered water molecule was observed in the Ni-L and Ni-C states. These results elucidate the organized proton transfer pathway during the catalytic reaction of a [NiFe] H2 ase, which is regulated by the H-bond network of Cys546, Glu34, and an ordered water molecule.
Collapse
Affiliation(s)
- Hulin Tai
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.,MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Koji Nishikawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| |
Collapse
|
15
|
Tai H, Nishikawa K, Higuchi Y, Mao Z, Hirota S. Cysteine SH and Glutamate COOH Contributions to [NiFe] Hydrogenase Proton Transfer Revealed by Highly Sensitive FTIR Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hulin Tai
- Division of Materials Science Graduate School of Science and Technology Nara Institute of Science and Technology 8916-5 Takayama, Ikoma Nara 630-0192 Japan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Koji Nishikawa
- Graduate School of Life Science University of Hyogo 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science University of Hyogo 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Zong‐wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Shun Hirota
- Division of Materials Science Graduate School of Science and Technology Nara Institute of Science and Technology 8916-5 Takayama, Ikoma Nara 630-0192 Japan
| |
Collapse
|
16
|
Song LC, Yang XY, Gao XY, Cao M. Nickel-Iron Dithiolato Hydrides Derived from H 2 Activation by Their μ-Hydroxo Ligand-Containing Analogues. Inorg Chem 2019; 58:39-42. [PMID: 30561201 DOI: 10.1021/acs.inorgchem.8b02648] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we describe the synthesis and characterization of the two μ-hydrido models of [NiFe]H2ases prepared from a new type of H2 activation by the corresponding two μ-hydroxo models. In addition, another μ-hydrido model prepared by the anionic exchange between one of the two μ-hydrido models and KPF6 is also reported. Interestingly, the synthesis of the two μ-hydrido models from H2 activation represents the first functional modeling of the H2 activation catalyzed by the [NiFe]H2ase (Ni-SIr)I state to give the Ni-R state.
Collapse
Affiliation(s)
- Li-Cheng Song
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300072 , China
| | - Xi-Yue Yang
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Xiu-Yun Gao
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Meng Cao
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| |
Collapse
|
17
|
Tai H, Higuchi Y, Hirota S. Comprehensive reaction mechanisms at and near the Ni-Fe active sites of [NiFe] hydrogenases. Dalton Trans 2018. [PMID: 29532823 DOI: 10.1039/c7dt04910b] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
[NiFe] hydrogenase (H2ase) catalyzes the oxidation of dihydrogen to two protons and two electrons and/or its reverse reaction. For this simple reaction, the enzyme has developed a sophisticated but intricate mechanism with heterolytic cleavage of dihydrogen (or a combination of a hydride and a proton), where its Ni-Fe active site exhibits various redox states. Recently, thermodynamic parameters of the acid-base equilibrium for activation-inactivation, a new intermediate in the catalytic reaction, and new crystal structures of [NiFe] H2ases have been reported, providing significant insights into the activation-inactivation and catalytic reaction mechanisms of [NiFe] H2ases. This Perspective provides an overview of the reaction mechanisms of [NiFe] H2ases based on these new findings.
Collapse
Affiliation(s)
- Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan.
