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Wang H, Huang SD, Yan L, Hu MY, Zhao J, Alp EE, Yoda Y, Petersen CM, Thompson MK. Europium-151 and iron-57 nuclear resonant vibrational spectroscopy of naturally abundant KEu(III)Fe(II)(CN) 6 and Eu(III)Fe(III)(CN) 6 complexes. Dalton Trans 2022; 51:17753-17761. [PMID: 36346270 PMCID: PMC9933908 DOI: 10.1039/d2dt02600g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have performed and analyzed the first combined 151Eu and 57Fe nuclear resonant vibrational spectroscopy (NRVS) for naturally abundant KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] complexes. Comparison of the observed 151Eu vs.57Fe NRVS spectroscopic features confirms that Eu(III) in both KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] occupies a position outside the [Fe(CN)6] core and coordinates to the N atoms of the CN- ions, whereas Fe(III) or Fe(II) occupies the site inside the [Fe(CN)6]4- core and coordinates to the C atoms of the CN- ions. In addition to the spectroscopic interest, the results from this study provide invaluable insights for the design and evaluation of the nanoparticles of such complexes as potential cellular contrast agents for their use in magnetic resonance imaging. The combined 151Eu and 57Fe NRVS measurements are also among the first few explorations of bi-isotopic NRVS experiments.
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Affiliation(s)
| | - Songping D Huang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
| | - Lifen Yan
- SETI Institute, Mountain View, CA 94043, USA.
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ercan E Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo 679-5198, Japan
| | - Courtney M Petersen
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Matthew K Thompson
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA
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2
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Wang J, Yoda Y, Wang H. Tracking energy scale variations from scan to scan in nuclear resonant vibrational spectroscopy: In situ correction using zero-energy position drifts ΔE i rather than making in situ calibration measurements. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:095101. [PMID: 36182504 DOI: 10.1063/5.0086332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/24/2022] [Indexed: 06/16/2023]
Abstract
Nuclear resonant vibrational spectroscopy (NRVS) is an excellent modern vibrational spectroscopy, in particular, for revealing site-specific information inside complicated molecules, such as enzymes. There are two different concepts about the energy calibration for a beamline or a monochromator (including a high resolution monochromator): the absolute energy calibration and the practical energy calibration. While the former pursues an as-fine-as-possible and as-repeatable-as-possible result, the latter includes the environment influenced variation from scan to scan, which often needs an in situ calibration measurement to track. However, an in situ measurement often shares a weak beam intensity and therefore has a noisy NRVS spectrum at the calibration sample location, not leading to a better energy calibration/correction in most cases. NRVS users for a long time have noticed that there are energy drifts in the vibrational spectra's zero-energy positions from scan to scan (ΔEi), but their trend has not been explored and utilized in the past. In this publication, after providing a brief introduction to the critical issue(s) in practical NRVS energy calibrations, we have evaluated the trend and the mechanism for these zero-energy drifts (ΔEi) and explored their link to the energy scales (αi) from scan to scan. Via detailed analyses, we have established a new stepwise procedure for carrying out practical energy calibrations, which includes the correction for the scan-dependent energy variations using ΔEi values rather than running additional in situ calibration measurements. We also proved that one additional instrument-fixed scaling constant (α0) exists to convert such "calibrated" energy axis (E') to the real energy axis (Ereal). The "calibrated" real energy axis (Ereal) has a preliminary error bar of ±0.1% (the 2σE divided by the vibrational energy position), which is 4-8 times better than that from the current practical energy calibration procedure.
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Affiliation(s)
- Jessie Wang
- School of Computer Science, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Yoshitaka Yoda
- Research and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Hongxin Wang
- SETI Institute, Mountain View, California 94043, USA
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3
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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4
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Popescu C, Dinh T, Chen H, Miller D, Washburn A, McGuire A, Dumarieh R, D'Antonio J, Ghiladi RA. Mössbauer studies of the ferryl, ferrous and ferric states of dehaloperoxidase from A. ornata. J Inorg Biochem 2022; 234:111867. [DOI: 10.1016/j.jinorgbio.2022.111867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/13/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
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5
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Wang H, Braun A, Cramer SP, Gee LB, Yoda Y. Nuclear Resonance Vibrational Spectroscopy: A Modern Tool to Pinpoint Site-Specific Cooperative Processes. Catalysts 2021; 11:909. [PMID: 35582460 PMCID: PMC9109880 DOI: 10.3390/cryst11080909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Nuclear resonant vibrational spectroscopy (NRVS) is a synchrotron radiation (SR)-based nuclear inelastic scattering spectroscopy that measures the phonons (i.e., vibrational modes) associated with the nuclear transition. It has distinct advantages over traditional vibration spectroscopy and has wide applications in physics, chemistry, bioinorganic chemistry, materials sciences, and geology, as well as many other research areas. In this article, we present a scientific and figurative description of this yet modern tool for the potential users in various research fields in the future. In addition to short discussions on its development history, principles, and other theoretical issues, the focus of this article is on the experimental aspects, such as the instruments, the practical measurement issues, the data process, and a few examples of its applications. The article concludes with introduction to non-57Fe NRVS and an outlook on the impact from the future upgrade of SR rings.
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Affiliation(s)
| | - Artur Braun
- Laboratory for High Performance Ceramics, Empa. Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland
| | | | - Leland B. Gee
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo 679-5198, Japan
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6
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Lorent C, Pelmenschikov V, Frielingsdorf S, Schoknecht J, Caserta G, Yoda Y, Wang H, Tamasaku K, Lenz O, Cramer SP, Horch M, Lauterbach L, Zebger I. Exploring Structure and Function of Redox Intermediates in [NiFe]-Hydrogenases by an Advanced Experimental Approach for Solvated, Lyophilized and Crystallized Metalloenzymes. Angew Chem Int Ed Engl 2021; 60:15854-15862. [PMID: 33783938 PMCID: PMC8360142 DOI: 10.1002/anie.202100451] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/20/2021] [Indexed: 01/28/2023]
Abstract
To study metalloenzymes in detail, we developed a new experimental setup allowing the controlled preparation of catalytic intermediates for characterization by various spectroscopic techniques. The in situ monitoring of redox transitions by infrared spectroscopy in enzyme lyophilizate, crystals, and solution during gas exchange in a wide temperature range can be accomplished as well. Two O2 -tolerant [NiFe]-hydrogenases were investigated as model systems. First, we utilized our platform to prepare highly concentrated hydrogenase lyophilizate in a paramagnetic state harboring a bridging hydride. This procedure proved beneficial for 57 Fe nuclear resonance vibrational spectroscopy and revealed, in combination with density functional theory calculations, the vibrational fingerprint of this catalytic intermediate. The same in situ IR setup, combined with resonance Raman spectroscopy, provided detailed insights into the redox chemistry of enzyme crystals, underlining the general necessity to complement X-ray crystallographic data with spectroscopic analyses.
