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Askins EJ, Sarkar A, Navabi P, Kumar K, Finkelmeyer SJ, Presselt M, Cabana J, Glusac KD. Interfacial Electrochemistry of Catalyst-Coordinated Graphene Nanoribbons. J Am Chem Soc 2024; 146:22360-22373. [PMID: 39087647 DOI: 10.1021/jacs.4c05250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
The immobilization of molecular electrocatalysts on conductive electrodes is an appealing strategy for enhancing their overall activity relative to those of analogous molecular compounds. In this study, we report on the interfacial electrochemistry of self-assembled two-dimensional nanosheets of graphene nanoribbons (GNR-2DNS) and analogs containing a Rh-based hydrogen evolution reaction (HER) catalyst (RhGNR-2DNS) immobilized on conductive electrodes. Proton-coupled electron transfer (PCET) taking place at N-centers of the nanoribbons was utilized as an indirect reporter of the interfacial electric fields experienced by the monolayer nanosheet located within the electric double layer. The experimental Pourbaix diagrams were compared with a theoretical model, which derives the experimental Pourbaix slopes as a function of parameter f, a fraction of the interfacial potential drop experienced by the redox-active group. Interestingly, our study revealed that GNR-2DNS was strongly coupled to glassy carbon electrodes (f = 1), while RhGNR-2DNS was not (f = 0.15). We further investigated the HER mechanism by RhGNR-2DNS using electrochemical and X-ray absorption spectroelectrochemical methods and compared it to homogeneous molecular model compounds. RhGNR-2DNS was found to be an active HER electrocatalyst over a broader set of aqueous pH conditions than its molecular analogs. We find that the improved HER performance in the immobilized catalyst arises due to two factors. First, redox-active bipyrimidine-based ligands were shown to dramatically alter the activity of Rh sites by increasing the electron density at the active Rh center and providing RhGNR-2DNS with improved catalysis. Second, catalyst immobilization was found to prevent catalyst aggregation that was found to occur for the molecular analog in the basic pH. Overall, this study provides valuable insights into the mechanism by which catalyst immobilization can affect the overall electrocatalytic performance.
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Affiliation(s)
- Erik J Askins
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Abdul Sarkar
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Pouyan Navabi
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Khagesh Kumar
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Sarah Jasmin Finkelmeyer
- Leibniz Institute of Photonic Technology (IPHT), Jena 07745, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Martin Presselt
- Leibniz Institute of Photonic Technology (IPHT), Jena 07745, Germany
- SciClus GmbH & Co. KG, Jena 07745, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Jena 07743, Germany
| | - Jordi Cabana
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Ksenija D Glusac
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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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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3
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Williams MT, Yee E, Larson GW, Apiche EA, Rama Damodaran A, Bhagi-Damodaran A. Metalloprotein enabled redox signal transduction in microbes. Curr Opin Chem Biol 2023; 76:102331. [PMID: 37311385 PMCID: PMC10524656 DOI: 10.1016/j.cbpa.2023.102331] [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: 03/09/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 06/15/2023]
Abstract
Microbes utilize numerous metal cofactor-containing proteins to recognize and respond to constantly fluctuating redox stresses in their environment. Gaining an understanding of how these metalloproteins sense redox events, and how they communicate such information downstream to DNA to modulate microbial metabolism, is a topic of great interest to both chemists and biologists. In this article, we review recently characterized examples of metalloprotein sensors, focusing on the coordination and oxidation state of the metals involved, how these metals are able to recognize redox stimuli, and how the signal is transmitted beyond the metal center. We discuss specific examples of iron, nickel, and manganese-based microbial sensors, and identify gaps in knowledge in the field of metalloprotein-based signal transduction pathways.
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Affiliation(s)
- Murphi T Williams
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Eaindra Yee
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Grant W Larson
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Elizabeth A Apiche
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA.
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Evans RM, Beaton SE, Rodriguez Macia P, Pang Y, Wong KL, Kertess L, Myers WK, Bjornsson R, Ash PA, Vincent KA, Carr SB, Armstrong FA. Comprehensive structural, infrared spectroscopic and kinetic investigations of the roles of the active-site arginine in bidirectional hydrogen activation by the [NiFe]-hydrogenase 'Hyd-2' from Escherichia coli. Chem Sci 2023; 14:8531-8551. [PMID: 37592998 PMCID: PMC10430524 DOI: 10.1039/d2sc05641k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/01/2023] [Indexed: 08/19/2023] Open
Abstract
The active site of [NiFe]-hydrogenases contains a strictly-conserved pendant arginine, the guanidine head group of which is suspended immediately above the Ni and Fe atoms. Replacement of this arginine (R479) in hydrogenase-2 from E. coli results in an enzyme that is isolated with a very tightly-bound diatomic ligand attached end-on to the Ni and stabilised by hydrogen bonding to the Nζ atom of the pendant lysine and one of the three additional water molecules located in the active site of the variant. The diatomic ligand is bound under oxidising conditions and is removed only after a prolonged period of reduction with H2 and reduced methyl viologen. Once freed of the diatomic ligand, the R479K variant catalyses both H2 oxidation and evolution but with greatly decreased rates compared to the native enzyme. Key kinetic characteristics are revealed by protein film electrochemistry: most importantly, a very low activation energy for H2 oxidation that is not linked to an increased H/D isotope effect. Native electrocatalytic reversibility is retained. The results show that the sluggish kinetics observed for the lysine variant arise most obviously because the advantage of a more favourable low-energy pathway is massively offset by an extremely unfavourable activation entropy. Extensive efforts to establish the identity of the diatomic ligand, the tight binding of which is an unexpected further consequence of replacing the pendant arginine, prove inconclusive.
