1
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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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2
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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3
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Bruska MK, Stiebritz MT, Reiher M. Binding of Reactive Oxygen Species at Fe-S Cubane Clusters. Chemistry 2015; 21:19081-9. [PMID: 26585994 DOI: 10.1002/chem.201503008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 01/05/2023]
Abstract
Reactive oxygen species (ROS) play an important role in the biochemistry of the cell and occur in degenerative processes as well as in signal transduction. Iron-sulfur proteins are particularly oxygen-sensitive and their inorganic cofactors frequently undergo ROS-induced decomposition reactions. As experimental knowledge about these processes is still incomplete we present here a quantum chemical study of the relative energetics for the binding of the most relevant ROS to [Fe4S4] clusters. We find that cubane clusters with one uncoordinated Fe atom (as found, for instance, in aconitase) bind all oxygen derivatives considered, whereas activation of triplet O2 to singlet O2 is required for binding to valence-saturated iron centers in these clusters. The radicals NO and OH feature the most exothermic binding energies to Fe atoms. Direct sulfoxidation of coordinating cysteine residues is only possible by OH or H2O2 as attacking agents. The thermodynamic picture of ROS binding to iron-sulfur clusters established here can serve as a starting point for studying reactivity-modulating effects of the cluster-embedding protein environment on ROS-induced decomposition of iron-sulfur proteins.
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Affiliation(s)
- Marta K Bruska
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland)
| | - Martin T Stiebritz
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland)
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland).
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4
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Orain C, Saujet L, Gauquelin C, Soucaille P, Meynial-Salles I, Baffert C, Fourmond V, Bottin H, Léger C. Electrochemical Measurements of the Kinetics of Inhibition of Two FeFe Hydrogenases by O2 Demonstrate That the Reaction Is Partly Reversible. J Am Chem Soc 2015; 137:12580-7. [DOI: 10.1021/jacs.5b06934] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Christophe Orain
- Laboratoire de
Bioénergétique et Ingénierie des Protéines,
CNRS/Aix-Marseille Université, 13402 Marseille, France
| | - Laure Saujet
- CEA, Institut
de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France
- Institut
de Biologie Intégrative de la Cellule I2BC, UMR 9198, CEA,
CNRS, Université Paris Sud, F-91191 Gif sur
Yvette, France
| | - Charles Gauquelin
- Université
de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135 CNRS:UMR 5504, avenue de Rangueil, 31077 Toulouse, France
| | - Philippe Soucaille
- Université
de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135 CNRS:UMR 5504, avenue de Rangueil, 31077 Toulouse, France
| | - Isabelle Meynial-Salles
- Université
de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135 CNRS:UMR 5504, avenue de Rangueil, 31077 Toulouse, France
| | - Carole Baffert
- Laboratoire de
Bioénergétique et Ingénierie des Protéines,
CNRS/Aix-Marseille Université, 13402 Marseille, France
| | - Vincent Fourmond
- Laboratoire de
Bioénergétique et Ingénierie des Protéines,
CNRS/Aix-Marseille Université, 13402 Marseille, France
| | - Hervé Bottin
- CEA, Institut
de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France
- Institut
de Biologie Intégrative de la Cellule I2BC, UMR 9198, CEA,
CNRS, Université Paris Sud, F-91191 Gif sur
Yvette, France
| | - Christophe Léger
- Laboratoire de
Bioénergétique et Ingénierie des Protéines,
CNRS/Aix-Marseille Université, 13402 Marseille, France
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5
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Stiebritz MT. MetREx: A protein design approach for the exploration of sequence-reactivity relationships in metalloenzymes. J Comput Chem 2015; 36:553-63. [DOI: 10.1002/jcc.23831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/12/2014] [Accepted: 12/16/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zürich; Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
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6
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Finkelmann AR, Stiebritz MT, Reiher M. Activation Barriers of Oxygen Transformation at the Active Site of [FeFe] Hydrogenases. Inorg Chem 2014; 53:11890-902. [DOI: 10.1021/ic501049z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arndt R. Finkelmann
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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7
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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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8
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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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10
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Abstract
The H(2)-evolving potential of [FeFe] hydrogenases is severely limited by the oxygen sensitivity of this class of enzymes. Recent experimental studies on hydrogenase from C. reinhardtii point to O(2)-induced structural changes in the [Fe(4)S(4)] subsite of the H cluster. Here, we investigate the mechanistic basis of this observation by means of density functional theory. Unexpectedly, we find that the isolated H cluster shows a pathological catalytic activity for the formation of reactive oxygen species such as O(2)(-) and HO(2)(-). After protonation of O(2)(-), an OOH radical may coordinate to the Fe atoms of the cubane, whereas H(2)O(2) specifically reacts with the S atoms of the cubane-coordinating cysteine residues. Both pathways are accompanied by significant structural distortions that compromise cluster integrity and thus catalytic activity. These results explain the experimental observation that O(2)-induced inhibition is accompanied by distortions of the [Fe(4)S(4)] moiety and account for the irreversibility of this process.