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Affiliation(s)
- Christian Lorent
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Vladimir Pelmenschikov
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Stefan Frielingsdorf
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Janna Schoknecht
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Giorgio Caserta
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Mikazuki-choSayo-gunHyogo679-5198Japan
| | - Hongxin Wang
- SETI Institute189 Bernardo AvenueMountain ViewCalifornia94043USA
| | - Kenji Tamasaku
- RIKEN SPring-8 center1-1-1 Kouto, Sayo-choSayo-gunHyogo679-5148Japan
| | - Oliver Lenz
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | | | - Marius Horch
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
- Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Lars Lauterbach
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Ingo Zebger
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
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7
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Lorent C, Pelmenschikov V, Frielingsdorf S, Schoknecht J, Caserta G, Yoda Y, Wang H, Tamasaku K, Lenz O, Cramer SP, Horch M, Lauterbach L, Zebger I. Ein neuer Aufbau zur Untersuchung der Struktur und Funktion von solvatisierten, lyophilisierten und kristallinen Metalloenzymen – veranschaulicht anhand von [NiFe]‐Hydrogenasen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christian Lorent
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Vladimir Pelmenschikov
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Stefan Frielingsdorf
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Janna Schoknecht
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Giorgio Caserta
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute SPring-8 1-1-1 Kouto, Mikazuki-cho Sayo-gun Hyogo 679-5198 Japan
| | - Hongxin Wang
- SETI Institute 189 Bernardo Avenue Mountain View California 94043 USA
| | - Kenji Tamasaku
- RIKEN SPring-8 center 1-1-1 Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Oliver Lenz
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Stephen P. Cramer
- SETI Institute 189 Bernardo Avenue Mountain View California 94043 USA
| | - Marius Horch
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
- Department of Physics Freie Universität Berlin Arnimallee 14 14195 Berlin Deutschland
| | - Lars Lauterbach
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Ingo Zebger
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
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8
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Murueta‐Cruz BA, Berlanga‐Vázquez A, Martínez‐Otero D, Benitez LN, Castillo I, Mondragón‐Díaz A. Planar or Bent? Redox Modulation of Hydrogenase Bimetallic Models by the [Ni
2
(μ‐SAr)
2
] Core Conformation. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brenda A. Murueta‐Cruz
- Departamento de Química Facultad de Ciencias Universidad del Valle Ciudad Universitaria Meléndez Calle 13 # 100-00 Cali Colombia
| | - Armando Berlanga‐Vázquez
- Instituto de Química Universidad Nacional Autónoma de México Ciudad Universitaria 04510 Ciudad de México México
| | - Diego Martínez‐Otero
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM Carretera Toluca-Atlacomulco km 14.5 Toluca 50200 Estado de México México
| | - Luis Norberto Benitez
- Departamento de Química Facultad de Ciencias Universidad del Valle Ciudad Universitaria Meléndez Calle 13 # 100-00 Cali Colombia
| | - Ivan Castillo
- Instituto de Química Universidad Nacional Autónoma de México Ciudad Universitaria 04510 Ciudad de México México
| | - Alexander Mondragón‐Díaz
- Departamento de Química Facultad de Ciencias Universidad del Valle Ciudad Universitaria Meléndez Calle 13 # 100-00 Cali Colombia
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9
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Orio M, Pantazis DA. Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research. Chem Commun (Camb) 2021; 57:3952-3974. [DOI: 10.1039/d1cc00705j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.
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Affiliation(s)
- Maylis Orio
- Aix-Marseille Université
- CNRS
- iSm2
- Marseille
- France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470 Mülheim an der Ruhr
- Germany
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10
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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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11
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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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12
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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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13
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Yaashikaa P, Senthil Kumar P, Varjani SJ, Saravanan A. A review on photochemical, biochemical and electrochemical transformation of CO2 into value-added products. J CO2 UTIL 2019. [DOI: 10.1016/j.jcou.2019.05.017] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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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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15
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Carlson MR, Gray DL, Richers CP, Wang W, Zhao PH, Rauchfuss TB, Pelmenschikov V, Pham CC, Gee LB, Wang H, Cramer SP. Sterically Stabilized Terminal Hydride of a Diiron Dithiolate. Inorg Chem 2018; 57:1988-2001. [PMID: 29384371 DOI: 10.1021/acs.inorgchem.7b02903] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The kinetically robust hydride [t-HFe2(Me2pdt)(CO)2(dppv)2]+ ([t-H1]+) (Me2pdt2- = Me2C(CH2S-)2; dppv = cis-1,2-C2H2(PPh2)2) and related derivatives were prepared with 57Fe enrichment for characterization by NMR, FT-IR, and NRVS. The experimental results were rationalized using DFT molecular modeling and spectral simulations. The spectroscopic analysis was aimed at supporting assignments of Fe-H vibrational spectra as they relate to recent measurements on [FeFe]-hydrogenase enzymes. The combination of bulky Me2pdt2- and dppv ligands stabilizes the terminal hydride with respect to its isomerization to the 5-16 kcal/mol more stable bridging hydride ([μ-H1]+) with t1/2(313.3 K) = 19.3 min. In agreement with the nOe experiments, the calculations predict that one methyl group in [t-H1]+ interacts with the hydride with a computed CH···HFe distance of 1.7 Å. Although [t-H571]+ exhibits multiple NRVS features in the 720-800 cm-1 region containing the bending Fe-H modes, the deuterated [t-D571]+ sample exhibits a unique Fe-D/CO band at ∼600 cm-1. In contrast, the NRVS spectra for [μ-H571]+ exhibit weaker bands near 670-700 cm-1 produced by the Fe-H-Fe wagging modes coupled to Me2pdt2- and dppv motions.
