1
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Sohraby F, Nunes-Alves A. Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase. J Chem Inf Model 2024; 64:4193-4203. [PMID: 38728115 PMCID: PMC11134402 DOI: 10.1021/acs.jcim.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
[NiFe] hydrogenases can act as efficient catalysts for hydrogen oxidation and biofuel production. However, some [NiFe] hydrogenases are inhibited by gas molecules present in the environment, such as O2 and CO. One strategy to engineer [NiFe] hydrogenases and achieve O2- and CO-tolerant enzymes is by introducing point mutations to block the access of inhibitors to the catalytic site. In this work, we characterized the unbinding pathways of CO in the complex with the wild-type and 10 different mutants of [NiFe] hydrogenase from Desulfovibrio fructosovorans using τ-random accelerated molecular dynamics (τRAMD) to enhance the sampling of unbinding events. The ranking provided by the relative residence times computed with τRAMD is in agreement with experiments. Extensive data analysis of the simulations revealed that from the two bottlenecks proposed in previous studies for the transit of gas molecules (residues 74 and 122 and residues 74 and 476), only one of them (residues 74 and 122) effectively modulates diffusion and residence times for CO. We also computed pathway probabilities for the unbinding of CO, O2, and H2 from the wild-type [NiFe] hydrogenase, and we observed that while the most probable pathways are the same, the secondary pathways are different. We propose that introducing mutations to block the most probable paths, in combination with mutations to open the main secondary path used by H2, can be a feasible strategy to achieve CO and O2 resistance in the [NiFe] hydrogenase from Desulfovibrio fructosovorans.
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Affiliation(s)
- Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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2
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Brocks C, Das CK, Duan J, Yadav S, Apfel UP, Ghosh S, Hofmann E, Winkler M, Engelbrecht V, Schäfer LV, Happe T. A Dynamic Water Channel Affects O 2 Stability in [FeFe]-Hydrogenases. CHEMSUSCHEM 2024; 17:e202301365. [PMID: 37830175 DOI: 10.1002/cssc.202301365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023]
Abstract
[FeFe]-hydrogenases are capable of reducing protons at a high rate. However, molecular oxygen (O2 ) induces the degradation of their catalytic cofactor, the H-cluster, which consists of a cubane [4Fe4S] subcluster (4FeH ) and a unique diiron moiety (2FeH ). Previous attempts to prevent O2 -induced damage have focused on enhancing the protein's sieving effect for O2 by blocking the hydrophobic gas channels that connect the protein surface and the 2FeH . In this study, we aimed to block an O2 diffusion pathway and shield 4FeH instead. Molecular dynamics (MD) simulations identified a novel water channel (WH ) surrounding the H-cluster. As this hydrophilic path may be accessible for O2 molecules we applied site-directed mutagenesis targeting amino acids along WH in proximity to 4FeH to block O2 diffusion. Protein film electrochemistry experiments demonstrate increased O2 stabilities for variants G302S and S357T, and MD simulations based on high-resolution crystal structures confirmed an enhanced local sieving effect for O2 in the environment of the 4FeH in both cases. The results strongly suggest that, in wild type proteins, O2 diffuses from the 4FeH to the 2FeH . These results reveal new strategies for improving the O2 stability of [FeFe]-hydrogenases by focusing on the O2 diffusion network near the active site.
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Affiliation(s)
- Claudia Brocks
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Chandan K Das
- Faculty of Chemistry and Biochemistry, Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Shanika Yadav
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Ulf-Peter Apfel
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Subhasri Ghosh
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Faculty of Biology and Biotechnology, X-ray structure analysis of proteins, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Martin Winkler
- Electrobiotechnology, TUM Campus Straubing, Schulgasse 22, Straubing, 94315, Germany
| | - Vera Engelbrecht
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Lars V Schäfer
- Faculty of Chemistry and Biochemistry, Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
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3
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Schumann C, Fernández Méndez J, Berggren G, Lindblad P. Novel concepts and engineering strategies for heterologous expression of efficient hydrogenases in photosynthetic microorganisms. Front Microbiol 2023; 14:1179607. [PMID: 37502399 PMCID: PMC10369191 DOI: 10.3389/fmicb.2023.1179607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/09/2023] [Indexed: 07/29/2023] Open
Abstract
Hydrogen is considered one of the key enablers of the transition towards a sustainable and net-zero carbon economy. When produced from renewable sources, hydrogen can be used as a clean and carbon-free energy carrier, as well as improve the sustainability of a wide range of industrial processes. Photobiological hydrogen production is considered one of the most promising technologies, avoiding the need for renewable electricity and rare earth metal elements, the demands for which are greatly increasing due to the current simultaneous electrification and decarbonization goals. Photobiological hydrogen production employs photosynthetic microorganisms to harvest solar energy and split water into molecular oxygen and hydrogen gas, unlocking the long-pursued target of solar energy storage. However, photobiological hydrogen production has to-date been constrained by several limitations. This review aims to discuss the current state-of-the art regarding hydrogenase-driven photobiological hydrogen production. Emphasis is placed on engineering strategies for the expression of improved, non-native, hydrogenases or photosynthesis re-engineering, as well as their combination as one of the most promising pathways to develop viable large-scale hydrogen green cell factories. Herein we provide an overview of the current knowledge and technological gaps curbing the development of photobiological hydrogenase-driven hydrogen production, as well as summarizing the recent advances and future prospects regarding the expression of non-native hydrogenases in cyanobacteria and green algae with an emphasis on [FeFe] hydrogenases.
