1
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Liu YC, Chu KT, Wang HR, Lee GH, Tseng MC, Wang CH, Horng YC, Chiang MH. Chloride- and Hydrosulfide-Bound 2Fe Complexes as Models of the Oxygen-Stable State of [FeFe] Hydrogenase. Angew Chem Int Ed Engl 2024; 63:e202408142. [PMID: 38818643 DOI: 10.1002/anie.202408142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024]
Abstract
[FeFe] hydrogenases demonstrate remarkable catalytic efficiency in hydrogen evolution and oxidation processes. However, susceptibility of these enzymes to oxygen-induced degradation impedes their practical deployment in hydrogen-production devices and fuel cells. Recent investigations into the oxygen-stable (Hinact) state of the H-cluster revealed its inherent capacity to resist oxygen degradation. Herein, we present findings on Cl- and SH-bound [2Fe-2S] complexes, bearing relevance to the oxygen-stable state within a biological context. A characteristic attribute of these complexes is the terminal Cl-/SH- ligation to the iron center bearing the CO bridge. Structural analysis of the t-Cl demonstrates a striking resemblance to the Hinact state of DdHydAB and CbA5H. The t-Cl/t-SH exhibit reversible oxidation, with both redox species, electronically, being the first biomimetic analogs to the Htrans and Hinact states. These complexes exhibit notable resistance against oxygen-induced decomposition, supporting the potential oxygen-resistant nature of the Htrans and Hinact states. The swift reductive release of the Cl-/SH-group demonstrates its labile and kinetically controlled binding. The findings garnered from these investigations offer valuable insights into properties of the enzymatic O2-stable state, and key factors governing deactivation and reactivation conversion. This work contributes to the advancement of bio-inspired molecular catalysts and the integration of enzymes and artificial catalysts into H2-evolution devices and fuel-cell applications.
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Affiliation(s)
- Yu-Chiao Liu
- Institute of Chemistry, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Kai-Ti Chu
- Institute of Chemistry, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Hong-Ru Wang
- Institute of Chemistry, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center, National Taiwan University, Taipei, 106, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Cheng-Hsin Wang
- Institute of Chemistry, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Yih-Chern Horng
- Department of Chemistry, National Changhua University of Education, Changhua, 500, Taiwan
| | - Ming-Hsi Chiang
- Institute of Chemistry, Academia Sinica, Nankang, Taipei, 115, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
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2
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Fasano A, Fourmond V, Léger C. Outer-sphere effects on the O 2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases. Chem Sci 2024; 15:5418-5433. [PMID: 38638217 PMCID: PMC11023054 DOI: 10.1039/d4sc00691g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
The comparison of homologous metalloenzymes, in which the same inorganic active site is surrounded by a variable protein matrix, has demonstrated that residues that are remote from the active site may have a great influence on catalytic properties. In this review, we summarise recent findings on the diverse molecular mechanisms by which the protein matrix may define the oxygen tolerance, catalytic directionality and catalytic reversibility of hydrogenases, enzymes that catalyse the oxidation and evolution of H2. These mechanisms involve residues in the second coordination sphere of the active site metal ion, more distant residues affecting protein flexibility through their side chains, residues lining the gas channel and even accessory subunits. Such long-distance effects, which contribute to making enzymes efficient, robust and different from one another, are a source of wonder for biochemists and a challenge for synthetic bioinorganic chemists.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
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3
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Rutz A, Das CK, Fasano A, Jaenecke J, Yadav S, Apfel UP, Engelbrecht V, Fourmond V, Léger C, Schäfer LV, Happe T. Increasing the O 2 Resistance of the [FeFe]-Hydrogenase CbA5H through Enhanced Protein Flexibility. ACS Catal 2022; 13:856-865. [PMID: 36733639 PMCID: PMC9886219 DOI: 10.1021/acscatal.2c04031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/08/2022] [Indexed: 12/29/2022]
Abstract
The high turnover rates of [FeFe]-hydrogenases under mild conditions and at low overpotentials provide a natural blueprint for the design of hydrogen catalysts. However, the unique active site (H-cluster) degrades upon contact with oxygen. The [FeFe]-hydrogenase fromClostridium beijerinckii (CbA5H) is characterized by the flexibility of its protein structure, which allows a conserved cysteine to coordinate to the active site under oxidative conditions. Thereby, intrinsic cofactor degradation induced by dioxygen is minimized. However, the protection from O2 is only partial, and the activity of the enzyme decreases upon each exposure to O2. By using site-directed mutagenesis in combination with electrochemistry, ATR-FTIR spectroscopy, and molecular dynamics simulations, we show that the kinetics of the conversion between the oxygen-protected inactive state (cysteine-bound) and the oxygen-sensitive active state can be accelerated by replacing a surface residue that is very distant from the active site. This sole exchange of methionine for a glutamate residue leads to an increased resistance of the hydrogenase to dioxygen. With our study, we aim to understand how local modifications of the protein structure can have a crucial impact on protein dynamics and how they can control the reactivity of inorganic active sites through outer sphere effects.
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Affiliation(s)
- Andreas Rutz
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical
Chemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Andrea Fasano
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Jan Jaenecke
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Shanika Yadav
- Inorganic
Chemistry Ι, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic
Chemistry Ι, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany,Fraunhofer
UMSICHT, 46047 Oberhausen, Germany
| | - Vera Engelbrecht
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vincent Fourmond
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Christophe Léger
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Lars V. Schäfer
- Theoretical
Chemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Thomas Happe
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany,
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4
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Chatelain L, Breton JB, Arrigoni F, Schollhammer P, Zampella G. Geometrical influence on the non-biomimetic heterolytic splitting of H 2 by bio-inspired [FeFe]-hydrogenase complexes: a rare example of inverted frustrated Lewis pair based reactivity. Chem Sci 2022; 13:4863-4873. [PMID: 35655865 PMCID: PMC9067592 DOI: 10.1039/d1sc06975f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/13/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the high levels of interest in the synthesis of bio-inspired [FeFe]-hydrogenase complexes, H2 oxidation, which is one specific aspect of hydrogenase enzymatic activity, is not observed for most reported complexes. To attempt H-H bond cleavage, two disubstituted diiron dithiolate complexes in the form of [Fe2(μ-pdt)L2(CO)4] (L: PMe3, dmpe) have been used to play the non-biomimetic role of a Lewis base, with frustrated Lewis pairs (FLPs) formed in the presence of B(C6F5)3 Lewis acid. These unprecedented FLPs, based on the bimetallic Lewis base partner, allow the heterolytic splitting of the H2 molecule, forming a protonated diiron cation and hydrido-borate anion. The substitution, symmetrical or asymmetrical, of two phosphine ligands at the diiron dithiolate core induces a strong difference in the H2 bond cleavage abilities, with the FLP based on the first complex being more efficient than the second. DFT investigations examined the different mechanistic pathways involving each accessible isomer and rationalized the experimental findings. One of the main DFT results highlights that the iron site acting as a Lewis base for the asymmetrical complex is the {Fe(CO)3} subunit, which is less electron-rich than the {FeL(CO)2} site of the symmetrical complex, diminishing the reactivity towards H2. Calculations relating to the different mechanistic pathways revealed the presence of a terminal hydride intermediate at the apical site of a rotated {Fe(CO)3} site, which is experimentally observed, and a semi-bridging hydride intermediate from H2 activation at the Fe-Fe site; these are responsible for a favourable back-reaction, reducing the conversion yield observed in the case of the asymmetrical complex. The use of two equivalents of Lewis acid allows for more complete and faster H2 bond cleavage due to the encapsulation of the hydrido-borate species by a second borane, favouring the reactivity of each FLP, in agreement with DFT calculations.