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Affiliation(s)
- Michaela R Carlson
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Danielle L Gray
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Casseday P Richers
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Wenguang Wang
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Pei-Hua Zhao
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | | | - Cindy C Pham
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Leland B Gee
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Hongxin Wang
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California , Davis, California 95616, United States
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16
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Abstract
For over 20 years, nuclear resonance vibrational spectroscopy (NRVS) has been used to study vibrational dynamics of iron-containing materials. With the only selection rule being iron motion, 57Fe NRVS has become an excellent tool to study iron-containing enzymes. Over the past decade, considerable progress has been made in the study of complex metalloenzymes using NRVS. Iron cofactors in heme-containing globins; [2Fe2S], [3Fe4S], [4Fe4S] proteins; the [NiFe] and [FeFe] hydrogenases; and nitrogenases have been explored in a fashion not possible through traditional vibrational spectroscopy. In this chapter, we discuss the basics of NRVS, a strategy to perform NRVS, and a discussion of the application of NRVS on rubredoxin and [FeFe] hydrogenase.
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Affiliation(s)
- Leland B Gee
- University of California, Davis, Davis, CA, United States.
| | - Hongxin Wang
- University of California, Davis, Davis, CA, United States
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17
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Zegkinoglou I, Zendegani A, Sinev I, Kunze S, Mistry H, Jeon HS, Zhao J, Hu MY, Alp EE, Piontek S, Smialkowski M, Apfel UP, Körmann F, Neugebauer J, Hickel T, Roldan Cuenya B. Operando Phonon Studies of the Protonation Mechanism in Highly Active Hydrogen Evolution Reaction Pentlandite Catalysts. J Am Chem Soc 2017; 139:14360-14363. [DOI: 10.1021/jacs.7b07902] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ali Zendegani
- Max-Planck-Institut für Eisenforschung, 40237 Düsseldorf, Germany
| | - Ilya Sinev
- Department
of Physics, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Sebastian Kunze
- Department
of Physics, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Hemma Mistry
- Department
of Physics, Ruhr-University Bochum, 44780 Bochum, Germany
- Department
of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Hyo Sang Jeon
- Department
of Physics, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Jiyong Zhao
- Advanced
Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Michael Y. Hu
- Advanced
Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Stefan Piontek
- Inorganic
Chemistry I, Ruhr-University Bochum, 44780 Bochum, Germany
| | | | - Ulf-Peter Apfel
- Inorganic
Chemistry I, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Fritz Körmann
- Max-Planck-Institut für Eisenforschung, 40237 Düsseldorf, Germany
| | - Jörg Neugebauer
- Max-Planck-Institut für Eisenforschung, 40237 Düsseldorf, Germany
| | - Tilmann Hickel
- Max-Planck-Institut für Eisenforschung, 40237 Düsseldorf, Germany
| | - Beatriz Roldan Cuenya
- Department
of Physics, Ruhr-University Bochum, 44780 Bochum, Germany
- Department
of Interface Science, Fritz-Haber Institute of the Max Planck Society, 14195 Berlin, Germany
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18
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O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors. Chembiochem 2017; 18:914-920. [PMID: 28253432 PMCID: PMC5445010 DOI: 10.1002/cbic.201700052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 11/11/2022]
Abstract
Isoprenoid biosynthesis is an important area for anti-infective drug development. One isoprenoid target is (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) reductase (IspH), which forms isopentenyl diphosphate and dimethylallyl diphosphate from HMBPP in a 2H+ /2e- reduction. IspH contains a 4 Fe-4 S cluster, and in this work, we first investigated how small molecules bound to the cluster by using HYSCORE and NRVS spectroscopies. The results of these, as well as other structural and spectroscopic investigations, led to the conclusion that, in most cases, ligands bound to IspH 4 Fe-4 S clusters by η1 coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2 O, O2 ) binding. Based on these ideas, we used in silico methods to find drug-like inhibitors that might occupy the HMBPP substrate binding pocket and bind to Fe, leading to the discovery of a barbituric acid analogue with a Ki value of ≈500 nm against Pseudomonas aeruginosa IspH.
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Affiliation(s)
- Bing O'Dowd
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Sarah Williams
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Hongxin Wang
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Joo Hwan No
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Weixue Wang
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093, USA
- National Biomedical Computation Resource, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Stephen P Cramer
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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19
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Reijerse EJ, Pham CC, Pelmenschikov V, Gilbert-Wilson R, Adamska-Venkatesh A, Siebel JF, Gee LB, Yoda Y, Tamasaku K, Lubitz W, Rauchfuss TB, Cramer SP. Direct Observation of an Iron-Bound Terminal Hydride in [FeFe]-Hydrogenase by Nuclear Resonance Vibrational Spectroscopy. J Am Chem Soc 2017; 139:4306-4309. [PMID: 28291336 PMCID: PMC5545132 DOI: 10.1021/jacs.7b00686] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
[FeFe]-hydrogenases catalyze the reversible reduction of protons to molecular hydrogen with extremely high efficiency. The active site ("H-cluster") consists of a [4Fe-4S]H cluster linked through a bridging cysteine to a [2Fe]H subsite coordinated by CN- and CO ligands featuring a dithiol-amine moiety that serves as proton shuttle between the protein proton channel and the catalytic distal iron site (Fed). Although there is broad consensus that an iron-bound terminal hydride species must occur in the catalytic mechanism, such a species has never been directly observed experimentally. Here, we present FTIR and nuclear resonance vibrational spectroscopy (NRVS) experiments in conjunction with density functional theory (DFT) calculations on an [FeFe]-hydrogenase variant lacking the amine proton shuttle which is stabilizing a putative hydride state. The NRVS spectra unequivocally show the bending modes of the terminal Fe-H species fully consistent with widely accepted models of the catalytic cycle.