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Affiliation(s)
- Rhiannon M Evans
- University of Oxford, Department of Chemistry South Parks Road Oxford UK
| | - Stephen E Beaton
- University of Oxford, Department of Chemistry South Parks Road Oxford UK
| | | | - Yunjie Pang
- College of Chemistry, Beijing Normal University 100875 Beijing China
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany
| | - Kin Long Wong
- University of Oxford, Department of Chemistry South Parks Road Oxford UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus Didcot UK
| | - Leonie Kertess
- University of Oxford, Department of Chemistry South Parks Road Oxford UK
| | - William K Myers
- University of Oxford, Department of Chemistry South Parks Road Oxford UK
| | - Ragnar Bjornsson
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire Chimie et Biologie des Métaux 17 Rue Des Martyrs F-38054 Grenoble Cedex France
| | - Philip A Ash
- School of Chemistry, The University of Leicester University Road Leicester LE1 7RH UK
| | - Kylie A Vincent
- University of Oxford, Department of Chemistry South Parks Road Oxford UK
| | - Stephen B Carr
- University of Oxford, Department of Chemistry South Parks Road Oxford UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus Didcot UK
| | - Fraser A Armstrong
- University of Oxford, Department of Chemistry South Parks Road Oxford UK
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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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Rennie BE, Price JS, Emslie DJH, Morris RH. Trans Ligand Determines the Stability of Paramagnetic Manganese(II) Hydrides of the Type trans-[MnH(L)(dmpe) 2] + Where L is PMe 3, C 2H 4, or CO. Inorg Chem 2023; 62:8123-8135. [PMID: 36812512 DOI: 10.1021/acs.inorgchem.2c04432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Paramagnetic metal hydride (PMH) complexes play important roles in catalytic applications and bioinorganic chemistry. 3d PMH chemistry has largely focused on Ti, Mn, Fe, and Co. Various MnII PMHs have been proposed as intermediates in catalysis, but isolated MnII PMHs are limited to dimeric high-spin MnII structures with bridging hydrides. In this paper, a series of the first low-spin monomeric MnII PMH complexes are generated by chemical oxidation of their MnI analogues. This series is of the type trans-[MnH(L)(dmpe)2]+/0 where the trans ligand L is PMe3, C2H4, or CO [dmpe is 1,2-bis(dimethylphosphino)ethane], and the thermal stability of the MnII hydride complexes was found to be strongly dependent on the identity of the trans ligand. When L is PMe3, the complex is the first example of an isolated monomeric MnII hydride complex. In contrast, when L is C2H4 or CO, the complexes are only stable at low temperatures; upon warming to room temperature, the former decomposed to afford [Mn(dmpe)3]+, accompanied by ethane and ethylene, whereas the latter eliminated H2, generating [Mn(MeCN)(CO)(dmpe)2]+ or a mixture of products including [Mn(κ1-PF6)(CO)(dmpe)2], depending on the reaction conditions. All PMHs were characterized by low-temperature electron paramagnetic resonance (EPR) spectroscopy, and stable [MnH(PMe3)(dmpe)2]+ was further characterized by UV-vis and IR spectroscopy, Superconducting Quantum Interference Device magnetometry, and single-crystal X-ray diffraction. Noteworthy spectral properties are the significant EPR superhyperfine coupling to the hydride (∼85 MHz) and an increase (+33 cm-1) in the Mn-H IR stretch upon oxidation. Density functional theory calculations were also employed to gain insights into the acidity and bond strengths of the complexes. MnII-H bond dissociation free energies are estimated to decrease in the series of complexes from 60 (L = PMe3) to 47 kcal/mol (L = CO).
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Affiliation(s)
- Benjamin E Rennie
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S3H6, Canada
| | - Jeffrey S Price
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S4M1, Canada
| | - David J H Emslie
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S4M1, Canada
| | - Robert H Morris
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S3H6, Canada
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7
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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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8
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Fan Q, Waldburger S, Neubauer P, Riedel SL, Gimpel M. Implementation of a high cell density fed-batch for heterologous production of active [NiFe]-hydrogenase in Escherichia coli bioreactor cultivations. Microb Cell Fact 2022; 21:193. [PMID: 36123684 PMCID: PMC9484157 DOI: 10.1186/s12934-022-01919-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background O2-tolerant [NiFe]-hydrogenases offer tremendous potential for applications in H2-based technology. As these metalloenzymes undergo a complicated maturation process that requires a dedicated set of multiple accessory proteins, their heterologous production is challenging, thus hindering their fundamental understanding and the development of related applications. Taking these challenges into account, we selected the comparably simple regulatory [NiFe]-hydrogenase (RH) from Cupriavidus necator as a model for the development of bioprocesses for heterologous [NiFe]-hydrogenase production. We already reported recently on the high-yield production of catalytically active RH in Escherichia coli by optimizing the culture conditions in shake flasks. Results In this study, we further increase the RH yield and ensure consistent product quality by a rationally designed high cell density fed-batch cultivation process. Overall, the bioreactor cultivations resulted in ˃130 mg L−1 of catalytically active RH which is a more than 100-fold increase compared to other RH laboratory bioreactor scale processes with C. necator. Furthermore, the process shows high reproducibility of the previously selected optimized conditions and high productivity. Conclusions This work provides a good opportunity to readily supply such difficult-to-express complex metalloproteins economically and at high concentrations to meet the demand in basic and applied studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01919-w.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Saskia Waldburger
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Sebastian L Riedel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany.