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Affiliation(s)
- Lucile Chatelain
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Jean-Baptiste Breton
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Federica Arrigoni
- Department of Biotechnology and Bioscience, University of Milano-Bicocca Piazza della Scienza 2 20126 Milan Italy
| | - Philippe Schollhammer
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Giuseppe Zampella
- Department of Biotechnology and Bioscience, University of Milano-Bicocca Piazza della Scienza 2 20126 Milan Italy
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5
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Fasano A, Land H, Fourmond V, Berggren G, Léger C. Reversible or Irreversible Catalysis of H +/H 2 Conversion by FeFe Hydrogenases. J Am Chem Soc 2021; 143:20320-20325. [PMID: 34813699 DOI: 10.1021/jacs.1c09554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies of molecular catalysts traditionally aim at understanding how a certain mechanism allows the reaction to be fast. A distinct question, which has only recently received attention in the case of bidirectional molecular catalysts, is how much thermodynamic driving force is required to achieve fast catalysis in either direction of the reaction. "Reversible" catalysts are bidirectional catalysts that work either way in response to even a small departure from equilibrium and thus do not waste input free energy as heat; conversely, "irreversible" catalysts require a large driving force to proceed at an appreciable rate [Fourmond et al. Nat. Rev. Chem. 2021, 5, 348-360]. Numerous mechanistic rationales for these contrasting behaviors have been proposed. To understand the determinants of catalytic (ir)reversibility, we examined the steady-state, direct electron transfer voltammetry of a particular FeFe hydrogenase, from Thermoanaerobacter mathranii, which is very unusual in that it irreversibly catalyzes H2 oxidation and production: a large overpotential is required for the reaction to proceed in either direction [Land et al. Chem. Sci. 2020, 11, 12789-12801]. In contrast to previous hypotheses, we demonstrate that in this particular enzyme catalytic irreversibility can be explained without invoking slow interfacial electron transfer or variations in the mechanism: the observed kinetics is fully consistent with the same catalytic pathway being used in both directions of the reaction.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
| | - Henrik Land
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Box-523, Uppsala 751 20, Sweden
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Box-523, Uppsala 751 20, Sweden
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
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6
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Abstract
[FeFe]-hydrogenases are efficient H2-catalysts, yet upon contact with dioxygen their catalytic cofactor (H-cluster) is irreversibly inactivated. Here, we combine X-ray crystallography, rational protein design, direct electrochemistry, and Fourier-transform infrared spectroscopy to describe a protein morphing mechanism that controls the reversible transition between the catalytic Hox-state and the inactive but oxygen-resistant Hinact-state in [FeFe]-hydrogenase CbA5H of Clostridium beijerinckii. The X-ray structure of air-exposed CbA5H reveals that a conserved cysteine residue in the local environment of the active site (H-cluster) directly coordinates the substrate-binding site, providing a safety cap that prevents O2-binding and consequently, cofactor degradation. This protection mechanism depends on three non-conserved amino acids situated approximately 13 Å away from the H-cluster, demonstrating that the 1st coordination sphere chemistry of the H-cluster can be remote-controlled by distant residues.
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7
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Jacq-Bailly A, Benvenuti M, Payne N, Kpebe A, Felbek C, Fourmond V, Léger C, Brugna M, Baffert C. Electrochemical Characterization of a Complex FeFe Hydrogenase, the Electron-Bifurcating Hnd From Desulfovibrio fructosovorans. Front Chem 2021; 8:573305. [PMID: 33490032 PMCID: PMC7820892 DOI: 10.3389/fchem.2020.573305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/10/2020] [Indexed: 12/02/2022] Open
Abstract
Hnd, an FeFe hydrogenase from Desulfovibrio fructosovorans, is a tetrameric enzyme that can perform flavin-based electron bifurcation. It couples the oxidation of H2 to both the exergonic reduction of NAD+ and the endergonic reduction of a ferredoxin. We previously showed that Hnd retains activity even when purified aerobically unlike other electron-bifurcating hydrogenases. In this study, we describe the purification of the enzyme under O2-free atmosphere and its biochemical and electrochemical characterization. Despite its complexity due to its multimeric composition, Hnd can catalytically and directly exchange electrons with an electrode. We characterized the catalytic and inhibition properties of this electron-bifurcating hydrogenase using protein film electrochemistry of Hnd by purifying Hnd aerobically or anaerobically, then comparing the electrochemical properties of the enzyme purified under the two conditions via protein film electrochemistry. Hydrogenases are usually inactivated under oxidizing conditions in the absence of dioxygen and can then be reactivated, to some extent, under reducing conditions. We demonstrate that the kinetics of this high potential inactivation/reactivation for Hnd show original properties: it depends on the enzyme purification conditions and varies with time, suggesting the coexistence and the interconversion of two forms of the enzyme. We also show that Hnd catalytic properties (Km for H2, diffusion and reaction at the active site of CO and O2) are comparable to those of standard hydrogenases (those which cannot catalyze electron bifurcation). These results suggest that the presence of the additional subunits, needed for electron bifurcation, changes neither the catalytic behavior at the active site, nor the gas diffusion kinetics but induces unusual rates of high potential inactivation/reactivation.
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Affiliation(s)
| | | | - Natalie Payne
- CNRS, Aix Marseille University, BIP, Marseille, France
| | - Arlette Kpebe
- CNRS, Aix Marseille University, BIP, Marseille, France
| | | | | | | | - Myriam Brugna
- CNRS, Aix Marseille University, BIP, Marseille, France
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8
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Zhang Y, Cheng P, Wang Y, Li Y, Su J, Chen Z, Yu X, Shen W. Genetic elucidation of hydrogen signaling in plant osmotic tolerance and stomatal closure via hydrogen sulfide. Free Radic Biol Med 2020; 161:1-14. [PMID: 32987125 DOI: 10.1016/j.freeradbiomed.2020.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Although ample evidence showed that exogenous hydrogen gas (H2) controls a diverse range of physiological functions in both animals and plants, the selective antioxidant mechanism, in some cases, is questioned. Importantly, most of the experiments on the function of H2 in plants were based on pharmacological approaches due to the synthesis pathway(s) in plants are still unclear. Here, we observed that the seedling growth inhibition of Arabidopsis caused by low doses of mannitol could progressively recover by recuperation, accompanied with the increased hydrogenase activity and H2 synthesis. To investigate the functions of endogenous H2, a hydrogenase gene (CrHYD1) for H2 biosynthesis from Chlamydomonas reinhardtii was expressed in Arabidopsis. Transgenic plants could intensify higher H2 synthesis compared with wild type and Arabidopsis transformed with the empty vector, and exhibited enhanced osmotic tolerance in both germination and post-germination stages. In response to mannitol, transgenic plants enhanced L-Cys desulfhydrase (DES)-dependent hydrogen sulfide (H2S) synthesis in guard cells and thereafter stomatal closure. The application of des mutant further highlights H2S acting as a downstream molecule of endogenous H2 control of stomatal closure. These results thus open a new window for increasing plant tolerance to osmotic stress.
