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Yadav S, Haas R, Boydas EB, Roemelt M, Happe T, Apfel UP, Stripp ST. Oxygen sensitivity of [FeFe]-hydrogenase: a comparative study of active site mimics inside vs. outside the enzyme. Phys Chem Chem Phys 2024; 26:19105-19116. [PMID: 38957092 DOI: 10.1039/d3cp06048a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
[FeFe]-hydrogenase is nature's most efficient proton reducing and H2-oxidizing enzyme. However, biotechnological applications are hampered by the O2 sensitivity of this metalloenzyme, and the mechanism of aerobic deactivation is not well understood. Here, we explore the oxygen sensitivity of four mimics of the organometallic active site cofactor of [FeFe]-hydrogenase, [Fe2(adt)(CO)6-x(CN)x]x- and [Fe2(pdt)(CO)6-x(CN)x]x- (x = 1, 2) as well as the corresponding cofactor variants of the enzyme by means of infrared, Mössbauer, and NMR spectroscopy. Additionally, we describe a straightforward synthetic recipe for the active site precursor complex Fe2(adt)(CO)6. Our data indicate that the aminodithiolate (adt) complex, which is the synthetic precursor of the natural active site cofactor, is most oxygen sensitive. This observation highlights the significance of proton transfer in aerobic deactivation, and supported by DFT calculations facilitates an identification of the responsible reactive oxygen species (ROS). Moreover, we show that the ligand environment of the iron ions critically influences the reactivity with O2 and ROS like superoxide and H2O2 as the oxygen sensitivity increases with the exchange of ligands from CO to CN-. The trends in aerobic deactivation observed for the model complexes are in line with the respective enzyme variants. Based on experimental and computational data, a model for the initial reaction of [FeFe]-hydrogenase with O2 is developed. Our study underscores the relevance of model systems in understanding biocatalysis and validates their potential as important tools for elucidating the chemistry of oxygen-induced deactivation of [FeFe]-hydrogenase.
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Affiliation(s)
- Shanika Yadav
- Inorganic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Rieke Haas
- Faculty of Biology & Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Esma Birsen Boydas
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor Str.2, 12489, Berlin, Germany
| | - Michael Roemelt
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor Str.2, 12489, Berlin, Germany
| | - Thomas Happe
- Faculty of Biology & Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
- Department of Electrosynthesi, Fraunhofer UMSICHT, Osterfelder Str. 3, 46047 Oberhausen, Germany
| | - Sven T Stripp
- Biophysical Chemistry, Technical University Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany.
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2
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Procacci B, Wrathall SLD, Farmer AL, Shaw DJ, Greetham GM, Parker AW, Rippers Y, Horch M, Lynam JM, Hunt NT. Understanding the [NiFe] Hydrogenase Active Site Environment through Ultrafast Infrared and 2D-IR Spectroscopy of the Subsite Analogue K[CpFe(CO)(CN) 2] in Polar and Protic Solvents. J Phys Chem B 2024; 128:1461-1472. [PMID: 38301127 PMCID: PMC10875664 DOI: 10.1021/acs.jpcb.3c07965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
The [CpFe(CO)(CN)2]- unit is an excellent structural model for the Fe(CO)(CN)2 moiety of the active site found in [NiFe] hydrogenases. Ultrafast infrared (IR) pump-probe and 2D-IR spectroscopy have been used to study K[CpFe(CO)(CN)2] (M1) in a range of protic and polar solvents and as a dry film. Measurements of anharmonicity, intermode vibrational coupling strength, vibrational relaxation time, and solvation dynamics of the CO and CN stretching modes of M1 in H2O, D2O, methanol, dimethyl sulfoxide, and acetonitrile reveal that H-bonding to the CN ligands plays an important role in defining the spectroscopic characteristics and relaxation dynamics of the Fe(CO)(CN)2 unit. Comparisons of the spectroscopic and dynamic data obtained for M1 in solution and in a dry film with those obtained for the enzyme led to the conclusion that the protein backbone forms an important part of the bimetallic active site environment via secondary coordination sphere interactions.
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Affiliation(s)
- Barbara Procacci
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Solomon L. D. Wrathall
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Amy L. Farmer
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Daniel J. Shaw
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Yvonne Rippers
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Marius Horch
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jason M. Lynam
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Neil T. Hunt
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
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3
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T Waffo AF, Lorent C, Katz S, Schoknecht J, Lenz O, Zebger I, Caserta G. Structural Determinants of the Catalytic Ni a-L Intermediate of [NiFe]-Hydrogenase. J Am Chem Soc 2023. [PMID: 37328284 DOI: 10.1021/jacs.3c01625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
[NiFe]-hydrogenases catalyze the reversible cleavage of H2 into two protons and two electrons at the inorganic heterobimetallic NiFe center of the enzyme. Their catalytic cycle involves at least four intermediates, some of which are still under debate. While the core reaction, including H2/H- binding, takes place at the inorganic cofactor, a major challenge lies in identifying those amino acid residues that contribute to the reactivity and how they stabilize (short-lived) intermediate states. Using cryogenic infrared and electron paramagnetic resonance spectroscopy on the regulatory [NiFe]-hydrogenase from Cupriavidus necator, a model enzyme for the analysis of catalytic intermediates, we deciphered the structural basis of the hitherto elusive Nia-L intermediates. We unveiled the protonation states of a proton-accepting glutamate and a Ni-bound cysteine residue in the Nia-L1, Nia-L2, and the hydride-binding Nia-C intermediates as well as previously unknown conformational changes of amino acid residues in proximity of the bimetallic active site. As such, this study unravels the complexity of the Nia-L intermediate and reveals the importance of the protein scaffold in fine-tuning proton and electron dynamics in [NiFe]-hydrogenase.
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Affiliation(s)
- Armel F T Waffo
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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4
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Stepwise assembly of the active site of [NiFe]-hydrogenase. Nat Chem Biol 2023; 19:498-506. [PMID: 36702959 DOI: 10.1038/s41589-022-01226-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 01/27/2023]
Abstract
[NiFe]-hydrogenases are biotechnologically relevant enzymes catalyzing the reversible splitting of H2 into 2e- and 2H+ under ambient conditions. Catalysis takes place at the heterobimetallic NiFe(CN)2(CO) center, whose multistep biosynthesis involves careful handling of two transition metals as well as potentially harmful CO and CN- molecules. Here, we investigated the sequential assembly of the [NiFe] cofactor, previously based on primarily indirect evidence, using four different purified maturation intermediates of the catalytic subunit, HoxG, of the O2-tolerant membrane-bound hydrogenase from Cupriavidus necator. These included the cofactor-free apo-HoxG, a nickel-free version carrying only the Fe(CN)2(CO) fragment, a precursor that contained all cofactor components but remained redox inactive and the fully mature HoxG. Through biochemical analyses combined with comprehensive spectroscopic investigation using infrared, electronic paramagnetic resonance, Mössbauer, X-ray absorption and nuclear resonance vibrational spectroscopies, we obtained detailed insight into the sophisticated maturation process of [NiFe]-hydrogenase.
