1
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Trevino RE, Fuller JT, Reid DJ, Laureanti JA, Ginovska B, Linehan JC, Shaw WJ. Understanding the role of negative charge in the scaffold of an artificial enzyme for CO 2 hydrogenation on catalysis. J Biol Inorg Chem 2024; 29:625-638. [PMID: 39207604 DOI: 10.1007/s00775-024-02070-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024]
Abstract
We have approached the construction of an artificial enzyme by employing a robust protein scaffold, lactococcal multidrug resistance regulator, LmrR, providing a structured secondary and outer coordination spheres around a molecular rhodium complex, [RhI(PEt2NglyPEt2)2]-. Previously, we demonstrated a 2-3 fold increase in activity for one Rh-LmrR construct by introducing positive charge in the secondary coordination sphere. In this study, a series of variants was made through site-directed mutagenesis where the negative charge is located in the secondary sphere or outer coordination sphere, with additional variants made with increasingly negative charge in the outer coordination sphere while keeping a positive charge in the secondary sphere. Placing a negative charge in the secondary or outer coordination sphere demonstrates decreased activity by a factor of two compared to the wild-type Rh-LmrR. Interestingly, addition of positive charge in the secondary sphere, with the negatively charged outer coordination sphere restores activity. Vibrational and NMR spectroscopy suggest minimal changes to the electronic density at the rhodium center, regardless of inclusion of a negative or positive charge in the secondary sphere, suggesting another mechanism is impacting catalytic activity, explored in the discussion.
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Affiliation(s)
- Regina E Trevino
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - Jack T Fuller
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - Deseree J Reid
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - Joseph A Laureanti
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
- Admiral Instruments, Tempe, AZ, 85281, USA
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - John C Linehan
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - Wendy J Shaw
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA.
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2
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Evans R, Krahn N, Weiss J, Vincent KA, Söll D, Armstrong FA. Replacing a Cysteine Ligand by Selenocysteine in a [NiFe]-Hydrogenase Unlocks Hydrogen Production Activity and Addresses the Role of Concerted Proton-Coupled Electron Transfer in Electrocatalytic Reversibility. J Am Chem Soc 2024; 146:16971-16976. [PMID: 38747098 PMCID: PMC11212049 DOI: 10.1021/jacs.4c03489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/27/2024]
Abstract
Hydrogenases catalyze hydrogen/proton interconversion that is normally electrochemically reversible (having minimal overpotential requirement), a special property otherwise almost exclusive to platinum metals. The mechanism of [NiFe]-hydrogenases includes a long-range proton-coupled electron-transfer process involving a specific Ni-coordinated cysteine and the carboxylate of a nearby glutamate. A variant in which this cysteine has been exchanged for selenocysteine displays two distinct changes in electrocatalytic properties, as determined by protein film voltammetry. First, proton reduction, even in the presence of H2 (a strong product inhibitor), is greatly enhanced relative to H2 oxidation: this result parallels a characteristic of natural [NiFeSe]-hydrogenases which are superior H2 production catalysts. Second, an inflection (an S-shaped "twist" in the trace) appears around the formal potential, the small overpotentials introduced in each direction (oxidation and reduction) signaling a departure from electrocatalytic reversibility. Concerted proton-electron transfer offers a lower energy pathway compared to stepwise transfers. Given the much lower proton affinity of Se compared to that of S, the inflection provides compelling evidence that concerted proton-electron transfer is important in determining why [NiFe]-hydrogenases are reversible electrocatalysts.
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Affiliation(s)
- Rhiannon
M. Evans
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Natalie Krahn
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United
States
| | - Joshua Weiss
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United
States
| | - Kylie A. Vincent
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Dieter Söll
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Fraser A. Armstrong
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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3
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Luhach S, Lalancette RA, Prokopchuk DE. "Catch and release" of the Cp N3 ligand using cobalt: dissociation, protonation, and C-H bond thermochemistry. Dalton Trans 2024. [PMID: 38916110 DOI: 10.1039/d4dt01560f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The coordination chemistry of an amine-rich CpN3 ligand has been explored with cobalt. We demonstrate that in the presence of NaCo(CO)4, the cationic precursor [CpN3]+ yields the complex CpN3CoI(CO)2. While 2e- oxidation generates new CoIII complexes such as [CpN3Co(NCMe)3]2+ and CpN3CoI2(CO), subsequent ligand loss is facile, generating free [CpN3]+ or the protonated dication [CpN3H]2+. We have structurally characterized both these ligand release products via single crystal X-ray diffraction and obtained thermochemical C-H bond strengths via experiment and density functional theory (DFT). Upon reversible 1e- reduction, the radical cation [CpN3H]˙+ has a weak C-H BDFE of 52 kcal mol-1 in acetonitrile. Mechanistic analysis shows that [CpN3H]˙+ undergoes radical-radical disproportionation in the absence of exogenous H-atom acceptors, which is supported by deuterium isotope labelling experiments. Structural comparison of these organic molecules shows a high degree of iminium-like electron delocalization over the C-N bonds connected to the central five-membered ring.
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Affiliation(s)
- Sanju Luhach
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, NJ 07102, USA.
| | - Roger A Lalancette
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, NJ 07102, USA.
| | - Demyan E Prokopchuk
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, NJ 07102, USA.