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Affiliation(s)
- Yihua Zhang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Center of Hydrogen Science, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pengfei Cheng
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yueqiao Wang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiuchang Su
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziping Chen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiuli Yu
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Center of Hydrogen Science, Shanghai Jiao Tong University, Shanghai, 200240, China.
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9
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Land H, Sekretareva A, Huang P, Redman HJ, Németh B, Polidori N, Mészáros LS, Senger M, Stripp ST, Berggren G. Characterization of a putative sensory [FeFe]-hydrogenase provides new insight into the role of the active site architecture. Chem Sci 2020; 11:12789-12801. [PMID: 34094474 PMCID: PMC8163306 DOI: 10.1039/d0sc03319g] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/19/2020] [Indexed: 12/12/2022] Open
Abstract
[FeFe]-hydrogenases are known for their high rates of hydrogen turnover, and are intensively studied in the context of biotechnological applications. Evolution has generated a plethora of different subclasses with widely different characteristics. The M2e subclass is phylogenetically distinct from previously characterized members of this enzyme family and its biological role is unknown. It features significant differences in domain- and active site architecture, and is most closely related to the putative sensory [FeFe]-hydrogenases. Here we report the first comprehensive biochemical and spectroscopical characterization of an M2e enzyme, derived from Thermoanaerobacter mathranii. As compared to other [FeFe]-hydrogenases characterized to-date, this enzyme displays an increased H2 affinity, higher activation enthalpies for H+/H2 interconversion, and unusual reactivity towards known hydrogenase inhibitors. These properties are related to differences in active site architecture between the M2e [FeFe]-hydrogenase and "prototypical" [FeFe]-hydrogenases. Thus, this study provides new insight into the role of this subclass in hydrogen metabolism and the influence of the active site pocket on the chemistry of the H-cluster.
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Affiliation(s)
- Henrik Land
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
| | - Alina Sekretareva
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
| | - Ping Huang
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
| | - Holly J Redman
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
| | - Brigitta Németh
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
| | - Nakia Polidori
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
| | - Lívia S Mészáros
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
| | - Moritz Senger
- Physical Chemistry, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin Arnimallee 14 DE-14195 Berlin Germany
| | - Sven T Stripp
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin Arnimallee 14 DE-14195 Berlin Germany
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 SE-75120 Uppsala Sweden
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10
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Corrigan PS, Tirsch JL, Silakov A. Investigation of the Unusual Ability of the [FeFe] Hydrogenase from Clostridium beijerinckii to Access an O 2-Protected State. J Am Chem Soc 2020; 142:12409-12419. [PMID: 32580545 DOI: 10.1021/jacs.0c04964] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe] hydrogenases are enzymes capable of producing and oxidizing H2 at staggering submillisecond time scales. A major limitation in applying these enzymes for industrial hydrogen production is their irreversible inactivation by oxygen. Recently, an [FeFe] hydrogenase from Clostridium beijerinckii (CbHydA1) was reported to regain its catalytic activity after exposure to oxygen. In this report, we have determined that artificially matured CbHydA1 is indeed oxygen tolerant in the absence of reducing agents and sulfides by means of reaching an O2-protected state (Hinact). We were also able to generate the Hinact state anaerobically via both chemical and electrochemical oxidation. We use a combination of spectroscopy, electrochemistry, and density functional theory (DFT) to uncover intrinsic properties of the active center of CbHydA1, leading to its unprecedented oxygen tolerance. We have observed that reversible, low-potential oxidation of the active center leads to the protection against O2-induced degradation. The transition between the active oxidized state (Hox) and the Hinact state appears to proceed without any detectable intermediates. We found that the Hinact state is stable for more than 40 h in air, highlighting the remarkable resilience of CbHydA1 to oxygen. Using a combination of DFT and FTIR, we also provide a hypothesis for the chemical identity of the Hinact state. These results demonstrate that CbHydA1 has remarkable stability in the presence of oxygen, which will drive future efforts to engineer more robust catalysts for biofuel production.
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Affiliation(s)
- Patrick S Corrigan
- The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Jonathan L Tirsch
- The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
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11
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Artz JH, Zadvornyy OA, Mulder DW, Keable SM, Cohen AE, Ratzloff MW, Williams SG, Ginovska B, Kumar N, Song J, McPhillips SE, Davidson CM, Lyubimov AY, Pence N, Schut GJ, Jones AK, Soltis SM, Adams MWW, Raugei S, King PW, Peters JW. Tuning Catalytic Bias of Hydrogen Gas Producing Hydrogenases. J Am Chem Soc 2019; 142:1227-1235. [PMID: 31816235 PMCID: PMC8653774 DOI: 10.1021/jacs.9b08756] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogenases display a wide range of catalytic rates and biases in reversible hydrogen gas oxidation catalysis. The interactions of the iron-sulfur-containing catalytic site with the local protein environment are thought to contribute to differences in catalytic reactivity, but this has not been demonstrated. The microbe Clostridium pasteurianum produces three [FeFe]-hydrogenases that differ in "catalytic bias" by exerting a disproportionate rate acceleration in one direction or the other that spans a remarkable 6 orders of magnitude. The combination of high-resolution structural work, biochemical analyses, and computational modeling indicates that protein secondary interactions directly influence the relative stabilization/destabilization of different oxidation states of the active site metal cluster. This selective stabilization or destabilization of oxidation states can preferentially promote hydrogen oxidation or proton reduction and represents a simple yet elegant model by which a protein catalytic site can confer catalytic bias.
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Affiliation(s)
- Jacob H. Artz
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - David W. Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Stephen M. Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Michael W. Ratzloff
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - S. Garrett Williams
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Scott E. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Catherine M. Davidson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Natasha Pence
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Anne K. Jones
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Simone Raugei
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Paul W. King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W. Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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12
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Esselborn J, Kertess L, Apfel UP, Hofmann E, Happe T. Loss of Specific Active-Site Iron Atoms in Oxygen-Exposed [FeFe]-Hydrogenase Determined by Detailed X-ray Structure Analyses. J Am Chem Soc 2019; 141:17721-17728. [PMID: 31609603 DOI: 10.1021/jacs.9b07808] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The [FeFe]-hydrogenases catalyze the uptake and evolution of hydrogen with unmatched speed at low overpotential. However, oxygen induces the degradation of the unique [6Fe-6S] cofactor within the active site, termed the H-cluster. We used X-ray structural analyses to determine possible modes of irreversible oxygen-driven inactivation. To this end, we exposed crystals of the [FeFe]-hydrogenase CpI from Clostridium pasteurianum to oxygen and quantitatively investigated the effects on the H-cluster structure over several time points using multiple data sets, while correlating it to decreases in enzyme activity. Our results reveal the loss of specific Fe atoms from both the diiron (2FeH) and the [4Fe-4S] subcluster (4FeH) of the H-cluster. Within the 2FeH, the Fe atom more distal to the 4FeH is strikingly more affected than the more proximal Fe atom. The 4FeH interconverts to a [2Fe-2S] cluster in parts of the population of active CpIADT, but not in crystals of the inactive apoCpI initially lacking the 2FeH. We thus propose two parallel processes: dissociation of the distal Fe atom and 4FeH interconversion. Both pathways appear to play major roles in the oxidative damage of [FeFe]-hydrogenases under electron-donor deprived conditions probed by our experimental setup.
