1
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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 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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3
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Gee LB, Pelmenschikov V, Mons C, Mishra N, Wang H, Yoda Y, Tamasaku K, Golinelli-Cohen MP, Cramer SP. NRVS and DFT of MitoNEET: Understanding the Special Vibrational Structure of a [2Fe-2S] Cluster with (Cys) 3(His) 1 Ligation. Biochemistry 2021; 60:2419-2424. [PMID: 34310123 DOI: 10.1021/acs.biochem.1c00252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human mitochondrial protein, mitoNEET (mNT), belongs to the family of small [2Fe-2S] NEET proteins that bind their iron-sulfur clusters with a novel and characteristic 3Cys:1His coordination motif. mNT has been implicated in the regulation of lipid and glucose metabolisms, iron/reactive oxygen species homeostasis, cancer, and possibly Parkinson's disease. The geometric structure of mNT as a function of redox state and pH is critical for its function. In this study, we combine 57Fe nuclear resonance vibrational spectroscopy with density functional theory calculations to understand the novel properties of this important protein.
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Affiliation(s)
- Leland B Gee
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | | | - Cécile Mons
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Nakul Mishra
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Hongxin Wang
- SETI Institute, Mountain View, California 94043, United States
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kenji Tamasaku
- Precision Spectroscopy Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Marie-Pierre Golinelli-Cohen
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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4
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Gee LB, Pelmenschikov V, Wang H, Mishra N, Liu YC, Yoda Y, Tamasaku K, Chiang MH, Cramer SP. Vibrational characterization of a diiron bridging hydride complex - a model for hydrogen catalysis. Chem Sci 2020; 11:5487-5493. [PMID: 34094075 PMCID: PMC8159291 DOI: 10.1039/d0sc01290d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/01/2020] [Indexed: 11/21/2022] Open
Abstract
A diiron complex containing a bridging hydride and a protonated terminal thiolate of the form [(μ,κ2-bdtH)(μ-PPh2)(μ-H)Fe2(CO)5]+ has been investigated through 57Fe nuclear resonance vibrational spectroscopy (NRVS) and interpreted using density functional theory (DFT) calculations. We report the Fe-μH-Fe wagging mode, and indications for Fe-μD stretching vibrations in the D-isotopologue, observed by 57Fe-NRVS. Our combined approach demonstrates an asymmetric sharing of the hydride between the two iron sites that yields two nondegenerate Fe-μH/D stretching vibrations. The studied complex provides an important model relevant to biological hydrogen catalysis intermediates. The complex mimics proposals for the binuclear metal sites in [FeFe] and [NiFe] hydrogenases. It is also an appealing prototype for the 'Janus intermediate' of nitrogenase, which has been proposed to contain two bridging Fe-H-Fe hydrides and two protonated sulfurs at the FeMo-cofactor. The significance of observing indirect effects of the bridging hydride, as well as obstacles in its direct observation, is discussed in the context of biological hydrogen intermediates.
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Affiliation(s)
- Leland B Gee
- Department of Chemistry, Stanford University 333 Campus Drive Stanford CA 94305 USA
| | - Vladimir Pelmenschikov
- 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
| | - Nakul Mishra
- Department of Chemistry, University of California, Davis One Shields Ave Davis CA 95616 USA
| | - Yu-Chiao Liu
- Institute of Chemistry, Academia Sinica Nankang Taipei 115 Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University Kaohsiung 807 Taiwan
| | - 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
| | - Ming-Hsi Chiang
- Institute of Chemistry, Academia Sinica Nankang Taipei 115 Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University Kaohsiung 807 Taiwan
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5
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Todorovic S, Teixeira M. Resonance Raman spectroscopy of Fe-S proteins and their redox properties. J Biol Inorg Chem 2018; 23:647-661. [PMID: 29368020 PMCID: PMC6006211 DOI: 10.1007/s00775-018-1533-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/14/2017] [Indexed: 12/02/2022]
Abstract
Resonance Raman spectra of Fe-S proteins are sensitive to the cluster type, structure and symmetry. Furthermore, bands that originate from bridging and terminal Fe-S vibrations in the 2Fe-2S, 3Fe-4S and 4Fe-4S clusters can be sensitively distinguished in the spectra, as well as the type of non-cysteinyl coordinating ligands, if present. For these reasons, resonance Raman spectroscopy has been playing an exceptionally active role in the studies of Fe-S proteins of diverse structures and functions. We provide here a concise overview of the structural information that can be obtained from resonance Raman spectroscopy on Fe-S clusters, and in parallel, refer to their thermodynamic properties (e.g., reduction potential), which together define the physiological roles of Fe-S proteins. We demonstrate how the knowledge gained over the past several decades on simple clusters nowadays enables studies of complex structures that include Fe-S clusters coupled to other centers and transient processes that involve cluster inter-conversion, biogenesis, disassembly and catalysis.