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9
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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: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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10
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Nayek A, Ahmed ME, Samanta S, Dinda S, Patra S, Dey SG, Dey A. Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling. J Am Chem Soc 2022; 144:8402-8429. [PMID: 35503922 DOI: 10.1021/jacs.2c01842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH+/ne-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH+/ne- reactions. Such control can allow functional modeling of hydrogenases (H+ + e- → 1/2 H2), cytochrome c oxidase (O2 + 4 e- + 4 H+ → 2 H2O), monooxygenases (RR'CH2 + O2 + 2 e- + 2 H+ → RR'CHOH + H2O) and dioxygenases (S + O2 → SO2; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.
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Affiliation(s)
- Abhijit Nayek
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Md Estak Ahmed
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Soumya Samanta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Souvik Dinda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Suman Patra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
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11
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Treviño RE, Shafaat HS. Protein-based models offer mechanistic insight into complex nickel metalloenzymes. Curr Opin Chem Biol 2022; 67:102110. [PMID: 35101820 DOI: 10.1016/j.cbpa.2021.102110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 11/03/2022]
Abstract
There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.
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Affiliation(s)
- Regina E Treviño
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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12
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Birrell JA, Rodríguez-Maciá P, Reijerse EJ, Martini MA, Lubitz W. The catalytic cycle of [FeFe] hydrogenase: A tale of two sites. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214191] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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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.
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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
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14
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The Challenge of Visualizing the Bridging Hydride at the Active Site and Proton Network of [NiFe]-Hydrogenase by Neutron Crystallography. Top Catal 2021. [DOI: 10.1007/s11244-021-01417-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Lorent C, Pelmenschikov V, Frielingsdorf S, Schoknecht J, Caserta G, Yoda Y, Wang H, Tamasaku K, Lenz O, Cramer SP, Horch M, Lauterbach L, Zebger I. Exploring Structure and Function of Redox Intermediates in [NiFe]-Hydrogenases by an Advanced Experimental Approach for Solvated, Lyophilized and Crystallized Metalloenzymes. Angew Chem Int Ed Engl 2021; 60:15854-15862. [PMID: 33783938 PMCID: PMC8360142 DOI: 10.1002/anie.202100451] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/20/2021] [Indexed: 01/28/2023]
Abstract
To study metalloenzymes in detail, we developed a new experimental setup allowing the controlled preparation of catalytic intermediates for characterization by various spectroscopic techniques. The in situ monitoring of redox transitions by infrared spectroscopy in enzyme lyophilizate, crystals, and solution during gas exchange in a wide temperature range can be accomplished as well. Two O2 -tolerant [NiFe]-hydrogenases were investigated as model systems. First, we utilized our platform to prepare highly concentrated hydrogenase lyophilizate in a paramagnetic state harboring a bridging hydride. This procedure proved beneficial for 57 Fe nuclear resonance vibrational spectroscopy and revealed, in combination with density functional theory calculations, the vibrational fingerprint of this catalytic intermediate. The same in situ IR setup, combined with resonance Raman spectroscopy, provided detailed insights into the redox chemistry of enzyme crystals, underlining the general necessity to complement X-ray crystallographic data with spectroscopic analyses.