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13
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Lu Y, Koo J. O 2 sensitivity and H 2 production activity of hydrogenases-A review. Biotechnol Bioeng 2019; 116:3124-3135. [PMID: 31403182 DOI: 10.1002/bit.27136] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 01/24/2023]
Abstract
Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H2 production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O2 sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O2 but proficient in H2 production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O2 tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O2 sensitivity of the enzyme while it catalyzes H2 production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H2 production and other industrial processes, as well as our own perspective on future applications.
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Affiliation(s)
- Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, Republic of Korea
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14
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Liu Y, Mohammadi M, Vashisth H. Diffusion network of CO in FeFe-Hydrogenase. J Chem Phys 2018; 149:204108. [PMID: 30501239 DOI: 10.1063/1.5054877] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
FeFe-hydrogenase is an efficient enzyme to produce H2 under optimal conditions. However, the activity of this enzyme is highly sensitive to the presence of inhibitory gases CO and O2 that cause irreversible damage to the active site. Therefore, a detailed knowledge of the diffusion pathways of these inhibitory gases is necessary to develop strategies for designing novel enzymes that are tolerant to these gases. In this work, we studied the diffusion pathways of CO in the CpI FeFe-hydrogenase from Clostridium pasteurianum. Specifically, we used several enhanced sampling and free-energy simulation methods to reconstruct a three-dimensional free-energy surface for CO diffusion which revealed 45 free-energy minima forming an interconnected network of pathways. We discovered multiple pathways of minimal free-energy as diffusion portals for CO and found that previously suggested hydrophobic pathways are not thermodynamically favorable for CO diffusion. We also observed that the global minimum in the free-energy surface is located in the vicinity of the active-site metal cluster, the H-cluster, which suggests a high-affinity for CO near the active site. Among 19 potential residues that we propose as candidates for future mutagenesis studies, 11 residues are shared with residues that have been previously proposed to increase the tolerance of this enzyme for O2. We hypothesize that these shared candidate residues are potentially useful for designing new variants of this enzyme that are tolerant to both inhibitory gases.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
| | - Mohammadjavad Mohammadi
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
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15
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Rodríguez-Maciá P, Reijerse EJ, van Gastel M, DeBeer S, Lubitz W, Rüdiger O, Birrell JA. Sulfide Protects [FeFe] Hydrogenases From O 2. J Am Chem Soc 2018; 140:9346-9350. [PMID: 30008217 DOI: 10.1021/jacs.8b04339] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe] hydrogenases catalyze proton reduction and hydrogen oxidation with high rates and efficiency under physiological conditions, but are highly oxygen sensitive. The [FeFe] hydrogenase from Desulfovibrio desulfuricans ( DdHydAB) can be purified under air in an oxygen stable inactive state Hoxair. The formation of the Hoxair state in vitro allows the handling of hydrogenases in air, making their implementation in biotechnological applications more feasible. Here, we report a simple and robust protocol for the formation of the Hoxair state in DdHydAB and the [FeFe] hydrogenase from Chlamydomonas reinhardtii, which is based on high potential inactivation in the presence of sulfide.
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Affiliation(s)
- Patricia Rodríguez-Maciá
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Edward J Reijerse
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Maurice van Gastel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany
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16
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Caserta G, Papini C, Adamska-Venkatesh A, Pecqueur L, Sommer C, Reijerse E, Lubitz W, Gauquelin C, Meynial-Salles I, Pramanik D, Artero V, Atta M, Del Barrio M, Faivre B, Fourmond V, Léger C, Fontecave M. Engineering an [FeFe]-Hydrogenase: Do Accessory Clusters Influence O 2 Resistance and Catalytic Bias? J Am Chem Soc 2018; 140:5516-5526. [PMID: 29595965 DOI: 10.1021/jacs.8b01689] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[FeFe]-hydrogenases, HydAs, are unique biocatalysts for proton reduction to H2. However, they suffer from a number of drawbacks for biotechnological applications: size, number and diversity of metal cofactors, oxygen sensitivity. Here we show that HydA from Megasphaera elsdenii (MeHydA) displays significant resistance to O2. Furthermore, we produced a shorter version of this enzyme (MeH-HydA), lacking the N-terminal domain harboring the accessory FeS clusters. As shown by detailed spectroscopic and biochemical characterization, MeH-HydA displays the following interesting properties. First, a functional active site can be assembled in MeH-HydA in vitro, providing the enzyme with excellent hydrogenase activity. Second, the resistance of MeHydA to O2 is conserved in MeH-HydA. Third, MeH-HydA is more biased toward proton reduction than MeHydA, as the result of the truncation changing the rate limiting steps in catalysis. This work shows that it is possible to engineer HydA to generate an active hydrogenase that combines the resistance of the most resistant HydAs and the simplicity of algal HydAs, containing only the H-cluster.
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Affiliation(s)
- Giorgio Caserta
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Cecilia Papini
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Agnieszka Adamska-Venkatesh
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Constanze Sommer
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Edward Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Charles Gauquelin
- LISBP , Université de Toulouse, CNRS, INRA, INSA , Toulouse , France
| | | | - Debajyoti Pramanik
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Melisa Del Barrio
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Vincent Fourmond
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Christophe Léger
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
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17
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Mohammadi M, Vashisth H. Pathways and Thermodynamics of Oxygen Diffusion in [FeFe]-Hydrogenase. J Phys Chem B 2017; 121:10007-10017. [DOI: 10.1021/acs.jpcb.7b06489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mohammadjavad Mohammadi
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
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18
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Morra S, Valetti F, Gilardi G. [FeFe]-hydrogenases as biocatalysts in bio-hydrogen production. RENDICONTI LINCEI 2016. [DOI: 10.1007/s12210-016-0584-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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19
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Rodríguez-Maciá P, Birrell JA, Lubitz W, Rüdiger O. Electrochemical Investigations on the Inactivation of the [FeFe] Hydrogenase from Desulfovibrio desulfuricans
by O2
or Light under Hydrogen-Producing Conditions. Chempluschem 2016; 82:540-545. [DOI: 10.1002/cplu.201600508] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Patricia Rodríguez-Maciá
- Max Planck Institute for Chemical Energy Conversion; Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
| | - James A. Birrell
- Max Planck Institute for Chemical Energy Conversion; Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion; Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion; Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
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20
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Kubas A, Orain C, De Sancho D, Saujet L, Sensi M, Gauquelin C, Meynial-Salles I, Soucaille P, Bottin H, Baffert C, Fourmond V, Best RB, Blumberger J, Léger C. Mechanism of O 2 diffusion and reduction in FeFe hydrogenases. Nat Chem 2016; 9:88-95. [PMID: 27995927 DOI: 10.1038/nchem.2592] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 07/08/2016] [Indexed: 11/09/2022]
Abstract
FeFe hydrogenases are the most efficient H2-producing enzymes. However, inactivation by O2 remains an obstacle that prevents them being used in many biotechnological devices. Here, we combine electrochemistry, site-directed mutagenesis, molecular dynamics and quantum chemical calculations to uncover the molecular mechanism of O2 diffusion within the enzyme and its reactions at the active site. We propose that the partial reversibility of the reaction with O2 results from the four-electron reduction of O2 to water. The third electron/proton transfer step is the bottleneck for water production, competing with formation of a highly reactive OH radical and hydroxylated cysteine. The rapid delivery of electrons and protons to the active site is therefore crucial to prevent the accumulation of these aggressive species during prolonged O2 exposure. These findings should provide important clues for the design of hydrogenase mutants with increased resistance to oxidative damage.