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5
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Fan Q, Waldburger S, Neubauer P, Riedel SL, Gimpel M. Implementation of a high cell density fed-batch for heterologous production of active [NiFe]-hydrogenase in Escherichia coli bioreactor cultivations. Microb Cell Fact 2022; 21:193. [PMID: 36123684 PMCID: PMC9484157 DOI: 10.1186/s12934-022-01919-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background O2-tolerant [NiFe]-hydrogenases offer tremendous potential for applications in H2-based technology. As these metalloenzymes undergo a complicated maturation process that requires a dedicated set of multiple accessory proteins, their heterologous production is challenging, thus hindering their fundamental understanding and the development of related applications. Taking these challenges into account, we selected the comparably simple regulatory [NiFe]-hydrogenase (RH) from Cupriavidus necator as a model for the development of bioprocesses for heterologous [NiFe]-hydrogenase production. We already reported recently on the high-yield production of catalytically active RH in Escherichia coli by optimizing the culture conditions in shake flasks. Results In this study, we further increase the RH yield and ensure consistent product quality by a rationally designed high cell density fed-batch cultivation process. Overall, the bioreactor cultivations resulted in ˃130 mg L−1 of catalytically active RH which is a more than 100-fold increase compared to other RH laboratory bioreactor scale processes with C. necator. Furthermore, the process shows high reproducibility of the previously selected optimized conditions and high productivity. Conclusions This work provides a good opportunity to readily supply such difficult-to-express complex metalloproteins economically and at high concentrations to meet the demand in basic and applied studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01919-w.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Saskia Waldburger
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Sebastian L Riedel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany.
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6
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Kulka-Peschke CJ, Schulz AC, Lorent C, Rippers Y, Wahlefeld S, Preissler J, Schulz C, Wiemann C, Bernitzky CCM, Karafoulidi-Retsou C, Wrathall SLD, Procacci B, Matsuura H, Greetham GM, Teutloff C, Lauterbach L, Higuchi Y, Ishii M, Hunt NT, Lenz O, Zebger I, Horch M. Reversible Glutamate Coordination to High-Valent Nickel Protects the Active Site of a [NiFe] Hydrogenase from Oxygen. J Am Chem Soc 2022; 144:17022-17032. [PMID: 36084022 DOI: 10.1021/jacs.2c06400] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NAD+-reducing [NiFe] hydrogenases are valuable biocatalysts for H2-based energy conversion and the regeneration of nucleotide cofactors. While most hydrogenases are sensitive toward O2 and elevated temperatures, the soluble NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus (HtSH) is O2-tolerant and thermostable. Thus, it represents a promising candidate for biotechnological applications. Here, we have investigated the catalytic activity and active-site structure of native HtSH and variants in which a glutamate residue in the active-site cavity was replaced by glutamine, alanine, and aspartate. Our biochemical, spectroscopic, and theoretical studies reveal that at least two active-site states of oxidized HtSH feature an unusual architecture in which the glutamate acts as a terminal ligand of the active-site nickel. This observation demonstrates that crystallographically observed glutamate coordination represents a native feature of the enzyme. One of these states is diamagnetic and characterized by a very high stretching frequency of an iron-bound active-site CO ligand. Supported by density-functional-theory calculations, we identify this state as a high-valent species with a biologically unprecedented formal Ni(IV) ground state. Detailed insights into its structure and dynamics were obtained by ultrafast and two-dimensional infrared spectroscopy, demonstrating that it represents a conformationally strained state with unusual bond properties. Our data further show that this state is selectively and reversibly formed under oxic conditions, especially upon rapid exposure to high O2 levels. We conclude that the kinetically controlled formation of this six-coordinate high-valent state represents a specific and precisely orchestrated stereoelectronic response toward O2 that could protect the enzyme from oxidative damage.
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Affiliation(s)
- Catharina J Kulka-Peschke
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anne-Christine Schulz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Stefan Wahlefeld
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Janina Preissler
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Claudia Schulz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Charlotte Wiemann
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | | | - Chara Karafoulidi-Retsou
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Solomon L D Wrathall
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Barbara Procacci
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, RIKEN/SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, U.K
| | - Christian Teutloff
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Lars Lauterbach
- Institute of Applied Microbiology, Synthetic Microbiology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Masaharu Ishii
- Graduate School of Agricultural and Life Sciences / Faculty of Agriculture, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Neil T Hunt
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Oliver Lenz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Marius Horch
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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7
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Fan Q, Caserta G, Lorent C, Zebger I, Neubauer P, Lenz O, Gimpel M. High-Yield Production of Catalytically Active Regulatory [NiFe]-Hydrogenase From Cupriavidus necator in Escherichia coli. Front Microbiol 2022; 13:894375. [PMID: 35572669 PMCID: PMC9100943 DOI: 10.3389/fmicb.2022.894375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Hydrogenases are biotechnologically relevant metalloenzymes that catalyze the reversible conversion of molecular hydrogen into protons and electrons. The O2-tolerant [NiFe]-hydrogenases from Cupriavidus necator (formerly Ralstonia eutropha) are of particular interest as they maintain catalysis even in the presence of molecular oxygen. However, to meet the demands of biotechnological applications and scientific research, a heterologous production strategy is required to overcome the low production yields in their native host. We have previously used the regulatory hydrogenase (RH) from C. necator as a model for the development of such a heterologous hydrogenase production process in E. coli. Although high protein yields were obtained, the purified enzyme was inactive due to the lack of the catalytic center, which contains an inorganic nickel-iron cofactor. In the present study, we significantly improved the production process to obtain catalytically active RH. We optimized important factors such as O2 content, metal availability, production temperature and time as well as the co-expression of RH-specific maturase genes. The RH was successfully matured during aerobic cultivation of E. coli by co-production of seven hydrogenase-specific maturases and a nickel permease, which was confirmed by activity measurements and spectroscopic investigations of the purified enzyme. The improved production conditions resulted in a high yield of about 80 mg L–1 of catalytically active RH and an up to 160-fold space-time yield in E. coli compared to that in the native host C. necator [<0.1 U (L d) –1]. Our strategy has important implications for the use of E. coli K-12 and B strains in the recombinant production of complex metalloenzymes, and provides a blueprint for the production of catalytically active [NiFe]-hydrogenases in biotechnologically relevant quantities.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Giorgio Caserta
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Christian Lorent
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Ingo Zebger
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
- *Correspondence: Matthias Gimpel,
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8
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Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Treviño RE, Shafaat HS. Protein-based models offer mechanistic insight into complex nickel metalloenzymes. Curr Opin Chem Biol 2022; 67:102110. [PMID: 35101820 DOI: 10.1016/j.cbpa.2021.102110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 11/03/2022]
Abstract
There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.