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4
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Kingsley G, Skagia A, Passaretti P, Fernandez-Cuesta C, Reynolds-Winczura A, Koscielniak K, Gambus A. DONSON facilitates Cdc45 and GINS chromatin association and is essential for DNA replication initiation. Nucleic Acids Res 2023; 51:9748-9763. [PMID: 37638758 PMCID: PMC10570026 DOI: 10.1093/nar/gkad694] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
Faithful cell division is the basis for the propagation of life and DNA replication must be precisely regulated. DNA replication stress is a prominent endogenous source of genome instability that not only leads to ageing, but also neuropathology and cancer development in humans. Specifically, the issues of how vertebrate cells select and activate origins of replication are of importance as, for example, insufficient origin firing leads to genomic instability and mutations in replication initiation factors lead to the rare human disease Meier-Gorlin syndrome. The mechanism of origin activation has been well characterised and reconstituted in yeast, however, an equal understanding of this process in higher eukaryotes is lacking. The firing of replication origins is driven by S-phase kinases (CDKs and DDK) and results in the activation of the replicative helicase and generation of two bi-directional replication forks. Our data, generated from cell-free Xenopus laevis egg extracts, show that DONSON is required for assembly of the active replicative helicase (CMG complex) at origins during replication initiation. DONSON has previously been shown to be essential during DNA replication, both in human cells and in Drosophila, but the mechanism of DONSON's action was unknown. Here we show that DONSON's presence is essential for replication initiation as it is required for Cdc45 and GINS association with Mcm2-7 complexes and helicase activation. To fulfil this role, DONSON interacts with the initiation factor, TopBP1, in a CDK-dependent manner. Following its initiation role, DONSON also forms a part of the replisome during the elongation stage of DNA replication. Mutations in DONSON have recently been shown to lead to the Meier-Gorlin syndrome; this novel replication initiation role of DONSON therefore provides the explanation for the phenotypes caused by DONSON mutations in patients.
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Affiliation(s)
- Georgia Kingsley
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Aggeliki Skagia
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Paolo Passaretti
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Cyntia Fernandez-Cuesta
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Alicja Reynolds-Winczura
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Kinga Koscielniak
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
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5
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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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6
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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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7
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Leone L, Sgueglia G, La Gatta S, Chino M, Nastri F, Lombardi A. Enzymatic and Bioinspired Systems for Hydrogen Production. Int J Mol Sci 2023; 24:ijms24108605. [PMID: 37239950 DOI: 10.3390/ijms24108605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/30/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases.
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Affiliation(s)
- Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Gianmattia Sgueglia
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
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8
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Jiang Q, Li T, Yang J, Aitchison CM, Huang J, Chen Y, Huang F, Wang Q, Cooper AI, Liu LN. Synthetic engineering of a new biocatalyst encapsulating [NiFe]-hydrogenases for enhanced hydrogen production. J Mater Chem B 2023; 11:2684-2692. [PMID: 36883480 PMCID: PMC10032307 DOI: 10.1039/d2tb02781j] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Hydrogenases are microbial metalloenzymes capable of catalyzing the reversible interconversion between molecular hydrogen and protons with high efficiency, and have great potential in the development of new electrocatalysts for renewable fuel production. Here, we engineered the intact proteinaceous shell of the carboxysome, a self-assembling protein organelle for CO2 fixation in cyanobacteria and proteobacteria, and sequestered heterologously produced [NiFe]-hydrogenases into the carboxysome shell. The protein-based hybrid catalyst produced in E. coli shows substantially improved hydrogen production under both aerobic and anaerobic conditions and enhanced material and functional robustness, compared to unencapsulated [NiFe]-hydrogenases. The catalytically functional nanoreactor as well as the self-assembling and encapsulation strategies provide a framework for engineering new bioinspired electrocatalysts to improve the sustainable production of fuels and chemicals in biotechnological and chemical applications.
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Affiliation(s)
- Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Tianpei Li
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jing Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, UK
| | - Catherine M Aitchison
- Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, UK
| | - Jiafeng Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Yu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Fang Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Andrew I Cooper
- Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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9
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Dragelj J, Karafoulidi-Retsou C, Katz S, Lenz O, Zebger I, Caserta G, Sacquin-Mora S, Mroginski MA. Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Front Microbiol 2023; 13:1073315. [PMID: 36733774 PMCID: PMC9886862 DOI: 10.3389/fmicb.2022.1073315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023] Open
Abstract
Comprising at least a bipartite architecture, the large subunit of [NiFe]-hydrogenase harbors the catalytic nickel-iron site while the small subunit houses an array of electron-transferring Fe-S clusters. Recently, some [NiFe]-hydrogenase large subunits have been isolated showing an intact and redox active catalytic cofactor. In this computational study we have investigated one of these metalloproteins, namely the large subunit HoxG of the membrane-bound hydrogenase from Cupriavidus necator (CnMBH), targeting its conformational and mechanical stability using molecular modelling and long all-atom Gaussian accelerated molecular dynamics (GaMD). Our simulations predict that isolated HoxG is stable in aqueous solution and preserves a large portion of its mechanical properties, but loses rigidity in regions around the active site, in contrast to the MBH heterodimer. Inspired by biochemical data showing dimerization of the HoxG protein and IR measurements revealing an increased stability of the [NiFe] cofactor in protein preparations with higher dimer content, corresponding simulations of homodimeric forms were also undertaken. While the monomeric subunit contains several flexible regions, our data predicts a regained rigidity in homodimer models. Furthermore, we computed the electrostatic properties of models obtained by enhanced sampling with GaMD, which displays a significant amount of positive charge at the protein surface, especially in solvent-exposed former dimer interfaces. These data offer novel insights on the way the [NiFe] core is protected from de-assembly and provide hints for enzyme anchoring to surfaces, which is essential information for further investigations on these minimal enzymes.
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Affiliation(s)
- Jovan Dragelj
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Sophie Sacquin-Mora
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
- CNRS, UPR, Laboratoire de Biochimie Théorique, Université de Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France
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10
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Formate hydrogenlyase, formic acid translocation and hydrogen production: dynamic membrane biology during fermentation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148919. [PMID: 36152681 DOI: 10.1016/j.bbabio.2022.148919] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Formate hydrogenlyase-1 (FHL-1) is a complex-I-like enzyme that is commonly found in gram-negative bacteria. The enzyme comprises a peripheral arm and a membrane arm but is not involved in quinone reduction. Instead, FHL-1 couples formate oxidation to the reduction of protons to molecular hydrogen (H2). Escherichia coli produces FHL-1 under fermentative conditions where it serves to detoxify formic acid in the environment. The membrane biology and bioenergetics surrounding E. coli FHL-1 have long held fascination. Here, we review recent work on understanding the molecular basis of formic acid efflux and influx. We also consider the structure and function of E. coli FHL-1, its relationship with formate transport, and pay particular attention to the molecular interface between the peripheral arm and the membrane arm. Finally, we highlight the interesting phenotype of genetic mutation of the ND1 Loop, which is located at that interface.