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Affiliation(s)
- Conrad Schumann
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Jorge Fernández Méndez
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
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4
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Martini MA, Bikbaev K, Pang Y, Lorent C, Wiemann C, Breuer N, Zebger I, DeBeer S, Span I, Bjornsson R, Birrell JA, Rodríguez-Maciá P. Binding of exogenous cyanide reveals new active-site states in [FeFe] hydrogenases. Chem Sci 2023; 14:2826-2838. [PMID: 36937599 PMCID: PMC10016341 DOI: 10.1039/d2sc06098a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/07/2023] [Indexed: 02/10/2023] Open
Abstract
[FeFe] hydrogenases are highly efficient metalloenyzmes for hydrogen conversion. Their active site cofactor (the H-cluster) is composed of a canonical [4Fe-4S] cluster ([4Fe-4S]H) linked to a unique organometallic di-iron subcluster ([2Fe]H). In [2Fe]H the two Fe ions are coordinated by a bridging 2-azapropane-1,3-dithiolate (ADT) ligand, three CO and two CN- ligands, leaving an open coordination site on one Fe where substrates (H2 and H+) as well as inhibitors (e.g. O2, CO, H2S) may bind. Here, we investigate two new active site states that accumulate in [FeFe] hydrogenase variants where the cysteine (Cys) in the proton transfer pathway is mutated to alanine (Ala). Our experimental data, including atomic resolution crystal structures and supported by calculations, suggest that in these two states a third CN- ligand is bound to the apical position of [2Fe]H. These states can be generated both by "cannibalization" of CN- from damaged [2Fe]H subclusters as well as by addition of exogenous CN-. This is the first detailed spectroscopic and computational characterisation of the interaction of exogenous CN- with [FeFe] hydrogenases. Similar CN--bound states can also be generated in wild-type hydrogenases, but do not form as readily as with the Cys to Ala variants. These results highlight how the interaction between the first amino acid in the proton transfer pathway and the active site tunes ligand binding to the open coordination site and affects the electronic structure of the H-cluster.
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Affiliation(s)
- Maria Alessandra Martini
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany
| | - Konstantin Bikbaev
- Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg Bioinorganic Chemistry Erlangen Germany
| | - Yunjie Pang
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany
- College of Chemistry, Beijing Normal University 100875 Beijing China
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Charlotte Wiemann
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
- Ruanda-Zentrum und Büro für Afrika-Kooperationen, Universität Koblenz-Landau, Universitätsstraße 1 56070 Koblenz Germany
| | - Nina Breuer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Serena DeBeer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany
| | - Ingrid Span
- Department of Chemistry and Pharmacy, Friedrich Alexander University Erlangen-Nürnberg Bioinorganic Chemistry Erlangen Germany
| | - Ragnar Bjornsson
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux 17 Rue des Martyrs F-38054 Grenoble Cedex France
| | - James A Birrell
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany
- School of Life Sciences, University of Essex Colchester CO4 3SQ UK
| | - Patricia Rodríguez-Maciá
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QR UK
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5
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Morra S. Fantastic [FeFe]-Hydrogenases and Where to Find Them. Front Microbiol 2022; 13:853626. [PMID: 35308355 PMCID: PMC8924675 DOI: 10.3389/fmicb.2022.853626] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/10/2022] [Indexed: 01/01/2023] Open
Abstract
[FeFe]-hydrogenases are complex metalloenzymes, key to microbial energy metabolism in numerous organisms. During anaerobic metabolism, they dissipate excess reducing equivalents by using protons from water as terminal electron acceptors, leading to hydrogen production. This reaction is coupled to reoxidation of specific redox partners [ferredoxins, NAD(P)H or cytochrome c3], that can be used either individually or simultaneously (via flavin-based electron bifurcation). [FeFe]-hydrogenases also serve additional physiological functions such as H2 uptake (oxidation), H2 sensing, and CO2 fixation. This broad functional spectrum is enabled by a modular architecture and vast genetic diversity, which is not fully explored and understood. This Mini Review summarises recent advancements in identifying and characterising novel [FeFe]-hydrogenases, which has led to expanding our understanding of their multiple roles in metabolism and functional mechanisms. For example, while numerous well-known [FeFe]-hydrogenases are irreversibly damaged by oxygen, some newly discovered enzymes display intrinsic tolerance. These findings demonstrate that oxygen sensitivity varies between different [FeFe]-hydrogenases: in some cases, protection requires the presence of exogenous compounds such as carbon monoxide or sulphide, while in other cases it is a spontaneous built-in mechanism that relies on a reversible conformational change. Overall, it emerges that additional research is needed to characterise new [FeFe]-hydrogenases as this will reveal further details on the physiology and mechanisms of these enzymes that will enable potential impactful applications.