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Affiliation(s)
- Regina E Treviño
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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10
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Heghmanns M, Günzel A, Brandis D, Kutin Y, Engelbrecht V, Winkler M, Happe T, Kasanmascheff M. Fine-tuning of FeS proteins monitored via pulsed EPR redox potentiometry at Q-band. BIOPHYSICAL REPORTS 2021; 1:100016. [PMID: 36425453 PMCID: PMC9680799 DOI: 10.1016/j.bpr.2021.100016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/30/2021] [Indexed: 06/16/2023]
Abstract
As essential electron translocating proteins in photosynthetic organisms, multiple plant-type ferredoxin (Fdx) isoforms are involved in a high number of reductive metabolic processes in the chloroplast. To allow quick cellular responses under changing environmental conditions, different plant-type Fdxs in Chlamydomonas reinhardtii were suggested to have adapted their midpoint potentials to a wide range of interaction partners. We performed pulsed electron paramagnetic resonance (EPR) monitored redox potentiometry at Q-band on three Fdx isoforms for a straightforward determination of their midpoint potentials. Additionally, site-directed mutagenesis was used to tune the midpoint potential of CrFdx1 in a range of approximately -338 to -511 mV, confirming the importance of single positions in the protein environment surrounding the [2Fe2S] cluster. Our results present a new target for future studies aiming to modify the catalytic activity of CrFdx1 that plays an essential role either as electron acceptor of photosystem I or as electron donor to hydrogenases under certain conditions. Additionally, the precisely determined redox potentials in this work using pulsed EPR demonstrate an alternative method that provides additional advantages compared with the well-established continuous wave EPR technique.
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Affiliation(s)
- Melanie Heghmanns
- TU Dortmund University, Department of Chemistry and Chemical Biology, Dortmund, Germany
| | - Alexander Günzel
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Photobiotechnology, Bochum, Germany
| | - Dörte Brandis
- TU Dortmund University, Department of Chemistry and Chemical Biology, Dortmund, Germany
| | - Yury Kutin
- TU Dortmund University, Department of Chemistry and Chemical Biology, Dortmund, Germany
| | - Vera Engelbrecht
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Photobiotechnology, Bochum, Germany
| | - Martin Winkler
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Photobiotechnology, Bochum, Germany
| | - Thomas Happe
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Photobiotechnology, Bochum, Germany
| | - Müge Kasanmascheff
- TU Dortmund University, Department of Chemistry and Chemical Biology, Dortmund, Germany
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11
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Fan Q, Neubauer P, Gimpel M. Production of soluble regulatory hydrogenase from Ralstonia eutropha in Escherichia coli using a fed-batch-based autoinduction system. Microb Cell Fact 2021; 20:201. [PMID: 34663324 PMCID: PMC8522226 DOI: 10.1186/s12934-021-01690-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
Background Autoinduction systems can regulate protein production in Escherichia coli without the need to monitor cell growth or add inducer at the proper time following culture growth. Compared to classical IPTG induction, autoinduction provides a simple and fast way to obtain high protein yields. In the present study, we report on the optimization process for the enhanced heterologous production of the Ralstonia eutropha regulatory hydrogenase (RH) in E. coli using autoinduction. These autoinduction methods were combined with the EnPresso B fed-batch like growth system, which applies slow in situ enzymatic glucose release from a polymer to control cell growth and protein synthesis rate. Results We were able to produce 125 mg L−1 RH corresponding to a productivity averaged over the whole process time of 3 mg (L h)−1 in shake flasks using classic single-shot IPTG induction. IPTG autoinduction resulted in a comparable volumetric RH yield of 112 mg L−1 and due to the shorter overall process time in a 1.6-fold higher productivity of 5 mg (L h)−1. In contrast, lactose autoinduction increased the volumetric yield more than 2.5-fold and the space time yield fourfold reaching 280 mg L−1 and 11.5 mg (L h)−1, respectively. Furthermore, repeated addition of booster increased RH production to 370 mg L−1, which to our knowledge is the highest RH concentration produced in E. coli to date. Conclusions The findings of this study confirm the general feasibility of the developed fed-batch based autoinduction system and provide an alternative to conventional induction systems for efficient recombinant protein production. We believe that the fed-batch based autoinduction system developed herein will favor the heterologous production of larger quantities of difficult-to-express complex enzymes to enable economical production of these kinds of proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01690-4.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
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12
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Electron inventory of the iron-sulfur scaffold complex HypCD essential in [NiFe]-hydrogenase cofactor assembly. Biochem J 2021; 478:3281-3295. [PMID: 34409988 PMCID: PMC8454700 DOI: 10.1042/bcj20210224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022]
Abstract
The [4Fe-4S] cluster containing scaffold complex HypCD is the central construction site for the assembly of the [Fe](CN)2CO cofactor precursor of [NiFe]-hydrogenase. While the importance of the HypCD complex is well established, not much is known about the mechanism by which the CN- and CO ligands are transferred and attached to the iron ion. We report an efficient expression and purification system producing the HypCD complex from E. coli with complete metal content. This enabled in-depth spectroscopic characterizations. The results obtained by EPR and Mössbauer spectroscopy demonstrate that the [Fe](CN)2CO cofactor and the [4Fe-4S] cluster of the HypCD complex are redox active. The data indicate a potential-dependent interconversion of the [Fe]2+/3+ and [4Fe-4S]2+/+ couple, respectively. Moreover, ATR FTIR spectroscopy reveals potential-dependent disulfide formation, which hints at an electron confurcation step between the metal centers. MicroScale thermophoresis indicates preferable binding between the HypCD complex and its in vivo interaction partner HypE under reducing conditions. Together, these results provide comprehensive evidence for an electron inventory fit to drive multi-electron redox reactions required for the assembly of the CN- and CO ligands on the scaffold complex HypCD.
