1
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Warmack RA, Rees DC. Nitrogenase beyond the Resting State: A Structural Perspective. Molecules 2023; 28:7952. [PMID: 38138444 PMCID: PMC10745740 DOI: 10.3390/molecules28247952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.
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Affiliation(s)
- Rebeccah A. Warmack
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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2
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Lai TY, Chen C, Chu K, Chien S, Ong T, Chiang M. Biologically inspired
3Fe4S
cluster as structural mimics of
FeMoco
M‐cluster. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202300062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Affiliation(s)
- Ting Yi Lai
- Institute of Chemistry Academia Sinica Taipei Taiwan
| | - Chang‐Ting Chen
- Institute of Chemistry Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - Kai‐Ti Chu
- Institute of Chemistry Academia Sinica Taipei Taiwan
| | - Su‐Ying Chien
- Instrumentation Center National Taiwan University Taipei Taiwan
| | - Tiow‐Gan Ong
- Institute of Chemistry Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - Ming‐Hsi Chiang
- Institute of Chemistry Academia Sinica Taipei Taiwan
- Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung Taiwan
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3
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Schneider C, Groß SJ, Demeshko S, Bontemps S, Meyer F, Werncke CG. Synthesis and characterisation of a very low-coordinate diferrous [2Fe-2S] 0 unit. Chem Commun (Camb) 2021; 57:10751-10754. [PMID: 34585677 DOI: 10.1039/d1cc04196g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Here we present the synthesis of a unique diferrous [2Fe-2S]0 complex with only three-coordinate iron ions via reduction of a four-coordinate diferric [2Fe-2S]2+ complex with concomitant ligand loss. The obtained compounds were thoroughly examined for their properties (e.g. by 57Fe Mössbauer spectroscopy and magnetic susceptibility measurements). Facile cleavage of the [2Fe-2S] rhombus, commonly seen as rather stable, by CS2 is also shown.
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Affiliation(s)
- Christian Schneider
- Chemistry Department, Philipps-University, Hans-Meerwein-Str. 4, 35043 Marburg, Germany.
| | - Sophie J Groß
- University of Göttingen, Institute of Inorganic Chemistry, Tammannstr. 4, D-37077 Göttingen, Germany
| | - Serhiy Demeshko
- University of Göttingen, Institute of Inorganic Chemistry, Tammannstr. 4, D-37077 Göttingen, Germany
| | - Sébastien Bontemps
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, 31077 Toulouse, France.,Université de Toulouse, UPS, INPT, 31077 Toulouse, France
| | - Franc Meyer
- University of Göttingen, Institute of Inorganic Chemistry, Tammannstr. 4, D-37077 Göttingen, Germany
| | - C Gunnar Werncke
- Chemistry Department, Philipps-University, Hans-Meerwein-Str. 4, 35043 Marburg, Germany.
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4
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Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine. Nat Commun 2021; 12:5925. [PMID: 34635654 PMCID: PMC8505563 DOI: 10.1038/s41467-021-26158-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Iron-sulfur (FeS) proteins are ancient and fundamental to life, being involved in electron transfer and CO2 fixation. FeS clusters have structures similar to the unit-cell of FeS minerals such as greigite, found in hydrothermal systems linked with the origin of life. However, the prebiotic pathway from mineral surfaces to biological clusters is unknown. Here we show that FeS clusters form spontaneously through interactions of inorganic Fe2+/Fe3+ and S2- with micromolar concentrations of the amino acid cysteine in water at alkaline pH. Bicarbonate ions stabilize the clusters and even promote cluster formation alone at concentrations >10 mM, probably through salting-out effects. We demonstrate robust, concentration-dependent formation of [4Fe4S], [2Fe2S] and mononuclear iron clusters using UV-Vis spectroscopy, 57Fe-Mössbauer spectroscopy and 1H-NMR. Cyclic voltammetry shows that the clusters are redox-active. Our findings reveal that the structures responsible for biological electron transfer and CO2 reduction could have formed spontaneously from monomers at the origin of life.
