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Maia LB, Maiti BK, Moura I, Moura JJG. Selenium-More than Just a Fortuitous Sulfur Substitute in Redox Biology. Molecules 2023; 29:120. [PMID: 38202704 PMCID: PMC10779653 DOI: 10.3390/molecules29010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Living organisms use selenium mainly in the form of selenocysteine in the active site of oxidoreductases. Here, selenium's unique chemistry is believed to modulate the reaction mechanism and enhance the catalytic efficiency of specific enzymes in ways not achievable with a sulfur-containing cysteine. However, despite the fact that selenium/sulfur have different physicochemical properties, several selenoproteins have fully functional cysteine-containing homologues and some organisms do not use selenocysteine at all. In this review, selected selenocysteine-containing proteins will be discussed to showcase both situations: (i) selenium as an obligatory element for the protein's physiological function, and (ii) selenium presenting no clear advantage over sulfur (functional proteins with either selenium or sulfur). Selenium's physiological roles in antioxidant defence (to maintain cellular redox status/hinder oxidative stress), hormone metabolism, DNA synthesis, and repair (maintain genetic stability) will be also highlighted, as well as selenium's role in human health. Formate dehydrogenases, hydrogenases, glutathione peroxidases, thioredoxin reductases, and iodothyronine deiodinases will be herein featured.
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Affiliation(s)
- Luisa B. Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - Biplab K. Maiti
- Department of Chemistry, School of Sciences, Cluster University of Jammu, Canal Road, Jammu 180001, India
| | - Isabel Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - José J. G. Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
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2
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Chaudière J. Biological and Catalytic Properties of Selenoproteins. Int J Mol Sci 2023; 24:10109. [PMID: 37373256 DOI: 10.3390/ijms241210109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Selenocysteine is a catalytic residue at the active site of all selenoenzymes in bacteria and mammals, and it is incorporated into the polypeptide backbone by a co-translational process that relies on the recoding of a UGA termination codon into a serine/selenocysteine codon. The best-characterized selenoproteins from mammalian species and bacteria are discussed with emphasis on their biological function and catalytic mechanisms. A total of 25 genes coding for selenoproteins have been identified in the genome of mammals. Unlike the selenoenzymes of anaerobic bacteria, most mammalian selenoenzymes work as antioxidants and as redox regulators of cell metabolism and functions. Selenoprotein P contains several selenocysteine residues and serves as a selenocysteine reservoir for other selenoproteins in mammals. Although extensively studied, glutathione peroxidases are incompletely understood in terms of local and time-dependent distribution, and regulatory functions. Selenoenzymes take advantage of the nucleophilic reactivity of the selenolate form of selenocysteine. It is used with peroxides and their by-products such as disulfides and sulfoxides, but also with iodine in iodinated phenolic substrates. This results in the formation of Se-X bonds (X = O, S, N, or I) from which a selenenylsulfide intermediate is invariably produced. The initial selenolate group is then recycled by thiol addition. In bacterial glycine reductase and D-proline reductase, an unusual catalytic rupture of selenium-carbon bonds is observed. The exchange of selenium for sulfur in selenoproteins, and information obtained from model reactions, suggest that a generic advantage of selenium compared with sulfur relies on faster kinetics and better reversibility of its oxidation reactions.
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Affiliation(s)
- Jean Chaudière
- CBMN (CNRS, UMR 5248), University of Bordeaux, 33600 Pessac, France
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3
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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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4
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Upadhyay A, Meena H, Jha RK, Kanika, Kumar S. Isolation of monomeric copper(II) phenolate selenoether complexes using chelating ortho-bisphenylselenide-phenolate ligands and their electrocatalytic hydrogen gas evolution activity. Dalton Trans 2022; 51:7284-7293. [PMID: 35481842 DOI: 10.1039/d2dt00678b] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of novel copper(II) phenolate selenoether complexes have been synthesized and structurally characterized for the first time from copper(I) phenanthroline and various substituted ortho-bisphenylselenide-phenol chelating ligands. The synthesized complexes exhibit Jahn-Teller distortion in their geometry and varied from distorted square planar to distorted octahedral by varying the substituent in the bis-selenophenolate ligand. The synthesized complexes electrocatalyze the hydrogen evolution reaction (HER) with a faradaic efficiency of up to 89%, and it was observed that the distorted square pyramidal geometry is the optimum geometry for the maximum efficiency of these copper complexes.
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Affiliation(s)
- Aditya Upadhyay
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India.
| | - Harshita Meena
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India.
| | - Raushan Kumar Jha
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India.
| | - Kanika
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India.
| | - Sangit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India.
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5
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Cysteine-Activated Small-Molecule H 2Se Donors Inspired by Synthetic H 2S Donors. J Am Chem Soc 2022; 144:3957-3967. [PMID: 35192764 DOI: 10.1021/jacs.1c12006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The importance of selenium (Se) in biology and health has become increasingly clear. Hydrogen selenide (H2Se), the biologically available and active form of Se, is suggested to be an emerging nitric oxide (NO)-like signaling molecule. Nevertheless, the research on H2Se chemical biology has technique difficulties due to the lack of well-characterized and controllable H2Se donors under physiological conditions, as well as a robust assay for direct H2Se quantification. Motivated by these needs, here, we demonstrate that selenocyclopropenones and selenoamides are tunable donor motifs that release H2Se upon reaction with cysteine (Cys) at pH 7.4 and that structural modifications enable the rate of Cys-mediated H2Se release to be tuned. We monitored the reaction pathways for the H2Se release and confirmed H2Se generation qualitatively using different methods. We further developed a quantitative assay for direct H2Se trapping and quantitation in an aqueous solution, which should also be operative for investigating future H2Se donor motifs. In addition, we demonstrate that arylselenoamide has the capability of Cys-mediated H2Se release in cellular environments. Importantly, mechanistic investigations and density functional theory (DFT) calculations illustrate the plausible pathways of Cys-activated H2Se release from arylselenoamides in detail, which may help understand the mechanistic issues of the H2S release from pharmacologically important arylthioamides. We anticipate that the well-defined chemistries of Cys-activated H2Se donor motifs will be useful for studying Se biology and for development of new H2Se donors and bioconjugate techniques.
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6
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Ruth JC, Spormann AM. Enzyme Electrochemistry for Industrial Energy Applications—A Perspective on Future Areas of Focus. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00708] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- John C. Ruth
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Alfred M. Spormann
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
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7
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Mauerhofer LM, Zwirtmayr S, Pappenreiter P, Bernacchi S, Seifert AH, Reischl B, Schmider T, Taubner RS, Paulik C, Rittmann SKMR. Hyperthermophilic methanogenic archaea act as high-pressure CH 4 cell factories. Commun Biol 2021; 4:289. [PMID: 33674723 PMCID: PMC7935968 DOI: 10.1038/s42003-021-01828-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyrα444 Glyα445 Tyrα446 in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH4 production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.