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Affiliation(s)
- Marta K. Bruska
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
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11
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Lautier T, Ezanno P, Baffert C, Fourmond V, Cournac L, Fontecilla-Camps JC, Soucaille P, Bertrand P, Meynial-Salles I, Léger C. The quest for a functional substrate access tunnel in FeFe hydrogenase. Faraday Discuss 2011; 148:385-407; discussion 421-41. [DOI: 10.1039/c004099c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Motiu S, Gogonea V. [Fe-Fe]-hydrogenase Reactivated by Residue Mutations as Bridging Carbonyl Rearranges: A QM/MM Study. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2010; 110:2705-2718. [PMID: 26045628 PMCID: PMC4452136 DOI: 10.1002/qua.22381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the current work, we found aqueous enzyme phase reaction pathways for the reactivation of the exogenously inhibited [Fe-Fe]-hydrogenases by O2, or OH-, which metabolizes to H2O1,2. We used the hybrid quantum mechanics/molecular mechanics (QM/MM) method to study the reactivation pathways of the exogenously inhibited enzyme matrix. The ONIOM calculations performed on the enzyme agree with experimental results3, i.e., wild-type [Fe-Fe]-hydrogenase H-cluster is inhibited by oxygen metabolites. An enzyme spherical region with a radius of 8 Å (from the distal iron, Fed) has been screened for residues that prevent H2O from leaving the catalytic site and reactivate the [Fe-Fe]-hydrogenase H-cluster. In the screening process, polar residues were removed, one at a time, and frequency calculations provided the change in the Gibbs' energy for the dissociation of water (due to their deletion). When residue deletion resulted in significant Gibbs' energy decrease, further residue substitutions have been carried out. Following each substitution, geometry optimization and frequency calculations have been performed to assess the change in the Gibbs' energy for the elimination H2O. Favorable thermodynamic results have been obtained for both single residue removal (ΔGΔGlu374 = -1.6 kcal/mol), single substitution (ΔGGlu374His = -3.1 kcal/mol), and combined residue substitutions (ΔGArg111Glu;Thr145Val;Glu374His;Tyr375Phe = -7.5 kcal/mol). Because the wild-type enzyme has only an endergonic step to overcome, i.e., for H2O removal, by eliminating several residues, one at a time, the endergonic step was made to proceed spontaneously. Thus, the most promising residue deletions which enhance H2O elimination are ΔArg111, ΔThr145, ΔSer177, ΔGlu240, ΔGlu374, and ΔTyr375. The thermodynamics and electronic structure analyses show that the bridging carbonyl (COb) of the H-cluster plays a concomitant role in the enzyme inhibition/reactivation. In gas phase, COb shifts towards Fed to compensate for the electron density donated to oxygen upon the elimination of H2O. However, this is not possible in the wild-type enzyme because the protein matrix hinders the displacement of COb towards Fed, which leads to enzyme inhibition. However, enzyme reactivation can be achieved by means of appropriate amino acid substitutions.
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Affiliation(s)
- Stefan Motiu
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195
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13
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Stiebritz MT, Reiher M. A unifying structural and electronic concept for Hmd and [FeFe] hydrogenase active sites. Inorg Chem 2010; 49:5818-23. [PMID: 20527808 DOI: 10.1021/ic902529c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydrogenases [FeFe] and Hmd feature at first sight rather different active sites. A closer inspection reveals striking similarities, which allow us to define swapped ligand spheres in such a way that the single active iron center of Hmd functions in a first-shell ligand environment resembling the reacting iron atom in [FeFe] hydrogenase and vice versa. These redesigned ligand environments can be conveniently studied with quantum chemical methods and point to general reactivity principles for iron centers with hydrogenase activity.
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Affiliation(s)
- Martin T Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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Dogaru D, Motiu S, Gogonea V. Residue Mutations in [Fe-Fe]-hydrogenase Impedes O(2) Binding: A QM/MM Investigation. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2009; 110:1784-1792. [PMID: 20485511 PMCID: PMC2872501 DOI: 10.1002/qua.22331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
[Fe-Fe]-hydrogenases are enzymes that reversibly catalyze the reaction of protons and electrons to molecular hydrogen, which occurs in anaerobic media. In living systems, [Fe-Fe]-hydrogenases are mostly used for H(2) production. The [Fe-Fe]-hydrogenase H-cluster is the active site, which contains two iron atoms. The latest theoretical investigations1,2 advocate that the structure of di-iron air inhibited species are either Fe(p) (II)-Fe(d) (II)-O-H(-), or Fe(p) (II)-Fe(d) (II)-O-O-H, thus O(2) has to be prevented from binding to Fe(d) in all di-iron subcluster oxidation states in order to retain a catalytically active enzyme. By performing residue mutations on [Fe-Fe]-hydrogenases, we were able to weaken O(2) binding to distal iron (Fe(d)) of Desulfovibrio desulfuricans hydrogenase (DdH). Individual residue deletions were carried out in the 8 A apoenzyme layer radial outward from Fe(d) to determine what residue substitutions should be made to weaken O(2) binding. Residue deletions and substitutions were performed for three di-iron subcluster oxidation states, Fe(p) (II)-Fe(d) (II), Fe(p) (II)-Fe(d) (I), and Fe(p) (I)-Fe(d) (I) of [Fe-Fe]-hydrogenase. Two deletions (DeltaThr(152) and DeltaSer(202)) were found most effective in weakening O(2) binding to Fe(d) in Fe(p) (II)-Fe(d) (I) hydrogenase (DeltaG(QM/MM) = +5.4 kcal/mol). An increase in Gibbs' energy (+2.2 kcal/mol and +4.4 kcal/mol) has also been found for Fe(p) (II)-Fe(d) (II), and Fe(p) (I)-Fe(d) (I) hydrogenase respectively. pi-backdonation considerations for frontier molecular orbital and geometrical analysis corroborate the Gibbs's energy results.
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Affiliation(s)
- Daniela Dogaru
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, Ohio 44115
| | - Stefan Motiu
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, Ohio 44115
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, Ohio 44115
- Department of Cell Biology, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195
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Stiebritz MT, Reiher M. Theoretical Study of Dioxygen Induced Inhibition of [FeFe]-Hydrogenase. Inorg Chem 2009; 48:7127-40. [DOI: 10.1021/ic9002127] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
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