| | | | | |
Collapse
|
18
|
Yu X, Pang M, Zhang S, Hu X, Tung CH, Wang W. Terminal Thiolate-Dominated H/D Exchanges and H2 Release: Diiron Thiol–Hydride. J Am Chem Soc 2018; 140:11454-11463. [DOI: 10.1021/jacs.8b06996] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xin Yu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, No. 27 South Shanda Road, Jinan, 250100, P. R. China
| | - Maofu Pang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, No. 27 South Shanda Road, Jinan, 250100, P. R. China
| | - Shengnan Zhang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, No. 27 South Shanda Road, Jinan, 250100, P. R. China
| | - Xinlong Hu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, No. 27 South Shanda Road, Jinan, 250100, P. R. China
| | - Chen-Ho Tung
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, No. 27 South Shanda Road, Jinan, 250100, P. R. China
| | - Wenguang Wang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, No. 27 South Shanda Road, Jinan, 250100, P. R. China
| |
Collapse
|
19
|
Song LC, Gao XY, Liu WB, Zhang HT, Cao M. Synthesis, Characterization, and Reactions of Functionalized Nickel–Iron Dithiolates Related to the Active Site of [NiFe]-Hydrogenases. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
20
|
Tai H, Xu L, Nishikawa K, Higuchi Y, Hirota S. Equilibrium between inactive ready Ni-SI r and active Ni-SI a states of [NiFe] hydrogenase studied by utilizing Ni-SI r-to-Ni-SI a photoactivation. Chem Commun (Camb) 2018; 53:10444-10447. [PMID: 28884761 DOI: 10.1039/c7cc06061k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Previously, the Ni-SIr state of [NiFe] hydrogenase was found to convert to the Ni-SIa state by light irradiation. Herein, large activation energies and a large kinetic isotope effect were obtained for the reconversion of the Ni-SIa state to the Ni-SIr state after the Ni-SIr-to-Ni-SIa photoactivation, suggesting that the Ni-SIa state reacts with H2O and leaves a bridging hydroxo ligand for the Ni-SIr state.
Collapse
Affiliation(s)
- Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan. and CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Liyang Xu
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan.
| | - Koji Nishikawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Higuchi
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan and Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan. and CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
21
|
Tai H, Xu L, Inoue S, Nishikawa K, Higuchi Y, Hirota S. Photoactivation of the Ni-SIr state to the Ni-SIa state in [NiFe] hydrogenase: FT-IR study on the light reactivity of the ready Ni-SIr state and as-isolated enzyme revisited. Phys Chem Chem Phys 2018; 18:22025-30. [PMID: 27456760 DOI: 10.1039/c6cp04628b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The Ni-SIr state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F was photoactivated to its Ni-SIa state by Ar(+) laser irradiation at 514.5 nm, whereas the Ni-SL state was light induced from a newly identified state, which was less active than any other identified state and existed in the "as-isolated" enzyme.
Collapse
Affiliation(s)
- Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan. and CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Liyang Xu
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan.
| | - Seiya Inoue
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Koji Nishikawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Higuchi
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan and Graduate School of Life Science, University of Hyogo, 3-2-1 Koto Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan. and CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Greene BL, Vansuch GE, Chica BC, Adams MWW, Dyer RB. Applications of Photogating and Time Resolved Spectroscopy to Mechanistic Studies of Hydrogenases. Acc Chem Res 2017; 50:2718-2726. [PMID: 29083854 DOI: 10.1021/acs.accounts.7b00356] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Rapid and facile redox chemistry is exemplified in nature by the oxidoreductases, the class of enzymes that catalyze electron transfer (ET) from a donor to an acceptor. The key role of oxidoreductases in metabolism and biosynthesis has imposed evolutionary pressure to enhance enzyme efficiency, pushing some toward the diffusion limit. Understanding the detailed molecular mechanisms of these highly optimized enzymes would provide an important foundation for the rational design of catalysts for multielectron chemistry, including fuel production. The hydrogenases (H2ases) are the oxidoreductases that catalyze the most basic electron and proton transfer reactions relevant to fuel production, the interconversion of protons and hydrogen, with kcat > 103 s-1. Thus, they provide a model system