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Affiliation(s)
- Simone Morra
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
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6
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Martini MA, Rüdiger O, Breuer N, Nöring B, DeBeer S, Rodríguez-Maciá P, Birrell JA. The Nonphysiological Reductant Sodium Dithionite and [FeFe] Hydrogenase: Influence on the Enzyme Mechanism. J Am Chem Soc 2021; 143:18159-18171. [PMID: 34668697 PMCID: PMC8569811 DOI: 10.1021/jacs.1c07322] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[FeFe] hydrogenases are highly active enzymes for interconverting protons and electrons with hydrogen (H2). Their active site H-cluster is formed of a canonical [4Fe-4S] cluster ([4Fe-4S]H) covalently attached to a unique [2Fe] subcluster ([2Fe]H), where both sites are redox active. Heterolytic splitting and formation of H2 takes place at [2Fe]H, while [4Fe-4S]H stores electrons. The detailed catalytic mechanism of these enzymes is under intense investigation, with two dominant models existing in the literature. In one model, an alternative form of the active oxidized state Hox, named HoxH, which forms at low pH in the presence of the nonphysiological reductant sodium dithionite (NaDT), is believed to play a crucial role. HoxH was previously suggested to have a protonated [4Fe-4S]H. Here, we show that HoxH forms by simple addition of sodium sulfite (Na2SO3, the dominant oxidation product of NaDT) at low pH. The low pH requirement indicates that sulfur dioxide (SO2) is the species involved. Spectroscopy supports binding at or near [4Fe-4S]H, causing its redox potential to increase by ∼60 mV. This potential shift detunes the redox potentials of the subclusters of the H-cluster, lowering activity, as shown in protein film electrochemistry (PFE). Together, these results indicate that HoxH and its one-electron reduced counterpart Hred'H are artifacts of using a nonphysiological reductant, and not crucial catalytic intermediates. We propose renaming these states as the "dithionite (DT) inhibited" states Hox-DTi and Hred-DTi. The broader potential implications of using a nonphysiological reductant in spectroscopic and mechanistic studies of enzymes are highlighted.
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Affiliation(s)
- Maria Alessandra Martini
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Nina Breuer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Birgit Nöring
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Patricia Rodríguez-Maciá
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, U.K
| | - James A Birrell
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
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7
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Laun K, Baranova I, Duan J, Kertess L, Wittkamp F, Apfel UP, Happe T, Senger M, Stripp ST. Site-selective protonation of the one-electron reduced cofactor in [FeFe]-hydrogenase. Dalton Trans 2021; 50:3641-3650. [PMID: 33629081 DOI: 10.1039/d1dt00110h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogenases are bidirectional redox enzymes that catalyze hydrogen turnover in archaea, bacteria, and algae. While all types of hydrogenase show H2 oxidation activity, [FeFe]-hydrogenases are excellent H2 evolution catalysts as well. Their active site cofactor comprises a [4Fe-4S] cluster covalently linked to a diiron site equipped with carbon monoxide and cyanide ligands. The active site niche is connected with the solvent by two distinct proton transfer pathways. To analyze the catalytic mechanism of [FeFe]-hydrogenase, we employ operando infrared spectroscopy and infrared spectro-electrochemistry. Titrating the pH under H2 oxidation or H2 evolution conditions reveals the influence of site-selective protonation on the equilibrium of reduced cofactor states. Governed by pKa differences across the active site niche and proton transfer pathways, we find that individual electrons are stabilized either at the [4Fe-4S] cluster (alkaline pH values) or at the diiron site (acidic pH values). This observation is discussed in the context of the complex interdependence of hydrogen turnover and bulk pH.
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Affiliation(s)
- Konstantin Laun
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany. sven.stripp@fu-berlin and Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | - Iuliia Baranova
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany. sven.stripp@fu-berlin and Faculty of Physics, St. Petersburg State University, 198504 St. Petersburg, Russian Federation
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Leonie Kertess
- Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Florian Wittkamp
- Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany and Fraunhofer UMSICHT, 46047 Oberhausen, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Moritz Senger
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany. sven.stripp@fu-berlin and Department of Chemistry, Uppsala University, 75120 Uppsala, Sweden.
| | - Sven T Stripp
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany. sven.stripp@fu-berlin
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8
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Land H, Senger M, Berggren G, Stripp ST. Current State of [FeFe]-Hydrogenase Research: Biodiversity and Spectroscopic Investigations. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01614] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Henrik Land
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
| | - Moritz Senger
- Physical Chemistry, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
| | - Sven T. Stripp
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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9
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Domene C, Jorgensen C, Schofield CJ. Mechanism of Molecular Oxygen Diffusion in a Hypoxia-Sensing Prolyl Hydroxylase Using Multiscale Simulation. J Am Chem Soc 2020; 142:2253-2263. [DOI: 10.1021/jacs.9b09236] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Carmen Domene
- Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, United Kingdom
- Department of Chemistry, Britannia House, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
- Department of Chemistry, University of Bath, Claverton Down Bath BA2 7AY, United Kingdom
| | - Christian Jorgensen
- Department of Chemistry, Britannia House, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, United Kingdom
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10
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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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11
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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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12
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Mebs S, Duan J, Wittkamp F, Stripp ST, Happe T, Apfel UP, Winkler M, Haumann M. Differential Protonation at the Catalytic Six-Iron Cofactor of [FeFe]-Hydrogenases Revealed by 57Fe Nuclear Resonance X-ray Scattering and Quantum Mechanics/Molecular Mechanics Analyses. Inorg Chem 2019; 58:4000-4013. [PMID: 30802044 DOI: 10.1021/acs.inorgchem.9b00100] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe]-hydrogenases are efficient biological hydrogen conversion catalysts and blueprints for technological fuel production. The relations between substrate interactions and electron/proton transfer events at their unique six-iron cofactor (H-cluster) need to be elucidated. The H-cluster comprises a four-iron cluster, [4Fe4S], linked to a diiron complex, [FeFe]. We combined 57Fe-specific X-ray nuclear resonance scattering experiments (NFS, nuclear forward scattering; NRVS, nuclear resonance vibrational spectroscopy) with quantum-mechanics/molecular-mechanics computations to study the [FeFe]-hydrogenase HYDA1 from a green alga. Selective 57Fe labeling at only [4Fe4S] or [FeFe], or at both subcomplexes was achieved by protein expression with a 57Fe salt and in vitro maturation with a synthetic diiron site precursor containing 57Fe. H-cluster states were populated under infrared spectroscopy control. NRVS spectral analyses facilitated assignment of the vibrational modes of the cofactor species. This approach revealed the H-cluster structure of the oxidized state (Hox) with a bridging carbon monoxide at [FeFe] and ligand rearrangement in the CO-inhibited state (Hox-CO). Protonation at a cysteine ligand of [4Fe4S] in the oxidized state occurring at low pH (HoxH) was indicated, in contrast to bridging hydride binding at [FeFe] in a one-electron reduced state (Hred). These findings are direct evidence for differential protonation either at the four-iron or diiron subcomplex of the H-cluster. NFS time-traces provided Mössbauer parameters such as the quadrupole splitting energy, which differ among cofactor states, thereby supporting selective protonation at either subcomplex. In combination with data for reduced states showing similar [4Fe4S] protonation as HoxH without (Hred') or with (Hhyd) a terminal hydride at [FeFe], our results imply that coordination geometry dynamics at the diiron site and proton-coupled electron transfer to either the four-iron or the diiron subcomplex discriminate catalytic and regulatory functions of [FeFe]-hydrogenases. We support a reaction cycle avoiding diiron site geometry changes during rapid H2 turnover.