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Affiliation(s)
- Lisa-Maria Mauerhofer
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
| | - Sara Zwirtmayr
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Patricia Pappenreiter
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | | | | | - Barbara Reischl
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria ,Krajete GmbH, Linz, Austria
| | - Tilman Schmider
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
| | - Ruth-Sophie Taubner
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria ,grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Christian Paulik
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Simon K.-M. R. Rittmann
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
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8
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Oberling M, Irran E, Ohki Y, Klare HFT, Oestreich M. Cationic Ru–Se Complexes for Cooperative Si–H Bond Activation. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marvin Oberling
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623 Berlin, Germany
| | - Elisabeth Irran
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623 Berlin, Germany
| | - Yasuhiro Ohki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hendrik F. T. Klare
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623 Berlin, Germany
| | - Martin Oestreich
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623 Berlin, Germany
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9
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Prasad P, Selvan D, Chakraborty S. Biosynthetic Approaches towards the Design of Artificial Hydrogen-Evolution Catalysts. Chemistry 2020; 26:12494-12509. [PMID: 32449989 DOI: 10.1002/chem.202001338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Indexed: 11/07/2022]
Abstract
Hydrogen is a clean and sustainable form of fuel that can minimize our heavy dependence on fossil fuels as the primary energy source. The need of finding greener ways to generate H2 gas has ignited interest in the research community to synthesize catalysts that can produce H2 by the reduction of H+ . The natural H2 producing enzymes hydrogenases have served as an inspiration to produce catalytic metal centers akin to these native enzymes. In this article we describe recent advances in the design of a unique class of artificial hydrogen evolving catalysts that combine the features of the active site metal(s) surrounded by a polypeptide component. The examples of these biosynthetic catalysts discussed here include i) assemblies of synthetic cofactors with native proteins; ii) peptide-appended synthetic complexes; iii) substitution of native cofactors with non-native cofactors; iv) metal substitution from rubredoxin; and v) a reengineered Cu storage protein into a Ni binding protein. Aspects of key design considerations in the construction of these artificial biocatalysts and insights gained into their chemical reactivity are discussed.
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Affiliation(s)
- Pallavi Prasad
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, 38677, USA
| | - Dhanashree Selvan
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, 38677, USA
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, 38677, USA
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10
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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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11
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Barbosa TM, Baltazar CSA, Cruz DR, Lousa D, Soares CM. Studying O 2 pathways in [NiFe]- and [NiFeSe]-hydrogenases. Sci Rep 2020; 10:10540. [PMID: 32601316 PMCID: PMC7324405 DOI: 10.1038/s41598-020-67494-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/02/2020] [Indexed: 12/25/2022] Open
Abstract
Hydrogenases are efficient biocatalysts for H2 production and oxidation with various potential biotechnological applications.[NiFe]-class hydrogenases are highly active in both production and oxidation processes—albeit primarily biased to the latter—but suffer from being sensitive to O2.[NiFeSe] hydrogenases are a subclass of [NiFe] hydrogenases with, usually, an increased insensitivity to aerobic environments. In this study we aim to understand the structural causes of the low sensitivity of a [NiFeSe]-hydrogenase, when compared with a [NiFe] class enzyme, by studying the diffusion of O2. To unravel the differences between the two enzymes, we used computational methods comprising Molecular Dynamics simulations with explicit O2 and Implicit Ligand Sampling methodologies. With the latter, we were able to map the free energy landscapes for O2 permeation in both enzymes. We derived pathways from these energy landscapes and selected the kinetically more relevant ones with reactive flux analysis using transition path theory. These studies evidence the existence of quite different pathways in both enzymes and predict a lower permeation efficiency for O2 in the case of the [NiFeSe]-hydrogenase when compared with the [NiFe] enzyme. These differences can explain the experimentally observed lower inhibition by O2 on [NiFeSe]-hydrogenases, when compared with [NiFe]-hydrogenases. A comprehensive map of the residues lining the most important O2 pathways in both enzymes is also presented.
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Affiliation(s)
- Tiago M Barbosa
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Carla S A Baltazar
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Davide R Cruz
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Diana Lousa
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Cláudio M Soares
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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12
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Yang X, Elrod LC, Le T, Vega VS, Naumann H, Rezenom Y, Reibenspies JH, Hall MB, Darensbourg MY. Controlling O2 Reactivity in Synthetic Analogues of [NiFeS]- and [NiFeSe]-Hydrogenase Active Sites. J Am Chem Soc 2019; 141:15338-15347. [DOI: 10.1021/jacs.9b07448] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuemei Yang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lindy C. Elrod
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Trung Le
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Valeria S. Vega
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Haley Naumann
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yohannes Rezenom
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Joseph H. Reibenspies
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael B. Hall
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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13
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Zacarias S, Temporão A, Barrio MD, Fourmond V, Léger C, Matias PM, Pereira IAC. A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02347] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Adriana Temporão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Melisa del Barrio
- Aix Marseille Univ., CNRS, Bioénergétique et Ingénierie des Protéines, UMR 7281 Marseille, France
| | - Vincent Fourmond
- Aix Marseille Univ., CNRS, Bioénergétique et Ingénierie des Protéines, UMR 7281 Marseille, France
| | - Christophe Léger
- Aix Marseille Univ., CNRS, Bioénergétique et Ingénierie des Protéines, UMR 7281 Marseille, France
| | - Pedro M. Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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14
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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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15
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Zacarias S, Vélez M, Pita M, De Lacey AL, Matias PM, Pereira IAC. Characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough. Methods Enzymol 2018; 613:169-201. [PMID: 30509465 DOI: 10.1016/bs.mie.2018.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The [NiFeSe] hydrogenases are a subgroup of the well-characterized family of [NiFe] hydrogenases, in which a selenocysteine is a ligand to the nickel atom in the binuclear NiFe active site instead of cysteine. These enzymes display very interesting catalytic properties for biological hydrogen production and bioelectrochemical applications: high H2 production activity, bias for H2 evolution, low H2 inhibition, and some degree of O2 tolerance. Here we describe the methodologies employed to study the [NiFeSe] hydrogenase isolated from the sulfate-reducing bacteria D. vulgaris Hildenborough and the creation of a homologous expression system for production of variant forms of the enzyme.