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Affiliation(s)
- Edward J. Reijerse
- Max-Planck-Institut für Chemische Energiekonversion, Stitstrasse 34-36, 45470 Mülheim, Germany
| | - Cindy C. Pham
- Department of Chemistry, University of California, Davis, California 95616, United States
| | | | - Ryan Gilbert-Wilson
- School of Chemical Sciences, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | | | - Judith F. Siebel
- Max-Planck-Institut für Chemische Energiekonversion, Stitstrasse 34-36, 45470 Mülheim, Germany
| | - Leland B. Gee
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Yoshitaka Yoda
- Materials Dynamics Laboratory, RIKEN SPring-8, Hyogo 679-5148, Japan
| | - Kenji Tamasaku
- Materials Dynamics Laboratory, RIKEN SPring-8, Hyogo 679-5148, Japan
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stitstrasse 34-36, 45470 Mülheim, Germany
| | - Thomas B. Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Stephen P. Cramer
- Department of Chemistry, University of California, Davis, California 95616, United States
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20
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Yoda Y, Okada K, Wang H, Cramer SP, Seto M. High-resolution monochromator for iron nuclear resonance vibrational spectroscopy of biological samples. JAPANESE JOURNAL OF APPLIED PHYSICS. PART 1, REGULAR PAPERS & SHORT NOTES 2016; 55:122401. [PMID: 29503983 PMCID: PMC5831540 DOI: 10.7567/jjap.55.122401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A new high-resolution monochromator for 14.4-keV X-rays has been designed and developed for the Fe nuclear resonance vibrational spectroscopy of biological samples. Higher flux and stability are especially important for measuring biological samples, because of the very weak signals produced due to the low concentrations of Fe-57. A 24% increase in flux while maintaining a high resolution below 0.9 meV is achieved in the calculation by adopting an asymmetric reflection of Ge, which is used as the first crystal of the three-bounce high-resolution monochromator. The small cost resulting from a 20% increase of the exit beam size is acceptable to our biological applications. The higher throughput of the new design has been experimentally verified. A fine rotation mechanics that that combines a weak-link hinge with a piezoelectric actuator was used for controlling the photon energy of the monochromatic beam. The resulting stability is sufficient to preserve the intrinsic resolution.
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Affiliation(s)
- Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute/SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kyoko Okada
- Japan Synchrotron Radiation Research Institute/SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Hongxin Wang
- Department of Chemistry, University of California, 1 Shields Ave., Davis, CA, 95616, United States
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA, 94720, United States
| | - Stephen P. Cramer
- Department of Chemistry, University of California, 1 Shields Ave., Davis, CA, 95616, United States
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA, 94720, United States
| | - Makoto Seto
- Research Reactor Institute, Kyoto University, 2-1010 Asashiro-nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan
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21
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Serrano PN, Wang H, Crack JC, Prior C, Hutchings MI, Thomson AJ, Kamali S, Yoda Y, Zhao J, Hu MY, Alp EE, Oganesyan VS, Le Brun NE, Cramer SP. Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes. Angew Chem Int Ed Engl 2016; 55:14575-14579. [PMID: 27778474 PMCID: PMC5204455 DOI: 10.1002/anie.201607033] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/05/2016] [Indexed: 12/13/2022]
Abstract
The reaction of protein-bound iron-sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2 (NO)4 (Cys)2 ]) and Roussin's Black Salt (RBS, [Fe4 (NO)7 S3 ]. In the latter case, the absence of 32 S/34 S shifts in the Fe-S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates.
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Affiliation(s)
| | - Hongxin Wang
- Department of ChemistryUniversity of CaliforniaDavisCA95616USA
- Physical Biosciences DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Jason C. Crack
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Christopher Prior
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | | | - Andrew J. Thomson
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Saeed Kamali
- University of Tennessee Space InstituteTullahomeTN37388-9700USA
| | - Yoshitaka Yoda
- Research and Utilization DivisionSPring-8/JASRI1-1-1 Kouto, SayoHyogo679-5198Japan
| | - Jiyong Zhao
- Advanced Photon SourceArgonne National LaboratoryArgonneIL60439USA
| | - Michael Y. Hu
- Advanced Photon SourceArgonne National LaboratoryArgonneIL60439USA
| | - Ercan E. Alp
- Advanced Photon SourceArgonne National LaboratoryArgonneIL60439USA
| | - Vasily S. Oganesyan
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Nick E. Le Brun
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Stephen P. Cramer
- Department of ChemistryUniversity of CaliforniaDavisCA95616USA
- Physical Biosciences DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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22
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Katz S, Noth J, Horch M, Shafaat HS, Happe T, Hildebrandt P, Zebger I. Vibrational spectroscopy reveals the initial steps of biological hydrogen evolution. Chem Sci 2016; 7:6746-6752. [PMID: 28451119 PMCID: PMC5355867 DOI: 10.1039/c6sc01098a] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/29/2016] [Indexed: 12/30/2022] Open
Abstract
[FeFe] hydrogenases are biocatalytic model systems for the exploitation and investigation of catalytic hydrogen evolution. Here, we used vibrational spectroscopic techniques to characterize, in detail, redox transformations of the [FeFe] and [4Fe4S] sub-sites of the catalytic centre (H-cluster) in a monomeric [FeFe] hydrogenase. Through the application of low-temperature resonance Raman spectroscopy, we discovered a novel metastable intermediate that is characterized by an oxidized [FeIFeII] centre and a reduced [4Fe4S]1+ cluster. Based on this unusual configuration, this species is assigned to the first, deprotonated H-cluster intermediate of the [FeFe] hydrogenase catalytic cycle. Providing insights into the sequence of initial reaction steps, the identification of this species represents a key finding towards the mechanistic understanding of biological hydrogen evolution.
