1
|
Kulka-Peschke CJ, Schulz AC, Lorent C, Rippers Y, Wahlefeld S, Preissler J, Schulz C, Wiemann C, Bernitzky CCM, Karafoulidi-Retsou C, Wrathall SLD, Procacci B, Matsuura H, Greetham GM, Teutloff C, Lauterbach L, Higuchi Y, Ishii M, Hunt NT, Lenz O, Zebger I, Horch M. Reversible Glutamate Coordination to High-Valent Nickel Protects the Active Site of a [NiFe] Hydrogenase from Oxygen. J Am Chem Soc 2022; 144:17022-17032. [PMID: 36084022 DOI: 10.1021/jacs.2c06400] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NAD+-reducing [NiFe] hydrogenases are valuable biocatalysts for H2-based energy conversion and the regeneration of nucleotide cofactors. While most hydrogenases are sensitive toward O2 and elevated temperatures, the soluble NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus (HtSH) is O2-tolerant and thermostable. Thus, it represents a promising candidate for biotechnological applications. Here, we have investigated the catalytic activity and active-site structure of native HtSH and variants in which a glutamate residue in the active-site cavity was replaced by glutamine, alanine, and aspartate. Our biochemical, spectroscopic, and theoretical studies reveal that at least two active-site states of oxidized HtSH feature an unusual architecture in which the glutamate acts as a terminal ligand of the active-site nickel. This observation demonstrates that crystallographically observed glutamate coordination represents a native feature of the enzyme. One of these states is diamagnetic and characterized by a very high stretching frequency of an iron-bound active-site CO ligand. Supported by density-functional-theory calculations, we identify this state as a high-valent species with a biologically unprecedented formal Ni(IV) ground state. Detailed insights into its structure and dynamics were obtained by ultrafast and two-dimensional infrared spectroscopy, demonstrating that it represents a conformationally strained state with unusual bond properties. Our data further show that this state is selectively and reversibly formed under oxic conditions, especially upon rapid exposure to high O2 levels. We conclude that the kinetically controlled formation of this six-coordinate high-valent state represents a specific and precisely orchestrated stereoelectronic response toward O2 that could protect the enzyme from oxidative damage.
Collapse
Affiliation(s)
- Catharina J Kulka-Peschke
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anne-Christine Schulz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Stefan Wahlefeld
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Janina Preissler
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Claudia Schulz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Charlotte Wiemann
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | | | - Chara Karafoulidi-Retsou
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Solomon L D Wrathall
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Barbara Procacci
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, RIKEN/SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, U.K
| | - Christian Teutloff
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Lars Lauterbach
- Institute of Applied Microbiology, Synthetic Microbiology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Masaharu Ishii
- Graduate School of Agricultural and Life Sciences / Faculty of Agriculture, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Neil T Hunt
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Oliver Lenz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Marius Horch
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| |
Collapse
|
2
|
Understanding 2D-IR Spectra of Hydrogenases: A Descriptive and Predictive Computational Study. Catalysts 2022. [DOI: 10.3390/catal12090988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to the presence of CO and ligands at this cofactor, infrared (IR) spectroscopy represents an ideal technique for studying these aspects, but molecular information from linear IR absorption experiments is limited. More detailed insights can be obtained from ultrafast nonlinear IR techniques like IRpump−IRprobe and two-dimensional (2D-)IR spectroscopy. However, fully exploiting these advanced techniques requires an in-depth understanding of experimental observables and the encoded molecular information. To address this challenge, we present a descriptive and predictive computational approach for the simulation and analysis of static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. Accurate reproduction of experimental spectra from a first-coordination-sphere model suggests a decisive role of the [NiFe] core in shaping the enzymatic potential energy surface. We also reveal spectrally encoded molecular information that is not accessible by experiments, thereby helping to understand the catalytic role of the diatomic ligands, structural differences between [NiFe] intermediates, and possible energy transfer mechanisms. Our studies demonstrate the feasibility and benefits of computational spectroscopy in the 2D-IR investigation of hydrogenases, thereby further strengthening the potential of this nonlinear IR technique as a powerful research tool for the investigation of complex bioinorganic molecules.