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Affiliation(s)
- Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | - Marcos Pita
- Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | | | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal; iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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16
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Yang X, Elrod LC, Reibenspies JH, Hall MB, Darensbourg MY. Oxygen uptake in complexes related to [NiFeS]- and [NiFeSe]-hydrogenase active sites. Chem Sci 2018; 10:1368-1373. [PMID: 30809352 PMCID: PMC6354737 DOI: 10.1039/c8sc04436h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/04/2018] [Indexed: 12/19/2022] Open
Abstract
The NiFe hydrogenase biomimetics are protected from oxygen invaders by sulfur and selenium castle guards.
A biomimetic study for S/Se oxygenation in Ni(μ-EPh)(μ-SN2)Fe, (E = S or Se; SN2 = Me-diazacycloheptane-CH2CH2S); Fe = (η5-C5H5)FeII(CO) complexes related to the oxygen-damaged active sites of [NiFeS]/[NiFeSe]-H2ases is described. Mono- and di-oxygenates (major and minor species, respectively) of the chalcogens result from exposure of the heterobimetallics to O2; one was isolated and structurally characterized to have Ni–O–SePh–Fe–S connectivity within a 5-membered ring. A compositionally analogous mono-oxy species was implicated by ν(CO) IR spectroscopy to be the corresponding Ni–O–SPh–Fe–S complex; treatment with O-abstraction agents such as P(o-tolyl)3 or PMe3 remediated the O damage. Computational studies (DFT) found that the lowest energy isomers of mono-oxygen derivatives of Ni(μ-EPh)(μ-SN2)Fe complexes were those with O attachment to Ni rather than Fe, a result consonant with experimental findings, but at odds with oxygenates found in oxygen-damaged [NiFeS]/[NiFeSe]-H2ase structures. A computer-generated model based on substituting –SMe for the N-CH2CH2S– sulfur donor of the N2S suggested that constraint within the chelate hindered O-atom uptake at that sulfur site.
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Affiliation(s)
- Xuemei Yang
- Texas A&M University , Department of Chemistry , College Station , TX 77843 , USA .
| | - Lindy C Elrod
- Texas A&M University , Department of Chemistry , College Station , TX 77843 , USA .
| | - Joseph H Reibenspies
- Texas A&M University , Department of Chemistry , College Station , TX 77843 , USA .
| | - Michael B Hall
- Texas A&M University , Department of Chemistry , College Station , TX 77843 , USA .
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17
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Maroney MJ, Hondal RJ. Selenium versus sulfur: Reversibility of chemical reactions and resistance to permanent oxidation in proteins and nucleic acids. Free Radic Biol Med 2018; 127:228-237. [PMID: 29588180 PMCID: PMC6158117 DOI: 10.1016/j.freeradbiomed.2018.03.035] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/14/2018] [Accepted: 03/18/2018] [Indexed: 12/16/2022]
Abstract
This review highlights the contributions of Jean Chaudière to the field of selenium biochemistry. Chaudière was the first to recognize that one of the main reasons that selenium in the form of selenocysteine is used in proteins is due to the fact that it strongly resists permanent oxidation. The foundations for this important concept was laid down by Al Tappel in the 1960's and even before by others. The concept of oxygen tolerance first recognized in the study of glutathione peroxidase was further advanced and refined by those studying [NiFeSe]-hydrogenases, selenosubtilisin, and thioredoxin reductase. After 200 years of selenium research, work by Marcus Conrad and coworkers studying glutathione peroxidase-4 has provided definitive evidence for Chaudière's original hypothesis (Ingold et al., 2018) [36]. While the reaction of selenium with oxygen is readily reversible, there are many other examples of this phenomenon of reversibility. Many reactions of selenium can be described as "easy in - easy out". This is due to the strong nucleophilic character of selenium to attack electrophiles, but then this reaction can be reversed due to the strong electrophilic character of selenium and the weakness of the selenium-carbon bond. Several examples of this are described.
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Affiliation(s)
- Michael J Maroney
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts, Life Sciences Laboratories, 240 Thatcher Road, Room N373, Amherst, MA 01003-9364, United States
| | - Robert J Hondal
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States.
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18
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Bortolus M, Costantini P, Doni D, Carbonera D. Overview of the Maturation Machinery of the H-Cluster of [FeFe]-Hydrogenases with a Focus on HydF. Int J Mol Sci 2018; 19:E3118. [PMID: 30314343 PMCID: PMC6212873 DOI: 10.3390/ijms19103118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/04/2018] [Accepted: 10/06/2018] [Indexed: 01/01/2023] Open
Abstract
Hydrogen production in nature is performed by hydrogenases. Among them, [FeFe]-hydrogenases have a peculiar active site, named H-cluster, that is made of two parts, synthesized in different pathways. The cubane sub-cluster requires the normal iron-sulfur cluster maturation machinery. The [2Fe] sub-cluster instead requires a dedicated set of maturase proteins, HydE, HydF, and HydG that work to assemble the cluster and deliver it to the apo-hydrogenase. In particular, the delivery is performed by HydF. In this review, we will perform an overview of the latest knowledge on the maturation machinery of the H-cluster, focusing in particular on HydF.
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Affiliation(s)
- Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
| | - Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
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19
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Harb MK, Alshurafa H, El-khateeb M, Al-Zuheiri A, Görls H, Abul-Futouh H, Weigand W. [FeFe]-Hydrogenase Models Containing Long Diselenolato Linkers. ChemistrySelect 2018. [DOI: 10.1002/slct.201801704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mohammad K. Harb
- Department of Pharmacy; Al-Zytoonah University of Jordan; P.O. Box 130 Amman 11733 Jordan
| | - Hadil Alshurafa
- Chemistry Department; Jordan University of Science and Technology; 22110 Irbid Jordan
| | - Mohammad El-khateeb
- Chemistry Department; Jordan University of Science and Technology; 22110 Irbid Jordan
| | - Aya Al-Zuheiri
- Department of Pharmacy; Al-Zytoonah University of Jordan; P.O. Box 130 Amman 11733 Jordan
| | - Helmar Görls
- Institute for Inorganic and Analytical Chemistry; Friedrich Schiller University Jena; Humbodt-Straße 8 07743 Jena Germany
| | - Hassan Abul-Futouh
- Institute for Inorganic and Analytical Chemistry; Friedrich Schiller University Jena; Humbodt-Straße 8 07743 Jena Germany
| | - Wolfgang Weigand
- Institute for Inorganic and Analytical Chemistry; Friedrich Schiller University Jena; Humbodt-Straße 8 07743 Jena Germany
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20
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Dolgova NV, Nehzati S, Choudhury S, MacDonald TC, Regnier NR, Crawford AM, Ponomarenko O, George GN, Pickering IJ. X-ray spectroscopy and imaging of selenium in living systems. Biochim Biophys Acta Gen Subj 2018; 1862:2383-2392. [PMID: 29729308 DOI: 10.1016/j.bbagen.2018.04.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Selenium is an essential element with a rich and varied chemistry in living organisms. It plays a variety of important roles ranging from being essential in enzymes that are critical for redox homeostasis to acting as a deterrent for herbivory in hyperaccumulating plants. Despite its importance there are many open questions, especially related to its chemistry in situ within living organisms. SCOPE OF REVIEW This review discusses X-ray spectroscopy and imaging of selenium in biological samples, with an emphasis on the methods, and in particular the techniques of X-ray absorption spectroscopy (XAS) and X-ray fluorescence imaging (XFI). We discuss the experimental methods and capabilities of XAS and XFI, and review their advantages and their limitations. A perspective on future possibilities and next-generation of experiments is also provided. MAJOR CONCLUSIONS XAS and XFI provide powerful probes of selenium chemistry, together with unique in situ capabilities. The opportunities and capabilities of the next generation of advanced X-ray spectroscopy experiments are particularly exciting. GENERAL SIGNIFICANCE XAS and XFI provide versatile tools that are generally applicable to any element with a convenient X-ray absorption edge, suitable for investigating complex systems essentially without pre-treatment.