for studying the efficiency exhibited by oxidoreductases. Because of the extraordinarily fast catalytic rates of these enzymes, their mechanisms have been difficult to study directly but instead have been inferred from structural and steady-state measurements. Although informative, the kinetic competency of observed equilibrium steps can only be suggested by these methods, not demonstrated, because the fundamental (fast) catalytic steps remain unresolved, resulting in minimal insight regarding the underlying ET and proton transfer (PT) events. Motivated by this gap in understanding, we developed an approach capable of observing elementary ET and PT during such fast enzyme turnover by combining a laser-induced potential jump with time-resolved spectroscopy. The potential jump initiates enzyme turnover by utilizing a short-pulsed laser to release a "caged" electron from a nanomaterial or NAD(P)H, which is then captured by a mediator such as methyl viologen. The subsequent enzyme reduction and turnover are monitored by transient absorption spectroscopy in the visible or mid-IR spectral regions. The method is completely general and in principle can be applied to any catalytic redox reaction. In the case of hydrogenases, time-resolved infrared spectroscopy of the active site CO ligands is particularly informative since the IR frequencies are exquisitely sensitive to the redox and protonation states. Using this methodology, we have developed a description of the catalytic mechanism of the Pyrococcus furiosus [NiFe]-hydrogenase by demonstrating the kinetic and chemical competency of equilibrium states and by invoking new intermediates. Additionally, the pre-steady-state kinetics revealed a distinct role of proton tunneling in concerted electron-proton transfer (EPT) modulated by a conserved glutamic acid residue. Similar multisite EPT processes have been implicated in numerous enzymes but have not been demonstrated explicitly. These methods have also been successfully applied to an electron bifurcating [FeFe]-H2ase from Thermotoga maritima, establishing the kinetic competency of the Hox, Hred, and Hsred intermediates of the [FeFe] enzyme. These results provide fundamental insight on the factors that control low barrier proton and electron flow in enzymes and thus provide a foundation for the rational design of reversible biomimetic catalysts.
Collapse
Affiliation(s)
- Brandon L. Greene
- Department
of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Gregory E. Vansuch
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Bryant C. Chica
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Michael W. W. Adams
- Department
of Biochemistry and Molecular Biology, University of Georgia, B122 Life
Sciences Bldg., Athens, Georgia 30602, United States
| | - R. Brian Dyer
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Song LC, Yang XY, Cao M, Gao XY, Liu BB, Zhu L, Jiang F. Dithiolato-bridged nickel–iron complexes as models for the active site of [NiFe]-hydrogenases. Chem Commun (Camb) 2017; 53:3818-3821. [DOI: 10.1039/c7cc00149e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
While the first NiFe-based μ-hydroxo model [3]+ can be prepared by reaction of a dicarbonyl model [1]2+ with Me3NO·2H2O, the functional modeling of H2 activation catalyzed by the Ni-SIa state gives the t-hydride model [2]+ in high yield.
Collapse
Affiliation(s)
- Li-Cheng Song
- Department of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Xi-Yue Yang
- Department of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Meng Cao
- Department of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Xiu-Yun Gao
- Department of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Bei-Bei Liu
- Department of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Liang Zhu
- Department of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Feng Jiang
- Department of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- China
| |
Collapse
|
26
|
Greene BL, Vansuch GE, Wu CH, Adams MWW, Dyer RB. Glutamate Gated Proton-Coupled Electron Transfer Activity of a [NiFe]-Hydrogenase. J Am Chem Soc 2016; 138:13013-13021. [DOI: 10.1021/jacs.6b07789] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brandon L. Greene
- Chemistry
Department, Emory University, Atlanta, Georgia 30322, United States
| | - Gregory E. Vansuch
- Chemistry
Department, Emory University, Atlanta, Georgia 30322, United States
| | - Chang-Hao Wu
- 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
| |
Collapse
|
27
|
Schilter D, Camara JM, Huynh MT, Hammes-Schiffer S, Rauchfuss TB. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides. Chem Rev 2016; 116:8693-749. [PMID: 27353631 PMCID: PMC5026416 DOI: 10.1021/acs.chemrev.6b00180] [Citation(s) in RCA: 397] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.