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5
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Dhara S, Panda S, Lahiri GK. Redox induced S-S bond cleavage of 2,2'-dithiobisbenzothiazole - leading to a [2Ru-2S] core analogous to [2Fe-2S] cluster. Dalton Trans 2021; 50:12408-12412. [PMID: 34378605 DOI: 10.1039/d1dt02211c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Facile reduction of 2,2'-dithiobisbenzothiazole by the mediation of metal-to-ligand charge transfer or by internal reducing equivalent is demonstrated. It leads to various binding modes of thiolates (κ1, κ2, μ) in a series of mononuclear and dinuclear ruthenium complexes. The dinuclear complex exhibited electron transfer processes similar to a [2Fe-2S] cluster.
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Affiliation(s)
- Suman Dhara
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Sanjib Panda
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Goutam Kumar Lahiri
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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6
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Wang CH, DeBeer S. Structure, reactivity, and spectroscopy of nitrogenase-related synthetic and biological clusters. Chem Soc Rev 2021; 50:8743-8761. [PMID: 34159992 DOI: 10.1039/d1cs00381j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The reduction of dinitrogen (N2) is essential for its incorporation into nucleic acids and amino acids, which are vital to life on earth. Nitrogenases convert atmospheric dinitrogen to two ammonia molecules (NH3) under ambient conditions. The catalytic active sites of these enzymes (known as FeM-cofactor clusters, where M = Mo, V, Fe) are the sites of N2 binding and activation and have been a source of great interest for chemists for decades. In this review, recent studies on nitrogenase-related synthetic molecular complexes and biological clusters are discussed, with a focus on their reactivity and spectroscopic characterization. The molecular models that are discussed span from simple mononuclear iron complexes to multinuclear iron complexes and heterometallic iron complexes. In addition, recent work on the extracted biological cofactors is discussed. An emphasis is placed on how these studies have contributed towards our understanding of the electronic structure and mechanism of nitrogenases.
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Affiliation(s)
- Chen-Hao Wang
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
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7
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Abstract
57Fe Mӧssbauer spectroscopy is unparalleled in the study of Fe-S cluster-containing proteins because of its unique ability to detect all forms of iron. Enrichment of biological samples with the 57Fe isotope and manipulation of experimental parameters such as temperature and magnetic field allow for elucidation of the number of Fe-S clusters present in a given protein, their nuclearity, oxidation state, geometry, and ligation environment, as well as any transient states relevant to enzyme chemistry. This chapter is arranged in five sections to help navigate an experimentalist to utilize 57Fe Mӧssbauer spectroscopy for delineating the role and structure of biological Fe-S clusters. The first section lays out the tools and technical considerations for the preparation of 57Fe-labeled samples. The choice of experimental parameters and their effects on the Mӧssbauer spectra are presented in the following two sections. The last two sections provide a theoretical and practical guide on spectral acquisition and analysis relevant to Fe-S centers.
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8
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Postbiosynthetic modification of a precursor to the nitrogenase iron-molybdenum cofactor. Proc Natl Acad Sci U S A 2021; 118:2015361118. [PMID: 33836573 DOI: 10.1073/pnas.2015361118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogenases utilize Fe-S clusters to reduce N2 to NH3 The large number of Fe sites in their catalytic cofactors has hampered spectroscopic investigations into their electronic structures, mechanisms, and biosyntheses. To facilitate their spectroscopic analysis, we are developing methods for incorporating 57Fe into specific sites of nitrogenase cofactors, and we report herein site-selective 57Fe labeling of the L-cluster-a carbide-containing, [Fe8S9C] precursor to the Mo nitrogenase catalytic cofactor. Treatment of the isolated L-cluster with the chelator ethylenediaminetetraacetate followed by reconstitution with 57Fe2+ results in 57Fe labeling of the terminal Fe sites in high yield and with high selectivity. This protocol enables the generation of L-cluster samples in which either the two terminal or the six belt Fe sites are selectively labeled with 57Fe. Mössbauer spectroscopic analysis of these samples bound to the nitrogenase maturase Azotobacter vinelandii NifX reveals differences in the primary coordination sphere of the terminal Fe sites and that one of the terminal sites of the L-cluster binds to H35 of Av NifX. This work provides molecular-level insights into the electronic structure and biosynthesis of the L-cluster and introduces postbiosynthetic modification as a promising strategy for studies of nitrogenase cofactors.