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Affiliation(s)
- S Katz
- Institut für Chemie , Technische Universitaet Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany . ;
| | - J Noth
- Fakultaet für Biologie und Biotechnologie , Lehrstuhl für Biochemie der Pflanzen , AG Photobiotechnologie , Ruhr-Universitaet Bochum , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - M Horch
- Institut für Chemie , Technische Universitaet Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany . ;
| | - H S Shafaat
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 , Muelheim an der Ruhr , Germany
| | - T Happe
- Fakultaet für Biologie und Biotechnologie , Lehrstuhl für Biochemie der Pflanzen , AG Photobiotechnologie , Ruhr-Universitaet Bochum , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - P Hildebrandt
- Institut für Chemie , Technische Universitaet Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany . ;
| | - I Zebger
- Institut für Chemie , Technische Universitaet Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany . ;
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23
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Serrano PN, Wang H, Crack JC, Prior C, Hutchings MI, Thomson AJ, Kamali S, Yoda Y, Zhao J, Hu MY, Alp EE, Oganesyan VS, Le Brun NE, Cramer SP. Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Hongxin Wang
- Department of Chemistry; University of California; Davis CA 95616 USA
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
| | - Jason C. Crack
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - Christopher Prior
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | | | - Andrew J. Thomson
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - Saeed Kamali
- University of Tennessee Space Institute; Tullahome TN 37388-9700 USA
| | - Yoshitaka Yoda
- Research and Utilization Division; SPring-8/JASRI; 1-1-1 Kouto, Sayo Hyogo 679-5198 Japan
| | - Jiyong Zhao
- Advanced Photon Source; Argonne National Laboratory; Argonne IL 60439 USA
| | - Michael Y. Hu
- Advanced Photon Source; Argonne National Laboratory; Argonne IL 60439 USA
| | - Ercan E. Alp
- Advanced Photon Source; Argonne National Laboratory; Argonne IL 60439 USA
| | - Vasily S. Oganesyan
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - Stephen P. Cramer
- Department of Chemistry; University of California; Davis CA 95616 USA
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
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24
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Schilter D, Camara JM, Huynh MT, Hammes-Schiffer S, Rauchfuss TB. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides. Chem Rev 2016; 116:8693-749. [PMID: 27353631 PMCID: PMC5026416 DOI: 10.1021/acs.chemrev.6b00180] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.
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Affiliation(s)
- David Schilter
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - James M. Camara
- Department of Chemistry, Yeshiva University, 500 West 185th Street, New York, New York 10033, United States
| | - Mioy T. Huynh
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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25
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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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26
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Lauterbach L, Gee LB, Pelmenschikov V, Jenney FE, Kamali S, Yoda Y, Adams MWW, Cramer SP. Characterization of the [3Fe-4S](0/1+) cluster from the D14C variant of Pyrococcus furiosus ferredoxin via combined NRVS and DFT analyses. Dalton Trans 2016; 45:7215-9. [PMID: 27063792 PMCID: PMC4940129 DOI: 10.1039/c5dt04760a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The D14C variant of Pyrococcus furiosus ferredoxin provides an extraordinary framework to investigate a [3Fe-4S] cluster at two oxidation levels and compare the results to its physiologic [4Fe-4S] counterpart in the very same protein. Our spectroscopic and computational study reveals vibrational property changes related to the electronic and structural aspects of both Fe-S clusters.
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Affiliation(s)
- Lars Lauterbach
- Department of Chemistry, University of California, Davis, CA 95616, USA and Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Leland B Gee
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | | | - Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA 30024, USA
| | - Saeed Kamali
- Department of Chemistry, University of California, Davis, CA 95616, USA and Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee Space Institute, Tullahoma, TN 37388, USA
| | | | - Michael W W Adams
- Department of Biochemistry & Molecular Biology, Life Sciences Building, University of Georgia, Athens, GA 30602, USA
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, USA and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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27
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Wang H, Yoda Y, Ogata H, Tanaka Y, Lubitz W. A strenuous experimental journey searching for spectroscopic evidence of a bridging nickel-iron-hydride in [NiFe] hydrogenase. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1334-44. [PMID: 26524296 PMCID: PMC4629863 DOI: 10.1107/s1600577515017816] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/23/2015] [Indexed: 05/24/2023]
Abstract
Direct spectroscopic evidence for a hydride bridge in the Ni-R form of [NiFe] hydrogenase has been obtained using iron-specific nuclear resonance vibrational spectroscopy (NRVS). The Ni-H-Fe wag mode at 675 cm(-1) is the first spectroscopic evidence for a bridging hydride in Ni-R as well as the first iron-hydride-related NRVS feature observed for a biological system. Although density function theory (DFT) calculation assisted the determination of the Ni-R structure, it did not predict the Ni-H-Fe wag mode at ∼ 675 cm(-1) before NRVS. Instead, the observed Ni-H-Fe mode provided a critical reference for the DFT calculations. While the overall science about Ni-R is presented and discussed elsewhere, this article focuses on the long and strenuous experimental journey to search for and experimentally identify the Ni-H-Fe wag mode in a Ni-R sample. As a methodology, the results presented here will go beyond Ni-R and hydrogenase research and will also be of interest to other scientists who use synchrotron radiation for measuring dilute samples or weak spectroscopic features.
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Affiliation(s)
- Hongxin Wang
- Department of Chemistry, University of California, 1 Cyclotron Road, Davis, CA 95616, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yoshitaka Yoda
- Research and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Yoshihito Tanaka
- Research and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
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28
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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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29
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoidbiosynthese in pathogenen Bakterien: Nukleare inelastische Streuung ermöglicht Einblicke in den ungewöhnlichen [4Fe-4S]-Cluster vom E.- coli-Protein LytB/IspH. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy. Nat Commun 2015; 6:7890. [PMID: 26259066 PMCID: PMC4531378 DOI: 10.1038/ncomms8890] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/18/2015] [Indexed: 11/28/2022] Open
Abstract
The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging' mode involving H− motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H− binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts. Understanding the catalytic mechanism of redox-active hydrogenases is a key to efficient hydrogen production and consumption. Here, the authors use nuclear resonance vibrational spectroscopy to study [NiFe]-hydrogenase, and observe a bridging hydride structure in an EPR silent intermediate.