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Affiliation(s)
- Christian Lorent
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Vladimir Pelmenschikov
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Stefan Frielingsdorf
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Janna Schoknecht
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Giorgio Caserta
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Mikazuki-choSayo-gunHyogo679-5198Japan
| | - Hongxin Wang
- SETI Institute189 Bernardo AvenueMountain ViewCalifornia94043USA
| | - Kenji Tamasaku
- RIKEN SPring-8 center1-1-1 Kouto, Sayo-choSayo-gunHyogo679-5148Japan
| | - Oliver Lenz
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | | | - Marius Horch
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
- Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Lars Lauterbach
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Ingo Zebger
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
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16
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Lorent C, Pelmenschikov V, Frielingsdorf S, Schoknecht J, Caserta G, Yoda Y, Wang H, Tamasaku K, Lenz O, Cramer SP, Horch M, Lauterbach L, Zebger I. Ein neuer Aufbau zur Untersuchung der Struktur und Funktion von solvatisierten, lyophilisierten und kristallinen Metalloenzymen – veranschaulicht anhand von [NiFe]‐Hydrogenasen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christian Lorent
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Vladimir Pelmenschikov
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Stefan Frielingsdorf
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Janna Schoknecht
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Giorgio Caserta
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute SPring-8 1-1-1 Kouto, Mikazuki-cho Sayo-gun Hyogo 679-5198 Japan
| | - Hongxin Wang
- SETI Institute 189 Bernardo Avenue Mountain View California 94043 USA
| | - Kenji Tamasaku
- RIKEN SPring-8 center 1-1-1 Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Oliver Lenz
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Stephen P. Cramer
- SETI Institute 189 Bernardo Avenue Mountain View California 94043 USA
| | - Marius Horch
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
- Department of Physics Freie Universität Berlin Arnimallee 14 14195 Berlin Deutschland
| | - Lars Lauterbach
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Ingo Zebger
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
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17
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Fan Q, Caserta G, Lorent C, Lenz O, Neubauer P, Gimpel M. Optimization of Culture Conditions for Oxygen-Tolerant Regulatory [NiFe]-Hydrogenase Production from Ralstonia eutropha H16 in Escherichia coli. Microorganisms 2021; 9:1195. [PMID: 34073092 PMCID: PMC8229454 DOI: 10.3390/microorganisms9061195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Hydrogenases are abundant metalloenzymes that catalyze the reversible conversion of molecular H2 into protons and electrons. Important achievements have been made over the past two decades in the understanding of these highly complex enzymes. However, most hydrogenases have low production yields requiring many efforts and high costs for cultivation limiting their investigation. Heterologous production of these hydrogenases in a robust and genetically tractable expression host is an attractive strategy to make these enzymes more accessible. In the present study, we chose the oxygen-tolerant H2-sensing regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha H16 owing to its relatively simple architecture compared to other [NiFe]-hydrogenases as a model to develop a heterologous hydrogenase production system in Escherichia coli. Using screening experiments in 24 deep-well plates with 3 mL working volume, we investigated relevant cultivation parameters, including inducer concentration, expression temperature, and expression time. The RH yield could be increased from 14 mg/L up to >250 mg/L by switching from a batch to an EnPresso B-based fed-batch like cultivation in shake flasks. This yield exceeds the amount of RH purified from the homologous host R. eutropha by several 100-fold. Additionally, we report the successful overproduction of the RH single subunits HoxB and HoxC, suitable for biochemical and spectroscopic investigations. Even though both RH and HoxC proteins were isolated in an inactive, cofactor free apo-form, the proposed strategy may powerfully accelerate bioprocess development and structural studies for both basic research and applied studies. These results are discussed in the context of the regulation mechanisms governing the assembly of large and small hydrogenase subunits.
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Affiliation(s)
- Qin Fan
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Giorgio Caserta
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Christian Lorent
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Peter Neubauer
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Matthias Gimpel
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
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18
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Hong DH, Ferreira RB, Catalano VJ, García-Serres R, Shearer J, Murray LJ. Access to Metal Centers and Fluxional Hydride Coordination Integral for CO 2 Insertion into [Fe 3(μ-H) 3] 3+ Clusters. Inorg Chem 2021; 60:7228-7239. [PMID: 33900076 DOI: 10.1021/acs.inorgchem.1c00244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CO2 insertion into tri(μ-hydrido)triiron(II) clusters ligated by a tris(β-diketiminate) cyclophane is demonstrated to be balanced by sterics for CO2 approach and hydride accessibility. Time-resolved NMR and UV-vis spectra for this reaction for a complex in which methoxy groups border the pocket of the hydride donor (Fe3H3L2, 4) result in a decreased activation barrier and increased kinetic isotope effect consistent with the reduced sterics. For the ethyl congener Fe3H3L1 (2), no correlation is found between rate and reaction solvent or added Lewis acids, implying CO2 coordination to an Fe center in the mechanism. The estimated hydricity (50 kcal/mol) based on observed H/D exchange with BD3 requires Fe-O bond formation in the product to offset an endergonic CO2 insertion. μ3-hydride coordination is noted to lower the activation barrier for the first CO2 insertion event in DFT calculations.
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Affiliation(s)
- Dae Ho Hong
- Center for Catalysis and Florida Center for Heterocyclic Chemistry, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Ricardo B Ferreira
- Center for Catalysis and Florida Center for Heterocyclic Chemistry, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Vincent J Catalano
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Ricardo García-Serres
- Université Grenoble Alpes, CNRS, CEA, BIG, LCBM (UMR 5249), F-38054 Grenoble, France
| | - Jason Shearer
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Leslie J Murray
- Center for Catalysis and Florida Center for Heterocyclic Chemistry, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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19
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Pribitzer S, Mannikko D, Stoll S. Determining electron-nucleus distances and Fermi contact couplings from ENDOR spectra. Phys Chem Chem Phys 2021; 23:8326-8335. [PMID: 33875997 DOI: 10.1039/d1cp00229e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hyperfine coupling between an electron spin and a nuclear spin depends on the Fermi contact coupling aiso and, through dipolar coupling, the distance r between the electron and the nucleus. It is measured with electron-nuclear double resonance (ENDOR) spectroscopy and provides insight into the electronic and spatial structure of paramagnetic centers. The analysis and interpretation of ENDOR spectra is commonly done by ordinary least-squares fitting. As this is an ill-posed, inverse mathematical problem, this is challenging, in particular for spectra that show features from several nuclei or where the hyperfine coupling parameters are distributed. We introduce a novel Tikhonov-type regularization approach that analyzes an experimental ENDOR spectrum in terms of a complete non-parametric distribution over r and aiso. The approach uses a penalty function similar to the cross entropy between the fitted distribution and a Bayesian prior distribution that is derived from density functional theory calculations. Additionally, we show that smoothness regularization, commonly used for a similar purpose in double electron-electron resonance (DEER) spectroscopy, is not suited for ENDOR. We demonstrate that the novel approach is able to identify and quantitate ligand protons with electron-nucleus distances between 4 and 9 Å in a series of vanadyl porphyrin compounds.