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9
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Solomon J, Rasekh MF, Hiller CJ, Lee CC, Tanifuji K, Ribbe MW, Hu Y. Probing the All-Ferrous States of Methanogen Nitrogenase Iron Proteins. JACS AU 2021; 1:119-123. [PMID: 34467276 PMCID: PMC8395668 DOI: 10.1021/jacsau.0c00072] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Fe protein of nitrogenase reduces two C1 substrates, CO2 and CO, under ambient conditions when its [Fe4S4] cluster adopts the all-ferrous [Fe4S4]0 state. Here, we show disparate reactivities of the nifH- and vnf-encoded Fe proteins from Methanosarcina acetivorans (designated MaNifH and MaVnfH) toward C1 substrates in the all-ferrous state, with the former capable of reducing both CO2 and CO to hydrocarbons, and the latter only capable of reducing CO to hydrocarbons at substantially reduced yields. EPR experiments conducted at varying solution potentials reveal that MaVnfH adopts the all-ferrous state at a more positive reduction potential than MaNifH, which could account for the weaker reactivity of the MaVnfH toward C1 substrates than MaNifH. More importantly, MaVnfH already displays the g = 16.4 parallel-mode EPR signal that is characteristic of the all-ferrous [Fe4S4]0 cluster at a reduction potential of -0.44 V, and the signal reaches 50% maximum intensity at a reduction potential of -0.59 V, suggesting the possibility of this Fe protein to access the all-ferrous [Fe4S4]0 state under physiological conditions. These results bear significant relevance to the long-lasting debate of whether the Fe protein can utilize the [Fe4S4]0/2+ redox couple to support a two-electron transfer during substrate turnover which, therefore, is crucial for expanding our knowledge of the reaction mechanism of nitrogenase and the cellular energetics of nitrogenase-based processes.
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Affiliation(s)
- Joseph
B. Solomon
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Mahtab F. Rasekh
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Caleb J. Hiller
- Department
of Physical Science, Southern Utah University, Cedar City, Utah 84720, United States
| | - Chi Chung Lee
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
| | - Kazuki Tanifuji
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
| | - Markus W. Ribbe
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
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10
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Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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11
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Gao X, Zhang Y, Li F, Tian B, Wang X, Wang Z, Carozza JC, Zhou Z, Han H, Xu C. Surface Modulation and Chromium Complexation: All-in-One Solution for the Cr(VI) Sequestration with Bifunctional Molecules. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8373-8379. [PMID: 32421314 DOI: 10.1021/acs.est.0c00710] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The sulfidation of zero valent iron (ZVI) to an Fe@FeSx (S-ZVI) composite has been intensively explored in the ZVI field. Yet, further benefits from the FeSx coating layer are seldom realized, especially those effectively using its intrinsic physical and chemical properties for elaborate design. Here, we demonstrate that in a traditional Cr(VI) sequestration reaction, the FeSx layer displays a great utility in immobilizing molecules containing hydroxyl groups (-OH) and hence, attracting Cr(VI) complexes chelated with carboxyl organics (RCOOH). Such intermolecular attraction readily promotes the diffusion of the Cr(VI) complexes to the S-ZVI surface, affording a higher reaction rate for the Cr(VI) sequestration process. In addition, the above mechanism was used to guide a rational selection of molecules incorporating both hydroxyl and carboxyl functional groups with a proper ratio and thereby, a significantly improved reaction efficiency was achieved. Furthermore, the FeSx phase was revealed to be consumed in the reaction, acting as a supplementary reductant. This work is the first to unveil the relationship between molecules with specific functionalization and the FeSx phase, providing a general rule in choosing appropriate reaction media for Cr(VI) sequestration and related reactions.
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Affiliation(s)
- Xuyan Gao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Yue Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Fengmin Li
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Boyang Tian
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Xiao Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Zhiwei Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Jesse C Carozza
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Zheng Zhou
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Haixiang Han
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Chunhua Xu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
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12
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Planar three-coordinate iron sulfide in a synthetic [4Fe-3S] cluster with biomimetic reactivity. Nat Chem 2019; 11:1019-1025. [PMID: 31611632 PMCID: PMC6858550 DOI: 10.1038/s41557-019-0341-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/19/2019] [Indexed: 11/25/2022]
Abstract
Iron-sulfur clusters are emerging as reactive sites for the reduction of small-molecule substrates. However, the four-coordinate iron sites of typical iron-sulfur clusters rarely react with substrates, implicating three-coordinate iron. This idea is untested because fully sulfide-coordinated three-coordinate iron is unprecedented. Here we report a new type of [4Fe-3S] cluster featuring an iron center with three bonds to sulfides. Although a high-spin electronic configuration is characteristic of other iron-sulfur clusters, the planar geometry and short Fe–S bonds lead to a surprising low-spin electronic configuration at the three-coordinate Fe center as determined by spectroscopy and ab initio calculations. In a demonstration of biomimetic reactivity, the [4Fe-3S] cluster reduces hydrazine, a natural substrate of nitrogenase. The product is the first example of NH2 bound to an iron-sulfur cluster. Our results demonstrate that three-coordinate iron supported by sulfide donors is a plausible precursor to reactivity in iron-sulfur clusters like the FeMoco of nitrogenase.