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Affiliation(s)
| | | | | | | | | | - Ulf-Peter Apfel
- Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
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13
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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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14
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Koo J, Swartz JR. System analysis and improved [FeFe] hydrogenase O2 tolerance suggest feasibility for photosynthetic H2 production. Metab Eng 2018; 49:21-27. [DOI: 10.1016/j.ymben.2018.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/27/2018] [Accepted: 04/29/2018] [Indexed: 11/16/2022]
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15
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Pham CC, Mulder DW, Pelmenschikov V, King PW, Ratzloff MW, Wang H, Mishra N, Alp EE, Zhao J, Hu MY, Tamasaku K, Yoda Y, Cramer SP. Terminal Hydride Species in [FeFe]-Hydrogenases Are Vibrationally Coupled to the Active Site Environment. Angew Chem Int Ed Engl 2018; 57:10605-10609. [PMID: 29923293 PMCID: PMC6812543 DOI: 10.1002/anie.201805144] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 01/01/2023]
Abstract
A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe-H/D bending modes in CrHydA1 [FeFe]-hydrogenase Cys-to-Ser variant C169S. Mutagenesis of cysteine to serine at position 169 changes the functional group adjacent to the H-cluster from a -SH to -OH, thus altering the proton transfer pathway. The catalytic activity of C169S is significantly reduced compared to that of native CrHydA1, presumably owing to less efficient proton transfer to the H-cluster. This mutation enabled effective capture of a hydride/deuteride intermediate and facilitated direct detection of the Fe-H/D normal modes. We observed a significant shift to higher frequency in an Fe-H bending mode of the C169S variant, as compared to previous findings with reconstituted native and oxadithiolate (ODT)-substituted CrHydA1. On the basis of DFT calculations, we propose that this shift is caused by the stronger interaction of the -OH group of C169S with the bridgehead -NH- moiety of the active site, as compared to that of the -SH group of C169 in the native enzyme.
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Affiliation(s)
- Cindy C. Pham
- Department of Chemistry, UC Davis, One Shields Ave, Davis, CA 95616, USA
| | - David W. Mulder
- National Renewable Energy Laboratory, 15013 Denver W. Pkwy., Golden, CO 80401, USA
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Paul W. King
- National Renewable Energy Laboratory, 15013 Denver W. Pkwy., Golden, CO 80401, USA
| | - Michael W. Ratzloff
- National Renewable Energy Laboratory, 15013 Denver W. Pkwy., Golden, CO 80401, USA
| | - Hongxin Wang
- Department of Chemistry, UC Davis, One Shields Ave, Davis, CA 95616, USA
| | - Nakul Mishra
- Department of Chemistry, UC Davis, One Shields Ave, Davis, CA 95616, USA
| | - Esen E. Alp
- Building 401, Argonne National Laboratory, 9700 Cass Ave, Lemont, IL 60439, USA
| | - Jiyong Zhao
- Building 401, Argonne National Laboratory, 9700 Cass Ave, Lemont, IL 60439, USA
| | - Michael Y. Hu
- Building 401, Argonne National Laboratory, 9700 Cass Ave, Lemont, IL 60439, USA
| | - Kenji Tamasaku
- JASRI, SPring-8, 1-1-1 Kouto, Mizauki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshitaka Yoda
- JASRI, SPring-8, 1-1-1 Kouto, Mizauki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Stephen P. Cramer
- Department of Chemistry, UC Davis, One Shields Ave, Davis, CA 95616, USA
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16
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Pham CC, Mulder DW, Pelmenschikov V, King PW, Ratzloff MW, Wang H, Mishra N, Alp EE, Zhao J, Hu MY, Tamasaku K, Yoda Y, Cramer SP. Terminal Hydride Species in [FeFe]‐Hydrogenases Are Vibrationally Coupled to the Active Site Environment. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Cindy C. Pham
- Department of Chemistry UC Davis One Shields Ave Davis CA 95616 USA
| | - David W. Mulder
- National Renewable Energy Laboratory 15013 Denver W. Pkwy. Golden CO 80401 USA
| | - Vladimir Pelmenschikov
- Institut für Chemie Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Paul W. King
- National Renewable Energy Laboratory 15013 Denver W. Pkwy. Golden CO 80401 USA
| | - Michael W. Ratzloff
- National Renewable Energy Laboratory 15013 Denver W. Pkwy. Golden CO 80401 USA
| | - Hongxin Wang
- Department of Chemistry UC Davis One Shields Ave Davis CA 95616 USA
| | - Nakul Mishra
- Department of Chemistry UC Davis One Shields Ave Davis CA 95616 USA
| | - Esen E. Alp
- Building 401 Argonne National Laboratory 9700 Cass Ave Lemont IL 60439 USA
| | - Jiyong Zhao
- Building 401 Argonne National Laboratory 9700 Cass Ave Lemont IL 60439 USA
| | - Michael Y. Hu
- Building 401 Argonne National Laboratory 9700 Cass Ave Lemont IL 60439 USA
| | - Kenji Tamasaku