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Affiliation(s)
- Natalia V Dolgova
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Susan Nehzati
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Sanjukta Choudhury
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Tracy C MacDonald
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Nathan R Regnier
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N0X2, Canada
| | - Andrew M Crawford
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Olena Ponomarenko
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada
| | - Graham N George
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada; Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N0X2, Canada.
| | - Ingrid J Pickering
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK S7N5E2, Canada; Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N0X2, Canada.
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21
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Ferentinos E, Chatziefthimiou S, Boudalis AK, Pissas M, Mathies G, Gast P, Groenen EJJ, Sanakis Y, Kyritsis P. The [Fe{(SePPh2
)2
N}2
] Complex Revisited: X-ray Crystallography, Magnetometry, High-Frequency EPR, and Mössbauer Studies Reveal Its Tetrahedral FeII
Se4
Coordination Sphere. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201701459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Eleftherios Ferentinos
- Inorganic Chemistry Laboratory; Department of Chemistry; National and Kapodistrian University of Athens; Panepistimiopolis 15771 Athens Greece
| | - Spyros Chatziefthimiou
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Athanassios K. Boudalis
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Michael Pissas
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Guinevere Mathies
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Peter Gast
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Edgar J. J. Groenen
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Yiannis Sanakis
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Panayotis Kyritsis
- Inorganic Chemistry Laboratory; Department of Chemistry; National and Kapodistrian University of Athens; Panepistimiopolis 15771 Athens Greece
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22
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Yuki M, Sakata K, Nakajima K, Kikuchi S, Sekine S, Kawai H, Nishibayashi Y. Dicationic Thiolate-Bridged Diruthenium Complexes for Catalytic Oxidation of Molecular Dihydrogen. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00764] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Masahiro Yuki
- Department
of Systems Innovation, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ken Sakata
- Faculty
of Pharmaceutical Sciences, Hoshi University, Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Kazunari Nakajima
- Department
of Systems Innovation, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Syoma Kikuchi
- Faculty
of Pharmaceutical Sciences, Hoshi University, Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Shinobu Sekine
- Fuel Cell System Engineering & Development Division, Toyota Motor Corporation, Mishuku, Susono, Shizuoka 410-1193, Japan
| | - Hiroyuki Kawai
- Fuel Cell System Engineering & Development Division, Toyota Motor Corporation, Mishuku, Susono, Shizuoka 410-1193, Japan
| | - Yoshiaki Nishibayashi
- Department
of Systems Innovation, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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23
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Artz JH, Zadvornyy OA, Mulder DW, King PW, Peters JW. Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases. Methods Enzymol 2017; 595:213-259. [PMID: 28882202 DOI: 10.1016/bs.mie.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.
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Affiliation(s)
- Jacob H Artz
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.
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24
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Therien JB, Artz JH, Poudel S, Hamilton TL, Liu Z, Noone SM, Adams MWW, King PW, Bryant DA, Boyd ES, Peters JW. The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5. Front Microbiol 2017; 8:1305. [PMID: 28747909 PMCID: PMC5506873 DOI: 10.3389/fmicb.2017.01305] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/28/2017] [Indexed: 12/02/2022] Open
Abstract
The first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5). Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI) is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction. A role for capturing reducing equivalents released as hydrogen during nitrogen fixation has been proposed for the second hydrogenase, CpII. Biochemical characterization of CpI and CpII indicated CpI has extremely high hydrogen production activity in comparison to CpII, while CpII has elevated hydrogen oxidation activity in comparison to CpI when assayed under the same conditions. This suggests that these enzymes have evolved a catalytic bias to support their respective physiological functions. Using the published genome of C. pasteurianum (strain W5) hydrogenase sequences were identified, including the already known [NiFe]-hydrogenase, CpI, and CpII sequences, and a third hydrogenase, CpIII was identified in the genome as well. Quantitative real-time PCR experiments were performed in order to analyze transcript abundance of the hydrogenases under diazotrophic and non-diazotrophic growth conditions. There is a markedly reduced level of CpI gene expression together with concomitant increases in CpII gene expression under nitrogen-fixing conditions. Structure-based analyses of the CpI and CpII sequences reveal variations in their catalytic sites that may contribute to their alternative physiological roles. This work demonstrates that the physiological roles of CpI and CpII are to evolve and to consume hydrogen, respectively, in concurrence with their catalytic activities in vitro, with CpII capturing excess reducing equivalents under nitrogen fixation conditions. Comparison of the primary sequences of CpI and CpII and their homologs provides an initial basis for identifying key structural determinants that modulate hydrogen production and hydrogen oxidation activities.