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13
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Fan Q, Caserta G, Lorent C, Lenz O, Neubauer P, Gimpel M. Optimization of Culture Conditions for Oxygen-Tolerant Regulatory [NiFe]-Hydrogenase Production from Ralstonia eutropha H16 in Escherichia coli. Microorganisms 2021; 9:1195. [PMID: 34073092 PMCID: PMC8229454 DOI: 10.3390/microorganisms9061195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Hydrogenases are abundant metalloenzymes that catalyze the reversible conversion of molecular H2 into protons and electrons. Important achievements have been made over the past two decades in the understanding of these highly complex enzymes. However, most hydrogenases have low production yields requiring many efforts and high costs for cultivation limiting their investigation. Heterologous production of these hydrogenases in a robust and genetically tractable expression host is an attractive strategy to make these enzymes more accessible. In the present study, we chose the oxygen-tolerant H2-sensing regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha H16 owing to its relatively simple architecture compared to other [NiFe]-hydrogenases as a model to develop a heterologous hydrogenase production system in Escherichia coli. Using screening experiments in 24 deep-well plates with 3 mL working volume, we investigated relevant cultivation parameters, including inducer concentration, expression temperature, and expression time. The RH yield could be increased from 14 mg/L up to >250 mg/L by switching from a batch to an EnPresso B-based fed-batch like cultivation in shake flasks. This yield exceeds the amount of RH purified from the homologous host R. eutropha by several 100-fold. Additionally, we report the successful overproduction of the RH single subunits HoxB and HoxC, suitable for biochemical and spectroscopic investigations. Even though both RH and HoxC proteins were isolated in an inactive, cofactor free apo-form, the proposed strategy may powerfully accelerate bioprocess development and structural studies for both basic research and applied studies. These results are discussed in the context of the regulation mechanisms governing the assembly of large and small hydrogenase subunits.
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Affiliation(s)
- Qin Fan
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Giorgio Caserta
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Christian Lorent
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (C.L.); (O.L.)
| | - Peter Neubauer
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Matthias Gimpel
- Institute of Biotechnology, Technische Universität Berlin, Chair of Bioprocess Engineering, Ackerstraße 76, D-13355 Berlin, Germany; (Q.F.); (P.N.)
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14
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Caserta G, Pelmenschikov V, Lorent C, Tadjoung Waffo AF, Katz S, Lauterbach L, Schoknecht J, Wang H, Yoda Y, Tamasaku K, Kaupp M, Hildebrandt P, Lenz O, Cramer SP, Zebger I. Hydroxy-bridged resting states of a [NiFe]-hydrogenase unraveled by cryogenic vibrational spectroscopy and DFT computations. Chem Sci 2020; 12:2189-2197. [PMID: 34163984 PMCID: PMC8179317 DOI: 10.1039/d0sc05022a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The catalytic mechanism of [NiFe]-hydrogenases is a subject of extensive research. Apart from at least four reaction intermediates of H2/H+ cycling, there are also a number of resting states, which are formed under oxidizing conditions. Although not directly involved in the catalytic cycle, the knowledge of their molecular structures and reactivity is important, because these states usually accumulate in the course of hydrogenase purification and may also play a role in vivo during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit (HoxC) of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure resting redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, 57Fe-labeled HoxC provided an unprecedented insight into the [NiFe] site modes, revealing their contributions in a spectral range otherwise superimposed by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data provide structural descriptions of the previously uncharacterized hydroxy- and water-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site. Active site vibrations of a [NiFe]-hydrogenase catalytic subunit are selectively probed by IR and NRV spectroscopy in two NiIIFeII and NiIIIFeII resting states, contributing in combination with DFT modeling to rationalized structural candidates.![]()
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Affiliation(s)
- Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Armel F Tadjoung Waffo
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Lars Lauterbach
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Hongxin Wang
- SETI Institute 189 Bernardo Avenue Mountain View CA 94043 USA
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute (JASRI) SPring-8, 1-1-1 Kouto, Sayo-gun Hyogo 679-5198 Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo-cho, Sayo-gun Hyogo 679-5148 Japan
| | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
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15
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Caserta G, Lorent C, Pelmenschikov V, Schoknecht J, Yoda Y, Hildebrandt P, Cramer SP, Zebger I, Lenz O. In Vitro Assembly as a Tool to Investigate Catalytic Intermediates of [NiFe]-Hydrogenase. ACS Catal 2020; 10:13890-13894. [PMID: 33680535 PMCID: PMC7932190 DOI: 10.1021/acscatal.0c04079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[NiFe]-hydrogenases catalyze the reversible reaction H2 ⇄ 2H+ + 2e-. Their basic module consists of a large subunit, coordinating the NiFe(CO)(CN)2 center, and a small subunit that carries electron-transferring iron-sulfur clusters. Here, we report the in vitro assembly of fully functional [NiFe]-hydrogenase starting from the isolated large and small subunits. Activity assays complemented by spectroscopic measurements revealed a native-like hydrogenase. This approach was used to label exclusively the NiFe(CO)(CN)2 center with 57Fe, enabling a clear view of the catalytic site by means of nuclear resonance vibrational spectroscopy. This strategy paves the way for in-depth studies of [NiFe]-hydrogenase catalytic intermediates.