- JASRI SPring-8 1-1-1 Kouto, Mizauki-cho Sayo-gun Hyogo 679-5198 Japan
| | - Yoshitaka Yoda
- JASRI SPring-8 1-1-1 Kouto, Mizauki-cho Sayo-gun Hyogo 679-5198 Japan
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17
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Roles of the F-domain in [FeFe] hydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:69-77. [DOI: 10.1016/j.bbabio.2017.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/16/2017] [Accepted: 08/19/2017] [Indexed: 12/31/2022]
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18
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Rewiring of Cyanobacterial Metabolism for Hydrogen Production: Synthetic Biology Approaches and Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:171-213. [PMID: 30091096 DOI: 10.1007/978-981-13-0854-3_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
With the demand for renewable energy growing, hydrogen (H2) is becoming an attractive energy carrier. Developing H2 production technologies with near-net zero carbon emissions is a major challenge for the "H2 economy." Certain cyanobacteria inherently possess enzymes, nitrogenases, and bidirectional hydrogenases that are capable of H2 evolution using sunlight, making them ideal cell factories for photocatalytic conversion of water to H2. With the advances in synthetic biology, cyanobacteria are currently being developed as a "plug and play" chassis to produce H2. This chapter describes the metabolic pathways involved and the theoretical limits to cyanobacterial H2 production and summarizes the metabolic engineering technologies pursued.
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19
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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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20
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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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21
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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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22
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Morra S, Arizzi M, Valetti F, Gilardi G. Oxygen Stability in the New [FeFe]-Hydrogenase from Clostridium beijerinckii SM10 (CbA5H). Biochemistry 2016; 55:5897-5900. [DOI: 10.1021/acs.biochem.6b00780] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Simone Morra
- Department of Life Sciences
and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Mariaconcetta Arizzi
- Department of Life Sciences
and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Francesca Valetti
- Department of Life Sciences
and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences
and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino 10123, Italy
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23
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Caserta G, Adamska-Venkatesh A, Pecqueur L, Atta M, Artero V, Roy S, Reijerse E, Lubitz W, Fontecave M. Chemical assembly of multiple metal cofactors: The heterologously expressed multidomain [FeFe]-hydrogenase from Megasphaera elsdenii. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1734-1740. [PMID: 27421233 DOI: 10.1016/j.bbabio.2016.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/03/2016] [Accepted: 07/10/2016] [Indexed: 10/21/2022]
Abstract
[FeFe]-hydrogenases are unique and fascinating enzymes catalyzing the reversible reduction of protons into hydrogen. These metalloenzymes display extremely large catalytic reaction rates at very low overpotential values and are, therefore, studied as potential catalysts for bioelectrodes of electrolyzers and fuel cells. Since they contain multiple metal cofactors whose biosynthesis depends on complex protein machineries, their preparation is difficult. As a consequence still few have been purified to homogeneity allowing spectroscopic and structural characterization. As part of a program aiming at getting easy access to new hydrogenases we report here a methodology based on a purely chemical assembly of their metal cofactors. This methodology is applied to the preparation and characterization of the hydrogenase from the fermentative anaerobic rumen bacterium Megasphaera elsdenii, which has only been incompletely characterized in the past.
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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, 11 place Marcelin Berthelot, 75005 Paris, France
| | | | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, 11 place Marcelin Berthelot, 75005 Paris, France
| | - Mohamed Atta
- 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
| | - Souvik Roy
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CEA/BIG, CNRS, 17 rue des martyrs, 38000 Grenoble, France
| | - 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
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, 11 place Marcelin Berthelot, 75005 Paris, France.
