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Schüren AO, Ridgway BM, Di Salvo F, Carella LM, Gramm VK, Metzger E, Doctorovich F, Rentschler E, Schünemann V, Ruschewitz U, Klein A. Structural insight into halide-coordinated [Fe 4S 4X nY 4-n] 2- clusters (X, Y = Cl, Br, I) by XRD and Mössbauer spectroscopy. Dalton Trans 2023; 52:1277-1290. [PMID: 36621931 DOI: 10.1039/d2dt03203a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron sulphur halide clusters [Fe4S4Br4]2- and [Fe4S4X2Y2]2- (X, Y = Cl, Br, I) were obtained in excellent yields (77 to 78%) and purity from [Fe(CO)5], elemental sulphur, I2 and benzyltrimethylammonium (BTMA+) iodide, bromide and chloride. Single crystals of (BTMA)2[Fe4S4Br4] (1), (BTMA)2[Fe4S4Br2Cl2] (2), (BTMA)2[Fe4S4Cl2I2] (3), and (BTMA)2[Fe4S4Br2I2] (4) were isostructural to the previously reported (BTMA)2[Fe4S4I4] (5) (monoclinic, Cc). Instead of the chloride cubane cluster [Fe4S4Cl4]2-, we found the prismane-shaped cluster (BTMA)3[Fe6S6Cl6] (6) (P1̄). 57Fe Mössbauer spectroscopy indicates complete delocalisation with Fe2.5+ oxidation states for all iron atoms. Magnetic measurements showed small χMT values at 298 K ranging from 1.12 to 1.54 cm3 K mol-1, indicating the dominant antiferromagnetic exchange interactions. With decreasing temperature, the χMT values decreased to reach a plateau at around 100 K. From about 20 K, the values drop significantly. Fitting the data in the Heisenberg-Dirac-van Vleck (HDvV) as well as the Heisenberg Double Exchange (HDE) formalism confirmed the delocalisation and antiferromagnetic coupling assumed from Mössbauer spectroscopy.
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Affiliation(s)
- Andreas O Schüren
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany. .,INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Benjamin M Ridgway
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Florencia Di Salvo
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Luca M Carella
- Johannes Gutenberg Universität Mainz, Department Chemie, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Verena K Gramm
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
| | - Elisa Metzger
- TU Kaiserlautern Department of Physics, 67663 Kaiserlautern, Germany
| | - Fabio Doctorovich
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Eva Rentschler
- Johannes Gutenberg Universität Mainz, Department Chemie, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Volker Schünemann
- TU Kaiserlautern Department of Physics, 67663 Kaiserlautern, Germany
| | - Uwe Ruschewitz
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
| | - Axel Klein
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
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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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Wittkamp F, Mishra N, Wang H, Wille HC, Steinbrügge R, Kaupp M, Cramer SP, Apfel UP, Pelmenschikov V. Insights from 125Te and 57Fe nuclear resonance vibrational spectroscopy: a [4Fe-4Te] cluster from two points of view. Chem Sci 2019; 10:7535-7541. [PMID: 31588304 PMCID: PMC6761874 DOI: 10.1039/c9sc02025j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/22/2019] [Indexed: 11/21/2022] Open
Abstract
Can sulfur-to-tellurium exchange serve as a method to understand iron–sulfur clusters of enzymatic systems?
Iron–sulfur clusters are common building blocks for electron transport and active sites of metalloproteins. Their comprehensive investigation is crucial for understanding these enzymes, which play important roles in modern biomimetic catalysis and biotechnology applications. We address this issue by utilizing (Et4N)3[Fe4Te4(SPh)4], a tellurium modified version of a conventional reduced [4Fe–4S]+ cluster, and performed both 57Fe- and 125Te-NRVS to reveal its characteristic vibrational features. Our analysis exposed major differences in the resulting 57Fe spectrum profile as compared to that of the respective [4Fe–4S] cluster, and between the 57Fe and 125Te profiles. DFT calculations are applied to rationalize structural, electronic, vibrational, and redox-dependent properties of the [4Fe–4Te]+ core. We herein highlight the potential of sulfur/tellurium exchange as a method to isolate the iron-only motion in enzymatic systems.