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Affiliation(s)
- Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, RIKEN SPring-8, Hyogo 679-5198, Japan
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Stephen P. Cramer
- SETI Institute, 189 Bernardo Avenue, Mountain View, CA 94043, United States
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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16
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Caserta G, Lorent C, Ciaccafava A, Keck M, Breglia R, Greco C, Limberg C, Hildebrandt P, Cramer SP, Zebger I, Lenz O. The large subunit of the regulatory [NiFe]-hydrogenase from Ralstonia eutropha - a minimal hydrogenase? Chem Sci 2020; 11:5453-5465. [PMID: 34094072 PMCID: PMC8159394 DOI: 10.1039/d0sc01369b] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Chemically synthesized compounds that are capable of facilitating the reversible splitting of dihydrogen into protons and electrons are rare in chemists' portfolio. The corresponding biocatalysts – hydrogenases – are, however, abundant in the microbial world. [NiFe]-hydrogenases represent a major subclass and display a bipartite architecture, composed of a large subunit, hosting the catalytic NiFe(CO)(CN)2 cofactor, and a small subunit whose iron–sulfur clusters are responsible for electron transfer. To analyze in detail the catalytic competence of the large subunit without its smaller counterpart, we purified the large subunit HoxC of the regulatory [NiFe]-hydrogenase of the model H2 oxidizer Ralstonia eutropha to homogeneity. Metal determination and infrared spectroscopy revealed a stoichiometric loading of the metal cofactor. This enabled for the first time the determination of the UV-visible extinction coefficient of the NiFe(CO)(CN)2 cofactor. Moreover, the absence of disturbing iron–sulfur clusters allowed an unbiased look into the low-spin Fe2+ of the active site by Mössbauer spectroscopy. Isolated HoxC was active in catalytic hydrogen–deuterium exchange, demonstrating its capacity to activate H2. Its catalytic activity was drastically lower than that of the bipartite holoenzyme. This was consistent with infrared and electron paramagnetic resonance spectroscopic observations, suggesting that the bridging position between the active site nickel and iron ions is predominantly occupied by water-derived ligands, even under reducing conditions. In fact, the presence of water-derived ligands bound to low-spin Ni2+ was reflected by the absorption bands occurring in the corresponding UV-vis spectra, as revealed by time-dependent density functional theory calculations conducted on appropriate in silico models. Thus, the isolated large subunits indeed represent simple [NiFe]-hydrogenase models, which could serve as blueprints for chemically synthesized mimics. Furthermore, our data point to a fundamental role of the small subunit in preventing water access to the catalytic center, which significantly increases the H2 splitting capacity of the enzyme. Spectroscopic investigation of an isolated [NiFe]-hydrogenase large subunit enables a unique view of the NiFe(CO)(CN)2 cofactor.![]()
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Affiliation(s)
- Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Alexandre Ciaccafava
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Matthias Keck
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Raffaella Breglia
- Department of Earth and Environmental Sciences, Milano-Bicocca University Piazza della Scienza 1 20126 Milan Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, Milano-Bicocca University Piazza della Scienza 1 20126 Milan Italy
| | - Christian Limberg
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
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17
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Ilina Y, Lorent C, Katz S, Jeoung J, Shima S, Horch M, Zebger I, Dobbek H. X‐ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yulia Ilina
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Philippstraße 13 10115 Berlin Germany
| | - Christian Lorent
- Institut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Jae‐Hun Jeoung
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Philippstraße 13 10115 Berlin Germany
| | - Seigo Shima
- Max-Planck-Institut für Terrestrische Mikrobiologie Karl-von-Frisch-Str. 10 35043 Marburg Germany
| | - Marius Horch
- Institut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
- Department of Chemistry and York Biomedical Research InstituteUniversity of York Heslington York YO10 5DD UK
| | - Ingo Zebger
- Institut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Philippstraße 13 10115 Berlin Germany
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18
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Ash PA, Kendall-Price SET, Vincent KA. Unifying Activity, Structure, and Spectroscopy of [NiFe] Hydrogenases: Combining Techniques To Clarify Mechanistic Understanding. Acc Chem Res 2019; 52:3120-3131. [PMID: 31675209 DOI: 10.1021/acs.accounts.9b00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Achieving a unified understanding of the mechanism of a multicenter redox enzyme such as [NiFe] hydrogenase is complicated by difficulties in reconciling information obtained by using different techniques and on samples in different physical forms. Measurements of the activity of the enzyme, and of factors which perturb activity, are generally carried out using biochemical assays in solution or with electrode-immobilized enzymes using protein film electrochemistry (PFE). Conversely, spectroscopy aimed at reporting on features of the metalloclusters in the enzyme, such as electron paramagnetic resonance (EPR) or X-ray absorption spectroscopy (XAS), is often conducted on frozen samples and is thus difficult to relate to catalytically relevant states as information about turnover and activity has been lost. To complicate matters further, most of our knowledge of the atomic-level structure of metalloenzymes comes from X-ray diffraction studies in the solid, crystalline state, which are again difficult to link to turnover conditions. Taking [NiFe] hydrogenases as our case study, we show here how it is possible to apply infrared (IR) spectroscopic sampling approaches to unite direct spectroscopic study with catalytic turnover. Using a method we have named protein film IR electrochemistry (PFIRE), we reveal the steady-state distribution of intermediates during catalysis and identify catalytic "bottlenecks" introduced by site-directed mutagenesis. We also show that it is possible to study dynamic transitions between active site states of enzymes in single crystals, uniting solid state and solution spectroscopic information. In all of these cases, the spectroscopic data complement and enhance interpretation of purely activity-based measurements by providing direct chemical insight that is otherwise hidden. The [NiFe] hydrogenases possess a bimetallic [NiFe] active site, coordinated by CO and CN- ligands, linked to the protein via bridging and terminal cysteine sulfur ligands, as well as an electron relay chain of iron sulfur clusters. Infrared spectroscopy is ideal for probing hydrogenases because the CO and CN- ligands are strong IR absorbers, but the suite of IR-based approaches we describe here will be equally valuable in studying substrate- or intermediate-bound states of other metalloenzymes where key mechanistic questions remain open, such as nitrogenase, formate dehydrogenase, or carbon monoxide dehydrogenase. We therefore hope that this Account will encourage future studies which unify information from different techniques across bioinorganic chemistry.
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Affiliation(s)
- Philip A. Ash
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | | | - Kylie A. Vincent
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
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19
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Ilina Y, Lorent C, Katz S, Jeoung JH, Shima S, Horch M, Zebger I, Dobbek H. X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2019; 58:18710-18714. [PMID: 31591784 PMCID: PMC6916344 DOI: 10.1002/anie.201908258] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Indexed: 11/23/2022]
Abstract
[NiFe] hydrogenases are complex model enzymes for the reversible cleavage of dihydrogen (H2). However, structural determinants of efficient H2 binding to their [NiFe] active site are not properly understood. Here, we present crystallographic and vibrational‐spectroscopic insights into the unexplored structure of the H2‐binding [NiFe] intermediate. Using an F420‐reducing [NiFe]‐hydrogenase from Methanosarcina barkeri as a model enzyme, we show that the protein backbone provides a strained chelating scaffold that tunes the [NiFe] active site for efficient H2 binding and conversion. The protein matrix also directs H2 diffusion to the [NiFe] site via two gas channels and allows the distribution of electrons between functional protomers through a subunit‐bridging FeS cluster. Our findings emphasize the relevance of an atypical Ni coordination, thereby providing a blueprint for the design of bio‐inspired H2‐conversion catalysts.