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24
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Impact of the chemicals, essential for the purification process of strict Fe-hydrogenase, on the corrosion of mild steel. Bioelectrochemistry 2016; 109:9-23. [DOI: 10.1016/j.bioelechem.2015.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/14/2015] [Accepted: 12/17/2015] [Indexed: 11/20/2022]
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25
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Mahinthichaichan P, Gennis RB, Tajkhorshid E. All the O2 Consumed by Thermus thermophilus Cytochrome ba3 Is Delivered to the Active Site through a Long, Open Hydrophobic Tunnel with Entrances within the Lipid Bilayer. Biochemistry 2016; 55:1265-78. [PMID: 26845082 DOI: 10.1021/acs.biochem.5b01255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cytochrome ba3 is a proton-pumping heme-copper oxygen reductase from the extreme thermophile Thermus thermophilus. Despite the fact that the enzyme's active site is buried deep within the protein, the apparent second order rate constant for the initial binding of O2 to the active-site heme has been experimentally found to be 10(9) M(-1) s(-1) at 298 K, at or near the diffusion limit, and 2 orders of magnitude faster than for O2 binding to myoglobin. To provide quantitative and microscopic descriptions of the O2 delivery pathway and mechanism in cytochrome ba3, extensive molecular dynamics simulations of the enzyme in its membrane-embedded form have been performed, including different protocols of explicit ligand sampling (flooding) simulations with O2, implicit ligand sampling analysis, and in silico mutagenesis. The results show that O2 diffuses to the active site exclusively via a Y-shaped hydrophobic tunnel with two 25-Å long membrane-accessible branches that coincide with the pathway previously suggested by the crystallographically identified xenon binding sites. The two entrances of the bifurcated tunnel of cytochrome ba3 are located within the lipid bilayer, where O2 is preferentially partitioned from the aqueous phase. The largest barrier to O2 migration within the tunnel is estimated to be only 1.5 kcal/mol, allowing O2 to reach the enzyme active site virtually impeded by one-dimensional diffusion once it reaches a tunnel entrance at the protein surface. Unlike other O2-utilizing proteins, the tunnel is "open" with no transient barriers observed due to protein dynamics. This unique low-barrier passage through the protein ensures that O2 transit through the protein is never rate-limiting.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Robert B Gennis
- Department of Biochemistry, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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26
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Vatsyayan P. Recent Advances in the Study of Electrochemistry of Redox Proteins. TRENDS IN BIOELECTROANALYSIS 2016. [DOI: 10.1007/11663_2015_5001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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27
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Morra S, Maurelli S, Chiesa M, Mulder DW, Ratzloff MW, Giamello E, King PW, Gilardi G, Valetti F. The effect of a C298D mutation in CaHydA [FeFe]-hydrogenase: Insights into the protein-metal cluster interaction by EPR and FTIR spectroscopic investigation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:98-106. [PMID: 26482707 DOI: 10.1016/j.bbabio.2015.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/17/2023]
Abstract
A conserved cysteine located in the signature motif of the catalytic center (H-cluster) of [FeFe]-hydrogenases functions in proton transfer. This residue corresponds to C298 in Clostridium acetobutylicum CaHydA. Despite the chemical and structural difference, the mutant C298D retains fast catalytic activity, while replacement with any other amino acid causes significant activity loss. Given the proximity of C298 to the H-cluster, the effect of the C298D mutation on the catalytic center was studied by continuous wave (CW) and pulse electron paramagnetic resonance (EPR) and by Fourier transform infrared (FTIR) spectroscopies. Comparison of the C298D mutant with the wild type CaHydA by CW and pulse EPR showed that the electronic structure of the center is not altered. FTIR spectroscopy confirmed that absorption peak values observed in the mutant are virtually identical to those observed in the wild type, indicating that the H-cluster is not generally affected by the mutation. Significant differences were observed only in the inhibited state Hox-CO: the vibrational modes assigned to the COexo and Fed-CO in this state are shifted to lower values in C298D, suggesting different interaction of these ligands with the protein moiety when C298 is changed to D298. More relevant to the catalytic cycle, the redox equilibrium between the Hox and Hred states is modified by the mutation, causing a prevalence of the oxidized state. This work highlights how the interactions between the protein environment and the H-cluster, a dynamic closely interconnected system, can be engineered and studied in the perspective of designing bio-inspired catalysts and mimics.
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Affiliation(s)
- Simone Morra
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy
| | - Sara Maurelli
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W Ratzloff
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Elio Giamello
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy.
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28
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Morra S, Cordara A, Gilardi G, Valetti F. Atypical effect of temperature tuning on the insertion of the catalytic iron-sulfur center in a recombinant [FeFe]-hydrogenase. Protein Sci 2015; 24:2090-4. [PMID: 26362685 DOI: 10.1002/pro.2805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 01/04/2023]
Abstract
The expression of recombinant [FeFe]-hydrogenases is an important step for the production of large amount of these enzymes for their exploitation in biotechnology and for the characterization of the protein-metal cofactor interactions. The correct assembly of the organometallic catalytic site, named H-cluster, requires a dedicated set of maturases that must be coexpressed in the microbial hosts or used for in vitro assembly of the active enzymes. In this work, the effect of the post-induction temperature on the recombinant expression of CaHydA [FeFe]-hydrogenase in E. coli is investigated. The results show a peculiar behavior: the enzyme expression is maximum at lower temperatures (20°C), while the specific activity of the purified CaHydA is higher at higher temperature (30°C), as a consequence of improved protein folding and active site incorporation.
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Affiliation(s)
- Simone Morra
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Alessandro Cordara
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
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29
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Oughli AA, Conzuelo F, Winkler M, Happe T, Lubitz W, Schuhmann W, Rüdiger O, Plumeré N. A redox hydrogel protects the O2 -sensitive [FeFe]-hydrogenase from Chlamydomonas reinhardtii from oxidative damage. Angew Chem Int Ed Engl 2015; 54:12329-33. [PMID: 26073322 DOI: 10.1002/anie.201502776] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 01/10/2023]
Abstract
The integration of sensitive catalysts in redox matrices opens up the possibility for their protection from deactivating molecules such as O2 . [FeFe]-hydrogenases are enzymes catalyzing H2 oxidation/production which are irreversibly deactivated by O2 . Therefore, their use under aerobic conditions has never been achieved. Integration of such hydrogenases in viologen-modified hydrogel films allows the enzyme to maintain catalytic current for H2 oxidation in the presence of O2 , demonstrating a protection mechanism independent of reactivation processes. Within the hydrogel, electrons from the hydrogenase-catalyzed H2 oxidation are shuttled to the hydrogel-solution interface for O2 reduction. Hence, the harmful O2 molecules do not reach the hydrogenase. We illustrate the potential applications of this protection concept with a biofuel cell under H2 /O2 mixed feed.