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Affiliation(s)
- Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal.
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
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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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7
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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.
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8
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Mao Z, Carroll EC, Kim PW, Cramer SP, Larsen DS. Ultrafast Charge-Transfer Dynamics in the Iron-Sulfur Complex of Rhodobacter capsulatus Ferredoxin VI. J Phys Chem Lett 2017; 8:4498-4503. [PMID: 28872878 PMCID: PMC7187928 DOI: 10.1021/acs.jpclett.7b02026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Iron-sulfur proteins play essential roles in various biological processes. Their electronic structure and vibrational dynamics are key to their rich chemistry but nontrivial to unravel. Here, the first ultrafast transient absorption and impulsive coherent vibrational spectroscopic (ICVS) studies on 2Fe-2S clusters in Rhodobacter capsulatus ferreodoxin VI are characterized. Photoexcitation initiated populations on multiple excited electronic states that evolve into each other in a long-lived charge-transfer state. This suggests a potential light-induced electron-transfer pathway as well as the possibility of using iron-sulfur proteins as photosensitizers for light-dependent enzymes. A tyrosine chain near the active site suggests potential hole-transfer pathways and affirms this electron-transfer pathway. The ICVS data revealed vibrational bands at 417 and 484 cm-1, with the latter attributed to an excited-state mode. The temperature dependence of the ICVS modes suggests that the temperature effect on protein structure or conformational heterogeneities needs to be considered during cryogenic temperature studies.
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Affiliation(s)
- Ziliang Mao
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elizabeth C. Carroll
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Peter W. Kim
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Stephen P. Cramer
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Corresponding Authors: &
| | - Delmar S. Larsen
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Corresponding Authors: &
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9
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Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center. PLoS One 2016; 11:e0162031. [PMID: 27656882 PMCID: PMC5033481 DOI: 10.1371/journal.pone.0162031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022] Open
Abstract
Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys2[2Fe-2S]His2 and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.
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10
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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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11
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Golinelli-Cohen MP, Lescop E, Mons C, Gonçalves S, Clémancey M, Santolini J, Guittet E, Blondin G, Latour JM, Bouton C. Redox Control of the Human Iron-Sulfur Repair Protein MitoNEET Activity via Its Iron-Sulfur Cluster. J Biol Chem 2016; 291:7583-93. [PMID: 26887944 DOI: 10.1074/jbc.m115.711218] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/06/2022] Open
Abstract
Human mitoNEET (mNT) is the first identified Fe-S protein of the mammalian outer mitochondrial membrane. Recently, mNT has been implicated in cytosolic Fe-S repair of a key regulator of cellular iron homeostasis. Here, we aimed to decipher the mechanism by which mNT triggers its Fe-S repair capacity. By using tightly controlled reactions combined with complementary spectroscopic approaches, we have determined the differential roles played by both the redox state of the mNT cluster and dioxygen in cluster transfer and protein stability. We unambiguously demonstrated that only the oxidized state of the mNT cluster triggers cluster transfer to a generic acceptor protein and that dioxygen is neither required for the cluster transfer reaction nor does it affect the transfer rate. In the absence of apo-acceptors, a large fraction of the oxidized holo-mNT form is converted back to reduced holo-mNT under low oxygen tension. Reduced holo-mNT, which holds a [2Fe-2S](+)with a global protein fold similar to that of the oxidized form is, by contrast, resistant in losing its cluster or in transferring it. Our findings thus demonstrate that mNT uses an iron-based redox switch mechanism to regulate the transfer of its cluster. The oxidized state is the "active state," which reacts promptly to initiate Fe-S transfer independently of dioxygen, whereas the reduced state is a "dormant form." Finally, we propose that the redox-sensing function of mNT is a key component of the cellular adaptive response to help stress-sensitive Fe-S proteins recover from oxidative injury.