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Affiliation(s)
- Florian Wittkamp
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - Nakul Mishra
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hans-Christian Wille
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - René Steinbrügge
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - Martin Kaupp
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Ulf-Peter Apfel
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . .,Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
| | - Vladimir Pelmenschikov
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
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Mebs S, Duan J, Wittkamp F, Stripp ST, Happe T, Apfel UP, Winkler M, Haumann M. Differential Protonation at the Catalytic Six-Iron Cofactor of [FeFe]-Hydrogenases Revealed by 57Fe Nuclear Resonance X-ray Scattering and Quantum Mechanics/Molecular Mechanics Analyses. Inorg Chem 2019; 58:4000-4013. [PMID: 30802044 DOI: 10.1021/acs.inorgchem.9b00100] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe]-hydrogenases are efficient biological hydrogen conversion catalysts and blueprints for technological fuel production. The relations between substrate interactions and electron/proton transfer events at their unique six-iron cofactor (H-cluster) need to be elucidated. The H-cluster comprises a four-iron cluster, [4Fe4S], linked to a diiron complex, [FeFe]. We combined 57Fe-specific X-ray nuclear resonance scattering experiments (NFS, nuclear forward scattering; NRVS, nuclear resonance vibrational spectroscopy) with quantum-mechanics/molecular-mechanics computations to study the [FeFe]-hydrogenase HYDA1 from a green alga. Selective 57Fe labeling at only [4Fe4S] or [FeFe], or at both subcomplexes was achieved by protein expression with a 57Fe salt and in vitro maturation with a synthetic diiron site precursor containing 57Fe. H-cluster states were populated under infrared spectroscopy control. NRVS spectral analyses facilitated assignment of the vibrational modes of the cofactor species. This approach revealed the H-cluster structure of the oxidized state (Hox) with a bridging carbon monoxide at [FeFe] and ligand rearrangement in the CO-inhibited state (Hox-CO). Protonation at a cysteine ligand of [4Fe4S] in the oxidized state occurring at low pH (HoxH) was indicated, in contrast to bridging hydride binding at [FeFe] in a one-electron reduced state (Hred). These findings are direct evidence for differential protonation either at the four-iron or diiron subcomplex of the H-cluster. NFS time-traces provided Mössbauer parameters such as the quadrupole splitting energy, which differ among cofactor states, thereby supporting selective protonation at either subcomplex. In combination with data for reduced states showing similar [4Fe4S] protonation as HoxH without (Hred') or with (Hhyd) a terminal hydride at [FeFe], our results imply that coordination geometry dynamics at the diiron site and proton-coupled electron transfer to either the four-iron or the diiron subcomplex discriminate catalytic and regulatory functions of [FeFe]-hydrogenases. We support a reaction cycle avoiding diiron site geometry changes during rapid H2 turnover.
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Affiliation(s)
| | | | | | | | | | - Ulf-Peter Apfel
- Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
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Lupan A, Silaghi-Dumitrescu R, King RB. Tetracapped tetrahedral ruthenium-sulfur clusters related to iron-sulfur structural units in metalloenzymes. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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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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7
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Schüren AO, Gramm VK, Dürr M, Foi A, Ivanović-Burmazović I, Doctorovich F, Ruschewitz U, Klein A. Halide coordinated homoleptic [Fe4S4X4](2-) and heteroleptic [Fe4S4X2Y2](2-) clusters (X, Y = Cl, Br, I)--alternative preparations, structural analogies and spectroscopic properties in solution and solid state. Dalton Trans 2016; 45:361-75. [PMID: 26618565 DOI: 10.1039/c5dt02769a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New facile methods to prepare iron sulphur halide clusters [Fe4S4X4](2-) from [Fe(CO)5] and elemental sulphur were elaborated. Reactions of ferrous precursors like tetrahalidoferrates(ii) or simple ferrous halides with [Fe(CO)5] and sulphur turned out to be efficient methods to prepare homoleptic [Fe4S4X4](2-) (X = Cl, Br) and heteroleptic clusters [Fe4S4X4-nYn](2-) (X = Cl, Br; Y = Br, I). Solid materials were obtained as salts of BTMA(+) (= benzyltrimethylammonium); the new compounds containing [Fe4S4Br4](2-) and [Fe4S4X2Y2](2-) (X, Y = Cl, Br, I) were all isostructural to (BTMA)2[Fe4S4I4] (monoclinic, Cc) as inferred from synchrotron X-ray powder diffraction. While the solid materials contain defined heteroleptic clusters with a halide X : Y ratio of 2 : 2, dissolving these compounds leads to rapid scrambling of the halide ligands forming mixtures of all five possible [Fe4S4X4-nYn](2-) clusters as could be shown by UHR-ESI MS. The variation of X and Y allowed assignment of the absorption bands in the visible and NIR; the long-wavelength bands around 1100 nm were tentatively assigned to intervalence charge transfer (IVCT) transitions.