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11
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Zamader A, Reuillard B, Pécaut J, Billon L, Bousquet A, Berggren G, Artero V. Non-Covalent Integration of a [FeFe]-Hydrogenase Mimic to Multiwalled Carbon Nanotubes for Electrocatalytic Hydrogen Evolution. Chemistry 2022; 28:e202202260. [PMID: 36069308 PMCID: PMC10092503 DOI: 10.1002/chem.202202260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 12/14/2022]
Abstract
Surface integration of molecular catalysts inspired from the active sites of hydrogenase enzymes represents a promising route towards developing noble metal-free and sustainable technologies for H2 production. Efficient and stable catalyst anchoring is a key aspect to enable this approach. Herein, we report the preparation and electrochemical characterization of an original diironhexacarbonyl complex including two pyrene groups per catalytic unit in order to allow for its smooth integration, through π-interactions, onto multiwalled carbon nanotube-based electrodes. In this configuration, the grafted catalyst could reach turnover numbers for H2 production (TONH2 ) of up to 4±2×103 within 20 h of bulk electrolysis, operating at neutral pH. Post operando analysis of catalyst functionalized electrodes revealed the degradation of the catalytic unit occurred via loss of the iron carbonyl units, while the anchoring groups and most part of the ligand remained attached onto multiwalled carbon nanotubes.
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Affiliation(s)
- Afridi Zamader
- Univ. Grenoble AlpesCNRSCEAIRIGLaboratoire de Chimie et Biologie des Métaux17 rue des MartyrsF-38054Grenoble, CedexFrance
- Molecular BiomimeticsDepartment of Chemistry – Ångström LaboratoryUppsala UniversityBox 523SE-75120UppsalaSweden
| | - Bertrand Reuillard
- Univ. Grenoble AlpesCNRSCEAIRIGLaboratoire de Chimie et Biologie des Métaux17 rue des MartyrsF-38054Grenoble, CedexFrance
| | - Jacques Pécaut
- Univ. Grenoble AlpesCEACNRSIRIG-SyMMESUMR 581938000GrenobleFrance
| | - Laurent Billon
- Universite Pau et des Pays de l'AdourE2S UPPACNRSIPREM64000PauFrance
- Bio-inspired Materials Group: Functionalities & Self-AssemblyUniversite de Pau et Pays de l'AdourE2S UPPA64053PauFrance
| | - Antoine Bousquet
- Bio-inspired Materials Group: Functionalities & Self-AssemblyUniversite de Pau et Pays de l'AdourE2S UPPA64053PauFrance
| | - Gustav Berggren
- Molecular BiomimeticsDepartment of Chemistry – Ångström LaboratoryUppsala UniversityBox 523SE-75120UppsalaSweden
| | - Vincent Artero
- Univ. Grenoble AlpesCNRSCEAIRIGLaboratoire de Chimie et Biologie des Métaux17 rue des MartyrsF-38054Grenoble, CedexFrance
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12
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McCool JD, Zhang S, Cheng I, Zhao X. Rational development of molecular earth-abundant metal complexes for electrocatalytic hydrogen production. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(22)64150-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Steinhilper R, Höff G, Heider J, Murphy BJ. Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli. Nat Commun 2022; 13:5395. [PMID: 36104349 PMCID: PMC9474812 DOI: 10.1038/s41467-022-32831-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 01/30/2023] Open
Abstract
The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H2 during fermentation, its reversibility, allowing H2-dependent CO2 reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex. New cryo-EM structures of the formate hydrogenlyase complex from the model bacterium E. coli clarify how electrons and protons move through the complex and are combined to make H2 gas. The complex shows important similarities and differences to related bioenergetic complexes across the tree of life.
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14
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Wang C, Lai Z, Huang G, Pan H. Current State of [Fe]‐Hydrogenase and Its Biomimetic Models. Chemistry 2022; 28:e202201499. [DOI: 10.1002/chem.202201499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Chao Wang
- Chemistry and Biomedicine Innovation Center (ChemBIC) State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue 210023 Nanjing P. R. China
| | - Zhenli Lai
- Key Laboratory of Development and Application of Rural Renewable Energy Biogas Institute of Ministry of Agriculture and Rural Affairs Section 4–13, Renmin South Road 610041 Chengdu P. R. China
| | - Gangfeng Huang
- Key Laboratory of Development and Application of Rural Renewable Energy Biogas Institute of Ministry of Agriculture and Rural Affairs Section 4–13, Renmin South Road 610041 Chengdu P. R. China
| | - Hui‐Jie Pan
- Chemistry and Biomedicine Innovation Center (ChemBIC) State Key Laboratory of Coordination Chemistry School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue 210023 Nanjing P. R. China
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15
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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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16
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Patel A, Mulder DW, Söll D, Krahn N. Harnessing selenocysteine to enhance microbial cell factories for hydrogen production. FRONTIERS IN CATALYSIS 2022; 2. [PMID: 36844461 PMCID: PMC9961374 DOI: 10.3389/fctls.2022.1089176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hydrogen is a clean, renewable energy source, that when combined with oxygen, produces heat and electricity with only water vapor as a biproduct. Furthermore, it has the highest energy content by weight of all known fuels. As a result, various strategies have engineered methods to produce hydrogen efficiently and in quantities that are of interest to the economy. To approach the notion of producing hydrogen from a biological perspective, we take our attention to hydrogenases which are naturally produced in microbes. These organisms have the machinery to produce hydrogen, which when cleverly engineered, could be useful in cell factories resulting in large production of hydrogen. Not all hydrogenases are efficient at hydrogen production, and those that are, tend to be oxygen sensitive. Therefore, we provide a new perspective on introducing selenocysteine, a highly reactive proteinogenic amino acid, as a strategy towards engineering hydrogenases with enhanced hydrogen production, or increased oxygen tolerance.