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Affiliation(s)
- Marie-Pierre Golinelli-Cohen
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France,
| | - Ewen Lescop
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Cécile Mons
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sergio Gonçalves
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Martin Clémancey
- Université Grenoble Alpes, Laboratoire Chimie et Biologie des Métaux (LCBM), and Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherche en Technologies et Sciences pour le Vivant (iRTSV), LCBM, Equipe Physicochimie des Métaux en Biologie (PMB), and CNRS UMR 5249, LCBM, 38054 Grenoble, France, and
| | - Jérôme Santolini
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Eric Guittet
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Geneviève Blondin
- Université Grenoble Alpes, Laboratoire Chimie et Biologie des Métaux (LCBM), and Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherche en Technologies et Sciences pour le Vivant (iRTSV), LCBM, Equipe Physicochimie des Métaux en Biologie (PMB), and CNRS UMR 5249, LCBM, 38054 Grenoble, France, and
| | - Jean-Marc Latour
- Université Grenoble Alpes, Laboratoire Chimie et Biologie des Métaux (LCBM), and Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherche en Technologies et Sciences pour le Vivant (iRTSV), LCBM, Equipe Physicochimie des Métaux en Biologie (PMB), and CNRS UMR 5249, LCBM, 38054 Grenoble, France, and
| | - Cécile Bouton
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France,
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12
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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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13
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Ali ME, Oppeneer PM. Unraveling the Electronic Structure, Spin States, Optical and Vibrational Spectra of Malaria Pigment. Chemistry 2015; 21:8544-53. [DOI: 10.1002/chem.201406208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 12/19/2022]
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14
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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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15
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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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16
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Mitra D, George SJ, Guo Y, Kamali S, Keable S, Peters JW, Pelmenschikov V, Case DA, Cramer SP. Characterization of [4Fe-4S] cluster vibrations and structure in nitrogenase Fe protein at three oxidation levels via combined NRVS, EXAFS, and DFT analyses. J Am Chem Soc 2013; 135:2530-43. [PMID: 23282058 DOI: 10.1021/ja307027n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm(-1) decrease in Fe-S stretching frequencies with each added electron. The "oxidized" [4Fe-4S](2+) state spectrum is consistent with and extends previous resonance Raman spectra. For the "reduced" [4Fe-4S](1+) state in Fe protein, and for any "all-ferrous" [4Fe-4S](0) cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å(-1) indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment.
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Affiliation(s)
- Devrani Mitra
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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17
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Kuchenreuther JM, Guo Y, Wang H, Myers WK, George SJ, Boyke CA, Yoda Y, Alp EE, Zhao J, Britt RD, Swartz JR, Cramer SP. Nuclear resonance vibrational spectroscopy and electron paramagnetic resonance spectroscopy of 57Fe-enriched [FeFe] hydrogenase indicate stepwise assembly of the H-cluster. Biochemistry 2013; 52:818-26. [PMID: 23249091 DOI: 10.1021/bi301336r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe-S clusters that facilitate the transfer of an electron to the H-cluster, a ligand-coordinated six-iron prosthetic group that catalyzes the redox interconversion of protons and H(2). Here, we have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron centers in CpI, and we compare our data to that for a [4Fe-4S] ferredoxin as well as a model complex resembling the [2Fe](H) catalytic domain of the H-cluster. To enrich the hydrogenase with (57)Fe nuclei, we used cell-free methods to post-translationally mature the enzyme. Specifically, inactive CpI apoprotein with (56)Fe-labeled Fe-S clusters was activated in vitro using (57)Fe-enriched maturation proteins. This approach enabled us to selectively label the [2Fe](H) subcluster with (57)Fe, which NRVS confirms by detecting (57)Fe-CO and (57)Fe-CN normal modes from the H-cluster nonprotein ligands. The NRVS and iron quantification results also suggest that the hydrogenase contains a second (57)Fe-S cluster. Electron paramagnetic resonance (EPR) spectroscopy indicates that this (57)Fe-enriched metal center is not the [4Fe-4S](H) subcluster of the H-cluster. This finding demonstrates that the CpI hydrogenase retained an (56)Fe-enriched [4Fe-4S](H) cluster during in vitro maturation, providing unambiguous evidence of stepwise assembly of the H-cluster. In addition, this work represents the first NRVS characterization of [FeFe] hydrogenases.
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Affiliation(s)
- Jon M Kuchenreuther
- Department of Chemistry, University of California-Davis, CA 95616, United States
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18
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Guo Y, Brecht E, Aznavour K, Nix JC, Xiao Y, Wang H, George SJ, Bau R, Keable S, Peters JW, Adams MWW, Jenney F, Sturhahn W, Alp EE, Zhao J, Yoda Y, Cramer SP. Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals. ACTA ACUST UNITED AC 2012; 222:77-90. [PMID: 26052177 DOI: 10.1007/s10751-012-0643-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Fe-S protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the X-ray crystal structure.