Collapse
|
3
|
Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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
| |
Collapse
|
7
|
Zorin NA, Khusnutdinova AN, Starodubov AS, Proskuryakov II, Tsygankov AA. Reconstruction of HydSL Hydrogenase from Thiocapsa roseopersicina after Cyanide Inhibition. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821030169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
8
|
Alaghmandfard A, Madaah Hosseini HR. A facile, two-step synthesis and characterization of Fe 3 O 4 - L Cysteine - graphene quantum dots as a multifunctional nanocomposite. APPLIED NANOSCIENCE 2021; 11:849-860. [PMID: 33425639 PMCID: PMC7778724 DOI: 10.1007/s13204-020-01642-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/27/2020] [Indexed: 01/15/2023]
Abstract
In this research, a facile, two-step synthesis of Fe3O4–LCysteine–graphene quantum dots (GQDs) nanocomposite is reported. This synthesis method comprises the preparation of GQDs via hydrothermal route, which should be conjugated to the LCysteine functionalized core–shell magnetic structure with the core of about 7.5-nm iron oxide nanoparticle and 3.5-nm LCysteine shell. LCysteine, as a biocompatible natural amino acid, was used to link magnetite nanoparticles (MNPs) with GQDs. X-ray powder diffraction, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray were used to investigate the presence and formation of MNPs, \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${\text{L}}_{{{\text{Cysteine}}}}$$\end{document}LCysteine functionalized MNPs, and final hybrid nanostructure. Morphology and size distribution of nanoparticles were demonstrated by scanning electron microscopy and transmission electron microscopy. Finally, the magnetic and optical properties of the prepared nanocomposite were measured by vibrating sample magnetometer, ultraviolet–visible, and photoluminescence spectroscopy. The results show that Fe3O4–LCysteine–GQDs nanocomposite exhibits a superparamagnetic behavior at room temperature with high saturation magnetization and low magnetic coercivity, which are 28.99 emu/g and 0.09 Oe, respectively. This nanocomposite also shows strong and stable emission at 460 nm and 530 nm when it is excited with the 235 nm wavelength. The magnetic GQDs structure also reveals the absorption wavelength at 270 nm. Therefore, Fe3O4–LCysteine–GQDs nanocomposite can be considered as a potential multifunctional hybrid structure with magnetic and optical properties simultaneously. This nanocomposite can be used for a wide range of biomedical applications like magnetic resonance imaging (MRI) contrast agents, biosensors, photothermal therapy, and hyperthermia.
Collapse
Affiliation(s)
- Amirhossein Alaghmandfard
- Department of Materials Science and Engineering, Sharif University of Technology, Azadi Avenue, P.O. Box 11155-9466, Tehran, Iran
| | - Hamid Reza Madaah Hosseini
- Department of Materials Science and Engineering, Sharif University of Technology, Azadi Avenue, P.O. Box 11155-9466, Tehran, Iran
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.![]()
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
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 .
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Leland B Gee
- University of California, Davis, Davis, CA, United States.
| | - Hongxin Wang
- University of California, Davis, Davis, CA, United States
| | | |
Collapse
|
13
|
Enzymatic and spectroscopic properties of a thermostable [NiFe]‑hydrogenase performing H 2-driven NAD +-reduction in the presence of O 2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:8-18. [PMID: 28970007 DOI: 10.1016/j.bbabio.2017.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/17/2017] [Accepted: 09/28/2017] [Indexed: 12/18/2022]
Abstract
Biocatalysts that mediate the H2-dependent reduction of NAD+ to NADH are attractive from both a fundamental and applied perspective. Here we present the first biochemical and spectroscopic characterization of an NAD+-reducing [NiFe]‑hydrogenase that sustains catalytic activity at high temperatures and in the presence of O2, which usually acts as an inhibitor. We isolated and sequenced the four structural genes, hoxFUYH, encoding the soluble NAD+-reducing [NiFe]‑hydrogenase (SH) from the thermophilic betaproteobacterium, Hydrogenophilus thermoluteolus TH-1T (Ht). The HtSH was recombinantly overproduced in a hydrogenase-free mutant of the well-studied, H2-oxidizing betaproteobacterium Ralstonia eutropha H16 (Re). The enzyme was purified and characterized with various biochemical and spectroscopic techniques. Highest H2-mediated NAD+ reduction activity was observed at 80°C and pH6.5, and catalytic activity was found to be sustained at low O2 concentrations. Infrared spectroscopic analyses revealed a spectral pattern for as-isolated HtSH that is remarkably different from those of the closely related ReSH and other [NiFe]‑hydrogenases. This indicates an unusual configuration of the oxidized catalytic center in HtSH. Complementary electron paramagnetic resonance spectroscopic analyses revealed spectral signatures similar to related NAD+-reducing [NiFe]‑hydrogenases. This study lays the groundwork for structural and functional analyses of the HtSH as well as application of this enzyme for H2-driven cofactor recycling under oxic conditions at elevated temperatures.
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
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.
Collapse
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 . ;
| |
Collapse
|
17
|
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
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|