Collapse
Affiliation(s)
- David Schilter
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - James M. Camara
- Department of Chemistry, Yeshiva University, 500 West 185th Street, New York, New York 10033, United States
| | - Mioy T. Huynh
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Greene BL, Wu CH, Vansuch GE, Adams MWW, Dyer RB. Proton Inventory and Dynamics in the Nia-S to Nia-C Transition of a [NiFe] Hydrogenase. Biochemistry 2016; 55:1813-25. [DOI: 10.1021/acs.biochem.5b01348] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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
| | - Gregory E. Vansuch
- Chemistry
Department, Emory University, Atlanta, Georgia 30322, 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
| |
Collapse
|
30
|
Lukoyanov D, Khadka N, Yang ZY, Dean DR, Seefeldt LC, Hoffman BM. Reversible Photoinduced Reductive Elimination of H2 from the Nitrogenase Dihydride State, the E(4)(4H) Janus Intermediate. J Am Chem Soc 2016; 138:1320-7. [PMID: 26788586 DOI: 10.1021/jacs.5b11650] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We recently demonstrated that N2 reduction by nitrogenase involves the obligatory release of one H2 per N2 reduced. These studies focus on the E4(4H) "Janus intermediate", which has accumulated four reducing equivalents as two [Fe-H-Fe] bridging hydrides. E4(4H) is poised to bind and reduce N2 through reductive elimination (re) of the two hydrides as H2, coupled to the binding/reduction of N2. To obtain atomic-level details of the re activation process, we carried out in situ 450 nm photolysis of E4(4H) in an EPR cavity at temperatures below 20 K. ENDOR and EPR measurements show that photolysis generates a new FeMo-co state, denoted E4(2H)*, through the photoinduced re of the two bridging hydrides of E4(4H) as H2. During cryoannealing at temperatures above 175 K, E4(2H)* reverts to E4(4H) through the oxidative addition (oa) of the H2. The photolysis quantum yield is temperature invariant at liquid helium temperatures and shows a rather large kinetic isotope effect, KIE = 10. These observations imply that photoinduced release of H2 involves a barrier to the combination of the two nascent H atoms, in contrast to a barrierless process for monometallic inorganic complexes, and further suggest that H2 formation involves nuclear tunneling through that barrier. The oa recombination of E4(2H)* with the liberated H2 offers compelling evidence for the Janus intermediate as the point at which H2 is necessarily lost during N2 reduction; this mechanistically coupled loss must be gated by N2 addition that drives the re/oa equilibrium toward reductive elimination of H2 with N2 binding/reduction.
Collapse
Affiliation(s)
- Dmitriy Lukoyanov
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| |
Collapse
|
31
|
Ash PA, Liu J, Coutard N, Heidary N, Horch M, Gudim I, Simler T, Zebger I, Lenz O, Vincent KA. Electrochemical and Infrared Spectroscopic Studies Provide Insight into Reactions of the NiFe Regulatory Hydrogenase from Ralstonia eutropha with O2 and CO. J Phys Chem B 2015; 119:13807-15. [PMID: 26115011 DOI: 10.1021/acs.jpcb.5b04164] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulatory hydrogenase (RH) from Ralstonia eutropha acts as the H2-sensing unit of a two-component system that regulates biosynthesis of the energy conserving hydrogenases of the organism according to the availability of H2. The H2 oxidation activity, which was so far determined in vitro with artificial electron acceptors, has been considered to be insensitive to O2 and CO. It is assumed that bulky isoleucine and phenylalanine amino acid residues close to the NiFe active site "gate" gas access, preventing molecules larger than H2 interacting with the active site. We have carried out sensitive electrochemical measurements to demonstrate that O2 is in fact an inhibitor of H2 oxidation by the RH, and that both H(+) reduction and H2 oxidation are inhibited by CO. Furthermore, we have demonstrated that the inhibitory effect of O2 arises due to interaction of O2 with the active site. Using protein film infrared electrochemistry (PFIRE) under H2 oxidation conditions, in conjunction with solution infrared measurements, we have identified previously unreported oxidized inactive and catalytically active reduced states of the RH active site. These findings suggest that the RH has a rich active site chemistry similar to that of other NiFe hydrogenases.