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Affiliation(s)
- Yisong Guo
- Department of Applied Science, University of California, Davis, CA 95616
| | - Eric Brecht
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Kristen Aznavour
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033
| | - Jay C Nix
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Yuming Xiao
- Department of Applied Science, University of California, Davis, CA 95616
| | - Hongxin Wang
- Department of Applied Science, University of California, Davis, CA 95616 ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Simon J George
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert Bau
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033
| | - Stephen Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | | | - Francis Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA 30024
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Ercan E Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Yoshitaka Yoda
- JASRI, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Stephen P Cramer
- Department of Applied Science, University of California, Davis, CA 95616 ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 ; Department of Chemistry, University of California, Davis, CA 95616
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19
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Hałas A, Orzechowska A, Derrien V, Chumakov AI, Sebban P, Fiedor J, Lipińska M, Zając M, Ślęzak T, Strzałka K, Matlak K, Korecki J, Fiedor L, Burda K. The dynamics of the non-heme iron in bacterial reaction centers from Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:2095-102. [PMID: 22921693 DOI: 10.1016/j.bbabio.2012.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 08/06/2012] [Accepted: 08/09/2012] [Indexed: 11/28/2022]
Abstract
We investigate the dynamical properties of the non-heme iron (NHFe) in His-tagged photosynthetic bacterial reaction centers (RCs) isolated from Rhodobacter (Rb.) sphaeroides. Mössbauer spectroscopy and nuclear inelastic scattering of synchrotron radiation (NIS) were applied to monitor the arrangement and flexibility of the NHFe binding site. In His-tagged RCs, NHFe was stabilized only in a high spin ferrous state. Its hyperfine parameters (IS=1.06±0.01mm/s and QS=2.12±0.01mm/s), and Debye temperature (θ(D0)~167K) are comparable to those detected for the high spin state of NHFe in non-His-tagged RCs. For the first time, pure vibrational modes characteristic of NHFe in a high spin ferrous state are revealed. The vibrational density of states (DOS) shows some maxima between 22 and 33meV, 33 and 42meV, and 53 and 60meV and a very sharp one at 44.5meV. In addition, we observe a large contribution of vibrational modes at low energies. This iron atom is directly connected to the protein matrix via all its ligands, and it is therefore extremely sensitive to the collective motions of the RC protein core. A comparison of the DOS spectra of His-tagged and non-His-tagged RCs from Rb. sphaeroides shows that in the latter case the spectrum was overlapped by the vibrations of the heme iron of residual cytochrome c(2), and a low spin state of NHFe in addition to its high spin one. This enabled us to pin-point vibrations characteristic for the low spin state of NHFe.
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Affiliation(s)
- A Hałas
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, al. Mickiewicza 30, 30-059 Kraków, Poland
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20
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Peng Q, Pavlik JW, Scheidt WR, Wiest O. Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)]. J Chem Theory Comput 2012; 8:214-223. [PMID: 23204948 PMCID: PMC3507453 DOI: 10.1021/ct2006456] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear Resonance Vibrational Spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds, but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP(2-)=octaethylporphyrinatio dianion) were performed. A test set of 21 methodology combinations including 8 functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86 and ωB97X-D) and 5 basis set (VTZ, TZVP, Lanl2DZ for iron and 6-31G*, 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e(2)), which can used to simulate the Vibrational Density Of States (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.
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Affiliation(s)
- Qian Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - Jeffrey W. Pavlik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - W. Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
- School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China
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21
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Paulsen H, Trautwein AX, Wegner P, Schmidt C, Chumakov AI, Schünemann V. Interpretation of Nuclear Resonant Vibrational Spectra of Rubredoxin Using a Combined Quantum Mechanics and Molecular Mechanics Approach. Chemphyschem 2011; 12:3434-41. [DOI: 10.1002/cphc.201100595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Indexed: 11/06/2022]
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22
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El Khoury Y, Hellwig P. A combined far-infrared spectroscopic and electrochemical approach for the study of iron-sulfur proteins. Chemphyschem 2011; 12:2669-74. [PMID: 21887734 DOI: 10.1002/cphc.201100165] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 06/15/2011] [Indexed: 11/11/2022]
Abstract
Herein, we present the development of a far-infrared spectroscopic approach for studying metalloenzyme active sites in a redox-dependent manner. An electrochemical cell with 5 mm path and based on silicon windows was found to be appropriate for the measurement of aqueous solutions down to 200 cm(-1) . The cell was probed with the infrared redox signature of the metal-ligand vibrations of different iron-sulfur proteins. Each Fe-S cluster type was found to show a specific spectral signature. As a common feature, a downshift of the frequency of the Fe-S vibrations was seen upon reduction, in line with the increase of the Fe-S bond. This downshift was found to be fully reversible. Electrochemically induced FTIR difference spectroscopy in the far infrared is now possible, opening new perspectives on the understanding of metalloproteins in function of the redox state.