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Affiliation(s)
- Armaan Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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17
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Sánchez P, Goel B, Neugebauer H, Lalancette RA, Grimme S, Hansen A, Prokopchuk DE. Ligand Protonation at Carbon, not Nitrogen, during H 2 Production with Amine-Rich Iron Electrocatalysts. Inorg Chem 2021; 60:17407-17413. [PMID: 34735115 DOI: 10.1021/acs.inorgchem.1c03142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present monometallic H2 production electrocatalysts containing electron-rich triamine-cyclopentadienyl (Cp) ligands coordinated to iron. After selective CO extrusion from the iron tricarbonyl precursors, electrocatalysis is observed via cyclic voltammetry in the presence of an exogenous acid. Contrary to the fact that amines in the secondary coordination sphere are often protonated during electrocatalysis, comprehensive quantum-chemical calculations indicate that the amines likely do not function as proton relays; instead, endo-Cp ring protonation is most favorable after 1e- reduction. This unusual mechanistic pathway emphasizes the need to consider a broad domain of H+/e- addition products by synergistically combining experimental and theoretical resources.
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Affiliation(s)
- Práxedes Sánchez
- Department of Chemistry, Rutgers University─Newark, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Bhumika Goel
- Department of Chemistry, Rutgers University─Newark, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Hagen Neugebauer
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, Bonn 53115, Germany
| | - Roger A Lalancette
- Department of Chemistry, Rutgers University─Newark, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, Bonn 53115, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, Bonn 53115, Germany
| | - Demyan E Prokopchuk
- Department of Chemistry, Rutgers University─Newark, 73 Warren Street, Newark, New Jersey 07102, United States
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18
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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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19
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Lučić M, Wilson MT, Svistunenko DA, Owen RL, Hough MA, Worrall JAR. Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of Fe IV = O formation in bacterial dye-decolorizing peroxidases. J Biol Inorg Chem 2021; 26:743-761. [PMID: 34477969 PMCID: PMC8463360 DOI: 10.1007/s00775-021-01896-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, Oxfordshire, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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20
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Isegawa M, Matsumoto T, Ogo S. H 2 activation by hydrogenase-inspired NiFe catalyst using frustrated Lewis pair: effect of buffer and halide ion in the heterolytic H-H bond cleavage. RSC Adv 2021; 11:28420-28432. [PMID: 35480737 PMCID: PMC9038005 DOI: 10.1039/d1ra05928a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Hydrogen is a clean fuel alternative to fossil fuels, and it is vital to develop catalysts for its efficient activation and production. We investigate the reaction mechanism of H2 activation in an aqueous solution by the recently developed NiFe complex (Ogo et al. Sci. Adv. 2020, 6, eaaz8181) using density functional theory (DFT) calculation. Our computational results showed that H2 is activated using frustrated Lewis pair. That is, H2 binds to the Fe site of the NiFe complex, acting as a Lewis acid, while the added buffer, acting as Lewis base, abstracts protons to form a hydride complex. Furthermore, the higher basicity in the proton abstraction reaction characterises reaction more exergonic and lowers the reaction barrier. In addition, in the proton abstraction by the water molecule, the reaction barrier was lowered when anion such as Cl− is in the vicinity of the water. Understanding the chemical species that contribute to the catalytic process in cooperation with the metal catalyst at the atomic level should help to maximise the function of the catalyst. Hydrogen is a clean fuel alternative to fossil fuels, and it is vital to develop catalysts for its efficient activation and production.![]()
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Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
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21
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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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22
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Kono F, Tamada T. Neutron crystallography for the elucidation of enzyme catalysis. Curr Opin Struct Biol 2021; 71:36-42. [PMID: 34214927 DOI: 10.1016/j.sbi.2021.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/08/2021] [Accepted: 05/22/2021] [Indexed: 11/26/2022]
Abstract
Hydrogen atoms and hydration water molecules in proteins are indispensable for many biochemical processes, especially enzymatic catalysis. The locations of hydrogen atoms in proteins are usually predicted based on X-ray structures, but it is still very difficult to know the ionization states of the catalytic residues, the hydration structure of the protein, and the characteristics of hydrogen-bonding interactions. Neutron crystallography allows the direct observation of hydrogen atoms that play crucial roles in molecular recognition and the catalytic reactions of enzymes. In this review, we present the current status of neutron crystallography in structural biology and recent neutron structural analyses of three enzymes: ascorbate peroxidase, the main protease of severe acute respiratory syndrome coronavirus 2, and copper-containing nitrite reductase.
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Affiliation(s)
- Fumiaki Kono
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan.
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23
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Joseph Srinivasan S, Cleary SE, Ramirez MA, Reeve HA, Paul CE, Vincent KA. E. coli Nickel-Iron Hydrogenase 1 Catalyses Non-native Reduction of Flavins: Demonstration for Alkene Hydrogenation by Old Yellow Enzyme Ene-reductases*. Angew Chem Int Ed Engl 2021; 60:13824-13828. [PMID: 33721401 PMCID: PMC8252551 DOI: 10.1002/anie.202101186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/26/2021] [Indexed: 11/10/2022]
Abstract
A new activity for the [NiFe] uptake hydrogenase 1 of Escherichia coli (Hyd1) is presented. Direct reduction of biological flavin cofactors FMN and FAD is achieved using H2 as a simple, completely atom-economical reductant. The robust nature of Hyd1 is exploited for flavin reduction across a broad range of temperatures (25-70 °C) and extended reaction times. The utility of this system as a simple, easy to implement FMNH2 or FADH2 regenerating system is then demonstrated by supplying reduced flavin to Old Yellow Enzyme "ene-reductases" to support asymmetric alkene reductions with up to 100 % conversion. Hyd1 turnover frequencies up to 20.4 min-1 and total turnover numbers up to 20 200 were recorded during flavin recycling.