Collapse
Affiliation(s)
- Philip A Ash
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Juan Liu
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nathan Coutard
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nina Heidary
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Marius Horch
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Ingvild Gudim
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Thomas Simler
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Kylie A Vincent
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Hidalgo R, Ash PA, Healy AJ, Vincent KA. Infrared Spectroscopy During Electrocatalytic Turnover Reveals the Ni-L Active Site State During H2 Oxidation by a NiFe Hydrogenase. Angew Chem Int Ed Engl 2015; 54:7110-3. [PMID: 25925315 PMCID: PMC4531817 DOI: 10.1002/anie.201502338] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/01/2015] [Indexed: 01/25/2023]
Abstract
A novel in situ IR spectroscopic approach is demonstrated for the characterization of hydrogenase during catalytic turnover. E. coli hydrogenase 1 (Hyd-1) is adsorbed on a high surface-area carbon electrode and subjected to the same electrochemical control and efficient supply of substrate as in protein film electrochemistry during spectral acquisition. The spectra reveal that the active site state known as Ni-L, observed in other NiFe hydrogenases only under illumination or at cryogenic temperatures, can be generated reversibly in the dark at ambient temperature under both turnover and non-turnover conditions. The observation that Ni-L is present at all potentials during turnover under H2 suggests that the final steps in the catalytic cycle of H2 oxidation by Hyd-1 involve sequential proton and electron transfer via Ni-L. A broadly applicable IR spectroscopic technique is presented for addressing electrode-adsorbed redox enzymes under fast catalytic turnover.
Collapse
Affiliation(s)
- Ricardo Hidalgo
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR (UK)
| | - Philip A Ash
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR (UK)
| | - Adam J Healy
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR (UK)
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR (UK).
| |
Collapse
|
34
|
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.
Collapse
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 . ;
| |
Collapse
|
35
|
Tai H, Nishikawa K, Inoue S, Higuchi Y, Hirota S. FT-IR Characterization of the Light-Induced Ni-L2 and Ni-L3 States of [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F. J Phys Chem B 2015; 119:13668-74. [PMID: 25898020 DOI: 10.1021/acs.jpcb.5b03075] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Different light-induced Ni-L states of [NiFe] hydrogenase from its Ni-C state have previously been observed by EPR spectroscopy. Herein, we succeeded in detecting simultaneously two Ni-L states of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F by FT-IR spectroscopy. A new light-induced νCO band at 1890 cm(-1) and νCN bands at 2034 and 2047 cm(-1) were detected in the FT-IR spectra of the H2-activated enzyme under N2 atmosphere at basic conditions, in addition to the 1910 cm(-1) νCO band and 2047 and 2061 cm(-1) νCN bands of the Ni-L2 state. The new bands were attributed to the Ni-L3 state by comparison of the FT-IR and EPR spectra. The νCO and νCN frequencies of the Ni-L3 state are the lowest frequencies observed among the corresponding frequencies of standard-type [NiFe] hydrogenases in various redox states. These results indicate that a residue, presumably Ni-coordinating Cys546, is protonated and deprotonated in the Ni-L2 and Ni-L3 states, respectively. Relatively small ΔH (6.4 ± 0.8 kJ mol(-1)) and ΔS (25.5 ± 10.3 J mol(-1) K(-1)) values were obtained for the conversion from the Ni-L2 to Ni-L3 state, which was in agreement with the previous proposals that deprotonation of Cys546 is important for the catalytic reaction of the enzyme.
Collapse
Affiliation(s)
- Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan.,CREST, Japan Science and Technology Agency , Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Koji Nishikawa
- Graduate School of Life Science, University of Hyogo , 3-2-1 Koto kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Seiya Inoue
- Graduate School of Life Science, University of Hyogo , 3-2-1 Koto kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Higuchi
- CREST, Japan Science and Technology Agency , Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.,Graduate School of Life Science, University of Hyogo , 3-2-1 Koto kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan.,CREST, Japan Science and Technology Agency , Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| |
Collapse
|
36
|
Hidalgo R, Ash PA, Healy AJ, Vincent KA. Infrared Spectroscopy During Electrocatalytic Turnover Reveals the Ni-L Active Site State During H2Oxidation by a NiFe Hydrogenase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502338] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
37
|
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.
Collapse
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
| |
Collapse
|