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Affiliation(s)
- Youssef El Khoury
- Institut de Chimie, UMR, Laboratoire de spectroscopie vibrationnelle et électrochimie des biomolécules Université de Strasbourg, France
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23
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Mitra D, Pelmenschikov V, Guo Y, Case DA, Wang H, Dong W, Tan ML, Ichiye T, Jenney FE, Adams MWW, Yoda Y, Zhao J, Cramer SP. Dynamics of the [4Fe-4S] cluster in Pyrococcus furiosus D14C ferredoxin via nuclear resonance vibrational and resonance Raman spectroscopies, force field simulations, and density functional theory calculations. Biochemistry 2011; 50:5220-35. [PMID: 21500788 DOI: 10.1021/bi200046p] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (Pf D14C Fd). To assist the normal-mode assignments, we conducted NRVS with D14C ferredoxin samples with (36)S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains, (Ph(4)P)(2)[Fe(4)S(4)Cl(4)]. Several distinct regions of NRVS intensity are identified, ranging from "protein" and torsional modes below 100 cm(-1), through bending and breathing modes near 150 cm(-1), to strong bands from Fe-S stretching modes between 250 and ∼400 cm(-1). The oxidized ferredoxin samples were also investigated by resonance Raman (RR) spectroscopy. We found good agreement between NRVS and RR frequencies, but because of different selection rules, the intensities vary dramatically between the two types of spectra. The (57)Fe partial vibrational densities of states for the oxidized samples were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields for local models of the [4Fe-4S] clusters. Full protein model calculations were also conducted using a supplemented CHARMM force field, and these calculations revealed low-frequency modes that may be relevant to electron transfer with Pf Fd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe(4)S(4)](2+/+) redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.
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Affiliation(s)
- Devrani Mitra
- Department of Applied Science, University of California , Davis, CA 95616, USA
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24
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Tinberg CE, Tonzetich ZJ, Wang H, Do LH, Yoda Y, Cramer SP, Lippard SJ. Characterization of iron dinitrosyl species formed in the reaction of nitric oxide with a biological Rieske center. J Am Chem Soc 2010; 132:18168-76. [PMID: 21133361 DOI: 10.1021/ja106290p] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reactions of nitric oxide with cysteine-ligated iron-sulfur cluster proteins typically result in disassembly of the iron-sulfur core and formation of dinitrosyl iron complexes (DNICs). Here we report the first evidence that DNICs also form in the reaction of NO with Rieske-type [2Fe-2S] clusters. Upon treatment of a Rieske protein, component C of toluene/o-xylene monooxygenase from Pseudomonas sp. OX1, with an excess of NO(g) or NO-generators S-nitroso-N-acetyl-D,L-pencillamine and diethylamine NONOate, the absorbance bands of the [2Fe-2S] cluster are extinguished and replaced by a new feature that slowly grows in at 367 nm. Analysis of the reaction products by electron paramagnetic resonance, Mössbauer, and nuclear resonance vibrational spectroscopy reveals that the primary product of the reaction is a thiolate-bridged diiron tetranitrosyl species, [Fe(2)(μ-SCys)(2)(NO)(4)], having a Roussin's red ester (RRE) formula, and that mononuclear DNICs account for only a minor fraction of nitrosylated iron. Reduction of this RRE reaction product with sodium dithionite produces the one-electron-reduced RRE, having absorptions at 640 and 960 nm. These results demonstrate that NO reacts readily with a Rieske center in a protein and suggest that dinuclear RRE species, not mononuclear DNICs, may be the primary iron dinitrosyl species responsible for the pathological and physiological effects of nitric oxide in such systems in biology.