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Affiliation(s)
- Alaa Alsheikh Oughli
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr (Germany)
| | - Felipe Conzuelo
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum (Germany)
| | - Martin Winkler
- Lehrstuhl Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr Universität Bochum, Universitätsstrasse 150, 44801 Bochum (Germany)
| | - Thomas Happe
- Lehrstuhl Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr Universität Bochum, Universitätsstrasse 150, 44801 Bochum (Germany)
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr (Germany)
| | - Wolfgang Schuhmann
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum (Germany)
| | - Olaf Rüdiger
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr (Germany).
| | - Nicolas Plumeré
- Center for Electrochemical Sciences-Molecular Nanostructures, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum (Germany).
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30
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Oughli AA, Conzuelo F, Winkler M, Happe T, Lubitz W, Schuhmann W, Rüdiger O, Plumeré N. Ein Redoxhydrogel schützt die O2-empfindliche [FeFe]-Hydrogenase ausChlamydomonas reinhardtiivor oxidativer Zerstörung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502776] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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31
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Gee LB, Leontyev I, Stuchebrukhov A, Scott AD, Pelmenschikov V, Cramer SP. Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics. Biochemistry 2015; 54:3314-9. [PMID: 25919807 DOI: 10.1021/acs.biochem.5b00216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.
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Affiliation(s)
- Leland B Gee
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | - Igor Leontyev
- §InterX Inc., Berkeley, California 94710, United States
| | - Alexei Stuchebrukhov
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | - Aubrey D Scott
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | | | - Stephen P Cramer
- †Department of Chemistry, University of California, Davis, California 95616, United States.,‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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32
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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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33
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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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34
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Chernev P, Lambertz C, Brünje A, Leidel N, Sigfridsson KGV, Kositzki R, Hsieh CH, Yao S, Schiwon R, Driess M, Limberg C, Happe T, Haumann M. Hydride Binding to the Active Site of [FeFe]-Hydrogenase. Inorg Chem 2014; 53:12164-77. [DOI: 10.1021/ic502047q] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Petko Chernev
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | - Camilla Lambertz
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Annika Brünje
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Nils Leidel
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | | | - Ramona Kositzki
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | - Chung-Hung Hsieh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shenglai Yao
- Department of Chemistry, Technical University Berlin, 10623 Berlin, Germany
| | - Rafael Schiwon
- Department of Chemistry, Humboldt University Berlin, 12489 Berlin, Germany
| | - Matthias Driess
- Department of Chemistry, Technical University Berlin, 10623 Berlin, Germany
| | - Christian Limberg
- Department of Chemistry, Humboldt University Berlin, 12489 Berlin, Germany
| | - Thomas Happe
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Michael Haumann
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
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35
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Mulder DW, Ratzloff MW, Bruschi M, Greco C, Koonce E, Peters JW, King PW. Investigations on the role of proton-coupled electron transfer in hydrogen activation by [FeFe]-hydrogenase. J Am Chem Soc 2014; 136:15394-402. [PMID: 25286239 DOI: 10.1021/ja508629m] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proton-coupled electron transfer (PCET) is a fundamental process at the core of oxidation-reduction reactions for energy conversion. The [FeFe]-hydrogenases catalyze the reversible activation of molecular H2 through a unique metallocofactor, the H-cluster, which is finely tuned by the surrounding protein environment to undergo fast PCET transitions. The correlation of electronic and structural transitions at the H-cluster with proton-transfer (PT) steps has not been well-resolved experimentally. Here, we explore how modification of the conserved PT network via a Cys → Ser substitution at position 169 proximal to the H-cluster of Chlamydomonas reinhardtii [FeFe]-hydrogenase (CrHydA1) affects the H-cluster using electron paramagnetic resonance (EPR) and Fourier transform infrared (FTIR) spectroscopy. Despite a substantial decrease in catalytic activity, the EPR and FTIR spectra reveal different H-cluster catalytic states under reducing and oxidizing conditions. Under H2 or sodium dithionite reductive treatments, the EPR spectra show signals that are consistent with a reduced [4Fe-4S]H(+) subcluster. The FTIR spectra showed upshifts of νCO modes to energies that are consistent with an increase in oxidation state of the [2Fe]H subcluster, which was corroborated by DFT analysis. In contrast to the case for wild-type CrHydA1, spectra associated with Hred and Hsred states are less populated in the Cys → Ser variant, demonstrating that the exchange of -SH with -OH alters how the H-cluster equilibrates among different reduced states of the catalytic cycle under steady-state conditions.
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Affiliation(s)
- David W Mulder
- Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
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36
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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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37
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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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38
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The oxidative inactivation of FeFe hydrogenase reveals the flexibility of the H-cluster. Nat Chem 2014; 6:336-42. [PMID: 24651202 DOI: 10.1038/nchem.1892] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 02/11/2014] [Indexed: 11/09/2022]
Abstract
Nature is a valuable source of inspiration in the design of catalysts, and various approaches are used to elucidate the mechanism of hydrogenases, the enzymes that oxidize or produce H2. In FeFe hydrogenases, H2 oxidation occurs at the H-cluster, and catalysis involves H2 binding on the vacant coordination site of an iron centre. Here, we show that the reversible oxidative inactivation of this enzyme results from the binding of H2 to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the coordination sphere around the reactive iron centre confers on the enzyme the ability to avoid harmful reactions under oxidizing conditions, including exposure to O2. The versatile chemistry of the diiron cluster in the natural system might inspire the design of novel synthetic catalysts for H2 oxidation.