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Affiliation(s)
- Shiny Joseph Srinivasan
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Sarah E Cleary
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Miguel A Ramirez
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Holly A Reeve
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
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24
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Joseph Srinivasan S, Cleary SE, Ramirez MA, Reeve HA, Paul CE, Vincent KA. E. coli Nickel-Iron Hydrogenase 1 Catalyses Non-native Reduction of Flavins: Demonstration for Alkene Hydrogenation by Old Yellow Enzyme Ene-reductases. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:13943-13947. [PMID: 38529476 PMCID: PMC10962552 DOI: 10.1002/ange.202101186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/26/2021] [Indexed: 11/10/2022]
Abstract
A new activity for the [NiFe] uptake hydrogenase 1 of Escherichia coli (Hyd1) is presented. Direct reduction of biological flavin cofactors FMN and FAD is achieved using H2 as a simple, completely atom-economical reductant. The robust nature of Hyd1 is exploited for flavin reduction across a broad range of temperatures (25-70 °C) and extended reaction times. The utility of this system as a simple, easy to implement FMNH2 or FADH2 regenerating system is then demonstrated by supplying reduced flavin to Old Yellow Enzyme "ene-reductases" to support asymmetric alkene reductions with up to 100 % conversion. Hyd1 turnover frequencies up to 20.4 min-1 and total turnover numbers up to 20 200 were recorded during flavin recycling.
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Affiliation(s)
- Shiny Joseph Srinivasan
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
| | - Sarah E. Cleary
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
| | - Miguel A. Ramirez
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
| | - Holly A. Reeve
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - Kylie A. Vincent
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
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25
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Evans RM, Krahn N, Murphy BJ, Lee H, Armstrong FA, Söll D. Selective cysteine-to-selenocysteine changes in a [NiFe]-hydrogenase confirm a special position for catalysis and oxygen tolerance. Proc Natl Acad Sci U S A 2021; 118:e2100921118. [PMID: 33753519 PMCID: PMC8020662 DOI: 10.1073/pnas.2100921118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In [NiFe]-hydrogenases, the active-site Ni is coordinated by four cysteine-S ligands (Cys; C), two of which are bridging to the Fe(CO)(CN)2 fragment. Substitution of a single Cys residue by selenocysteine (Sec; U) occurs occasionally in nature. Using a recent method for site-specific Sec incorporation into proteins, each of the four Ni-coordinating cysteine residues in the oxygen-tolerant Escherichia coli [NiFe]-hydrogenase-1 (Hyd-1) has been replaced by U to identify its importance for enzyme function. Steady-state solution activity of each Sec-substituted enzyme (on a per-milligram basis) is lowered, although this may reflect the unquantified presence of recalcitrant inactive/immature/misfolded forms. Protein film electrochemistry, however, reveals detailed kinetic data that are independent of absolute activities. Like native Hyd-1, the variants have low apparent KMH2 values, do not produce H2 at pH 6, and display the same onset overpotential for H2 oxidation. Mechanistically important differences were identified for the C576U variant bearing the equivalent replacement found in native [NiFeSe]-hydrogenases, its extreme O2 tolerance (apparent KMH2 and Vmax [solution] values relative to native Hyd-1 of 0.13 and 0.04, respectively) implying the importance of a selenium atom in the position cis to the site where exogenous ligands (H-, H2, O2) bind. Observation of the same unusual electrocatalytic signature seen earlier for the proton transfer-defective E28Q variant highlights the direct role of the chalcogen atom (S/Se) at position 576 close to E28, with the caveat that Se is less effective than S in facilitating proton transfer away from the Ni during H2 oxidation by this enzyme.
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Affiliation(s)
- Rhiannon M Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Bonnie J Murphy
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Harrison Lee
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom;
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511;
- Department of Chemistry, Yale University, New Haven, CT 06520
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26
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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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Caserta G, Pelmenschikov V, Lorent C, Tadjoung Waffo AF, Katz S, Lauterbach L, Schoknecht J, Wang H, Yoda Y, Tamasaku K, Kaupp M, Hildebrandt P, Lenz O, Cramer SP, Zebger I. Hydroxy-bridged resting states of a [NiFe]-hydrogenase unraveled by cryogenic vibrational spectroscopy and DFT computations. Chem Sci 2020; 12:2189-2197. [PMID: 34163984 PMCID: PMC8179317 DOI: 10.1039/d0sc05022a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The catalytic mechanism of [NiFe]-hydrogenases is a subject of extensive research. Apart from at least four reaction intermediates of H2/H+ cycling, there are also a number of resting states, which are formed under oxidizing conditions. Although not directly involved in the catalytic cycle, the knowledge of their molecular structures and reactivity is important, because these states usually accumulate in the course of hydrogenase purification and may also play a role in vivo during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit (HoxC) of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure resting redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, 57Fe-labeled HoxC provided an unprecedented insight into the [NiFe] site modes, revealing their contributions in a spectral range otherwise superimposed by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data provide structural descriptions of the previously uncharacterized hydroxy- and water-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site. Active site vibrations of a [NiFe]-hydrogenase catalytic subunit are selectively probed by IR and NRV spectroscopy in two NiIIFeII and NiIIIFeII resting states, contributing in combination with DFT modeling to rationalized structural candidates.![]()
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Affiliation(s)
- Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Armel F Tadjoung Waffo
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Lars Lauterbach
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Hongxin Wang
- SETI Institute 189 Bernardo Avenue Mountain View CA 94043 USA
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute (JASRI) SPring-8, 1-1-1 Kouto, Sayo-gun Hyogo 679-5198 Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo-cho, Sayo-gun Hyogo 679-5148 Japan
| | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation. Angew Chem Int Ed Engl 2020; 59:21656-21662. [PMID: 32780931 PMCID: PMC7756461 DOI: 10.1002/anie.202008622] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 01/06/2023]
Abstract
Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (FeIV =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the FeIII and FeIV =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | | | - Michael T. Wilson
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Amanda K. Chaplin
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Bradley Davy
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Ali Ebrahim
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Danny Axford
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | | | | | - Shigeki Owada
- RIKEN Spring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Ivo Tews
- Biological SciencesInstitute for Life SciencesUniversity of SouthamptonUniversity RoadSouthamptonSO17 1BJUK
| | - Robin L. Owen
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Michael A. Hough
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
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29
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water‐Free Distal Heme Site in a Dye‐Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe
IV
=O Formation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marina Lučić
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | | | - Michael T. Wilson
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Amanda K. Chaplin
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Bradley Davy