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Affiliation(s)
- Stephan Pribitzer
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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20
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Ghosh AC, Duboc C, Gennari M. Synergy between metals for small molecule activation: Enzymes and bio-inspired complexes. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213606] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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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.
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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
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22
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Abstract
The role of deuterium in disentangling key steps of the mechanisms of H2 activation by mimics of hydrogenases is presented. These studies have allowed to a better understanding of the mode of action of the natural enzymes and their mimics.
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Affiliation(s)
- Mar Gómez-Gallego
- Departamento de Química Orgánica I and Center for Innovation in Advanced Chemistry (ORFEO-CINQA). Facultad de Química
- Universidad Complutense
- 28040-Madrid
- Spain
| | - Miguel A. Sierra
- Departamento de Química Orgánica I and Center for Innovation in Advanced Chemistry (ORFEO-CINQA). Facultad de Química
- Universidad Complutense
- 28040-Madrid
- Spain
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23
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Amanullah S, Saha P, Nayek A, Ahmed ME, Dey A. Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis. Chem Soc Rev 2021; 50:3755-3823. [DOI: 10.1039/d0cs01405b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Paramita Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhijit Nayek
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Md Estak Ahmed
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhishek Dey
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
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24
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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.
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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
| | - 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
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25
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Salvadori E, Chiesa M, Buonerba A, Grassi A. Structure and dynamics of catalytically competent but labile paramagnetic metal-hydrides: the Ti(iii)-H in homogeneous olefin polymerization. Chem Sci 2020; 11:12436-12445. [PMID: 34123229 PMCID: PMC8162776 DOI: 10.1039/d0sc04967k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 11/29/2022] Open
Abstract
Metal hydride complexes find widespread application in catalysis and their properties are often understood on the basis of the available crystal structures. However, some catalytically relevant metal hydrides are only spontaneously formed in situ, cannot be isolated in large quantities or crystallised and their structure is therefore ill defined. One such example is the paramagnetic Ti(iii)-hydride involved in homogeneous Ziegler-Natta catalysis, formed upon activation of CpTi(iv)Cl3 with modified methylalumoxane (MMAO). In this contribution, through a combined use of electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR) and hyperfine sublevel correlation (HYSCORE) spectroscopies we identify the nature of the ligands, their bonding interaction and the extent of the spin distribution. From the data, an atomistic and electronic model is proposed, which supports the presence of a self-assembled ion pair between a cationic terminal Ti-hydride and an aluminate anion, with a hydrodynamic radius of ca. 16 Å.
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Affiliation(s)
- Enrico Salvadori
- Department of Chemistry, University of Turin Via Pietro Giuria 7 Torino 10125 Italy
| | - Mario Chiesa
- Department of Chemistry, University of Turin Via Pietro Giuria 7 Torino 10125 Italy
| | - Antonio Buonerba
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno Via Giovanni Paolo II, 132 I-84084 Fisciano SA Italy
| | - Alfonso Grassi
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno Via Giovanni Paolo II, 132 I-84084 Fisciano SA Italy
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26
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Vansuch GE, Wu CH, Haja DK, Blair SA, Chica B, Johnson MK, Adams MWW, Dyer RB. Metal-ligand cooperativity in the soluble hydrogenase-1 from Pyrococcus furiosus. Chem Sci 2020; 11:8572-8581. [PMID: 34123117 PMCID: PMC8163435 DOI: 10.1039/d0sc00628a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Metal–ligand cooperativity is an essential feature of bioinorganic catalysis. The design principles of such cooperativity in metalloenzymes are underexplored, but are critical to understand for developing efficient catalysts designed with earth abundant metals for small molecule activation. The simple substrate requirements of reversible proton reduction by the [NiFe]-hydrogenases make them a model bioinorganic system. A highly conserved arginine residue (R355) directly above the exogenous ligand binding position of the [NiFe]-catalytic core is known to be essential for optimal function because mutation to a lysine results in lower catalytic rates. To expand on our studies of soluble hydrogenase-1 from Pyrococcus furiosus (Pf SH1), we investigated the role of R355 by site-directed-mutagenesis to a lysine (R355K) using infrared and electron paramagnetic resonance spectroscopic probes sensitive to active site redox and protonation events. It was found the mutation resulted in an altered ligand binding environment at the [NiFe] centre. A key observation was destabilization of the Nia3+–C state, which contains a bridging hydride. Instead, the tautomeric Nia+–L states were observed. Overall, the results provided insight into complex metal–ligand cooperativity between the active site and protein scaffold that modulates the bridging hydride stability and the proton inventory, which should prove valuable to design principles for efficient bioinspired catalysts. Metal–ligand cooperativity is an essential feature of bioinorganic catalysis.![]()
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Affiliation(s)
| | - Chang-Hao Wu
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA.,AskGene Pharma Inc. Camarillo CA 93012 USA
| | - Dominik K Haja
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA
| | - Soshawn A Blair
- Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - Bryant Chica