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31
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Gilbert-Wilson R, Siebel JF, Adamska-Venkatesh A, Pham CC, Reijerse E, Wang H, Cramer SP, Lubitz W, Rauchfuss TB. Spectroscopic Investigations of [FeFe] Hydrogenase Maturated with [(57)Fe2(adt)(CN)2(CO)4](2-). J Am Chem Soc 2015; 137:8998-9005. [PMID: 26091969 DOI: 10.1021/jacs.5b03270] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The preparation and spectroscopic characterization of a CO-inhibited [FeFe] hydrogenase with a selectively (57)Fe-labeled binuclear subsite is described. The precursor [(57)Fe2(adt)(CN)2(CO)4](2-) was synthesized from the (57)Fe metal, S8, CO, (NEt4)CN, NH4Cl, and CH2O. (Et4N)2[(57)Fe2(adt)(CN)2(CO)4] was then used for the maturation of the [FeFe] hydrogenase HydA1 from Chlamydomonas reinhardtii, to yield the enzyme selectively labeled at the [2Fe]H subcluster. Complementary (57)Fe enrichment of the [4Fe-4S]H cluster was realized by reconstitution with (57)FeCl3 and Na2S. The Hox-CO state of [2(57)Fe]H and [4(57)Fe-4S]H HydA1 was characterized by Mössbauer, HYSCORE, ENDOR, and nuclear resonance vibrational spectroscopy.
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Affiliation(s)
- Ryan Gilbert-Wilson
- †School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Judith F Siebel
- ‡Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Agnieszka Adamska-Venkatesh
- ‡Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Cindy C Pham
- §Department of Chemistry, University of California, Davis, California 95616, United States
| | - Edward Reijerse
- ‡Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hongxin Wang
- §Department of Chemistry, University of California, Davis, California 95616, United States.,∥Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stephen P Cramer
- §Department of Chemistry, University of California, Davis, California 95616, United States.,∥Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Wolfgang Lubitz
- ‡Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Thomas B Rauchfuss
- †School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoid Biosynthesis in Pathogenic Bacteria: Nuclear Resonance Vibrational Spectroscopy Provides Insight into the Unusual [4Fe-4S] Cluster of the E. coli LytB/IspH Protein. Angew Chem Int Ed Engl 2015; 54:12584-7. [PMID: 26118554 DOI: 10.1002/anie.201502494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/10/2022]
Abstract
The LytB/IspH protein catalyzes the last step of the methylerythritol phosphate (MEP) pathway which is used for the biosynthesis of essential terpenoids in most pathogenic bacteria. Therefore, the MEP pathway is a target for the development of new antimicrobial agents as it is essential for microorganisms, yet absent in humans. Substrate-free LytB has a special [4Fe-4S](2+) cluster with a yet unsolved structure. This motivated us to use synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) in combination with quantum chemical-molecular mechanical (QM/MM) calculations to gain more insight into the structure of substrate-free LytB. The apical iron atom of the [4Fe-4S](2+) is clearly linked to three water molecules. We additionally present NRVS data of LytB bound to its natural substrate, (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) and to the inhibitors (E)-4-amino-3-methylbut-2-en-1-yl diphosphate and (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate.
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Affiliation(s)
- Isabelle Faus
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Annegret Reinhard
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Sergej Rackwitz
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Juliusz A Wolny
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Kai Schlage
- P01, Petra III, DESY, Notkestrasse 85, D-22607 Hamburg (Germany)
| | | | - Aleksandr Chumakov
- ESRF - The European Synchrotron, CS40220, 38043 Grenoble Cedex 9 (France)
| | - Sergiy Krasutsky
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Philippe Chaignon
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France)
| | - C Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Myriam Seemann
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France).
| | - Volker Schünemann
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany).
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33
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Schilter D, Pelmenschikov V, Wang H, Meier F, Gee LB, Yoda Y, Kaupp M, Rauchfuss TB, Cramer SP. Synthesis and vibrational spectroscopy of (57)Fe-labeled models of [NiFe] hydrogenase: first direct observation of a nickel-iron interaction. Chem Commun (Camb) 2015; 50:13469-72. [PMID: 25237680 PMCID: PMC4191989 DOI: 10.1039/c4cc04572f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isotopically labelled Ni57Fe models of the [NiFe] hydrogenase active site have been prepared and studied with nuclear resonant vibrational spectroscopy, enabling direct characterization of metal–metal bonding.
A new route to iron carbonyls has enabled synthesis of 57Fe-labeled [NiFe] hydrogenase mimic (OC)357Fe(pdt)Ni(dppe). Its study by nuclear resonance vibrational spectroscopy revealed Ni–57Fe vibrations, as confirmed by calculations. The modes are absent for [(OC)357Fe(pdt)Ni(dppe)]+, which lacks Ni–57Fe bonding, underscoring the utility of the analyses in identifying metal–metal interactions.
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Affiliation(s)
- David Schilter
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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34
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Horch M, Hildebrandt P, Zebger I. Concepts in bio-molecular spectroscopy: vibrational case studies on metalloenzymes. Phys Chem Chem Phys 2015; 17:18222-37. [DOI: 10.1039/c5cp02447a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Challenges and chances in bio-molecular spectroscopy are exemplified by vibrational case studies on metalloenzymes.
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Affiliation(s)
- M. Horch
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - P. Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - I. Zebger
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
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35
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Lauterbach L, Wang H, Horch M, Gee LB, Yoda Y, Tanaka Y, Zebger I, Lenz O, Cramer SP. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O 2-tolerant NAD +-reducing [NiFe] hydrogenase. Chem Sci 2015; 6:1055-1060. [PMID: 25678951 PMCID: PMC4321745 DOI: 10.1039/c4sc02982h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nuclear resonance vibrational spectroscopy is used to characterize all Fe-containing cofactors in a complex multicofactor enzyme.
Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.