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Affiliation(s)
- Adam Kubas
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK.,Institute of Physical Chemistry, Polish Academy of Science, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Christophe Orain
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - David De Sancho
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,CIC nanoGUNE, Tolosa Hiribidea 76, 20018 Donostia-San Sebastián, Spain.,IKERBASQUE; Basque Foundation for Science, María Díaz de Haro 3, 48013 Bilbao, Spain
| | - Laure Saujet
- Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France.,Institut de Biologie Intégrative de la Cellule I2BC, UMR 9198, CEA, CNRS, Université Paris Sud, F-91191 Gif sur Yvette, France
| | - Matteo Sensi
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Charles Gauquelin
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792, CNRS:UMR 5504, 135 avenue de Rangueil, Toulouse 31077 Cedex 04, France
| | - Isabelle Meynial-Salles
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792, CNRS:UMR 5504, 135 avenue de Rangueil, Toulouse 31077 Cedex 04, France
| | - Philippe Soucaille
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792, CNRS:UMR 5504, 135 avenue de Rangueil, Toulouse 31077 Cedex 04, France
| | - Hervé Bottin
- Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France.,Institut de Biologie Intégrative de la Cellule I2BC, UMR 9198, CEA, CNRS, Université Paris Sud, F-91191 Gif sur Yvette, France
| | - Carole Baffert
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Vincent Fourmond
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
| | - Christophe Léger
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
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21
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Mirmohades M, Adamska-Venkatesh A, Sommer C, Reijerse E, Lomoth R, Lubitz W, Hammarström L. Following [FeFe] Hydrogenase Active Site Intermediates by Time-Resolved Mid-IR Spectroscopy. J Phys Chem Lett 2016; 7:3290-3293. [PMID: 27494400 DOI: 10.1021/acs.jpclett.6b01316] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Time-resolved nanosecond mid-infrared spectroscopy is for the first time employed to study the [FeFe] hydrogenase from Chlamydomonas reinhardtii and to investigate relevant intermediates of the enzyme active site. An actinic 355 nm, 10 ns laser flash triggered photodissociation of a carbonyl group from the CO-inhibited state Hox-CO to form the state Hox, which is an intermediate of the catalytic proton reduction cycle. Time-resolved infrared spectroscopy allowed us to directly follow the subsequent rebinding of the carbonyl, re-forming Hox-CO, and determine the reaction half-life to be t1/2 ≈ 13 ± 5 ms at room temperature. This gives direct information on the dynamics of CO inhibition of the enzyme.
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Affiliation(s)
- Mohammad Mirmohades
- Department of Chemistry - Ångström Laboratory, Uppsala University , Box 523, 751 20 Uppsala, Sweden
| | - Agnieszka Adamska-Venkatesh
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Constanze Sommer
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Reiner Lomoth
- Department of Chemistry - Ångström Laboratory, Uppsala University , Box 523, 751 20 Uppsala, Sweden
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Leif Hammarström
- Department of Chemistry - Ångström Laboratory, Uppsala University , Box 523, 751 20 Uppsala, Sweden
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22
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Mechanism of inhibition of NiFe hydrogenase by nitric oxide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:454-61. [DOI: 10.1016/j.bbabio.2016.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/20/2015] [Accepted: 01/25/2016] [Indexed: 11/23/2022]
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23
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Merrouch M, Hadj‐Saïd J, Domnik L, Dobbek H, Léger C, Dementin S, Fourmond V. O
2
Inhibition of Ni‐Containing CO Dehydrogenase Is Partly Reversible. Chemistry 2015; 21:18934-8. [DOI: 10.1002/chem.201502835] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Meriem Merrouch
- Aix‐Marseille University, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille cedex 20, (France)
| | - Jessica Hadj‐Saïd
- Aix‐Marseille University, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille cedex 20, (France)
| | - Lilith Domnik
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt‐Universität zu Berlin, Unter den Linden 6, 10099 Berlin (Germany)
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt‐Universität zu Berlin, Unter den Linden 6, 10099 Berlin (Germany)
| | - Christophe Léger
- Aix‐Marseille University, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille cedex 20, (France)
| | - Sébastien Dementin
- Aix‐Marseille University, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille cedex 20, (France)
| | - Vincent Fourmond
- Aix‐Marseille University, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille cedex 20, (France)
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24
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Orain C, Saujet L, Gauquelin C, Soucaille P, Meynial-Salles I, Baffert C, Fourmond V, Bottin H, Léger C. Electrochemical Measurements of the Kinetics of Inhibition of Two FeFe Hydrogenases by O2 Demonstrate That the Reaction Is Partly Reversible. J Am Chem Soc 2015; 137:12580-7. [DOI: 10.1021/jacs.5b06934] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Christophe Orain
- Laboratoire de
Bioénergétique et Ingénierie des Protéines,
CNRS/Aix-Marseille Université, 13402 Marseille, France
| | - Laure Saujet
- CEA, Institut
de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France
- Institut
de Biologie Intégrative de la Cellule I2BC, UMR 9198, CEA,
CNRS, Université Paris Sud, F-91191 Gif sur
Yvette, France
| | - Charles Gauquelin
- Université
de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135 CNRS:UMR 5504, avenue de Rangueil, 31077 Toulouse, France
| | - Philippe Soucaille
- Université
de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135 CNRS:UMR 5504, avenue de Rangueil, 31077 Toulouse, France
| | - Isabelle Meynial-Salles
- Université
de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135 CNRS:UMR 5504, avenue de Rangueil, 31077 Toulouse, France
| | - Carole Baffert
- Laboratoire de
Bioénergétique et Ingénierie des Protéines,
CNRS/Aix-Marseille Université, 13402 Marseille, France
| | - Vincent Fourmond
- Laboratoire de
Bioénergétique et Ingénierie des Protéines,
CNRS/Aix-Marseille Université, 13402 Marseille, France
| | - Hervé Bottin
- CEA, Institut
de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France
- Institut
de Biologie Intégrative de la Cellule I2BC, UMR 9198, CEA,
CNRS, Université Paris Sud, F-91191 Gif sur
Yvette, France
| | - Christophe Léger
- Laboratoire de
Bioénergétique et Ingénierie des Protéines,
CNRS/Aix-Marseille Université, 13402 Marseille, France
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25
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Stiebritz MT. MetREx: A protein design approach for the exploration of sequence-reactivity relationships in metalloenzymes. J Comput Chem 2015; 36:553-63. [DOI: 10.1002/jcc.23831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/12/2014] [Accepted: 12/16/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zürich; Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
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26
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Swanson KD, Ratzloff MW, Mulder DW, Artz JH, Ghose S, Hoffman A, White S, Zadvornyy OA, Broderick JB, Bothner B, King PW, Peters JW. [FeFe]-Hydrogenase Oxygen Inactivation Is Initiated at the H Cluster 2Fe Subcluster. J Am Chem Soc 2015; 137:1809-16. [DOI: 10.1021/ja510169s] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin D. Swanson
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Michael W. Ratzloff
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W. Mulder
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jacob H. Artz
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Shourjo Ghose
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Andrew Hoffman
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Spencer White
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Oleg A. Zadvornyy
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B. Broderick
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Brian Bothner
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Paul W. King
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W. Peters
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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27
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Boyd ES, Hamilton TL, Swanson KD, Howells AE, Baxter BK, Meuser JE, Posewitz MC, Peters JW. [FeFe]-hydrogenase abundance and diversity along a vertical redox gradient in Great Salt Lake, USA. Int J Mol Sci 2014; 15:21947-66. [PMID: 25464382 PMCID: PMC4284687 DOI: 10.3390/ijms151221947] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022] Open
Abstract