- Department of Chemistry, Emory University Atlanta Georgia 30222 USA .,Biosciences Center, National Renewable Energy Laboratory Golden Colorado 80401 USA
| | - Michael K Johnson
- Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - Michael W W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA.,Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - R Brian Dyer
- Department of Chemistry, Emory University Atlanta Georgia 30222 USA
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27
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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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28
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Gu NX, Oyala PH, Peters JC. H 2 Evolution from a Thiolate-Bound Ni(III) Hydride. J Am Chem Soc 2020; 142:7827-7835. [PMID: 32249575 DOI: 10.1021/jacs.0c00712] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Terminal NiIII hydrides are proposed intermediates in proton reduction catalyzed by both molecular electrocatalysts and metalloenzymes, but well-defined examples of paramagnetic nickel hydride complexes are largely limited to bridging hydrides. Herein, we report the synthesis of an S = 1/2, terminally bound thiolate-NiIII-H complex. This species and its terminal hydride ligand in particular have been thoroughly characterized by vibrational and EPR techniques, including pulse EPR studies. Corresponding DFT calculations suggest appreciable spin leakage onto the thiolate ligand. The hyperfine coupling to the terminal hydride ligand of the thiolate-NiIII-H species is comparable to that of the hydride ligand proposed for the Ni-C hydrogenase intermediate (NiIII-H-FeII). Upon warming, the featured thiolate-NiIII-H species undergoes bimolecular reductive elimination of H2. Associated kinetic studies are discussed and compared with a structurally related FeIII-H species that has also recently been reported to undergo bimolecular H-H coupling.
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Affiliation(s)
- Nina X Gu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jonas C Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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29
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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
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30
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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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31
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Horch M, Schoknecht J, Wrathall SLD, Greetham GM, Lenz O, Hunt NT. Understanding the structure and dynamics of hydrogenases by ultrafast and two-dimensional infrared spectroscopy. Chem Sci 2019; 10:8981-8989. [PMID: 31762978 PMCID: PMC6857670 DOI: 10.1039/c9sc02851j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
Hydrogenases are valuable model enzymes for sustainable energy conversion approaches using H2, but rational utilization of these base-metal biocatalysts requires a detailed understanding of the structure and dynamics of their complex active sites. The intrinsic CO and CN- ligands of these metalloenzymes represent ideal chromophores for infrared (IR) spectroscopy, but structural and dynamic insight from conventional IR absorption experiments is limited. Here, we apply ultrafast and two-dimensional (2D) IR spectroscopic techniques, for the first time, to study hydrogenases in detail. Using an O2-tolerant [NiFe] hydrogenase as a model system, we demonstrate that IR pump-probe spectroscopy can explore catalytically relevant ligand bonding by accessing high-lying vibrational states. This ultrafast technique also shows that the protein matrix is influential in vibrational relaxation, which may be relevant for energy dissipation from the active site during fast reaction steps. Further insights into the relevance of the active site environment are provided by 2D-IR spectroscopy, which reveals equilibrium dynamics and structural constraints imposed on the H2-accepting intermediate of [NiFe] hydrogenases. Both techniques offer new strategies for uniquely identifying redox-structural states in complex catalytic mixtures via vibrational quantum beats and 2D-IR off-diagonal peaks. Together, these findings considerably expand the scope of IR spectroscopy in hydrogenase research, and new perspectives for the characterization of these enzymes and other (bio-)organometallic targets are presented.
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Affiliation(s)
- Marius Horch
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Janna Schoknecht
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Solomon L D Wrathall
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , Oxford , OX110PE , UK
| | - Oliver Lenz
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Neil T Hunt
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
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32
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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.
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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
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33
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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
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34
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Rao G, Altman AB, Brown AC, Tao L, Stich TA, Arnold J, Britt RD. Metal Bonding with 3d and 6d Orbitals: An EPR and ENDOR Spectroscopic Investigation of Ti 3+-Al and Th 3+-Al Heterobimetallic Complexes. Inorg Chem 2019; 58:7978-7988. [PMID: 31185562 PMCID: PMC6584900 DOI: 10.1021/acs.inorgchem.9b00720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Accessing covalent
bonding interactions between actinides and ligating atoms remains
a central problem in the field. Our current understanding of actinide
bonding is limited because of a paucity of diverse classes of compounds
and the lack of established models. We recently synthesized a thorium
(Th)–aluminum (Al) heterobimetallic molecule that represents
a new class of low-valent Th-containing compounds. To gain further
insight into this system and actinide–metal bonding more generally,
it is useful to study their underlying electronic structures. Here,
we report characterization by electron paramagnetic resonance (EPR)
and electron–nuclear double resonance (ENDOR) spectroscopy
of two heterobimetallic compounds: (i) a Cptt2ThH3AlCTMS3 [TMS = Si(CH3)3; Cptt = 1,3-di-tert-butylcyclopentadienyl]
complex with bridging hydrides and (ii) an actinide-free Cp2TiH3AlCTMS3 (Cp = cyclopentadienyl) analogue.