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Affiliation(s)
- Christine E Tinberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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25
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Orzechowska A, Lipińska M, Fiedor J, Chumakov A, Zając M, Ślęzak T, Matlak K, Strzałka K, Korecki J, Fiedor L, Burda K. Coupling of collective motions of the protein matrix to vibrations of the non-heme iron in bacterial photosynthetic reaction centers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1696-704. [DOI: 10.1016/j.bbabio.2010.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 06/23/2010] [Accepted: 06/26/2010] [Indexed: 10/19/2022]
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26
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Delfino I, Cerullo G, Cannistraro S, Manzoni C, Polli D, Dapper C, Newton WE, Guo Y, Cramer SP. Observation of terahertz vibrations in the nitrogenase FeMo cofactor by femtosecond pump-probe spectroscopy. Angew Chem Int Ed Engl 2010; 49:3912-5. [PMID: 20411554 PMCID: PMC3129498 DOI: 10.1002/anie.200906787] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have used Impulsive Coherent Vibrational Spectroscopy (ICVS) to study the FeMo-cofactor of nitrogenase from Azotobacter vinelandii as the extracted small molecule ‘FeMoco’. In the ICVS experiment, a 15 fs visible laser pulse pumps the sample to an excited electronic state, and a second <10 fs pulse probes the change in transmission as a function of the time delay. FeMoco was observed to relax to the ground state by a single exponential decay with a time constant of ~200 fs. Superimposed on this relaxation are oscillations caused by the coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the FeMoco vibrational frequencies that are coherently excited by the short laser pulse. The frequencies obtained by the ICVS technique were compared with values from normal mode calculations. The strongest ICVS bands are at 215 and 420 cm−1. The 420 cm−1 band is attributed to Fe-S stretching motion, whereas the 215 cm−1 band, which is the strongest feature in the spectrum, is attributed to a breathing mode of FeMoco. Over the years, nitrogenase and FeMoco have resisted characterization by resonance Raman spectroscopy. The current results demonstrate the promise of ICVS as an alternative probe of FeMoco dynamics.
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Affiliation(s)
- Ines Delfino
- Biophysics & Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, I-01100 Viterbo, Italy
| | - Giulio Cerullo
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Salvatore Cannistraro
- Biophysics & Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, I-01100 Viterbo, Italy
| | - Cristian Manzoni
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Dario Polli
- National Laboratory for Ultrafast and Ultraintense Optical Science-CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Christie Dapper
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061
| | - William E. Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061
| | - Yisong Guo
- Department of Applied Science, University of California, Davis, CA 95616
| | - Stephen P. Cramer
- Department of Applied Science, University of California, Davis, CA 95616
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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27
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Delfino I, Cerullo G, Cannistraro S, Manzoni C, Polli D, Dapper C, Newton W, Guo Y, Cramer S. Observation of Terahertz Vibrations in the Nitrogenase FeMo Cofactor by Femtosecond Pump-Probe Spectroscopy. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Lipińska M, Orzechowska A, Fiedor J, Chumakov AI, Ślȩzak T, Zaja̧c M, Matlak K, Korecki J, Hałas A, Strzałka K, Fiedor L, Burda K. Influence of Cd2+on the spin state of non-heme iron and on protein local motions in reactions centers from purple photosynthetic bacteriumRhodospirilium rubrum. ACTA ACUST UNITED AC 2010. [DOI: 10.1088/1742-6596/217/1/012021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Bell CB, Wong SD, Xiao Y, Klinker EJ, Tenderholt AL, Smith MC, Rohde JU, Que L, Cramer SP, Solomon EI. A combined NRVS and DFT study of Fe(IV)=O model complexes: a diagnostic method for the elucidation of non-heme iron enzyme intermediates. Angew Chem Int Ed Engl 2008; 47:9071-4. [PMID: 18925598 DOI: 10.1002/anie.200803740] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Caleb B Bell
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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Bell C, Wong S, Xiao Y, Klinker E, Tenderholt A, Smith M, Rohde JU, Que L, Cramer S, Solomon E. A Combined NRVS and DFT Study of FeIVO Model Complexes: A Diagnostic Method for the Elucidation of Non-Heme Iron Enzyme Intermediates. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803740] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Guo Y, Wang H, Xiao Y, Vogt S, Thauer RK, Shima S, Volkers PI, Rauchfuss TB, Pelmenschikov V, Case DA, Alp EE, Sturhahn W, Yoda Y, Cramer SP. Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS). Inorg Chem 2008; 47:3969-77. [PMID: 18407624 DOI: 10.1021/ic701251j] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm(-1), consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at approximately 311 cm(-1) and another reproducible feature at approximately 380 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.
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Affiliation(s)
- Yisong Guo
- Department of Applied Science, University of California, Davis, California 95616, USA
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