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Affiliation(s)
- Andreas O Schüren
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany. and Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Verena K Gramm
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
| | - Maximilian Dürr
- Department Chemie und Pharmazie, Lehrstuhl für Bioanorgansiche Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Ana Foi
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Ivana Ivanović-Burmazović
- Department Chemie und Pharmazie, Lehrstuhl für Bioanorgansiche Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Fabio Doctorovich
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Uwe Ruschewitz
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
| | - Axel Klein
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
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8
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoidbiosynthese in pathogenen Bakterien: Nukleare inelastische Streuung ermöglicht Einblicke in den ungewöhnlichen [4Fe-4S]-Cluster vom E.- coli-Protein LytB/IspH. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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9
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoid Biosynthesis in Pathogenic Bacteria: Nuclear Resonance Vibrational Spectroscopy Provides Insight into the Unusual [4Fe-4S] Cluster of the E. coli LytB/IspH Protein. Angew Chem Int Ed Engl 2015; 54:12584-7. [PMID: 26118554 DOI: 10.1002/anie.201502494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/10/2022]
Abstract
The LytB/IspH protein catalyzes the last step of the methylerythritol phosphate (MEP) pathway which is used for the biosynthesis of essential terpenoids in most pathogenic bacteria. Therefore, the MEP pathway is a target for the development of new antimicrobial agents as it is essential for microorganisms, yet absent in humans. Substrate-free LytB has a special [4Fe-4S](2+) cluster with a yet unsolved structure. This motivated us to use synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) in combination with quantum chemical-molecular mechanical (QM/MM) calculations to gain more insight into the structure of substrate-free LytB. The apical iron atom of the [4Fe-4S](2+) is clearly linked to three water molecules. We additionally present NRVS data of LytB bound to its natural substrate, (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) and to the inhibitors (E)-4-amino-3-methylbut-2-en-1-yl diphosphate and (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate.
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Affiliation(s)
- Isabelle Faus
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Annegret Reinhard
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Sergej Rackwitz
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Juliusz A Wolny
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Kai Schlage
- P01, Petra III, DESY, Notkestrasse 85, D-22607 Hamburg (Germany)
| | | | - Aleksandr Chumakov
- ESRF - The European Synchrotron, CS40220, 38043 Grenoble Cedex 9 (France)
| | - Sergiy Krasutsky
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Philippe Chaignon
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France)
| | - C Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Myriam Seemann
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France).
| | - Volker Schünemann
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany).
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10
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Leu BM, Zgierski MZ, Bischoff C, Li M, Hu MY, Zhao J, Martin SW, Alp EE, Scheidt WR. Quantitative vibrational dynamics of the metal site in a tin porphyrin: an IR, NRVS, and DFT study. Inorg Chem 2013; 52:9948-53. [PMID: 23962374 PMCID: PMC3787516 DOI: 10.1021/ic401152b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We used a newer, synchrotron-based, spectroscopic technique (nuclear resonance vibrational spectroscopy, NRVS) in combination with a more traditional one (infrared absorption, IR) to obtain a complete, quantitative picture of the metal center vibrational dynamics in a six-coordinated tin porphyrin. From the NRVS (119)Sn site-selectivity and the sensitivity of the IR signal to (112)Sn/(119)Sn isotope substitution, we identified the frequency of the antisymmetric stretching of the axial bonds (290 cm(-1)) and all the other vibrations involving Sn. Experimentally authenticated density functional theory (DFT) calculations aid the data interpretation by providing detailed normal mode descriptions for each observed vibration. These results may represent a starting point toward the characterization of the local vibrational dynamics of the metallic site in tin porphyrins and compounds with related structures. The quantitative complementariness between IR, NRVS, and DFT is emphasized.
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Affiliation(s)
- Bogdan M Leu
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States.
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11
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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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12
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Kamali S, Wang H, Mitra D, Ogata H, Lubitz W, Manor BC, Rauchfuss TB, Byrne D, Bonnefoy V, Jenney FE, Adams MWW, Yoda Y, Alp E, Zhao J, Cramer SP. Observation of the Fe-CN and Fe-CO vibrations in the active site of [NiFe] hydrogenase by nuclear resonance vibrational spectroscopy. Angew Chem Int Ed Engl 2013; 52:724-8. [PMID: 23136119 PMCID: PMC3535562 DOI: 10.1002/anie.201204616] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/09/2012] [Indexed: 11/06/2022]
Abstract
Nuclear inelastic scattering of (57)Fe labeled [NiFe] hydrogenase is shown to give information on different states of the enzyme. It was thus possible to detect and assign Fe-CO and Fe-CN bending and stretching vibrations of the active site outside the spectral range of the Fe-S cluster normal modes.