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13
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Hoeke V, Tociu L, Case DA, Seefeldt LC, Raugei S, Hoffman BM. High-Resolution ENDOR Spectroscopy Combined with Quantum Chemical Calculations Reveals the Structure of Nitrogenase Janus Intermediate E 4(4H). J Am Chem Soc 2019; 141:11984-11996. [PMID: 31310109 DOI: 10.1021/jacs.9b04474] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have shown that the key state in N2 reduction to two NH3 molecules by the enzyme nitrogenase is E4(4H), the "Janus" intermediate, which has accumulated four [e-/H+] and is poised to undergo reductive elimination of H2 coupled to N2 binding and activation. Initial 1H and 95Mo ENDOR studies of freeze-trapped E4(4H) revealed that the catalytic multimetallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted as E4(4H)(a), with two parallel Fe-H-Fe planes bridging pairs of "anchor" Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E4(4H)(b), with one bridging and one terminal hydride, and E4(4H)(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties in the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E4(4H)(c), and additional structures have been proposed in the DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1H-ENDOR experiments using improved instrumentation, Mims 2H ENDOR, and a recently developed pulsed-ENDOR protocol ("PESTRE") to obtain absolute hyperfine interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its "anchoring" Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result is the freeze-trapped, lowest-energy Janus intermediate structure, E4(4H)(a).
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Affiliation(s)
- Veronika Hoeke
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Laura Tociu
- Department of Chemistry , University of Chicago , Chicago , Illinois 60637 , United States
| | - David A Case
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States
| | - Simone Raugei
- Physical Sciences Division , Pacific Northwestern National Laboratory , Richland , Washington 99352 , United States
| | - Brian M Hoffman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
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14
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DeRosha DE, Arnet NA, Mercado BQ, Holland PL. A [2Fe-1S] Complex That Affords Access to Bimetallic and Higher-Nuclearity Iron-Sulfur Clusters. Inorg Chem 2019; 58:8829-8834. [PMID: 31247861 DOI: 10.1021/acs.inorgchem.9b01212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small, coordinatively unsaturated iron-sulfur clusters are conceived as building blocks for the diverse set of shapes of iron-sulfur clusters in biological and synthetic chemistry. Here we describe a synthetic method for preparing [2Fe-1S] clusters containing two iron(II) ions, which are supported by a relatively unhindered β-diketiminate supporting ligand. The [2Fe-1S] cluster can be isolated in the presence of trimethylphosphine, and the compound with one PMe3 on each iron(II) ion has been crystallographically characterized. The PMe3 ligands may be removed with B(C6F5)3 to give a spectroscopically characterized species with solvent ligands. This species is a versatile synthon for [2Fe-2S], [4Fe-3S], and [10Fe-8S] clusters. Crystallographic characterization of the 10Fe cluster shows that it has all iron(II) ions, and the core has two [4Fe-4S] cubes that share a face in a novel arrangement. This cluster also has two iron sites that are coordinated to solvent donors, suggesting the potential for using this type of cluster for reactivity in the future.