Analyses of the hyperfine interactions between the paramagnetic trivalent
metal centers and the surrounding magnetic nuclei, 1H and 27Al, yield spin distributions over both complexes. These results
show that while the bridging hydrides in the two complexes have similar
hyperfine couplings (aiso = −9.7
and −10.7 MHz, respectively), the spin density on the Al ion
in the Th3+ complex is ∼5-fold larger than that
in the titanium(3+) (Ti3+) analogue. This suggests a direct
orbital overlap between Th and Al, leading to a covalent interaction
between Th and Al. Our quantitative investigation by a pulse EPR technique
deepens our understanding of actinide bonding to main-group elements. The electronic structures of Ti3+−Al and Th3+−Al heterobimetallic complexes are probed by electron−nuclear
double resonance spectroscopy, revealing a much larger spin density
on the Al center in the latter and the presence of a covalent Th−Al
bonding interaction caused by the direct orbital overlap between Th
and Al.
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Affiliation(s)
- Guodong Rao
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
| | - Alison B Altman
- Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Alexandra C Brown
- Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Lizhi Tao
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
| | - Troy A Stich
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
| | - John Arnold
- Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - R David Britt
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
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35
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Qiu S, Li Q, Xu Y, Shen S, Sun C. Learning from nature: Understanding hydrogenase enzyme using computational approach. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Qinye Li
- School of Chemical Engineering Monash University Clayton Victoria Australia
| | - Yongjun Xu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Shaohua Shen
- International Research Center for Renewable Energy, State Key Laboratory of Multiphase Flow in Power Engineering Xi'an Jiaotong University Shaanxi China
| | - Chenghua Sun
- Department of Chemistry and Biotechnology, and Center for Translational Atomaterials Swinburne University of Technology Hawthorn Victoria Australia
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36
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Borthakur B, Vargas A, Phukan AK. A Computational Study of Carbene Ligand Stabilization of Biomimetic Models of the Rotated H
red
State of [FeFe]‐Hydrogenase. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Bitupon Borthakur
- Department of Chemical Sciences Tezpur University Napaam 784028 Assam India
| | - Alfredo Vargas
- Department of Chemistry, School of Life Sciences University of Sussex Brighton BN1 9QJ Sussex United Kingdom
| | - Ashwini K. Phukan
- Department of Chemical Sciences Tezpur University Napaam 784028 Assam India
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37
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Qiu S, Azofra LM, Macfarlane DR, Sun C. Hydrogen Evolution in [NiFe] Hydrogenases: A Case of Heterolytic Approach between Proton and Hydride. Inorg Chem 2019; 58:2979-2986. [DOI: 10.1021/acs.inorgchem.8b02812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
| | - Luis Miguel Azofra
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Douglas R. Macfarlane
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Electromaterials Science (ACES), School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
| | - Chenghua Sun
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
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38
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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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39
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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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40
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Maroney MJ, Hondal RJ. Selenium versus sulfur: Reversibility of chemical reactions and resistance to permanent oxidation in proteins and nucleic acids. Free Radic Biol Med 2018; 127:228-237. [PMID: 29588180 PMCID: PMC6158117 DOI: 10.1016/j.freeradbiomed.2018.03.035] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/14/2018] [Accepted: 03/18/2018] [Indexed: 12/16/2022]
Abstract
This review highlights the contributions of Jean Chaudière to the field of selenium biochemistry. Chaudière was the first to recognize that one of the main reasons that selenium in the form of selenocysteine is used in proteins is due to the fact that it strongly resists permanent oxidation. The foundations for this important concept was laid down by Al Tappel in the 1960's and even before by others. The concept of oxygen tolerance first recognized in the study of glutathione peroxidase was further advanced and refined by those studying [NiFeSe]-hydrogenases, selenosubtilisin, and thioredoxin reductase. After 200 years of selenium research, work by Marcus Conrad and coworkers studying glutathione peroxidase-4 has provided definitive evidence for Chaudière's original hypothesis (Ingold et al., 2018) [36]. While the reaction of selenium with oxygen is readily reversible, there are many other examples of this phenomenon of reversibility. Many reactions of selenium can be described as "easy in - easy out". This is due to the strong nucleophilic character of selenium to attack electrophiles, but then this reaction can be reversed due to the strong electrophilic character of selenium and the weakness of the selenium-carbon bond. Several examples of this are described.
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Affiliation(s)
- Michael J Maroney
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts, Life Sciences Laboratories, 240 Thatcher Road, Room N373, Amherst, MA 01003-9364, United States
| | - Robert J Hondal
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States.
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41
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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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42
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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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43
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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.
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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.
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44
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Ash PA, Carr SB, Reeve HA, Skorupskaitė A, Rowbotham JS, Shutt R, Frogley MD, Evans RM, Cinque G, Armstrong FA, Vincent KA. Generating single metalloprotein crystals in well-defined redox states: electrochemical control combined with infrared imaging of a NiFe hydrogenase crystal. Chem Commun (Camb) 2018; 53:5858-5861. [PMID: 28504793 PMCID: PMC5708527 DOI: 10.1039/c7cc02591b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We describe an approach to generating and verifying well-defined redox states in metalloprotein single crystals by combining electrochemical control with synchrotron infrared microspectroscopic imaging. For NiFe hydrogenase 1 from Escherichia coli we demonstrate fully reversible and uniform electrochemical reduction from the oxidised inactive to the fully reduced state, and temporally resolve steps during this reduction.