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Affiliation(s)
- Lars Lauterbach
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany ; Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA
| | - Hongxin Wang
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA
| | - Marius Horch
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Leland B Gee
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA
| | - Yoshitaka Yoda
- JASRI, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshihito Tanaka
- RIKEN, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Ingo Zebger
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Stephen P Cramer
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA
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36
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Liu K, Rykov AI, Wang J, Zhang T. Recent Advances in the Application of Mößbauer Spectroscopy in Heterogeneous Catalysis. ADVANCES IN CATALYSIS 2015. [DOI: 10.1016/bs.acat.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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37
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Scott A, Pelmenschikov V, Guo Y, Yan L, Wang H, George SJ, Dapper CH, Newton WE, Yoda Y, Tanaka Y, Cramer SP. Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom. J Am Chem Soc 2014; 136:15942-54. [PMID: 25275608 PMCID: PMC4235365 DOI: 10.1021/ja505720m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 01/21/2023]
Abstract
The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.
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Affiliation(s)
- Aubrey
D. Scott
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | | | - Yisong Guo
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Lifen Yan
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Hongxin Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
| | - Simon J. George
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Christie H. Dapper
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - William E. Newton
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - Yoshitaka Yoda
- Research
and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshihito Tanaka
- SR
Materials Science Instrumentation Unit, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Stephen P. Cramer
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
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38
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Vedha SA, Solomon RV, Venuvanalingam P. Atomic partitioning of M-H2 bonds in [NiFe] hydrogenase--a test case of concurrent binding. Phys Chem Chem Phys 2014; 16:10698-707. [PMID: 24756140 DOI: 10.1039/c4cp00526k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility of simultaneous addition of η(2)-H2 to both the metals (Ni and Fe) in the active site of the as isolated state of the enzyme (Ni-SI) is examined here by an atom-by-atom electronic energy partitioning based on the QTAIM method. Results show that the 4LS state prefers H2 removal than addition. Destabilization of the atomic basins of the thiolate bridges and decrease of the electrophilicity of the Fe and Ni, resulting in poor back donation to the CO ligand, are the bottlenecks that hamper dihydrogen activation simultaneously. The study helps to understand why such states are seldom accessed in the activation of dihydrogen. Moreover, Ni has been found to be the natural choice for the dihydrogen binding.
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Affiliation(s)
- Swaminathan Angeline Vedha
- Theoretical & Computational Chemistry Laboratory, School of Chemistry, Bharathidasan University, Tiruchirappalli 24, India.
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39
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Humboldt and Bessel Research Awards. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201401120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Humboldt- und Bessel-Forschungspreise. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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42
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Carroll M, Chen J, Gray DE, Lansing JC, Rauchfuss TB, Schilter D, Volkers PI, Wilson S. Ferrous Carbonyl Dithiolates as Precursors to FeFe, FeCo, and FeMn Carbonyl Dithiolates. Organometallics 2014; 33:858-867. [PMID: 24803716 PMCID: PMC3999794 DOI: 10.1021/om400752a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Indexed: 01/23/2023]
Abstract
Reported are complexes of the formula Fe(dithiolate)(CO)2(diphos) and their use to prepare homo- and heterobimetallic dithiolato derivatives. The starting iron dithiolates were prepared by a one-pot reaction of FeCl2 and CO with chelating diphosphines and dithiolates, where dithiolate = S2(CH2)22- (edt2-), S2(CH2)32- (pdt2-), S2(CH2)2(C(CH3)2)2- (Me2pdt2-) and diphos = cis-C2H2(PPh2)2 (dppv), C2H4(PPh2)2 (dppe), C6H4(PPh2)2 (dppbz), C2H4[P(C6H11)2]2 (dcpe). The incorporation of 57Fe into such building block complexes commenced with the conversion of 57Fe into 57Fe2I4( i PrOH)4, which then was treated with K2pdt, CO, and dppe to give 57Fe(pdt)(CO)2(dppe). NMR and IR analyses show that these complexes exist as mixtures of all-cis and trans-CO isomers, edt2- favoring the former and pdt2- the latter. Treatment of Fe(dithiolate)(CO)2(diphos) with the Fe(0) reagent (benzylideneacetone)Fe(CO)3 gave Fe2(dithiolate)(CO)4(diphos), thereby defining a route from simple ferrous salts to models for hydrogenase active sites. Extending the building block route to heterobimetallic complexes, treatment of Fe(pdt)(CO)2(dppe) with [(acenaphthene)Mn(CO)3]+ gave [(CO)3Mn(pdt)Fe(CO)2(dppe)]+ ([3d(CO)]+). Reduction of [3d(CO)]+ with BH4- gave the Cs -symmetric μ-hydride (CO)3Mn(pdt)(H)Fe(CO)(dppe) (H3d). Complex H3d is reversibly protonated by strong acids, the proposed site of protonation being sulfur. Treatment of Fe(dithiolate)(CO)2(diphos) with CpCoI2(CO) followed by reduction by Cp2Co affords CpCo(dithiolate)Fe(CO)(diphos) (4), which can also be prepared from Fe(dithiolate)(CO)2(diphos) and CpCo(CO)2. Like the electronically related (CO)3Fe(pdt)Fe(CO)(diphos), these complexes undergo protonation to afford the μ-hydrido complexes [CpCo(dithiolate)HFe(CO)(diphos)]+. Low-temperature NMR studies indicate that Co is the kinetic site of protonation.
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Affiliation(s)
- Maria
E. Carroll
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Jinzhu Chen
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Danielle E. Gray
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - James C. Lansing
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - David Schilter
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Phillip I. Volkers
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott
R. Wilson
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
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A practical guide for nuclear resonance vibrational spectroscopy (NRVS) of biochemical samples and model compounds. Methods Mol Biol 2014; 1122:125-37. [PMID: 24639257 DOI: 10.1007/978-1-62703-794-5_9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) has been used by physicists for many years. However, it is still a relatively new technique for bioinorganic users. This technique yields a vibrational spectrum for a specific element, which can be easily interpreted. Furthermore, isotopic labeling allows for site-specific experiments. In this chapter, we discuss how to access specific beamlines, what kind of equipment is used in NRVS, and how the sample should be prepared and the data collected and analyzed.