The use of [FeFe]-hydrogenase enzymes for the biotechnological production of H2 or other reduced products has been limited by their sensitivity to oxygen (O2). Here, we apply a PCR-directed approach to determine the distribution, abundance, and diversity of hydA gene fragments along co-varying salinity and O2 gradients in a vertical water column of Great Salt Lake (GSL), UT. The distribution of hydA was constrained to water column transects that had high salt and relatively low O2 concentrations. Recovered HydA deduced amino acid sequences were enriched in hydrophilic amino acids relative to HydA from less saline environments. In addition, they harbored interesting variations in the amino acid environment of the complex H-cluster metalloenzyme active site and putative gas transfer channels that may be important for both H2 transfer and O2 susceptibility. A phylogenetic framework was created to infer the accessory cluster composition and quaternary structure of recovered HydA protein sequences based on phylogenetic relationships and the gene contexts of known complete HydA sequences. Numerous recovered HydA are predicted to harbor multiple N- and C-terminal accessory iron-sulfur cluster binding domains and are likely to exist as multisubunit complexes. This study indicates an important role for [FeFe]-hydrogenases in the functioning of the GSL ecosystem and provides new target genes and variants for use in identifying O2 tolerant enzymes for biotechnological applications.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
| | - Trinity L Hamilton
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Kevin D Swanson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Alta E Howells
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Bonnie K Baxter
- Department of Biology and the Great Salt Lake Institute, Westminster College, Salt Lake City, UT 84105, USA.
| | - Jonathan E Meuser
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Matthew C Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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28
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Finkelmann AR, Stiebritz MT, Reiher M. Activation Barriers of Oxygen Transformation at the Active Site of [FeFe] Hydrogenases. Inorg Chem 2014; 53:11890-902. [DOI: 10.1021/ic501049z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arndt R. Finkelmann
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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29
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Kubas A, De Sancho D, Best RB, Blumberger J. Aerobic damage to [FeFe]-hydrogenases: activation barriers for the chemical attachment of O2. Angew Chem Int Ed Engl 2014; 53:4081-4. [PMID: 24615978 PMCID: PMC4143129 DOI: 10.1002/anie.201400534] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Indexed: 11/11/2022]
Abstract
[FeFe]-hydrogenases are the best natural hydrogen-producing enzymes but their biotechnological exploitation is hampered by their extreme oxygen sensitivity. The free energy profile for the chemical attachment of O2 to the enzyme active site was investigated by using a range-separated density functional re-parametrized to reproduce high-level ab initio data. An activation free-energy barrier of 13 kcal mol(-1) was obtained for chemical bond formation between the di-iron active site and O2, a value in good agreement with experimental inactivation rates. The oxygen binding can be viewed as an inner-sphere electron-transfer process that is strongly influenced by Coulombic interactions with the proximal cubane cluster and the protein environment. The implications of these results for future mutation studies with the aim of increasing the oxygen tolerance of this enzyme are discussed.
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Affiliation(s)
- Adam Kubas
- Department of Physics and Astronomy, University College LondonGower Street, London WC1E 6BT (UK)
| | - David De Sancho
- Department of Chemistry, Cambridge UniversityLensfield Road, Cambridge CB2 1EW (UK)
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD 20892-0520 (USA)
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College LondonGower Street, London WC1E 6BT (UK)
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30
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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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31
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Kubas A, De Sancho D, Best RB, Blumberger J. Aerobic Damage to [FeFe]-Hydrogenases: Activation Barriers for the Chemical Attachment of O2. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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32
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Engineering Hydrogenases for H2 Production: Bolts and Goals. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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33
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Szot K, de Poulpiquet A, Ciaccafava A, Marques H, Jönsson-Niedziolka M, Niedziolka-Jönsson J, Marken F, Lojou E, Opallo M. Carbon nanoparticulate films as effective scaffolds for mediatorless bioelectrocatalytic hydrogen oxidation. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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34
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Richau KH, Kudahettige RL, Pujic P, Kudahettige NP, Sellstedt A. Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia. J Biosci 2013; 38:703-12. [DOI: 10.1007/s12038-013-9372-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- K H Richau
- Department of Plant Physiology, UPSC, Umea University, S-90187 Umea, Sweden
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35
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Fourmond V, Baffert C, Sybirna K, Dementin S, Abou-Hamdan A, Meynial-Salles I, Soucaille P, Bottin H, Léger C. The mechanism of inhibition by H2 of H2-evolution by hydrogenases. Chem Commun (Camb) 2013; 49:6840-2. [PMID: 23792933 DOI: 10.1039/c3cc43297a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By analysing the results of experiments carried out with two FeFe hydrogenases and several "channel mutants" of a NiFe hydrogenase, we demonstrate that whether or not hydrogen evolution is significantly inhibited by H2 is not a consequence of active site chemistry, but rather relates to H2 transport within the enzyme.
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Affiliation(s)
- Vincent Fourmond
- CNRS, Aix-Marseille Université, BIP UMR 7281, 13009, Marseille, France
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36
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Does the environment around the H-cluster allow coordination of the pendant amine to the catalytic iron center in [FeFe] hydrogenases? Answers from theory. J Biol Inorg Chem 2013; 18:693-700. [DOI: 10.1007/s00775-013-1014-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 05/29/2013] [Indexed: 01/08/2023]
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37
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Fourmond V, Baffert C, Sybirna K, Lautier T, Abou Hamdan A, Dementin S, Soucaille P, Meynial-Salles I, Bottin H, Léger C. Steady-state catalytic wave-shapes for 2-electron reversible electrocatalysts and enzymes. J Am Chem Soc 2013; 135:3926-38. [PMID: 23362993 DOI: 10.1021/ja311607s] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Using direct electrochemistry to learn about the mechanism of electrocatalysts and redox enzymes requires that kinetic models be developed. Here we thoroughly discuss the interpretation of electrochemical signals obtained with adsorbed enzymes and molecular catalysts that can reversibly convert their substrate and product. We derive analytical relations between electrochemical observables (overpotentials for catalysis in each direction, positions, and magnitudes of the features of the catalytic wave) and the characteristics of the catalytic cycle (redox properties of the catalytic intermediates, kinetics of intramolecular and interfacial electron transfer, etc.). We discuss whether or not the position of the wave is determined by the redox potential of a redox relay when intramolecular electron transfer is slow. We demonstrate that there is no simple relation between the reduction potential of the active site and the catalytic bias of the enzyme, defined as the ratio of the oxidative and reductive limiting currents; this explains the recent experimental observation that the catalytic bias of NiFe hydrogenase depends on steps of the catalytic cycle that occur far from the active site [Abou Hamdan et al., J. Am. Chem. Soc. 2012, 134, 8368]. On the experimental side, we examine which models can best describe original data obtained with various NiFe and FeFe hydrogenases, and we illustrate how the presence of an intramolecular electron transfer chain affects the voltammetry by comparing the data obtained with the FeFe hydrogenases from Chlamydomonas reinhardtii and Clostridium acetobutylicum, only one of which has a chain of redox relays. The considerations herein will help the interpretation of electrochemical data previously obtained with various other bidirectional oxidoreductases, and, possibly, synthetic inorganic catalysts.