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Affiliation(s)
- Daniel E DeRosha
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Nicholas A Arnet
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Brandon Q Mercado
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Patrick L Holland
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
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15
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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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16
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Khodour Y, Kaguni LS, Stiban J. Iron-sulfur clusters in nucleic acid metabolism: Varying roles of ancient cofactors. Enzymes 2019; 45:225-256. [PMID: 31627878 DOI: 10.1016/bs.enz.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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17
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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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18
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
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19
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Ollagnier de Choudens S, Barras F. Genetic, Biochemical, and Biophysical Methods for Studying FeS Proteins and Their Assembly. Methods Enzymol 2017; 595:1-32. [PMID: 28882198 DOI: 10.1016/bs.mie.2017.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
FeS clusters containing proteins are structurally and functionally diverse and present in most organisms. Our understanding of FeS cluster production and insertion into polypeptides has benefited from collaborative efforts between in vitro and in vivo studies. The former allows a detailed description of FeS-containing protein and a deep understanding of the molecular mechanisms catalyzing FeS cluster assembly. The second allows to include metabolic and environmental constraints within the analysis of FeS homeostasis. The interplay and the cross talk between the two approaches have been a key strategy to reach a multileveled integrated understanding of FeS cluster homeostasis. In this chapter, we describe the genetic and biochemical/biophysical strategies that were used in the field of FeS cluster biogenesis, with the aim of providing the reader with a critical view of both approaches. In addition to the description of classic tricks and a series of recommendations, we will also discuss models as well as spectroscopic techniques useful to characterize FeS clusters such as UV-visible, Mössbauer, electronic paramagnetic resonance, resonance Raman, circular dichroism, and nuclear magnetic resonance.
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Affiliation(s)
- Sandrine Ollagnier de Choudens
- Université Grenoble Alpes, Laboratoire de Chimie et Biologie des Métaux, BioCat, Grenoble, France; CNRS, Laboratoire de Chimie et Biologie des Métaux, BioCat, UMR, Grenoble, France; CEA-Grenoble, DRF/BIG/CBM, Grenoble, France.
| | - Frédéric Barras
- Laboratoire Chimie Bactérienne, Université Aix-Marseille, CNRS, Marseille, France.
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20
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Stiban J, So M, Kaguni LS. Iron-Sulfur Clusters in Mitochondrial Metabolism: Multifaceted Roles of a Simple Cofactor. BIOCHEMISTRY (MOSCOW) 2017; 81:1066-1080. [PMID: 27908232 DOI: 10.1134/s0006297916100059] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis. Whereas the identification of iron-sulfur containing proteins and their roles in numerous aspects of cellular function has been a long-standing research area, that in mitochondria is comparatively recent, and it is likely that their roles within mitochondria have been only partially revealed. We review the status of the field and provide examples of other cellular iron-sulfur proteins to highlight their multifarious roles.
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Affiliation(s)
- Johnny Stiban
- Birzeit University, Department of Biology and Biochemistry, West Bank Birzeit, 627, Palestine.
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21
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Lee Y, Abboud KA, García-Serres R, Murray LJ. A three-coordinate Fe(ii) center within a [3Fe-(μ3-S)] cluster that provides an accessible coordination site. Chem Commun (Camb) 2016; 52:9295-8. [PMID: 27363672 DOI: 10.1039/c6cc04671a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A μ3-sulfide bridged triiron cluster(ii,ii,iii) supported by a cyclophane ligand undergoes metal-based reduction to yield an all-ferrous species. The latter complex incorporates a three-coordinate iron center that provides an accessible coordination site to a solvent molecule.
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Affiliation(s)
- Yousoon Lee
- University of Florida, Department of Chemistry, Center for Catalysis, Gainesville, FL 32611-7200, USA.
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22
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Yao S, Meier F, Lindenmaier N, Rudolph R, Blom B, Adelhardt M, Sutter J, Mebs S, Haumann M, Meyer K, Kaupp M, Driess M. Biomimetische [2Fe-2S]-Cluster mit stark delokalisierten gemischtvalenten Eisenzentren. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506788] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Yao S, Meier F, Lindenmaier N, Rudolph R, Blom B, Adelhardt M, Sutter J, Mebs S, Haumann M, Meyer K, Kaupp M, Driess M. Biomimetic [2Fe-2S] Clusters with Extensively Delocalized Mixed-Valence Iron Centers. Angew Chem Int Ed Engl 2015; 54:12506-10. [DOI: 10.1002/anie.201506788] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Indexed: 11/09/2022]
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25
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Reesbeck ME, Rodriguez MM, Brennessel WW, Mercado BQ, Vinyard D, Holland PL. Oxidized and reduced [2Fe-2S] clusters from an iron(I) synthon. J Biol Inorg Chem 2015; 20:875-83. [PMID: 26044124 DOI: 10.1007/s00775-015-1272-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/20/2015] [Indexed: 02/06/2023]
Abstract
Synthetic [2Fe-2S] clusters are often used to elucidate ligand effects on the reduction potentials and spectroscopy of natural electron-transfer sites, which can have anionic Cys ligands or neutral His ligands. Current synthetic routes to [2Fe-2S] clusters are limited in their feasibility with a range of supporting ligands. Here, we report a new synthetic route to synthetic [2Fe-2S] clusters, through oxidation of an iron(I) source with elemental sulfur. This method yields a neutral diketiminate-supported [2Fe-2S] cluster in the diiron(III)-oxidized form. The oxidized [2Fe-2S] cluster can be reduced to a mixed valent iron(II)-iron(III) compound. Both the diferric and reduced mixed valent clusters are characterized using X-ray crystallography, Mössbauer spectroscopy, EPR spectroscopy and cyclic voltammetry. The reduced compound is particularly interesting because its X-ray crystal structure shows a difference in Fe-S bond lengths to one of the iron atoms, consistent with valence localization. The valence localization is also evident from Mössbauer spectroscopy.