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Ali Ebrahim
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Danny Axford
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Takehiko Tosha
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Shigeki Owada
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
- Japan Synchrotron Radiation Research Institute 1-1-1 Kouto Sayo Hyogo 679-5198 Japan
| | | | - Ivo Tews
- Biological Sciences Institute for Life Sciences University of Southampton University Road Southampton SO17 1BJ UK
| | - Robin L. Owen
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Michael A. Hough
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
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30
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Towards molecular understanding of local chemical environment effects in electro- and photocatalytic CO2 reduction. Nat Catal 2020. [DOI: 10.1038/s41929-020-00512-x] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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31
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Yang X, Darensbourg MY. The roles of chalcogenides in O 2 protection of H 2ase active sites. Chem Sci 2020; 11:9366-9377. [PMID: 34094202 PMCID: PMC8161538 DOI: 10.1039/d0sc02584d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/11/2020] [Indexed: 12/31/2022] Open
Abstract
At some point, all HER (Hydrogen Evolution Reaction) catalysts, important in sustainable H2O splitting technology, will encounter O2 and O2-damage. The [NiFeSe]-H2ases and some of the [NiFeS]-H2ases, biocatalysts for reversible H2 production from protons and electrons, are exemplars of oxygen tolerant HER catalysts in nature. In the hydrogenase active sites oxygen damage may be extensive (irreversible) as it is for the [FeFe]-H2ase or moderate (reversible) for the [NiFe]-H2ases. The affinity of oxygen for sulfur, in [NiFeS]-H2ase, and selenium, in [NiFeSe]-H2ase, yielding oxygenated chalcogens results in maintenance of the core NiFe unit, and myriad observable but inactive states, which can be reductively repaired. In contrast, the [FeFe]-H2ase active site has less possibilities for chalcogen-oxygen uptake and a greater chance for O2-attack on iron. Exposure to O2 typically leads to irreversible damage. Despite the evidence of S/Se-oxygenation in the active sites of hydrogenases, there are limited reported synthetic models. This perspective will give an overview of the studies of O2 reactions with the hydrogenases and biomimetics with focus on our recent studies that compare sulfur and selenium containing synthetic analogues of the [NiFe]-H2ase active sites.
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Affiliation(s)
- Xuemei Yang
- Texas A&M University, Department of Chemistry College Station TX 77843 USA
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32
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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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33
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34
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Thammavongsy Z, Ziller JW, Yang JY. Modular synthesis of symmetric proazaphosphatranes bearing heteroatom groups. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Zhang L, Morello G, Carr SB, Armstrong FA. Aerobic Photocatalytic H2 Production by a [NiFe] Hydrogenase Engineered to Place a Silver Nanocluster in the Electron Relay. J Am Chem Soc 2020; 142:12699-12707. [DOI: 10.1021/jacs.0c04302] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Liyun Zhang
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, Oxfordshire United Kingdom
| | - Giorgio Morello
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, Oxfordshire United Kingdom
| | - Stephen B. Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot OX11 0QX, United Kingdom
| | - Fraser A. Armstrong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, Oxfordshire United Kingdom
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36
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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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37
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Affiliation(s)
- Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Rong-Zhen Liao
- Key Laboratory for Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Media, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, People’s Republic of China
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38
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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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39
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Kwon H, Basran J, Devos JM, Suardíaz R, van der Kamp MW, Mulholland AJ, Schrader TE, Ostermann A, Blakeley MP, Moody PCE, Raven EL. Visualizing the protons in a metalloenzyme electron proton transfer pathway. Proc Natl Acad Sci U S A 2020; 117:6484-6490. [PMID: 32152099 PMCID: PMC7104402 DOI: 10.1073/pnas.1918936117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In redox metalloenzymes, the process of electron transfer often involves the concerted movement of a proton. These processes are referred to as proton-coupled electron transfer, and they underpin a wide variety of biological processes, including respiration, energy conversion, photosynthesis, and metalloenzyme catalysis. The mechanisms of proton delivery are incompletely understood, in part due to an absence of information on exact proton locations and hydrogen bonding structures in a bona fide metalloenzyme proton pathway. Here, we present a 2.1-Å neutron crystal structure of the complex formed between a redox metalloenzyme (ascorbate peroxidase) and its reducing substrate (ascorbate). In the neutron structure of the complex, the protonation states of the electron/proton donor (ascorbate) and all of the residues involved in the electron/proton transfer pathway are directly observed. This information sheds light on possible proton movements during heme-catalyzed oxygen activation, as well as on ascorbate oxidation.
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Affiliation(s)
- Hanna Kwon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Juliette M Devos
- Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Reynier Suardíaz
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | | | - Tobias E Schrader
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85748 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, D-85748 Garching, Germany
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Peter C E Moody
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom;
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
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40
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Methanogenesis involves direct hydride transfer from H2 to an organic substrate. Nat Rev Chem 2020; 4:213-221. [PMID: 37128042 DOI: 10.1038/s41570-020-0167-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2020] [Indexed: 01/02/2023]
Abstract
Certain anaerobic microorganisms evolved a mechanism to use H2 as a reductant in their energy metabolisms. For these purposes, the microorganisms developed H2-activating enzymes, which are aspirational catalysts in a sustainable hydrogen economy. In the case of the hydrogenotrophic pathway performed by methanogenic archaea, 8e- are extracted from 4H2 and used as reducing equivalents to convert CO2 into CH4. Under standard cultivation conditions, these archaea express [NiFe]-hydrogenases, which are Ni-dependent and Fe-dependent enzymes and heterolytically cleave H2 into 2H+ and 2e-, the latter being supplied into the central metabolism. Under Ni-limiting conditions, F420-reducing [NiFe]-hydrogenases are downregulated and their functions are predominantly taken over by an upregulated [Fe]-hydrogenase. Unique in biology, this Fe-dependent hydrogenase cleaves H2 and directly transfers H- to an imidazolium-containing substrate. [Fe]-hydrogenase activates H2 at an Fe cofactor ligated by two CO molecules, an acyl group, a pyridinol N atom and a cysteine thiolate as the central constituent. This Fe centre has inspired chemists to not only design synthetic mimics to catalytically cleave H2 in solution but also for incorporation into apo-[Fe]-hydrogenase to give semi-synthetic proteins. This Perspective describes the enzymes involved in hydrogenotrophic methanogenesis, with a focus on those performing the reduction steps. Of these, we describe [Fe]-hydrogenases in detail and cover recent progress in their synthetic modelling.