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Affiliation(s)
- Saeed Kamali
- Department of Chemistry, University of California Davis, CA 95616 (USA)
| | - Hongxin Wang
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA)
- Department of Chemistry, University of California Davis, CA 95616 (USA)
| | - Devrani Mitra
- Department of Chemistry, University of California Davis, CA 95616 (USA)
| | - Hideaki Ogata
- Max-Planck-Institut für Chemische Energiekonversion 45470 Mülheim an der Ruhr (Germany)
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion 45470 Mülheim an der Ruhr (Germany)
| | - Brian C. Manor
- Department of Chemistry, University of Illinois Champaign-Urbana, IL 61801 (USA)
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois Champaign-Urbana, IL 61801 (USA)
| | - Deborah Byrne
- Institut de Microbiologie de la Méditerranée Aix-Marseille-Universit , Marseille 13009 (France)
| | - Violaine Bonnefoy
- CNRS, IMM, Laboratoire de Chimie Bactérienne Marseille Cedex 20 (France)
| | - Francis E. Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine Suwanee, GA 30024 (USA)
| | - Michael W. W. Adams
- Department of Biochemistry & Molecular Biology University of Georgia, Athens, GA 30602 (USA)
| | - Yoshitaka Yoda
- JASRI, SPring-8 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)
| | - Ercan Alp
- Advanced Photon Source, Argonne National Laboratory Argonne, IL 60439 (USA)
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory Argonne, IL 60439 (USA)
| | - Stephen P. Cramer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA)
- Department of Chemistry, University of California Davis, CA 95616 (USA)
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Kamali S, Wang H, Mitra D, Ogata H, Lubitz W, Manor BC, Rauchfuss TB, Byrne D, Bonnefoy V, Jenney FE, Adams MWW, Yoda Y, Alp E, Zhao J, Cramer SP. Detektion von Fe-CN- und Fe-CO-Schwingungen im aktiven Zentrum der [NiFe]-Hydrogenase durch inelastische kernresonante Streuung. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204616] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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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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15
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George SJ, Barney BM, Mitra D, Igarashi RY, Guo Y, Dean DR, Cramer SP, Seefeldt LC. EXAFS and NRVS reveal a conformational distortion of the FeMo-cofactor in the MoFe nitrogenase propargyl alcohol complex. J Inorg Biochem 2012; 112:85-92. [PMID: 22564272 DOI: 10.1016/j.jinorgbio.2012.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Revised: 01/03/2012] [Accepted: 02/07/2012] [Indexed: 10/14/2022]
Abstract
We have used EXAFS and NRVS spectroscopies to examine the structural changes in the FeMo-cofactor active site of the α-70(Ala) variant of Azotobacter vinelandii nitrogenase on binding and reduction of propargyl alcohol (PA). The Mo K-edge near-edge and EXAFS spectra are very similar in the presence and absence of PA, suggesting PA does not bind at Mo. By contrast, Fe EXAFS spectra show a clear and reproducible change in the long Fe-Fe interaction at ~3.7 Å on PA binding with the apparent appearance of a new Fe-Fe interaction at 3.99 Å. An analogous change in the long Mo-Fe 5.1 Å interaction is not seen. The NRVS spectra exclude the possibility of large-scale structural change of the FeMo-cofactor involving breaking the μ(2) Fe-S-Fe bonds of the Fe(6)S(9)X core. The simplest chemically consistent structural change is that the bound form of PA is coordinated at Fe atoms (Fe6 or Fe7) adjacent to the Mo terminus, with a concomitant movement of the Fe away from the central atom X and along the Fe-X bond by about 0.35 Å. This study comprises the first experimental evidence of the conformational changes of the FeMo-cofactor active site on binding a substrate or product.
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Affiliation(s)
- Simon J George
- Department of Chemistry, University of California, Davis, CA 95616, USA.