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Affiliation(s)
- Megan E Reesbeck
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06520, USA
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26
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Terranova U, de Leeuw NH. Aqueous Fe2S2 cluster: structure, magnetic coupling, and hydration behaviour from Hubbard U density functional theory. Phys Chem Chem Phys 2015; 16:13426-33. [PMID: 24881882 DOI: 10.1039/c4cp00984c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We present a DFT + U investigation of the all-ferrous Fe2S2 cluster in aqueous solution. We determine the value of U by tuning the geometry of the cluster in the gas-phase to that obtained by the highly accurate CCSD(T) method. When the optimised value of U is employed for the aqueous Fe2S2 cluster (Fe2S2(aq)), the resulting geometry agrees well with the X-ray diffraction structure, while the magnetic coupling is in line with the estimate from Mössbauer data. Molecular dynamics trajectories predict Fe2S2(aq) to be stable in water, regardless of the introduction of U. However, significant differences arise in the geometry, hydration, and exchange constant of the solvated clusters.
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Affiliation(s)
- Umberto Terranova
- Department of Chemistry, University College London, London, WC1H 0AJ, UK.
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27
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Ali ME, Staemmler V, Marx D. Magnetostructural dynamics of Rieske versus ferredoxin iron-sulfur cofactors. Phys Chem Chem Phys 2015; 17:6289-96. [PMID: 25648433 DOI: 10.1039/c4cp05465b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The local chemical environment of the [2Fe-2S] cofactor hosted by ferredoxin and Rieske-type proteins is fundamentally different due to the presence of distinct ligands at the two iron centers in the case of Rieske proteins, whereas they are identical in ferredoxins. This renders Rieske [2Fe-2S] cores chemically asymmetric and results in more complex vibrational spectra as compared to ferredoxin. Likewise, one would expect other properties, for instance the dynamics of the magnetic exchange coupling constant J, to be also more complex. Applying ab initio molecular dynamics using our recently introduced spin-constrained two-determinant extended broken symmetry (CEBS) approach to Rieske and ferredoxin model complexes at 300 K, we extract the molecular fluctuations and the resulting magnetostructural cross-correlations involving the antiferromagnetic exchange interaction J(t). This analysis demonstrates that the details of the magnetostructural dynamics are indeed distinctly different for Rieske and ferredoxin cofactors, while the time averages of 〈J〉 are shown to be essentially identical. In particular, the frequency window between about 200 and 350 cm(-1), is a "fingerprint region" that allows one to distinguish chemically asymmetric from symmetric cofactors and thus Rieske proteins from ferredoxins.
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Affiliation(s)
- Md Ehesan Ali
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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28
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Mössbauer spectroscopy of Fe/S proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1395-405. [PMID: 25498248 DOI: 10.1016/j.bbamcr.2014.12.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/17/2014] [Accepted: 12/03/2014] [Indexed: 01/02/2023]
Abstract
Iron-sulfur (Fe/S) clusters are structurally and functionally diverse cofactors that are found in all domains of life. (57)Fe Mössbauer spectroscopy is a technique that provides information about the chemical nature of all chemically distinct Fe species contained in a sample, such as Fe oxidation and spin state, nuclearity of a cluster with more than one metal ion, electron spin ground state of the cluster, and delocalization properties in mixed-valent clusters. Moreover, the technique allows for quantitation of all Fe species, when it is used in conjunction with electron paramagnetic resonance (EPR) spectroscopy and analytical methods. (57)Fe-Mössbauer spectroscopy played a pivotal role in unraveling the electronic structures of the "well-established" [2Fe-2S](2+/+), [3Fe-4S](1+/0), and [4Fe-4S](3+/2+/1+/0) clusters and -more-recently- was used to characterize novel Fe/S clustsers, including the [4Fe-3S] cluster of the O2-tolerant hydrogenase from Aquifex aeolicus and the 3Fe-cluster intermediate observed during the reaction of lipoyl synthase, a member of the radical SAM enzyme superfamily.