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39
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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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40
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Long H, King PW, Chang CH. Proton Transport in Clostridium pasteurianum [FeFe] Hydrogenase I: A Computational Study. J Phys Chem B 2014; 118:890-900. [PMID: 24405487 DOI: 10.1021/jp408621r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Hai Long
- National Renewable Energy Laboratory, MS ESIF301, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Paul W. King
- National Renewable Energy Laboratory, MS ESIF301, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Christopher H. Chang
- National Renewable Energy Laboratory, MS ESIF301, 15013 Denver West Parkway, Golden, Colorado 80401, United States
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41
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Lambertz C, Chernev P, Klingan K, Leidel N, Sigfridsson KGV, Happe T, Haumann M. Electronic and molecular structures of the active-site H-cluster in [FeFe]-hydrogenase determined by site-selective X-ray spectroscopy and quantum chemical calculations. Chem Sci 2014. [DOI: 10.1039/c3sc52703d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Site-selective X-ray spectroscopy discriminated the cubane and diiron units in the H-cluster of [FeFe]-hydrogenase revealing its electronic and structural configurations.
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Affiliation(s)
- Camilla Lambertz
- Institute for Biochemistry of Plants
- Department of Photobiotechnology
- Ruhr-University Bochum
- 44780 Bochum, Germany
| | - Petko Chernev
- Institute for Experimental Physics
- Freie Universität Berlin
- FB Physik
- 14195 Berlin, Germany
| | - Katharina Klingan
- Institute for Experimental Physics
- Freie Universität Berlin
- FB Physik
- 14195 Berlin, Germany
| | - Nils Leidel
- Institute for Experimental Physics
- Freie Universität Berlin
- FB Physik
- 14195 Berlin, Germany
| | | | - Thomas Happe
- Institute for Biochemistry of Plants
- Department of Photobiotechnology
- Ruhr-University Bochum
- 44780 Bochum, Germany
| | - Michael Haumann
- Institute for Experimental Physics
- Freie Universität Berlin
- FB Physik
- 14195 Berlin, Germany
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42
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43
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Photobiological hydrogen production: Bioenergetics and challenges for its practical application. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2013. [DOI: 10.1016/j.jphotochemrev.2013.05.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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44
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Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules 2013; 3:778-811. [PMID: 24970191 PMCID: PMC4030971 DOI: 10.3390/biom3040778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.
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45
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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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46
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Winkler M, Esselborn J, Happe T. Molecular basis of [FeFe]-hydrogenase function: an insight into the complex interplay between protein and catalytic cofactor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:974-85. [PMID: 23507618 DOI: 10.1016/j.bbabio.2013.03.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/21/2013] [Accepted: 03/08/2013] [Indexed: 12/20/2022]
Abstract
The precise electrochemical features of metal cofactors that convey the functions of redox enzymes are essentially determined by the specific interaction pattern between cofactor and enclosing protein environment. However, while biophysical techniques allow a detailed understanding of the features characterizing the cofactor itself, knowledge about the contribution of the protein part is much harder to obtain. [FeFe]-hydrogenases are an interesting class of enzymes that catalyze both, H2 oxidation and the reduction of protons to molecular hydrogen with significant efficiency. The active site of these proteins consists of an unusual prosthetic group (H-cluster) with six iron and six sulfur atoms. While H-cluster architecture and catalytic states during the different steps of H2 turnover have been thoroughly investigated during the last 20 years, possible functional contributions from the polypeptide framework were only assumed according to the level of conservancy and X-ray structure analyses. Due to the recent development of simpler and more efficient expression systems the role of single amino acids can now be experimentally investigated. This article summarizes, compares and categorizes the results of recent investigations based on site directed and random mutagenesis according to their informative value about structure function relationships in [FeFe]-hydrogenases. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Martin Winkler
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Bochum, Germany
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47
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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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48
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Site saturation mutagenesis demonstrates a central role for cysteine 298 as proton donor to the catalytic site in CaHydA [FeFe]-hydrogenase. PLoS One 2012; 7:e48400. [PMID: 23133586 PMCID: PMC3485046 DOI: 10.1371/journal.pone.0048400] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/25/2012] [Indexed: 01/24/2023] Open
Abstract
[FeFe]-hydrogenases reversibly catalyse molecular hydrogen evolution by reduction of two protons. Proton supply to the catalytic site (H-cluster) is essential for enzymatic activity. Cysteine 298 is a highly conserved residue in all [FeFe]-hydrogenases; moreover C298 is structurally very close to the H-cluster and it is important for hydrogenase activity. Here, the function of C298 in catalysis was investigated in detail by means of site saturation mutagenesis, simultaneously studying the effect of C298 replacement with all other 19 amino acids and selecting for mutants with high retained activity. We demonstrated that efficient enzymatic turnover was maintained only when C298 was replaced by aspartic acid, despite the structural diversity between the two residues. Purified CaHydA C298D does not show any significant structural difference in terms of secondary structure and iron incorporation, demonstrating that the mutation does not affect the overall protein fold. C298D retains the hydrogen evolution activity with a decrease of kcat only by 2-fold at pH 8.0 and it caused a shift of the optimum pH from 8.0 to 7.0. Moreover, the oxygen inactivation rate was not affected demonstrating that the mutation does not influence O2 diffusion to the active site or its reactivity with the H-cluster. Our results clearly demonstrate that, in order to maintain the catalytic efficiency and the high turnover number typical of [FeFe] hydrogenases, the highly conserved C298 can be replaced only by another ionisable residue with similar steric hindrance, giving evidence of its involvement in the catalytic function of [FeFe]-hydrogenases in agreement with an essential role in proton transfer to the active site.
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49
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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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50
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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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