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Affiliation(s)
- Vincent Fourmond
- CNRS, Aix-Marseille Univ, BIP UMR 7281, IMM FR 3479, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France
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38
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Oxygen tolerance of an in silico-designed bioinspired hydrogen-evolving catalyst in water. Proc Natl Acad Sci U S A 2013; 110:2017-22. [PMID: 23341607 DOI: 10.1073/pnas.1215149110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Certain bacterial enzymes, the diiron hydrogenases, have turnover numbers for hydrogen production from water as large as 10(4)/s. Their much smaller common active site, composed of earth-abundant materials, has a structure that is an attractive starting point for the design of a practical catalyst for electrocatalytic or solar photocatalytic hydrogen production from water. In earlier work, our group has reported the computational design of [FeFe](P)/FeS(2), a hydrogenase-inspired catalyst/electrode complex, which is efficient and stable throughout the production cycle. However, the diiron hydrogenases are highly sensitive to ambient oxygen by a mechanism not yet understood in detail. An issue critical for practical use of [FeFe](P)/FeS(2) is whether this catalyst/electrode complex is tolerant to the ambient oxygen. We report demonstration by ab initio simulations that the complex is indeed tolerant to dissolved oxygen over timescales long enough for practical application, reducing it efficiently. This promising hydrogen-producing catalyst, composed of earth-abundant materials and with a diffusion-limited rate in acidified water, is efficient as well as oxygen tolerant.
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39
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Baffert C, Sybirna K, Ezanno P, Lautier T, Hajj V, Meynial-Salles I, Soucaille P, Bottin H, Léger C. Covalent attachment of FeFe hydrogenases to carbon electrodes for direct electron transfer. Anal Chem 2012; 84:7999-8005. [PMID: 22891965 DOI: 10.1021/ac301812s] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Direct electron transfer between enzymes and electrodes is now commonly achieved, but obtaining protein films that are very stable may be challenging. This is particularly crucial in the case of hydrogenases, the enzymes that catalyze the biological conversion between dihydrogen and protons, because the instability of the hydrogenase films may prevent the use of these enzymes as electrocatalysts of H(2) oxidation and production in biofuel cells and photoelectrochemical cells. Here we show that two different FeFe hydrogenases (from Chamydomonas reinhardtii and Clostridium acetobutylicum) can be covalently attached to functionalized pyrolytic graphite electrodes using peptidic coupling. In both cases, a surface patch of lysine residues makes it possible to favor an orientation that is efficient for fast, direct electron transfer. High hydrogen-oxidation current densities are maintained for up to one week, the only limitation being the intrinsic stability of the enzyme. We also show that covalent attachment has no effect on the catalytic properties of the enzyme, which means that this strategy can also used be for electrochemical studies of the catalytic mechanism.
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Affiliation(s)
- Carole Baffert
- CNRS, Aix Marseille Université, BIP UMR, IMM FR, France.
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40
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Hong G, Pachter R. Inhibition of biocatalysis in [Fe-Fe] hydrogenase by oxygen: molecular dynamics and density functional theory calculations. ACS Chem Biol 2012; 7:1268-75. [PMID: 22563793 DOI: 10.1021/cb3001149] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Designing O(2)-tolerant hydrogenases is a major challenge in applying [Fe-Fe]H(2)ases for H(2) production. The inhibition involves transport of oxygen through the enzyme to the H-cluster, followed by binding and subsequent deactivation of the active site. To explore the nature of the oxygen diffusion channel for the hydrogenases from Desulfovibrio desulfuricans (Dd) and Clostridium pasteurianum (Cp), empirical molecular dynamics simulations were performed. The dynamic nature of the oxygen pathways in Dd and Cp was elucidated, and insight is provided, in part, into the experimental observation on the difference of oxygen inhibition in Dd and the hydrogenase from Clostridium acetobutylicum (Ca, assumed homologous to Cp). Further, to gain an understanding of the mechanism of oxygen inhibition of the [Fe-Fe]H(2)ase, density functional theory calculations of model compounds composed of the H-cluster and proximate amino acids are reported. Confirmation of the experimentally based suppositions on inactivation by oxygen at the [2Fe](H) domain is provided, validating the model compounds used and oxidation state assumptions, further explaining the mode of damage. This unified approach provides insight into oxygen diffusion in the enzyme, followed by deactivation at the H-cluster.
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Affiliation(s)
- Gongyi Hong
- Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433,
United States
- General Dynamics Information Technology, Inc., Dayton, Ohio 45433, United
States
| | - Ruth Pachter
- Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433,
United States
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41
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Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation. Proc Natl Acad Sci U S A 2012; 109:6399-404. [PMID: 22493222 DOI: 10.1073/pnas.1121176109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[NiFe]-hydrogenases are fascinating biological catalysts with potential application in biofuel cells. However, a severe problem in practical application is the strong sensitivity of hydrogenase to gaseous inhibitor molecules such as CO and O(2). Recently, a number of successful protein engineering studies have been reported that aimed at lowering the access of diatomic inhibitors to the active site pocket, but the molecular mechanism conferring increased resistance remained unclear. Here we use a multiscale simulation approach combining molecular dynamics with a master equation formalism to explain the steady drop in CO diffusion rate observed for the mutants V74M L122A, V74M L122M, and V74M of Desulfovibrio fructosovorans [NiFe]-hydrogenase. We find that diffusion in these variants is controlled by two gates, one between residues 74 and 476 and the other between residues 74 and 122. The existence of two control points in different locations explains why the reduction in the experimental diffusion rate does not simply correlate with the width of the main gas channel. We also find that in the more effective mutation (V74M) CO molecules are still able to reach the active site through transitions that are gated by the microsecond dihedral motions of the side chain of R476 and the thermal fluctuations of the width of the gas channel defined by M74 and L122. Reflecting on the molecular information gained from simulation, we discuss future mutation experiments that could further lower the diffusion rates of small ligands inhibiting [NiFe]-hydrogenase.