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41
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Ishibashi T. Therapeutic Efficacy of Molecular Hydrogen: A New Mechanistic Insight. Curr Pharm Des 2020; 25:946-955. [PMID: 31057105 PMCID: PMC6806612 DOI: 10.2174/1381612825666190506123038] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/25/2019] [Indexed: 02/02/2023]
Abstract
Background: Molecular hydrogen (H2) is now recognized as a therapeutic gas for the treatment of numerous diseases including neurodegenerative diseases, metabolic disorders, and inflammatory diseases. Non-polar, neutral H2 is assumed to have health benefits facilitated by its passive diffusion across the human body immediately after administration and is considered a safe therapeutic inert gas that does not interfere with physiological enzymatic reactions. The effects of H2 on mammalian cells are assumed to be based on non-enzymatic reactions with Reactive Oxygen Species (ROS) exhibiting extremely high reactivity. However, many reports on therapeutic applications of H2 have the limitation to regard H2 only as a scavenger for the hydroxyl radical and peroxynitrite. Methods: Apart from this proposed principle, a new possible mechanism of H2 activation and consumption in mammalian cells is considered in this review, which is specifically focused on the mitochondrial complex I that has a close evolutionary relationship with energy-converting, membrane-bound [NiFe]-hydrogenases (MBH). Notably, the possibility that H2 may function as both electron and proton donor in the ubiquinone-binding chamber of complex I is discussed. Results: H2 is proposed to act as the rectifier of the mitochondrial electron flow in the disordered or pathological state when the accumulation of electrons leads to ROS production, specifically during the re-supply of O2 after hypoxia in the mitochondria. Conclusion: Furthermore, H2 is proposed to convert the quinone intermediates to the fully reduced ubiquinol, thereby increasing the antioxidant capacity of the quinone pool as well as preventing the generation of ROS.
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Affiliation(s)
- Toru Ishibashi
- Department of Rheumatology, Orthopaedic Surgery and Health Care, Huis Ten Bosch Satellite H2 Clinic Hakata, Fukuoka, Japan
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42
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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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43
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Weder N, Probst B, Sévery L, Fernández-Terán RJ, Beckord J, Blacque O, Tilley SD, Hamm P, Osterwalder J, Alberto R. Mechanistic insights into photocatalysis and over two days of stable H 2 generation in electrocatalysis by a molecular cobalt catalyst immobilized on TiO 2. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00330a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular and heterogeneous water reduction combined: Over 2 days of electrocatalysis of a cobalt polypyridyl catalyst immobilized on TiO2.
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Affiliation(s)
- Nicola Weder
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
| | - Benjamin Probst
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
| | - Laurent Sévery
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
| | | | - Jan Beckord
- Department of Physics
- University of Zurich
- 8057 Zurich
- Switzerland
| | - Olivier Blacque
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
| | - S. David Tilley
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
| | - Peter Hamm
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
| | | | - Roger Alberto
- Department of Chemistry
- University of Zurich
- 8057 Zurich
- Switzerland
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44
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Ash PA, Kendall-Price SET, Vincent KA. Unifying Activity, Structure, and Spectroscopy of [NiFe] Hydrogenases: Combining Techniques To Clarify Mechanistic Understanding. Acc Chem Res 2019; 52:3120-3131. [PMID: 31675209 DOI: 10.1021/acs.accounts.9b00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Achieving a unified understanding of the mechanism of a multicenter redox enzyme such as [NiFe] hydrogenase is complicated by difficulties in reconciling information obtained by using different techniques and on samples in different physical forms. Measurements of the activity of the enzyme, and of factors which perturb activity, are generally carried out using biochemical assays in solution or with electrode-immobilized enzymes using protein film electrochemistry (PFE). Conversely, spectroscopy aimed at reporting on features of the metalloclusters in the enzyme, such as electron paramagnetic resonance (EPR) or X-ray absorption spectroscopy (XAS), is often conducted on frozen samples and is thus difficult to relate to catalytically relevant states as information about turnover and activity has been lost. To complicate matters further, most of our knowledge of the atomic-level structure of metalloenzymes comes from X-ray diffraction studies in the solid, crystalline state, which are again difficult to link to turnover conditions. Taking [NiFe] hydrogenases as our case study, we show here how it is possible to apply infrared (IR) spectroscopic sampling approaches to unite direct spectroscopic study with catalytic turnover. Using a method we have named protein film IR electrochemistry (PFIRE), we reveal the steady-state distribution of intermediates during catalysis and identify catalytic "bottlenecks" introduced by site-directed mutagenesis. We also show that it is possible to study dynamic transitions between active site states of enzymes in single crystals, uniting solid state and solution spectroscopic information. In all of these cases, the spectroscopic data complement and enhance interpretation of purely activity-based measurements by providing direct chemical insight that is otherwise hidden. The [NiFe] hydrogenases possess a bimetallic [NiFe] active site, coordinated by CO and CN- ligands, linked to the protein via bridging and terminal cysteine sulfur ligands, as well as an electron relay chain of iron sulfur clusters. Infrared spectroscopy is ideal for probing hydrogenases because the CO and CN- ligands are strong IR absorbers, but the suite of IR-based approaches we describe here will be equally valuable in studying substrate- or intermediate-bound states of other metalloenzymes where key mechanistic questions remain open, such as nitrogenase, formate dehydrogenase, or carbon monoxide dehydrogenase. We therefore hope that this Account will encourage future studies which unify information from different techniques across bioinorganic chemistry.