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Affiliation(s)
- Yulia Ilina
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Jae-Hun Jeoung
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
| | - Seigo Shima
- Max-Planck-Institut für Terrestrische Mikrobiologie, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Marius Horch
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
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20
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Horch M, Schoknecht J, Wrathall SLD, Greetham GM, Lenz O, Hunt NT. Understanding the structure and dynamics of hydrogenases by ultrafast and two-dimensional infrared spectroscopy. Chem Sci 2019; 10:8981-8989. [PMID: 31762978 PMCID: PMC6857670 DOI: 10.1039/c9sc02851j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
Hydrogenases are valuable model enzymes for sustainable energy conversion approaches using H2, but rational utilization of these base-metal biocatalysts requires a detailed understanding of the structure and dynamics of their complex active sites. The intrinsic CO and CN- ligands of these metalloenzymes represent ideal chromophores for infrared (IR) spectroscopy, but structural and dynamic insight from conventional IR absorption experiments is limited. Here, we apply ultrafast and two-dimensional (2D) IR spectroscopic techniques, for the first time, to study hydrogenases in detail. Using an O2-tolerant [NiFe] hydrogenase as a model system, we demonstrate that IR pump-probe spectroscopy can explore catalytically relevant ligand bonding by accessing high-lying vibrational states. This ultrafast technique also shows that the protein matrix is influential in vibrational relaxation, which may be relevant for energy dissipation from the active site during fast reaction steps. Further insights into the relevance of the active site environment are provided by 2D-IR spectroscopy, which reveals equilibrium dynamics and structural constraints imposed on the H2-accepting intermediate of [NiFe] hydrogenases. Both techniques offer new strategies for uniquely identifying redox-structural states in complex catalytic mixtures via vibrational quantum beats and 2D-IR off-diagonal peaks. Together, these findings considerably expand the scope of IR spectroscopy in hydrogenase research, and new perspectives for the characterization of these enzymes and other (bio-)organometallic targets are presented.
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Affiliation(s)
- Marius Horch
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Janna Schoknecht
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Solomon L D Wrathall
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , Oxford , OX110PE , UK
| | - Oliver Lenz
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Neil T Hunt
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
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21
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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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22
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Abstract
Hydrogenases catalyze the simple yet important interconversion between H2 and protons and electrons. Found throughout prokaryotes, lower eukaryotes, and archaea, hydrogenases are used for a variety of redox and signaling purposes and are found in many different forms. This diverse group of metalloenzymes is divided into [NiFe], [FeFe], and [Fe] variants, based on the transition metal contents of their active sites. A wide array of biochemical and spectroscopic methods has been used to elucidate hydrogenases, and this along with a general description of the main enzyme types and catalytic mechanisms is discussed in this chapter.
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23
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Hartmann S, Frielingsdorf S, Ciaccafava A, Lorent C, Fritsch J, Siebert E, Priebe J, Haumann M, Zebger I, Lenz O. O2-Tolerant H2 Activation by an Isolated Large Subunit of a [NiFe] Hydrogenase. Biochemistry 2018; 57:5339-5349. [DOI: 10.1021/acs.biochem.8b00760] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sven Hartmann
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Stefan Frielingsdorf
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Alexandre Ciaccafava
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Christian Lorent
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Johannes Fritsch
- Department of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Elisabeth Siebert
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Jacqueline Priebe
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ingo Zebger
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Oliver Lenz
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
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24
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Moula G, Matsumoto T, Miehlich ME, Meyer K, Tatsumi K. Synthesis of an All-Ferric Cuboidal Iron-Sulfur Cluster [Fe III4 S 4 (SAr) 4 ]. Angew Chem Int Ed Engl 2018; 57:11594-11597. [PMID: 29775229 DOI: 10.1002/anie.201803679] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Indexed: 11/11/2022]
Abstract
An unprecedented, super oxidized all-ferric iron-sulfur cubanoid cluster with all terminal thiolates, Fe4 S4 (STbt)4 (3) [Tbt=2,4,6-tris{bis(trimethylsilyl)methyl}phenyl], has been isolated from the reaction of the bis-thiolate complex Fe(STbt)2 (2) with elemental sulfur. This cluster 3 has been characterized by X-ray crystallography, zero-field 57 Fe Mössbauer spectroscopy, cyclic voltammetry, and other relevant physico-chemical methods. Based on all the data, the electronic ground state of the cluster has been assigned to be Stot =0.
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Affiliation(s)
- Golam Moula
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan),
| | - Tsuyoshi Matsumoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Matthias E Miehlich
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Egerlandstrasse 1, 91058, Erlangen, Bavaria, Germany
| | - Karsten Meyer
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Egerlandstrasse 1, 91058, Erlangen, Bavaria, Germany
| | - Kazuyuki Tatsumi
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan),
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25
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Moula G, Matsumoto T, Miehlich ME, Meyer K, Tatsumi K. Synthesis of an All-Ferric Cuboidal Iron-Sulfur Cluster [FeIII
4
S4
(SAr)4
]. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Golam Moula
- Research Center for Materials Science; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan),
| | - Tsuyoshi Matsumoto
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Matthias E. Miehlich
- Department of Chemistry and Pharmacy; Inorganic Chemistry; Friedrich-Alexander-University Erlangen-Nürnberg (FAU); Egerlandstrasse 1 91058 Erlangen Bavaria Germany
| | - Karsten Meyer
- Department of Chemistry and Pharmacy; Inorganic Chemistry; Friedrich-Alexander-University Erlangen-Nürnberg (FAU); Egerlandstrasse 1 91058 Erlangen Bavaria Germany
| | - Kazuyuki Tatsumi
- Research Center for Materials Science; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan),
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26
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Kamnev AA, Tugarova AV. Sample treatment in Mössbauer spectroscopy for protein-related analyses: Nondestructive possibilities to look inside metal-containing biosystems. Talanta 2017; 174:819-837. [PMID: 28738659 DOI: 10.1016/j.talanta.2017.06.057] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/01/2017] [Accepted: 06/19/2017] [Indexed: 01/07/2023]
Abstract
In this review, the unique possibilities are considered of the 57Fe transmission (TMS) and 57Co emission (EMS) variants of Mössbauer (nuclear γ-resonance) spectroscopy as nondestructive techniques with minimal sample preparation/treatment and a significant analytical potential, with a focus on the analysis of cation-binding sites in metalloproteins. The techniques are shown to provide unique structural and quantitative information on the coordination microenvironment, the chemical state and transformations of the Mössbauer nuclides in sophisticated metal-containing proteins, including those within complicated supramolecular structures, and in microbial cells or tissues. Recent representative examples of analyses of Fe-containing proteins by 57Fe TMS are briefly discussed, along with the newly emerging data on using 57Co EMS for probing the structural organisation of 57Co-doped cation-binding sites in sophisticated biocomplexes including metalloenzymes. Finally, some rare or exotic applications of Mössbauer spectroscopy (including the synchrotron-based methodology) in protein-related studies are outlined.