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29
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The iron-sulfur core in Rieske proteins is not symmetric. J Biol Inorg Chem 2014; 19:1287-93. [PMID: 25151276 DOI: 10.1007/s00775-014-1185-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
At variance with ferredoxins, Rieske-type proteins contain a chemically asymmetric iron-sulfur cluster. Nevertheless, X-ray crystallography apparently finds their [2Fe-2S] cores to be structurally symmetric or very close to symmetric (i.e. the four iron-sulfur bonds in the [2Fe-2S] core are equidistant). Using a combination of advanced density-based approaches, including finite-temperature molecular dynamics to access thermal fluctuations and free-energy profiles, in conjunction with correlated wavefunction-based methods we clearly predict an asymmetric core structure. This reveals a fundamental and intrinsic difference within the iron-sulfur clusters hosted by Rieske proteins and ferredoxins and thus opens up a new dimension for the ongoing efforts in understanding the role of Rieske-type [2Fe-2S] cluster in electron transfer processes that occur in almost all biological systems.
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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31
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Albers A, Demeshko S, Pröpper K, Dechert S, Bill E, Meyer F. A Super-Reduced Diferrous [2Fe–2S] Cluster. J Am Chem Soc 2013; 135:1704-7. [DOI: 10.1021/ja311563y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Antonia Albers
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Serhiy Demeshko
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Kevin Pröpper
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Sebastian Dechert
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Eckhard Bill
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstrasse 34 −
36, D-45470 Mülheim an der Ruhr, Germany
| | - Franc Meyer
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
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Ullmann GM, Kloppmann E, Essigke T, Krammer EM, Klingen AR, Becker T, Bombarda E. Investigating the mechanisms of photosynthetic proteins using continuum electrostatics. PHOTOSYNTHESIS RESEARCH 2008; 97:33-53. [PMID: 18478354 DOI: 10.1007/s11120-008-9306-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Accepted: 04/10/2008] [Indexed: 05/26/2023]
Abstract
Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions.
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Affiliation(s)
- G Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, Bayreuth 95447, Germany.
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Orio M, Mouesca JM. Variation of average g values and effective exchange coupling constants among [2Fe-2S] clusters: a density functional theory study of the impact of localization (trapping forces) versus delocalization (double-exchange) as competing factors. Inorg Chem 2008; 47:5394-416. [PMID: 18491857 DOI: 10.1021/ic701730h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A phenomenological model aimed at rationalizing variations in both average g-tensor values (gav identical with 1/3Sigmaigi ) and effective exchange coupling constants Jeff (defined as two-thirds of the energy difference between the S = 3/2 and S = 1/2 spin states) has been derived in order to describe the great variety of magnetic properties exhibited by reduced [2Fe-2S] clusters in proteins. The key quantity in the present analysis is the ratio Delta E/B computed from two competing terms. Delta Ecomprises various effects that result in trapping-site asymmetries: vibronic coupling and the chemical nature (S/N/O) and conformations of the ligands on the one hand and solvation terms, the hydrogen bonding network, etc., on the other. All of these additive terms (in a "bottom-up" approach) favor valence localization of the reducing electron onto one of the two iron sites. In contrast, the B term is the double-exchange term, which favors electronic delocalization. Both gav and Jeff can be expressed as functions of Delta E/ B. We have also shown that electronic localization generally favors small gav and large Jeff values (while the opposite is true for electronic delocalization) in a comparative study of the spectroscopic features of plant-type ferredoxins (Fd's) and Rieske centers (and related mutants). Two other types of problems were particularly challenging. The first of these involved deprotonated Rieske centers and the xanthine oxidase clusters II, which are characterized by very small Jeff values (40-45 cm (-1) with a J S A. S B model) correlated with unusually large gav values (in the range 1.97-2.01) as a result of an antisymmetric exchange coupling mechanism. The second concerned the analogous Fd's from Clostridium pasteurianum (Cp) and Aquifex aeolicus (Aa). Detailed Mössbauer studies of the C56S mutant of the Cp system revealed a mixture of clusters with valence-localized S = 1/2 and valence-delocalized S = 9/2 ground states. We relied on crystallographic structures of wild-type and mutant Aa Fd's in order to explain such a distribution of spin states.