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Affiliation(s)
- Jesse B Therien
- Department of Chemistry and Biochemistry, Montana State University, BozemanMT, United States
| | - Jacob H Artz
- Department of Chemistry and Biochemistry, Montana State University, BozemanMT, United States
| | - Saroj Poudel
- Department of Microbiology and Immunology, Montana State University, BozemanMT, United States
| | - Trinity L Hamilton
- Department of Chemistry and Biochemistry, Montana State University, BozemanMT, United States
| | - Zhenfeng Liu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States
| | - Seth M Noone
- National Renewable Energy Laboratory, Biosciences Center, GoldenCO, United States
| | - Michael W W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, AthensGA, United States
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, GoldenCO, United States
| | - Donald A Bryant
- Department of Chemistry and Biochemistry, Montana State University, BozemanMT, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, BozemanMT, United States
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, BozemanMT, United States
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25
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El-Khouly ME, El-Mohsnawy E, Fukuzumi S. Solar energy conversion: From natural to artificial photosynthesis. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.02.001] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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26
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Ruff A, Szczesny J, Zacarias S, Pereira IA, Plumeré N, Schuhmann W. Protection and Reactivation of the [NiFeSe] Hydrogenase from Desulfovibrio vulgaris Hildenborough under Oxidative Conditions. ACS ENERGY LETTERS 2017; 2:964-968. [PMID: 32226822 PMCID: PMC7098691 DOI: 10.1021/acsenergylett.7b00167] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/03/2017] [Indexed: 06/02/2023]
Abstract
We report on the fabrication of bioanodes for H2 oxidation based on [NiFeSe] hydrogenase. The enzyme was electrically wired by means of a specifically designed low-potential viologen-modified polymer, which delivers benchmark H2 oxidizing currents even under deactivating conditions owing to efficient protection against O2 combined with a viologen-induced reactivation of the O2 inhibited enzyme. Moreover, the viologen-modified polymer allows for electrochemical co-deposition of polymer and biocatalyst and, by this, for control of the film thickness. Protection and reactivation of the enzyme was demonstrated in thick and thin reaction layers.
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Affiliation(s)
- Adrian Ruff
- Analytical
Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Julian Szczesny
- Analytical
Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Sónia Zacarias
- Instituto
de Tecnologia Quimica e Biologica Antonio Xavier, Universidade Nova de Lisboa, 278o-157 Oeiras, Portugal
| | - Inês A.
C. Pereira
- Instituto
de Tecnologia Quimica e Biologica Antonio Xavier, Universidade Nova de Lisboa, 278o-157 Oeiras, Portugal
| | - Nicolas Plumeré
- Center
for Electrochemical Sciences (CES) - Molecular Nanostructures, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Wolfgang Schuhmann
- Analytical
Chemistry - Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
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27
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The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis. Nat Chem Biol 2017; 13:544-550. [DOI: 10.1038/nchembio.2335] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/21/2016] [Indexed: 01/14/2023]
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28
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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29
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Gezer G, Durán Jiménez D, Siegler MA, Bouwman E. Electrocatalytic proton reduction by a model for [NiFeSe] hydrogenases. Dalton Trans 2017; 46:7506-7514. [DOI: 10.1039/c7dt00972k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrocatalytic proton reduction was studied using [NiFe] complexes as models of [NiFeSe] hydrogenases.
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Affiliation(s)
- Gamze Gezer
- Leiden Institute of Chemistry
- Leiden University
- 2300 RA Leiden
- the Netherlands
| | | | | | - Elisabeth Bouwman
- Leiden Institute of Chemistry
- Leiden University
- 2300 RA Leiden
- the Netherlands
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30
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Hutton GAM, Reuillard B, Martindale BCM, Caputo CA, Lockwood CWJ, Butt JN, Reisner E. Carbon Dots as Versatile Photosensitizers for Solar-Driven Catalysis with Redox Enzymes. J Am Chem Soc 2016; 138:16722-16730. [PMID: 27977174 DOI: 10.1021/jacs.6b10146] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Light-driven enzymatic catalysis is enabled by the productive coupling of a protein to a photosensitizer. Photosensitizers used in such hybrid systems are typically costly, toxic, and/or fragile, with limited chemical versatility. Carbon dots (CDs) are low-cost, nanosized light-harvesters that are attractive photosensitizers for biological systems as they are water-soluble, photostable, nontoxic, and their surface chemistry can be easily modified. We demonstrate here that CDs act as excellent light-absorbers in two semibiological photosynthetic systems utilizing either a fumarate reductase (FccA) for the solar-driven hydrogenation of fumarate to succinate or a hydrogenase (H2ase) for reduction of protons to H2. The tunable surface chemistry of the CDs was exploited to synthesize positively charged ammonium-terminated CDs (CD-NHMe2+), which were capable of transferring photoexcited electrons directly to the negatively charged enzymes with high efficiency and stability. Enzyme-based turnover numbers of 6000 mol succinate (mol FccA)-1 and 43,000 mol H2 (mol H2ase)-1 were reached after 24 h. Negatively charged carboxylate-terminated CDs (CD-CO2-) displayed little or no activity, and the electrostatic interactions at the CD-enzyme interface were determined to be essential to the high photocatalytic activity observed with CD-NHMe2+. The modular surface chemistry of CDs together with their photostability and aqueous solubility make CDs versatile photosensitizers for redox enzymes with great scope for their utilization in photobiocatalysis.
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Affiliation(s)
- Georgina A M Hutton
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Bertrand Reuillard
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | | | - Christine A Caputo
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Colin W J Lockwood
- School of Chemistry and School of Biological Sciences, University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Julea N Butt
- School of Chemistry and School of Biological Sciences, University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Erwin Reisner
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
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31
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Tapia C, Zacarias S, Pereira IAC, Conesa JC, Pita M, De Lacey AL. In Situ Determination of Photobioproduction of H2 by In2S3-[NiFeSe] Hydrogenase from Desulfovibrio vulgaris Hildenborough Using Only Visible Light. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01512] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cristina Tapia
- Instituto
de Catálisis y Petroleoquímica, CSIC, c/Marie Curie
2, 28049 Madrid, Spain
| | - Sonia Zacarias
- Instituto
de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Apartado
127, 2781-901 Oeiras, Portugal
| | - Inês A. C. Pereira
- Instituto
de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Apartado
127, 2781-901 Oeiras, Portugal
| | - Jose C. Conesa
- Instituto
de Catálisis y Petroleoquímica, CSIC, c/Marie Curie
2, 28049 Madrid, Spain
| | - Marcos Pita
- Instituto
de Catálisis y Petroleoquímica, CSIC, c/Marie Curie
2, 28049 Madrid, Spain
| | - Antonio L. De Lacey
- Instituto
de Catálisis y Petroleoquímica, CSIC, c/Marie Curie
2, 28049 Madrid, Spain
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32
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Abstract
[NiFe]-hydrogenases catalyze the reversible conversion of hydrogen gas into protons and electrons and are vital metabolic components of many species of bacteria and archaea. At the core of this enzyme is a sophisticated catalytic center comprising nickel and iron, as well as cyanide and carbon monoxide ligands, which is anchored to the large hydrogenase subunit through cysteine residues. The production of this multicomponent active site is accomplished by a collection of accessory proteins and can be divided into discrete stages. The iron component is fashioned by the proteins HypC, HypD, HypE, and HypF, which functionalize iron with cyanide and carbon monoxide. Insertion of the iron center signals to the metallochaperones HypA, HypB, and SlyD to selectively deliver the nickel to the active site. A specific protease recognizes the completed metal cluster and then cleaves the C-terminus of the large subunit, resulting in a conformational change that locks the active site in place. Finally, the large subunit associates with the small subunit, and the complete holoenzyme translocates to its final cellular position. Beyond this broad overview of the [NiFe]-hydrogenase maturation process, biochemical and structural studies are revealing the fundamental underlying molecular mechanisms. Here, we review recent work illuminating how the accessory proteins contribute to the maturation of [NiFe]-hydrogenase and discuss some of the outstanding questions that remain to be resolved.