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Affiliation(s)
- P A Ash
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
| | - S B Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK and Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - H A Reeve
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
| | - A Skorupskaitė
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
| | - J S Rowbotham
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
| | - R Shutt
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
| | - M D Frogley
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, UK
| | - R M Evans
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
| | - G Cinque
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, UK
| | - F A Armstrong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
| | - K A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
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45
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Qiu S, Azofra LM, MacFarlane DR, Sun C. Hydrogen bonding effect between active site and protein environment on catalysis performance in H 2-producing [NiFe] hydrogenases. Phys Chem Chem Phys 2018; 20:6735-6743. [PMID: 29457815 DOI: 10.1039/c7cp07685a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction between the active site and the surrounding protein environment plays a fundamental role in the hydrogen evolution reaction (HER) in [NiFe] hydrogenases. Our density functional theory (DFT) findings demonstrate that the reaction Gibbs free energy required for the rate determining step decreases by 7.1 kcal mol-1 when the surrounding protein environment is taken into account, which is chiefly due to free energy decreases for the two H+/e- addition steps (the so-called Ni-SIa to I1, and Ni-C to Ni-R), being the largest thermodynamic impediments of the whole reaction. The variety of hydrogen bonds (H-bonds) between the amino acids and the active site is hypothesised to be the main reason for such stability: H-bonds not only work as electrostatic attractive forces that influence the charge redistribution, but more importantly, they act as an electron 'pull' taking electrons from the active site towards the amino acids. Moreover, the electron 'pull' effect through H-bonds via the S- in cysteine residues shows a larger influence on the energy profile than that via the CN- ligands on Fe.
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Affiliation(s)
- Siyao Qiu
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia.
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46
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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.
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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
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47
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Tang H, Hall MB. Biomimetics of [NiFe]-Hydrogenase: Nickel- or Iron-Centered Proton Reduction Catalysis? J Am Chem Soc 2017; 139:18065-18070. [DOI: 10.1021/jacs.7b10425] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hao Tang
- Department of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - Michael B. Hall
- Department of Chemistry, Texas A&M University, College Station, Texas 77845, United States
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48
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Maiti BK, Almeida RM, Moura I, Moura JJ. Rubredoxins derivatives: Simple sulphur-rich coordination metal sites and its relevance for biology and chemistry. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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49
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Artz JH, Zadvornyy OA, Mulder DW, King PW, Peters JW. Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases. Methods Enzymol 2017; 595:213-259. [PMID: 28882202 DOI: 10.1016/bs.mie.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.
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Affiliation(s)
- Jacob H Artz
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.
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50
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Winkler M, Senger M, Duan J, Esselborn J, Wittkamp F, Hofmann E, Apfel UP, Stripp ST, Happe T. Accumulating the hydride state in the catalytic cycle of [FeFe]-hydrogenases. Nat Commun 2017; 8:16115. [PMID: 28722011 PMCID: PMC5524980 DOI: 10.1038/ncomms16115] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/30/2017] [Indexed: 01/07/2023] Open
Abstract
H2 turnover at the [FeFe]-hydrogenase cofactor (H-cluster) is assumed to follow a reversible heterolytic mechanism, first yielding a proton and a hydrido-species which again is double-oxidized to release another proton. Three of the four presumed catalytic intermediates (Hox, Hred/Hred and Hsred) were characterized, using various spectroscopic techniques. However, in catalytically active enzyme, the state containing the hydrido-species, which is eponymous for the proposed heterolytic mechanism, has yet only been speculated about. We use different strategies to trap and spectroscopically characterize this transient hydride state (Hhyd) for three wild-type [FeFe]-hydrogenases. Applying a novel set-up for real-time attenuated total-reflection Fourier-transform infrared spectroscopy, we monitor compositional changes in the state-specific infrared signatures of [FeFe]-hydrogenases, varying buffer pH and gas composition. We selectively enrich the equilibrium concentration of Hhyd, applying Le Chatelier’s principle by simultaneously increasing substrate and product concentrations (H2/H+). Site-directed manipulation, targeting either the proton-transfer pathway or the adt ligand, significantly enhances Hhyd accumulation independent of pH. Of the four intermediates in the catalytic cycle of [FeFe]-hydrogenases, the hydride state still has eluded characterization. Here, the authors shift the reaction equilibrium for three hydrogenases and enrich the hydride-bound species, characterizing them using a real-time IR spectroscopic technique.
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Affiliation(s)
- Martin Winkler
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Moritz Senger
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jifu Duan
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Julian Esselborn
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Florian Wittkamp
- Fakultät für Chemie und Biochemie, Lehrstuhl für Anorganische Chemie I/Bioanorganische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Eckhard Hofmann
- AG Proteinkristallographie, Lehrstuhl für Biophysik, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Fakultät für Chemie und Biochemie, Lehrstuhl für Anorganische Chemie I/Bioanorganische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Sven Timo Stripp
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Thomas Happe
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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