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Affiliation(s)
- Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049, Saratov, Russia.
| | - Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049, Saratov, Russia
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27
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Ash PA, Hidalgo R, Vincent KA. Proton Transfer in the Catalytic Cycle of [NiFe] Hydrogenases: Insight from Vibrational Spectroscopy. ACS Catal 2017; 7:2471-2485. [PMID: 28413691 PMCID: PMC5387674 DOI: 10.1021/acscatal.6b03182] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/30/2017] [Indexed: 12/11/2022]
Abstract
![]()
Catalysis
of H2 production and oxidation reactions is
critical in renewable energy systems based around H2 as
a clean fuel, but the present reliance on platinum-based catalysts
is not sustainable. In nature, H2 is oxidized at minimal
overpotential and high turnover frequencies at [NiFe] catalytic sites
in hydrogenase enzymes. Although an outline mechanism has been established
for the [NiFe] hydrogenases involving heterolytic cleavage of H2 followed by a first and then second transfer of a proton
and electron away from the active site, details remain vague concerning
how the proton transfers are facilitated by the protein environment
close to the active site. Furthermore, although [NiFe] hydrogenases
from different organisms or cellular environments share a common active
site, they exhibit a broad range of catalytic characteristics indicating
the importance of subtle changes in the surrounding protein in controlling
their behavior. Here we review recent time-resolved infrared (IR)
spectroscopic studies and IR spectroelectrochemical studies carried
out in situ during electrocatalytic turnover. Additionally, we re-evaluate
the significant body of IR spectroscopic data on hydrogenase active
site states determined through more conventional solution studies,
in order to highlight mechanistic steps that seem to apply generally
across the [NiFe] hydrogenases, as well as steps which so far seem
limited to specific groups of these enzymes. This analysis is intended
to help focus attention on the key open questions where further work
is needed to assess important aspects of proton and electron transfer
in the mechanism of [NiFe] hydrogenases.
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Affiliation(s)
- Philip A. Ash
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ricardo Hidalgo
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kylie A. Vincent
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
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28
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Puggioni V, Tempel S, Latifi A. Distribution of Hydrogenases in Cyanobacteria: A Phylum-Wide Genomic Survey. Front Genet 2016; 7:223. [PMID: 28083017 PMCID: PMC5186783 DOI: 10.3389/fgene.2016.00223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/13/2016] [Indexed: 01/02/2023] Open
Abstract
Microbial Molecular hydrogen (H2) cycling plays an important role in several ecological niches. Hydrogenases (H2ases), enzymes involved in H2 metabolism, are of great interest for investigating microbial communities, and producing BioH2. To obtain an overall picture of the genetic ability of Cyanobacteria to produce H2ases, we conducted a phylum wide analysis of the distribution of the genes encoding these enzymes in 130 cyanobacterial genomes. The concomitant presence of the H2ase and genes involved in the maturation process, and that of well-conserved catalytic sites in the enzymes were the three minimal criteria used to classify a strain as being able to produce a functional H2ase. The [NiFe] H2ases were found to be the only enzymes present in this phylum. Fifty-five strains were found to be potentially able produce the bidirectional Hox enzyme and 33 to produce the uptake (Hup) enzyme. H2 metabolism in Cyanobacteria has a broad ecological distribution, since only the genomes of strains collected from the open ocean do not possess hox genes. In addition, the presence of H2ase was found to increase in the late branching clades of the phylogenetic tree of the species. Surprisingly, five cyanobacterial genomes were found to possess homologs of oxygen tolerant H2ases belonging to groups 1, 3b, and 3d. Overall, these data show that H2ases are widely distributed, and are therefore probably of great functional importance in Cyanobacteria. The present finding that homologs to oxygen-tolerant H2ases are present in this phylum opens new perspectives for applying the process of photosynthesis in the field of H2 production.
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Affiliation(s)
- Vincenzo Puggioni
- Laboratoire de Chimie Bactérienne UMR 7283, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University Marseille, France
| | - Sébastien Tempel
- Laboratoire de Chimie Bactérienne UMR 7283, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University Marseille, France
| | - Amel Latifi
- Laboratoire de Chimie Bactérienne UMR 7283, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University Marseille, France
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29
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Ogata H, Lubitz W, Higuchi Y. Structure and function of [NiFe] hydrogenases. J Biochem 2016; 160:251-258. [PMID: 27493211 DOI: 10.1093/jb/mvw048] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/06/2016] [Indexed: 12/22/2022] Open
Abstract
Hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons via a heterolytic splitting mechanism. The active sites of [NiFe] hydrogenases comprise a dinuclear Ni-Fe center carrying CO and CN- ligands. The catalytic activity of the standard (O2-sensitive) [NiFe] hydrogenases vanishes under aerobic conditions. The O2-tolerant [NiFe] hydrogenases can sustain H2 oxidation activity under atmospheric conditions. These hydrogenases have very similar active site structures that change the ligand sphere during the activation/catalytic process. An important structural difference between these hydrogenases has been found for the proximal iron-sulphur cluster located in the vicinity of the active site. This unprecedented [4Fe-3S]-6Cys cluster can supply two electrons, which lead to rapid recovery of the O2 inactivation, to the [NiFe] active site.