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Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6.,Department of Biochemistry, University of Toronto , Toronto, Ontario, Canada M5S 1A8
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33
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Vedha SA, Velmurugan G, Venuvanalingam P. Noncovalent interactions between the second coordination sphere and the active site of [NiFeSe] hydrogenase. RSC Adv 2016. [DOI: 10.1039/c6ra11295a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
QM/MM studies on seven truncated models of the oxidized as-isolated state of the [NiFeSe] Hases reveal the influence of the residues in the second coordination sphere on the active site.
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Affiliation(s)
- Swaminathan Angeline Vedha
- Theoretical and Computational Chemistry Laboratory
- School of Chemistry
- Bharathidasan University
- Tiruchirappalli-620 024
- India
| | - Gunasekaran Velmurugan
- Theoretical and Computational Chemistry Laboratory
- School of Chemistry
- Bharathidasan University
- Tiruchirappalli-620 024
- India
| | - Ponnambalam Venuvanalingam
- Theoretical and Computational Chemistry Laboratory
- School of Chemistry
- Bharathidasan University
- Tiruchirappalli-620 024
- India
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34
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Abstract
The development of technology for the inexpensive generation of the renewable energy vector H2 through water splitting is of immediate economic, ecological, and humanitarian interest. Recent interest in hydrogenases has been fueled by their exceptionally high catalytic rates for H2 production at a marginal overpotential, which is presently only matched by the nonscalable noble metal platinum. The mechanistic understanding of hydrogenase function guides the design of synthetic catalysts, and selection of a suitable hydrogenase enables direct applications in electro- and photocatalysis. [FeFe]-hydrogenases display excellent H2 evolution activity, but they are irreversibly damaged upon exposure to O2, which currently prevents their use in full water splitting systems. O2-tolerant [NiFe]-hydrogenases are known, but they are typically strongly biased toward H2 oxidation, while H2 production by [NiFe]-hydrogenases is often product (H2) inhibited. [NiFeSe]-hydrogenases are a subclass of [NiFe]-hydrogenases with a selenocysteine residue coordinated to the active site nickel center in place of a cysteine. They exhibit a combination of unique properties that are highly advantageous for applications in water splitting compared with other hydrogenases. They display a high H2 evolution rate with marginal inhibition by H2 and tolerance to O2. [NiFeSe]-hydrogenases are therefore one of the most active molecular H2 evolution catalysts applicable in water splitting. Herein, we summarize our recent progress in exploring the unique chemistry of [NiFeSe]-hydrogenases through biomimetic model chemistry and the chemistry with [NiFeSe]-hydrogenases in semiartificial photosynthetic systems. We gain perspective from the structural, spectroscopic, and electrochemical properties of the [NiFeSe]-hydrogenases and compare them with the chemistry of synthetic models of this hydrogenase active site. Our synthetic models give insight into the effects on the electronic properties and reactivity of the active site upon the introduction of selenium. We have utilized the exceptional properties of the [NiFeSe]-hydrogenase from Desulfomicrobium baculatum in a number of photocatalytic H2 production schemes, which are benchmark systems in terms of single site activity, tolerance toward O2, and in vitro water splitting with biological molecules. Each system comprises a light-harvesting component, which allows for light-driven electron transfer to the hydrogenase in order for it to catalyze H2 production. A system with [NiFeSe]-hydrogenase on a dye-sensitized TiO2 nanoparticle gives an enzyme-semiconductor hybrid for visible light-driven generation of H2 with an enzyme-based turnover frequency of 50 s(-1). A stable and inexpensive polymeric carbon nitride as a photosensitizer in combination with the [NiFeSe]-hydrogenase shows good activity for more than 2 days. Light-driven H2 evolution with the enzyme and an organic dye under high O2 levels demonstrates the excellent robustness and feasibility of water splitting with a hydrogenase-based scheme. This has led, most recently, to the development of a light-driven full water splitting system with a [NiFeSe]-hydrogenase wired to the water oxidation enzyme photosystem II in a photoelectrochemical cell. In contrast to the other systems, this photoelectrochemical system does not rely on a sacrificial electron donor and allowed us to establish the long sought after light-driven water splitting with an isolated hydrogenase.
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Affiliation(s)
- Claire Wombwell
- Christian Doppler Laboratory
for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Christine A. Caputo
- Christian Doppler Laboratory
for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Erwin Reisner
- Christian Doppler Laboratory
for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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35
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Vedha SA, Velmurugan G, Jagadeesan R, Venuvanalingam P. Insights from the computational studies on the oxidized as-isolated state of [NiFeSe] hydrogenase from D. vulgaris Hildenborough. Phys Chem Chem Phys 2015. [PMID: 26205195 DOI: 10.1039/c5cp03071d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A density functional theory study of the active site structure and features of the oxygen tolerant [NiFeSe] Hase in the oxidized as-isolated state of the enzyme D. vulgaris Hildenborough (DvH) is reported here. The three conformers reported to be present in the X-ray structure (PDB ID: ) have been studied. The novel bidentate interchalcogen ligand (S-Se) in Conf-I of the [NiFeSe] Hase reported for the first time in hydrogenases (Hase) is found to be of donor-acceptor type with an uneven η(2) L → M σ-bond. The symmetry mismatch at the sp orbital of Se and at the dz(2) orbital of Ni has been identified to be the reason for the inability of Conf-II to convert to Conf-I. NBO analysis shows that the sulfinate ligand peculiar to the state stabilizes the active site through n →π* interactions. The results reveal that the isolated oxidized state of the [NiFeSe] Hase is significantly different from the well-known [NiFe] Hase.
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Affiliation(s)
- Swaminathan Angeline Vedha
- Theoretical and Computational Chemistry Laboratory, School of Chemistry, Bharathidasan University, Tiruchirappalli-620 024, India.
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36
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Ceccaldi P, Marques MC, Fourmond V, Pereira IC, Léger C. Oxidative inactivation of NiFeSe hydrogenase. Chem Commun (Camb) 2015; 51:14223-6. [PMID: 26260963 DOI: 10.1039/c5cc05930e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We propose a resolution to the paradox that spectroscopic studies of NiFeSe hydrogenase have not revealed any major signal attributable to Ni(III) states formed upon reaction with O2, despite the fact that two inactive states are formed upon either aerobic or anaerobic oxidation.