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Riethausen J, Rüdiger O, Gärtner W, Lubitz W, Shafaat HS. Spectroscopic and electrochemical characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Miyazaki F: reversible redox behavior and interactions between electron transfer centers. Chembiochem 2013; 14:1714-9. [PMID: 24038675 DOI: 10.1002/cbic.201300120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 12/18/2022]
Abstract
Characterizing a new hydrogenase: The newly isolated [NiFeSe] hydrogenase from Desulfovibrio vulgaris Miyazaki F displays catalytic properties distinct from other hydrogenase proteins. Here we apply site-specific spectroscopic and electrochemical techniques to characterize these unique features at the molecular level.
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Affiliation(s)
- Jana Riethausen
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, Muelheim an der Ruhr 45470 (Germany)
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45
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Wang H, Yoda Y, Dong W, Huang SD. Energy calibration issues in nuclear resonant vibrational spectroscopy: observing small spectral shifts and making fast calibrations. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:683-90. [PMID: 23955030 PMCID: PMC3747949 DOI: 10.1107/s0909049513021201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 07/30/2013] [Indexed: 05/24/2023]
Abstract
The conventional energy calibration for nuclear resonant vibrational spectroscopy (NRVS) is usually long. Meanwhile, taking NRVS samples out of the cryostat increases the chance of sample damage, which makes it impossible to carry out an energy calibration during one NRVS measurement. In this study, by manipulating the 14.4 keV beam through the main measurement chamber without moving out the NRVS sample, two alternative calibration procedures have been proposed and established: (i) an in situ calibration procedure, which measures the main NRVS sample at stage A and the calibration sample at stage B simultaneously, and calibrates the energies for observing extremely small spectral shifts; for example, the 0.3 meV energy shift between the 100%-(57)Fe-enriched [Fe4S4Cl4](=) and 10%-(57)Fe and 90%-(54)Fe labeled [Fe4S4Cl4](=) has been well resolved; (ii) a quick-switching energy calibration procedure, which reduces each calibration time from 3-4 h to about 30 min. Although the quick-switching calibration is not in situ, it is suitable for normal NRVS measurements.
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Affiliation(s)
- Hongxin Wang
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
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46
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Appel AM, Bercaw JE, Bocarsly AB, Dobbek H, DuBois DL, Dupuis M, Ferry JG, Fujita E, Hille R, Kenis PJA, Kerfeld CA, Morris RH, Peden CHF, Portis AR, Ragsdale SW, Rauchfuss TB, Reek JNH, Seefeldt LC, Thauer RK, Waldrop GL. Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO2 fixation. Chem Rev 2013; 113:6621-58. [PMID: 23767781 PMCID: PMC3895110 DOI: 10.1021/cr300463y] [Citation(s) in RCA: 1262] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Aaron M. Appel
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - John E. Bercaw
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Andrew B. Bocarsly
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Daniel L. DuBois
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Michel Dupuis
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - James G. Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, United States
| | - Etsuko Fujita
- Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Paul J. A. Kenis
- Department of Chemical and Biochemical Engineering, University of Illinois, Urbana, Illinois 61801, United States
| | - Cheryl A. Kerfeld
- DOE Joint Genome Institute, 2800 Mitchell Drive Walnut Creek, California 94598, United States, and Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall Berkeley, California 94720, United States
| | - Robert H. Morris
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Charles H. F. Peden
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Archie R. Portis
- Departments of Crop Sciences and Plant Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Joost N. H. Reek
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Rudolf K. Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse 10, D-35043 Marburg, Germany
| | - Grover L. Waldrop
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Siebert E, Horch M, Rippers Y, Fritsch J, Frielingsdorf S, Lenz O, Velazquez Escobar F, Siebert F, Paasche L, Kuhlmann U, Lendzian F, Mroginski M, Zebger I, Hildebrandt P. Resonance Raman Spectroscopy as a Tool to Monitor the Active Site of Hydrogenases. Angew Chem Int Ed Engl 2013; 52:5162-5. [DOI: 10.1002/anie.201209732] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/22/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Elisabeth Siebert
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Marius Horch
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Yvonne Rippers
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Johannes Fritsch
- Institut für Biologie/Mikrobiologie, Humboldt Universität zu Berlin, Chausseestrasse 117, 10115 Berlin (Germany)
| | - Stefan Frielingsdorf
- Institut für Biologie/Mikrobiologie, Humboldt Universität zu Berlin, Chausseestrasse 117, 10115 Berlin (Germany)
| | - Oliver Lenz
- Institut für Biologie/Mikrobiologie, Humboldt Universität zu Berlin, Chausseestrasse 117, 10115 Berlin (Germany)
| | - Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Friedrich Siebert
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Lars Paasche
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Uwe Kuhlmann
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Friedhelm Lendzian
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Maria‐Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Ingo Zebger
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
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48
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Siebert E, Horch M, Rippers Y, Fritsch J, Frielingsdorf S, Lenz O, Velazquez Escobar F, Siebert F, Paasche L, Kuhlmann U, Lendzian F, Mroginski MA, Zebger I, Hildebrandt P. Resonanz-Raman-Spektroskopie als Methode zur Untersuchung des aktiven Zentrums von Hydrogenasen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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[NiFe] hydrogenases: a common active site for hydrogen metabolism under diverse conditions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:986-1002. [PMID: 23399489 DOI: 10.1016/j.bbabio.2013.01.015] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/06/2012] [Accepted: 01/26/2013] [Indexed: 01/05/2023]
Abstract
Hydrogenase proteins catalyze the reversible conversion of molecular hydrogen to protons and electrons. The most abundant hydrogenases contain a [NiFe] active site; these proteins are generally biased towards hydrogen oxidation activity and are reversibly inhibited by oxygen. However, there are [NiFe] hydrogenase that exhibit unique properties, including aerobic hydrogen oxidation and preferential hydrogen production activity; these proteins are highly relevant in the context of biotechnological devices. This review describes four classes of these "nonstandard" [NiFe] hydrogenases and discusses the electrochemical, spectroscopic, and structural studies that have been used to understand the mechanisms behind this exceptional behavior. A revised classification protocol is suggested in the conclusions, particularly with respect to the term "oxygen-tolerance". This article is part of a special issue entitled: metals in bioenergetics and biomimetics systems.
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