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42
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43
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Abstract
The H(2)-evolving potential of [FeFe] hydrogenases is severely limited by the oxygen sensitivity of this class of enzymes. Recent experimental studies on hydrogenase from C. reinhardtii point to O(2)-induced structural changes in the [Fe(4)S(4)] subsite of the H cluster. Here, we investigate the mechanistic basis of this observation by means of density functional theory. Unexpectedly, we find that the isolated H cluster shows a pathological catalytic activity for the formation of reactive oxygen species such as O(2)(-) and HO(2)(-). After protonation of O(2)(-), an OOH radical may coordinate to the Fe atoms of the cubane, whereas H(2)O(2) specifically reacts with the S atoms of the cubane-coordinating cysteine residues. Both pathways are accompanied by significant structural distortions that compromise cluster integrity and thus catalytic activity. These results explain the experimental observation that O(2)-induced inhibition is accompanied by distortions of the [Fe(4)S(4)] moiety and account for the irreversibility of this process.
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Affiliation(s)
- Marta K. Bruska
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
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44
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Madden C, Vaughn MD, Díez-Pérez I, Brown KA, King PW, Gust D, Moore AL, Moore TA. Catalytic Turnover of [FeFe]-Hydrogenase Based on Single-Molecule Imaging. J Am Chem Soc 2011; 134:1577-82. [DOI: 10.1021/ja207461t] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher Madden
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Michael D. Vaughn
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Ismael Díez-Pérez
- Center for Bioelectronics and Biosensors, Biodesign Institute and Department of Electrical Engineering, Arizona State University, Tempe, Arizona 85287, United States
- Department of Physical Chemistry, University of Barcelona, Barcelona, Spain 08028
| | - Katherine A. Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Paul W. King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Devens Gust
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Ana L. Moore
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas A. Moore
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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45
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Lambertz C, Leidel N, Havelius KGV, Noth J, Chernev P, Winkler M, Happe T, Haumann M. O2 reactions at the six-iron active site (H-cluster) in [FeFe]-hydrogenase. J Biol Chem 2011; 286:40614-23. [PMID: 21930709 DOI: 10.1074/jbc.m111.283648] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Irreversible inhibition by molecular oxygen (O(2)) complicates the use of [FeFe]-hydrogenases (HydA) for biotechnological hydrogen (H(2)) production. Modification by O(2) of the active site six-iron complex denoted as the H-cluster ([4Fe4S]-2Fe(H)) of HydA1 from the green alga Chlamydomonas reinhardtii was characterized by x-ray absorption spectroscopy at the iron K-edge. In a time-resolved approach, HydA1 protein samples were prepared after increasing O(2) exposure periods at 0 °C. A kinetic analysis of changes in their x-ray absorption near edge structure and extended X-ray absorption fine structure spectra revealed three phases of O(2) reactions. The first phase (τ(1) ≤ 4 s) is characterized by the formation of an increased number of Fe-O,C bonds, elongation of the Fe-Fe distance in the binuclear unit (2Fe(H)), and oxidation of one iron ion. The second phase (τ(2) ≈ 15 s) causes a ∼50% decrease of the number of ∼2.7-Å Fe-Fe distances in the [4Fe4S] subcluster and the oxidation of one more iron ion. The final phase (τ(3) ≤ 1000 s) leads to the disappearance of most Fe-Fe and Fe-S interactions and further iron oxidation. These results favor a reaction sequence, which involves 1) oxygenation at 2Fe(H(+)) leading to the formation of a reactive oxygen species-like superoxide (O(2)(-)), followed by 2) H-cluster inactivation and destabilization due to ROS attack on the [4Fe4S] cluster to convert it into an apparent [3Fe4S](+) unit, leading to 3) complete O(2)-induced degradation of the remainders of the H-cluster. This mechanism suggests that blocking of ROS diffusion paths and/or altering the redox potential of the [4Fe4S] cubane by genetic engineering may yield improved O(2) tolerance in [FeFe]-hydrogenase.
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Affiliation(s)
- Camilla Lambertz
- Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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46
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A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism. J Biol Eng 2011; 5:7. [PMID: 21615937 PMCID: PMC3130634 DOI: 10.1186/1754-1611-5-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/26/2011] [Indexed: 01/11/2023] Open
Abstract
Background FeFe-hydrogenases are the most active class of H2-producing enzymes known in nature and may have important applications in clean H2 energy production. Many potential uses are currently complicated by a crucial weakness: the active sites of all known FeFe-hydrogenases are irreversibly inactivated by O2. Results We have developed a synthetic metabolic pathway in E. coli that links FeFe-hydrogenase activity to the production of the essential amino acid cysteine. Our design includes a complementary host strain whose endogenous redox pool is insulated from the synthetic metabolic pathway. Host viability on a selective medium requires hydrogenase expression, and moderate O2 levels eliminate growth. This pathway forms the basis for a genetic selection for O2 tolerance. Genetically selected hydrogenases did not show improved stability in O2 and in many cases had lost H2 production activity. The isolated mutations cluster significantly on charged surface residues, suggesting the evolution of binding surfaces that may accelerate hydrogenase electron transfer. Conclusions Rational design can optimize a fully heterologous three-component pathway to provide an essential metabolic flux while remaining insulated from the endogenous redox pool. We have developed a number of convenient in vivo assays to aid in the engineering of synthetic H2 metabolism. Our results also indicate a H2-independent redox activity in three different FeFe-hydrogenases, with implications for the future directed evolution of H2-activating catalysts.
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Baffert C, Bertini L, Lautier T, Greco C, Sybirna K, Ezanno P, Etienne E, Soucaille P, Bertrand P, Bottin H, Meynial-Salles I, De Gioia L, Léger C. CO disrupts the reduced H-cluster of FeFe hydrogenase. A combined DFT and protein film voltammetry study. J Am Chem Soc 2011; 133:2096-9. [PMID: 21271703 DOI: 10.1021/ja110627b] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Carbon monoxide is often described as a competitive inhibitor of FeFe hydrogenases, and it is used for probing H(2) binding to synthetic or in silico models of the active site H-cluster. Yet it does not always behave as a simple inhibitor. Using an original approach which combines accurate electrochemical measurements and theoretical calculations, we elucidate the mechanism by which, under certain conditions, CO binding can cause permanent damage to the H-cluster. Like in the case of oxygen inhibition, the reaction with CO engages the entire H-cluster, rather than only the Fe(2) subsite.
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Affiliation(s)
- Carole Baffert
- Bioenergetics and Engineering of Proteins, CNRS, UPR 9036, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Lautier T, Ezanno P, Baffert C, Fourmond V, Cournac L, Fontecilla-Camps JC, Soucaille P, Bertrand P, Meynial-Salles I, Léger C. The quest for a functional substrate access tunnel in FeFe hydrogenase. Faraday Discuss 2011; 148:385-407; discussion 421-41. [DOI: 10.1039/c004099c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Morra S, Valetti F, Sadeghi SJ, King PW, Meyer T, Gilardi G. Direct electrochemistry of an [FeFe]-hydrogenase on a TiO2 Electrode. Chem Commun (Camb) 2011; 47:10566-8. [DOI: 10.1039/c1cc14535e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Krassen H, Ott S, Heberle J. In vitro hydrogen production—using energy from the sun. Phys Chem Chem Phys 2011; 13:47-57. [DOI: 10.1039/c0cp01163k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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