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Affiliation(s)
- Pierre Ceccaldi
- CNRS, Aix-Marseille Univ., BIP UMR 7281, IMM FR 3479, 31 Chemin J. Aiguier, 13402 Marseille Cedex 20, France.
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37
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Caputo CA, Wang L, Beranek R, Reisner E. Carbon nitride-TiO 2 hybrid modified with hydrogenase for visible light driven hydrogen production. Chem Sci 2015; 6:5690-5694. [PMID: 28757952 PMCID: PMC5512016 DOI: 10.1039/c5sc02017d] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 06/29/2015] [Indexed: 01/18/2023] Open
Abstract
A system consisting of a [NiFeSe]-hydrogenase (H2ase) grafted on the surface of a TiO2 nanoparticle modified with polyheptazine carbon nitride polymer, melon (CN x ) is reported. This semi-biological assembly shows a turnover number (TON) of more than 5.8 × 105 mol H2 (mol H2ase)-1 after 72 h in a sacrificial electron donor solution at pH 6 during solar AM 1.5 G irradiation. An external quantum efficiency up to 4.8% for photon-to-hydrogen conversion was achieved under irradiation with monochromatic light. The CN x -TiO2-H2ase construct was also active under UV-free solar light irradiation (λ > 420 nm), where it showed a substantially higher activity than TiO2-H2ase and CN x -H2ase due, in part, to the formation of a CN x -TiO2 charge transfer complex and highly productive electron transfer to the H2ase. The CN x -TiO2-H2ase system sets a new benchmark for photocatalytic H2 production with a H2ase immobilised on a noble- and toxic-metal free light absorber in terms of visible light utilisation and stability.
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Affiliation(s)
- Christine A Caputo
- Christian Doppler Laboratory for Sustainable SynGas Chemistry , Department of Chemistry , Cambridge University , Lensfied Road , Cambridge CB2 1EW , UK . ; http://www-reisner.ch.cam.ac.uk
| | - Lidong Wang
- Faculty of Chemistry and Biochemistry , Ruhr-Universität Bochum , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Radim Beranek
- Faculty of Chemistry and Biochemistry , Ruhr-Universität Bochum , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Erwin Reisner
- Christian Doppler Laboratory for Sustainable SynGas Chemistry , Department of Chemistry , Cambridge University , Lensfied Road , Cambridge CB2 1EW , UK . ; http://www-reisner.ch.cam.ac.uk
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38
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Roncaroli F, Bill E, Friedrich B, Lenz O, Lubitz W, Pandelia ME. Cofactor composition and function of a H 2-sensing regulatory hydrogenase as revealed by Mössbauer and EPR spectroscopy. Chem Sci 2015; 6:4495-4507. [PMID: 29142700 PMCID: PMC5665086 DOI: 10.1039/c5sc01560j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/26/2015] [Indexed: 01/22/2023] Open
Abstract
The regulatory hydrogenase (RH) from Ralstonia eutropha H16 acts as a sensor for the detection of environmental H2 and regulates gene expression related to hydrogenase-mediated cellular metabolism. In marked contrast to prototypical energy-converting [NiFe] hydrogenases, the RH is apparently insensitive to inhibition by O2 and CO. While the physiological function of regulatory hydrogenases is well established, little is known about the redox cycling of the [NiFe] center and the nature of the iron-sulfur (FeS) clusters acting as electron relay. The absence of any FeS cluster signals in EPR had been attributed to their particular nature, whereas the observation of essentially only two active site redox states, namely Ni-SI and Ni-C, invoked a different operant mechanism. In the present work, we employ a combination of Mössbauer, FTIR and EPR spectroscopic techniques to study the RH, and the results are consistent with the presence of three [4Fe-4S] centers in the small subunit. In the as-isolated, oxidized RH all FeS clusters reside in the EPR-silent 2+ state. Incubation with H2 leads to reduction of two of the [4Fe-4S] clusters, whereas only strongly reducing agents lead to reduction of the third cluster, which is ascribed to be the [4Fe-4S] center in 'proximal' position to the [NiFe] center. In the two different active site redox states, the low-spin FeII exhibits distinct Mössbauer features attributed to changes in the electronic and geometric structure of the catalytic center. The results are discussed with regard to the spectral characteristics and physiological function of H2-sensing regulatory hydrogenases.
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Affiliation(s)
- Federico Roncaroli
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ; .,Department of Condensed Matter Physics , Centro Atómico Constituyentes , Comisión Nacional de Energía Atómica (CNEA) , Argentina
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Bärbel Friedrich
- Institut für Biologie/Mikrobiologie , Humboldt-Universität zu Berlin , Chausseestraße 117 , 10115 Berlin , Germany
| | - Oliver Lenz
- Institut für Biologie/Mikrobiologie , Humboldt-Universität zu Berlin , Chausseestraße 117 , 10115 Berlin , Germany.,Institut für Chemie , Technische Universität Berlin , Max-Volmer-Laboratorium , Straße des 17. Juni 135 , 10623 Berlin , Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Maria-Eirini Pandelia
- The Pennsylvania State University , Department of Chemistry , State College , PA 16802 , USA . .,Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
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39
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Abstract
A dinuclear synthetic model of the [NiFeSe] hydrogenase active site and a structural, spectroscopic and electrochemical analysis of this complex is reported. [NiFe(‘S2Se2’)(CO)3] (H2‘S2Se2’=1,2-bis(2-thiabutyl-3,3-dimethyl-4-selenol)benzene) has been synthesized by reacting the nickel selenolate complex [Ni(‘S2Se2’)] with [Fe(CO)3bda] (bda=benzylideneacetone). X-ray crystal structure analysis confirms that [NiFe(‘S2Se2’)(CO)3] mimics the key structural features of the enzyme active site, including a doubly bridged heterobimetallic nickel and iron center with a selenolate terminally coordinated to the nickel center. Comparison of [NiFe(‘S2Se2’)(CO)3] with the previously reported thiolate analogue [NiFe(‘S4’)(CO)3] (H2‘S4’=H2xbsms=1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) showed that the selenolate groups in [NiFe(‘S2Se2’)(CO)3] give lower carbonyl stretching frequencies in the IR spectrum. Electrochemical studies of [NiFe(‘S2Se2’)(CO)3] and [NiFe(‘S4’)(CO)3] demonstrated that both complexes do not operate as homogenous H2 evolution catalysts, but are precursors to a solid deposit on an electrode surface for H2 evolution catalysis in organic and aqueous solution.