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Affiliation(s)
- Maylis Orio
- Laboratory of Inorganic and Biological Chemistry, Grenoble cedex, France
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35
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Hirst J. Elucidating the mechanisms of coupled electron transfer and catalytic reactions by protein film voltammetry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:225-39. [PMID: 16730325 DOI: 10.1016/j.bbabio.2006.04.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/28/2006] [Accepted: 04/01/2006] [Indexed: 11/30/2022]
Abstract
Protein film voltammetry, the direct electrochemistry of redox enzymes and proteins, provides precise and comprehensive information on complicated reaction mechanisms. By controlling the driving force for a reaction (using the applied potential) and monitoring the reaction in real time (using the current), it allows thermodynamic and kinetic information to be determined simultaneously. Two challenges are inherent to protein film voltammetry: (i) to adsorb the protein or enzyme in a native and active configuration on the electrode surface, and (ii) to understand and interpret voltammetric results on both a qualitative and quantitative level, allowing mechanistic models to be proposed and rigorous experiments to test these models to be devised. This review focuses on the second of these two challenges. It describes how to use protein film voltammetry to derive mechanistic and biochemically relevant information about redox proteins and enzymes, and how to evaluate and interpret voltammetric results. Selected key studies are described in detail, to illustrate their underlying principles, strategies and physical interpretations.
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Affiliation(s)
- Judy Hirst
- Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK.
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36
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Igarashi RY, Laryukhin M, Dos Santos PC, Lee HI, Dean DR, Seefeldt LC, Hoffman BM. Trapping H- Bound to the Nitrogenase FeMo-Cofactor Active Site during H2 Evolution: Characterization by ENDOR Spectroscopy. J Am Chem Soc 2005; 127:6231-41. [PMID: 15853328 DOI: 10.1021/ja043596p] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We here show that the iron-molybdenum (FeMo)-cofactor of the nitrogenase alpha-70(Ile) molybdenum-iron (MoFe) protein variant accumulates a novel S = (1)/(2) state that can be trapped during the reduction of protons to H(2). (1,2)H-ENDOR measurements disclose the presence of two protons/hydrides (H(+/)(-)) whose hyperfine tensors have been determined from two-dimensional field-frequency (1)H ENDOR plots. The two H(+/)(-) have large isotropic hyperfine couplings, A(iso)( )() approximately 23 MHz, which shows they are bound to the cofactor. The favored analysis for these plots indicates that the two H(+/)(-) have the same principal values, which indicates that they are chemically equivalent. The tensors are further related to each other by a permutation of the tensor components, which indicates an underlying symmetry of binding relative to the cofactor. At present, no model for the structure of the iron-molybdenum (FeMo)-cofactor in the S = (1)/(2) state trapped during the reduction of H(+) can be shown unequivocally to satisfy all of the constraints generated by the ENDOR analysis. The data disfavors any model that involves protonation of sulfides, and thus suggests that the intermediate instead contains two chemically equivalent bound hydrides; it appears unlikely that these are terminal monohydrides.
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Affiliation(s)
- Robert Y Igarashi
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, USA
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Armstrong FA. Recent developments in dynamic electrochemical studies of adsorbed enzymes and their active sites. Curr Opin Chem Biol 2005; 9:110-7. [PMID: 15811794 DOI: 10.1016/j.cbpa.2005.02.011] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
This review outlines recent developments in electrochemical investigations of proteins adsorbed on electrodes. The important point about 'protein film voltammetry' is that it addresses the rates of reactions that occur in enzymes - catalysis, inhibition, electron flow - as a function of potential; in other words, it introduces the 'potential dimension' into enzyme kinetics. Some surprisingly subtle, yet significant observations are made, including demonstration of a special role for Mo(V) in the catalytic cycle of Mo enzymes, quantitation of the catalytic bias in multi-centred enzymes such as mitochondrial Complex I, insight into mechanisms of proton transfer in enzymes, and properties of proteins that are covalently attached directly to a gold surface.
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