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16
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Jayasooriya UA, Peck JN, Elaine Barclay J, Hardy SM, Chumakov AI, Evans DJ, Pickett CJ, Oganesyan VS. Nuclear inelastic scattering spectroscopy of tris(acetylacetonate)iron(III); A vibrational probe via the iron atom. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.10.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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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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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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Pelmenschikov V, Guo Y, Wang H, Cramer SP, Case DA. Fe-H/D stretching and bending modes in nuclear resonant vibrational, Raman and infrared spectroscopies: comparisons of density functional theory and experiment. Faraday Discuss 2011; 148:409-20; discussion 421-41. [PMID: 21322496 PMCID: PMC3058621 DOI: 10.1039/c004367m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infrared, Raman, and nuclear resonant vibrational (NRVS) spectroscopies have been used to address the Fe-H bonding in trans-HFe(CO) iron hydride compound, HFe(CO)(dppe)2, dppe = 1,2-bis(diphenylphosphino)ethane. H and D isotopomers of the compound, with selective substitution at the metal-coordinated hydrogen, have been considered in order to address the Fe-H/D stretching and bending modes. Experimental results are compared to the normal mode analysis by density functional theory (DFT). The results are that (i) the IR spectrum does not clearly show Fe-H stretching or bending modes; (ii) Fe-H stretching modes are clear but weak in the Raman spectrum, and Fe-H bending modes are weak; (iii) NRVS 57Fe spectroscopy resolves Fe-H bending clearly, but Fe-H or Fe-D stretching is above its experimentally resolved frequency range. DFT calculations (with no scaling of frequencies) show intensities and peak locations that allow unambiguous correlations between observed and calculated features, with frequency errors generally less than 15 cm(-1). Prospects for using these techniques to unravel vibrational modes of protein active sites are discussed.
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Affiliation(s)
- Vladimir Pelmenschikov
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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Tonzetich ZJ, Wang H, Mitra D, Tinberg CE, Do LH, Jenney FE, Adams MWW, Cramer SP, Lippard SJ. Identification of protein-bound dinitrosyl iron complexes by nuclear resonance vibrational spectroscopy. J Am Chem Soc 2010; 132:6914-6. [PMID: 20429508 DOI: 10.1021/ja101002f] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We have applied (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to identify protein-bound dinitrosyl iron complexes. Intense NRVS peaks due to vibrations of the N-Fe-N unit can be observed between 500 and 700 cm(-1) and are diagnostic indicators of the type of iron dinitrosyl species present. NRVS spectra for four iron dinitrosyl model compounds are presented and used as benchmarks for the identification of species formed in the reaction of Pyrococcus furiosus ferredoxin D14C with nitric oxide.
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Affiliation(s)
- Zachary J Tonzetich
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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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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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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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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George SJ, Igarashi RY, Xiao Y, Hernandez JA, Demuez M, Zhao D, Yoda Y, Ludden PW, Rubio LM, Cramer SP. Extended X-ray absorption fine structure and nuclear resonance vibrational spectroscopy reveal that NifB-co, a FeMo-co precursor, comprises a 6Fe core with an interstitial light atom. J Am Chem Soc 2008; 130:5673-80. [PMID: 18386899 DOI: 10.1021/ja0755358] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NifB-co, an Fe-S cluster produced by the enzyme NifB, is an intermediate on the biosynthetic pathway to the iron molybdenum cofactor (FeMo-co) of nitrogenase. We have used Fe K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy together with (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the structure of NifB-co while bound to the NifX protein from Azotobacter vinelandii. The spectra have been interpreted in part by comparison with data for the completed FeMo-co attached to the NafY carrier protein: the NafY:FeMo-co complex. EXAFS analysis of the NifX:NifB-co complex yields an average Fe-S distance of 2.26 A and average Fe-Fe distances of 2.66 and 3.74 A. Search profile analyses reveal the presence of a single Fe-X (X = C, N, or O) interaction at 2.04 A, compared to a 2.00 A Fe-X interaction found in the NafY:FeMo-co EXAFS. This suggests that the interstitial light atom (X) proposed to be present in FeMo-co has already inserted at the NifB-co stage of biosynthesis. The NRVS exhibits strong bands from Fe-S stretching modes peaking around 270, 315, 385, and 408 cm(-1). Additional intensity at approximately 185-200 cm(-1) is interpreted as a set of cluster "breathing" modes similar to those seen for the FeMo-cofactor. The strength and location of these modes also suggest that the FeMo-co interstitial light atom seen in the crystal structure is already in place in NifB-co. Both the EXAFS and NRVS data for NifX:NifB-co are best simulated using a Fe 6S 9X trigonal prism structure analogous to the 6Fe core of FeMo-co, although a 7Fe structure made by capping one trigonal 3S terminus with Fe cannot be ruled out. The results are consistent with the conclusion that the interstitial light atom is already present at an early stage in FeMo-co biosynthesis prior to the incorporation of Mo and R-homocitrate.
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Affiliation(s)
- Simon J George
- Advanced Biological and Environmental X-ray Facility, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Cramer SP, Xiao Y, Wang H, Guo Y, Smith MC. Nuclear Resonance Vibrational Spectroscopy (NRVS) of Fe–S model compounds, Fe–S proteins, and nitrogenase. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s10751-006-9473-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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