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Affiliation(s)
- Claire Wombwell
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK) E-mail: Homepage: http://www-reisner.ch.cam.ac.uk/
| | - Erwin Reisner
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK) E-mail: Homepage: http://www-reisner.ch.cam.ac.uk/
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40
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Caputo CA, Gross MA, Lau VW, Cavazza C, Lotsch BV, Reisner E. Photocatalytic hydrogen production using polymeric carbon nitride with a hydrogenase and a bioinspired synthetic Ni catalyst. Angew Chem Int Ed Engl 2014; 53:11538-42. [PMID: 25205168 PMCID: PMC4497605 DOI: 10.1002/anie.201406811] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/07/2014] [Indexed: 11/30/2022]
Abstract
Solar-light-driven H2 production in water with a [NiFeSe]-hydrogenase (H2ase) and a bioinspired synthetic nickel catalyst (NiP) in combination with a heptazine carbon nitride polymer, melon (CN(x)), is reported. The semibiological and purely synthetic systems show catalytic activity during solar light irradiation with turnover numbers (TONs) of more than 50,000 mol H2(mol H2ase)(-1) and approximately 155 mol H2 (mol NiP)(-1) in redox-mediator-free aqueous solution at pH 6 and 4.5, respectively. Both systems maintained a reduced photoactivity under UV-free solar light irradiation (λ>420 nm).
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Affiliation(s)
- Christine A Caputo
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
| | - Manuela A Gross
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
| | - Vincent W Lau
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
| | - Christine Cavazza
- CEA, CNRS, Université Grenoble Alpes, IBS71 Avenue des Martyrs, 38044 Grenoble (France)
| | - Bettina V Lotsch
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
| | - Erwin Reisner
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
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41
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Caputo CA, Gross MA, Lau VW, Cavazza C, Lotsch BV, Reisner E. Photocatalytic Hydrogen Production using Polymeric Carbon Nitride with a Hydrogenase and a Bioinspired Synthetic Ni Catalyst. ACTA ACUST UNITED AC 2014; 126:11722-11726. [PMID: 26300567 PMCID: PMC4535659 DOI: 10.1002/ange.201406811] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/07/2014] [Indexed: 11/30/2022]
Abstract
Solar-light-driven H2 production in water with a [NiFeSe]-hydrogenase (H2ase) and a bioinspired synthetic nickel catalyst (NiP) in combination with a heptazine carbon nitride polymer, melon (CNx), is reported. The semibiological and purely synthetic systems show catalytic activity during solar light irradiation with turnover numbers (TONs) of more than 50 000 mol H2 (mol H2ase)−1 and approximately 155 mol H2 (mol NiP)−1 in redox-mediator-free aqueous solution at pH 6 and 4.5, respectively. Both systems maintained a reduced photoactivity under UV-free solar light irradiation (λ>420 nm).
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Affiliation(s)
- Christine A Caputo
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW (UK) E-mail: Homepage: http://www-reisner.ch.cam.ac.uk/
| | - Manuela A Gross
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW (UK) E-mail: Homepage: http://www-reisner.ch.cam.ac.uk/
| | - Vincent W Lau
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW (UK) E-mail: Homepage: http://www-reisner.ch.cam.ac.uk/
| | - Christine Cavazza
- CEA, CNRS, Université Grenoble Alpes IBS, 71 Avenue des Martyrs, 38044 Grenoble (France)
| | - Bettina V Lotsch
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW (UK) E-mail: Homepage: http://www-reisner.ch.cam.ac.uk/
| | - Erwin Reisner
- Christian Doppler Laboratory for Sustainable SynGas Chemistry, Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW (UK) E-mail: Homepage: http://www-reisner.ch.cam.ac.uk/
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42
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Song LC, Sun XJ, Jia GJ, Wang MM, Song HB. Synthesis, structural characterization, and electrochemical properties of (diphosphine)Ni-bridged butterfly Fe2E2 (E = S, Se, Te) cluster complexes related to [NiFe]-hydrogenases. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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43
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The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member. J Mol Biol 2014; 426:2813-26. [DOI: 10.1016/j.jmb.2014.05.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/02/2014] [Accepted: 05/23/2014] [Indexed: 11/21/2022]
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44
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Abbas G, Mariya-al-Rashida, Irfan A, Rana UA, Shakir I. DFT studies on the tetranuclear cubane complex [Ni4(ampd)4(Cl4)]·MeCN. J STRUCT CHEM+ 2014. [DOI: 10.1134/s0022476614010053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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46
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Boer JL, Mulrooney SB, Hausinger RP. Nickel-dependent metalloenzymes. Arch Biochem Biophys 2014; 544:142-52. [PMID: 24036122 PMCID: PMC3946514 DOI: 10.1016/j.abb.2013.09.002] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
Abstract
This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.
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Affiliation(s)
- Jodi L Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Scott B Mulrooney
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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47
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48
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Abstract
AbstractEnzymes that naturally contain an organometallic complex are highly rare. Hydrogenases commonly include iron carbonyl(s) at the active site and play central roles in the hydrogen metabolism of microorganisms. [NiFe]-hydrogenases that harbor an Ni-Fe(CN)2CO complex at the active site most widely exist among organisms, compared with the other two types, [FeFe]- and [Fe]-hydrogenases. Since the first crystal structure report in 1995, structural information of the Ni-Fe cluster with various redox/substrate-bound states has been obtained, although details of the reaction mechanisms are poorly understood. While the subunit composition, physiological function, and spectroscopic/biochemical properties of [NiFe]-hydrogenases are diverse, structural information of only a limited group of the enzymes is available so far. In this paper, structural aspects of [NiFe]-hydrogenases are reviewed and recent progresses in understanding the mechanism of an O2-tolerant property of limited members and active site assembling of [NiFe]-hydrogenases are described.
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Sakai T, Mersch D, Reisner E. Photocatalytic hydrogen evolution with a hydrogenase in a mediator-free system under high levels of oxygen. Angew Chem Int Ed Engl 2013; 52:12313-6. [PMID: 24115736 PMCID: PMC4138992 DOI: 10.1002/anie.201306214] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Indexed: 12/03/2022]
Abstract
Take a breath: An oxygen-tolerant hydrogenase can be employed with a dye in a photocatalytic scheme for the generation of H2 . The homogeneous system does not require a redox mediator and visible-light irradiation yields high amounts of H2 even in the presence of air.
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Affiliation(s)
- Tsubasa Sakai
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
| | - Dirk Mersch
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
| | - Erwin Reisner
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
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Sakai T, Mersch D, Reisner E. Photocatalytic Hydrogen Evolution with a Hydrogenase in a Mediator-Free System under High Levels of Oxygen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306214] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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