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Affiliation(s)
- Philip A. Ash
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | | | - Kylie A. Vincent
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
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45
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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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46
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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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47
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Slater JW, Marguet SC, Gray ME, Monaco HA, Sotomayor M, Shafaat HS. Power of the Secondary Sphere: Modulating Hydrogenase Activity in Nickel-Substituted Rubredoxin. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01720] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeffrey W. Slater
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sean C. Marguet
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Michelle E. Gray
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Haleigh A. Monaco
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Marcos Sotomayor
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S. Shafaat
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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48
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Sutthirat N, Ziller JW, Yang JY, Thammavongsy Z. Crystal structure of NiFe(CO) 5[tris(pyridyl-meth-yl)aza-phosphatrane]: a synthetic mimic of the NiFe hydrogenase active site incorporating a pendant pyridine base. Acta Crystallogr E Crystallogr Commun 2019; 75:438-442. [PMID: 31161052 PMCID: PMC6509684 DOI: 10.1107/s2056989019003256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 11/22/2022]
Abstract
The reaction of Ni(TPAP)(COD) {where TPAP = [(NC5H4)CH2]3P(NC2H4)3N} with Fe(CO)5 resulted in the isolation of the title heterobimetallic NiFe(TPAP)(CO)5 complex di-μ-carbonyl-tricarbon-yl[2,8,9-tris-(pyridin-2-yl-meth-yl)-2,5,8,9-tetra-aza-1-phosphabi-cyclo-[3.3.3]undeca-ne]ironnickel, [FeNi(C24H30N7P)(CO)5]. Characterization of the complex by 1H and 31P NMR as well as IR spectroscopy are presented. The structure of NiFe(TPAP)(CO)5 reveals three terminally bound CO mol-ecules on Fe0, two bridging CO mol-ecules between Ni0 and Fe0, and TPAP coordinated to Ni0. The Ni-Fe bond length is 2.4828 (4) Å, similar to that of the reduced form of the active site of NiFe hydrogenase (∼2.5 Å). Additionally, a proximal pendant base from one of the non-coordinating pyridine groups of TPAP is also present. Although involvement of a pendant base has been cited in the mechanism of NiFe hydrogenase, this moiety has yet to be incorporated in a structurally characterized synthetic mimic with key structural motifs (terminally bound CO or CN ligands on Fe). Thus, the title complex NiFe(TPAP)(CO)5 is an unique synthetic model for NiFe hydrogenase. In the crystal, the complex mol-ecules are linked by C-H⋯O hydrogen bonds, forming undulating layers parallel to (100). Within the layers, there are offset π-π [inter-centroid distance = 3.2739 (5) Å] and C-H⋯π inter-actions present. The layers are linked by further C-H⋯π inter-actions, forming a supra-molecular framework.
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Affiliation(s)
- Natwara Sutthirat
- Department of Chemistry, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - Joseph W. Ziller
- Department of Chemistry, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - Jenny Y. Yang
- Department of Chemistry, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - Zachary Thammavongsy
- Department of Chemistry, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
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49
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Dalle K, Warnan J, Leung JJ, Reuillard B, Karmel IS, Reisner E. Electro- and Solar-Driven Fuel Synthesis with First Row Transition Metal Complexes. Chem Rev 2019; 119:2752-2875. [PMID: 30767519 PMCID: PMC6396143 DOI: 10.1021/acs.chemrev.8b00392] [Citation(s) in RCA: 440] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Indexed: 12/31/2022]
Abstract
The synthesis of renewable fuels from abundant water or the greenhouse gas CO2 is a major step toward creating sustainable and scalable energy storage technologies. In the last few decades, much attention has focused on the development of nonprecious metal-based catalysts and, in more recent years, their integration in solid-state support materials and devices that operate in water. This review surveys the literature on 3d metal-based molecular catalysts and focuses on their immobilization on heterogeneous solid-state supports for electro-, photo-, and photoelectrocatalytic synthesis of fuels in aqueous media. The first sections highlight benchmark homogeneous systems using proton and CO2 reducing 3d transition metal catalysts as well as commonly employed methods for catalyst immobilization, including a discussion of supporting materials and anchoring groups. The subsequent sections elaborate on productive associations between molecular catalysts and a wide range of substrates based on carbon, quantum dots, metal oxide surfaces, and semiconductors. The molecule-material hybrid systems are organized as "dark" cathodes, colloidal photocatalysts, and photocathodes, and their figures of merit are discussed alongside system stability and catalyst integrity. The final section extends the scope of this review to prospects and challenges in targeting catalysis beyond "classical" H2 evolution and CO2 reduction to C1 products, by summarizing cases for higher-value products from N2 reduction, C x>1 products from CO2 utilization, and other reductive organic transformations.
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Affiliation(s)
| | | | - Jane J. Leung
- Christian Doppler Laboratory
for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Bertrand Reuillard
- Christian Doppler Laboratory
for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Isabell S. Karmel
- Christian Doppler Laboratory
for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Erwin Reisner
- Christian Doppler Laboratory
for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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50
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part IV. Canonical, non-canonical and hybrid iron-sulfur proteins. J Struct Biol 2019; 205:103-120. [PMID: 30677521 DOI: 10.1016/j.jsb.2019.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 12/26/2022]
Abstract
A plethora of proteins are able to express iron-sulfur clusters, but have a clear picture of the different types of proteins and the different iron-sulfur clusters they harbor it is not easy. In the last five years we have reviewed structure/electrochemistry of metalloproteins expressing: (i) single types of iron-sulfur clusters (namely: {Fe(Cys)4}, {[Fe2S2](Cys)4}, {[Fe2S2](Cys)3(X)} (X = Asp, Arg, His), {[Fe2S2](Cys)2(His)2}, {[Fe3S4](Cys)3}, {[Fe4S4](Cys)4} and {[Fe4S4](Cys)3(nonthiolate ligand)} cores); (ii) metalloproteins harboring iron-sulfur centres of different nuclearities (namely: [4Fe-4S] and [2Fe-2S], [4Fe-4S] and [3Fe-4S], and [4Fe-4S], [3Fe-4S] and [2Fe-2S] clusters. Our target is now to review structure and electrochemistry of proteins harboring canonical, non-canonical and hybrid iron-sulfur proteins.
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Affiliation(s)
- Piero Zanello
- Dipartimento di Biotecnologie, Chimica e Farmacia dell'Università di Siena, Via A. De Gasperi 2, 53100 Siena, Italy
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