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Affiliation(s)
- Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, Mülheim an der Ruhr 45470, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, Mülheim an der Ruhr 45470, Germany
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan .,RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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30
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Brazzolotto D, Gennari M, Queyriaux N, Simmons TR, Pécaut J, Demeshko S, Meyer F, Orio M, Artero V, Duboc C. Nickel-centred proton reduction catalysis in a model of [NiFe] hydrogenase. Nat Chem 2016; 8:1054-1060. [PMID: 27768098 DOI: 10.1038/nchem.2575] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 06/13/2016] [Indexed: 02/07/2023]
Abstract
Hydrogen production through water splitting is one of the most promising solutions for the storage of renewable energy. [NiFe] hydrogenases are organometallic enzymes containing nickel and iron centres that catalyse hydrogen evolution with performances that rival those of platinum. These enzymes provide inspiration for the design of new molecular catalysts that do not require precious metals. However, all heterodinuclear NiFe models reported so far do not reproduce the Ni-centred reactivity found at the active site of [NiFe] hydrogenases. Here, we report a structural and functional NiFe mimic that displays reactivity at the Ni site. This is shown by the detection of two catalytic intermediates that reproduce structural and electronic features of the Ni-L and Ni-R states of the enzyme during catalytic turnover. Under electrocatalytic conditions, this mimic displays high rates for H2 evolution (second-order rate constant of 2.5 × 104 M-1 s-1; turnover frequency of 250 s-1 at 10 mM H+ concentration) from mildly acidic solutions.
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Affiliation(s)
- Deborah Brazzolotto
- Univ. Grenoble Alpes, CNRS UMR 5250, DCM, F-38000 Grenoble, France.,Univ. Grenoble Alpes, CNRS UMR 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Marcello Gennari
- Univ. Grenoble Alpes, CNRS UMR 5250, DCM, F-38000 Grenoble, France
| | - Nicolas Queyriaux
- Univ. Grenoble Alpes, CNRS UMR 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Trevor R Simmons
- Univ. Grenoble Alpes, CNRS UMR 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Jacques Pécaut
- Univ. Grenoble Alpes, INAC-LCIB, F-38000 Grenoble, France.,CEA, DRF-INAC-SyMMES, Reconnaissance Ionique et Chimie de Coordination, F-38000 Grenoble, France
| | - Serhiy Demeshko
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Franc Meyer
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.,International Center for Advanced Studies of Energy Conversion (ICASEC), Georg-August-University, D-37077 Göttingen, Germany
| | - Maylis Orio
- Institut des Sciences Moléculaires de Marseille, Aix Marseille Université, CNRS, Centrale Marseille, ISM2 UMR 7313, 13397, Marseille, France
| | - Vincent Artero
- Univ. Grenoble Alpes, CNRS UMR 5249, CEA, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Carole Duboc
- Univ. Grenoble Alpes, CNRS UMR 5250, DCM, F-38000 Grenoble, France
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31
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Chambers GM, Huynh MT, Li Y, Hammes-Schiffer S, Rauchfuss TB, Reijerse E, Lubitz W. Models of the Ni-L and Ni-SIa States of the [NiFe]-Hydrogenase Active Site. Inorg Chem 2016; 55:419-31. [PMID: 26421729 PMCID: PMC4807737 DOI: 10.1021/acs.inorgchem.5b01662] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new class of synthetic models for the active site of [NiFe]-hydrogenases are described. The Ni(I/II)(SCys)2 and Fe(II)(CN)2CO sites are represented with (RC5H4)Ni(I/II) and Fe(II)(diphos)(CO) modules, where diphos = 1,2-C2H4(PPh2)2(dppe) or cis-1,2-C2H2(PPh2)2(dppv). The two bridging thiolate ligands are represented by CH2(CH2S)2(2-) (pdt(2-)), Me2C(CH2S)2(2-) (Me2pdt(2-)), and (C6H5S)2(2-). The reaction of Fe(pdt)(CO)2(dppe) and [(C5H5)3Ni2]BF4 affords [(C5H5)Ni(pdt)Fe(dppe)(CO)]BF4 ([1a]BF4). Monocarbonyl [1a]BF4 features an S = 0 Ni(II)Fe(II) center with five-coordinated iron, as proposed for the Ni-SIa state of the enzyme. One-electron reduction of [1a](+) affords the S = 1/2 derivative [1a](0), which, according to density functional theory (DFT) calculations and electron paramagnetic resonance and Mössbauer spectroscopies, is best described as a Ni(I)Fe(II) compound. The Ni(I)Fe(II) assignment matches that for the Ni-L state in [NiFe]-hydrogenase, unlike recently reported Ni(II)Fe(I)-based models. Compound [1a](0) reacts with strong acids to liberate 0.5 equiv of H2 and regenerate [1a](+), indicating that H2 evolution is catalyzed by [1a](0). DFT calculations were used to investigate the pathway for H2 evolution and revealed that the mechanism can proceed through two isomers of [1a](0) that differ in the stereochemistry of the Fe(dppe)CO center. Calculations suggest that protonation of [1a](0) (both isomers) affords Ni(III)-H-Fe(II) intermediates, which represent mimics of the Ni-C state of the enzyme.
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32
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Behnke SL, Shafaat HS. Heterobimetallic Models of the [NiFe] Hydrogenases: A Structural and Spectroscopic Comparison. COMMENT INORG CHEM 2015. [DOI: 10.1080/02603594.2015.1108914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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Ash PA, Liu J, Coutard N, Heidary N, Horch M, Gudim I, Simler T, Zebger I, Lenz O, Vincent KA. Electrochemical and Infrared Spectroscopic Studies Provide Insight into Reactions of the NiFe Regulatory Hydrogenase from Ralstonia eutropha with O2 and CO. J Phys Chem B 2015; 119:13807-15. [PMID: 26115011 DOI: 10.1021/acs.jpcb.5b04164] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulatory hydrogenase (RH) from Ralstonia eutropha acts as the H2-sensing unit of a two-component system that regulates biosynthesis of the energy conserving hydrogenases of the organism according to the availability of H2. The H2 oxidation activity, which was so far determined in vitro with artificial electron acceptors, has been considered to be insensitive to O2 and CO. It is assumed that bulky isoleucine and phenylalanine amino acid residues close to the NiFe active site "gate" gas access, preventing molecules larger than H2 interacting with the active site. We have carried out sensitive electrochemical measurements to demonstrate that O2 is in fact an inhibitor of H2 oxidation by the RH, and that both H(+) reduction and H2 oxidation are inhibited by CO. Furthermore, we have demonstrated that the inhibitory effect of O2 arises due to interaction of O2 with the active site. Using protein film infrared electrochemistry (PFIRE) under H2 oxidation conditions, in conjunction with solution infrared measurements, we have identified previously unreported oxidized inactive and catalytically active reduced states of the RH active site. These findings suggest that the RH has a rich active site chemistry similar to that of other NiFe hydrogenases.
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Affiliation(s)
- Philip A Ash
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Juan Liu
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nathan Coutard
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nina Heidary
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Marius Horch
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Ingvild Gudim
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Thomas Simler
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Kylie A Vincent
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
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