1
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Warmack RA, Wenke BB, Spatzal T, Rees DC. Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins. Nat Protoc 2024:10.1038/s41596-024-00973-5. [PMID: 38575747 DOI: 10.1038/s41596-024-00973-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/11/2024] [Indexed: 04/06/2024]
Abstract
Single-particle cryo-electron microscopy (cryoEM) provides an attractive avenue for advancing our atomic resolution understanding of materials, molecules and living systems. However, the vast majority of published cryoEM methodologies focus on the characterization of aerobically purified samples. Air-sensitive enzymes and microorganisms represent important yet understudied systems in structural biology. We have recently demonstrated the success of an anaerobic single-particle cryoEM workflow applied to the air-sensitive nitrogenase enzymes. In this protocol, we detail the use of Schlenk lines and anaerobic chambers to prepare samples, including a protein tag for monitoring sample exposure to oxygen in air. We describe how to use a plunge freezing apparatus inside of a soft-sided vinyl chamber of the type we routinely use for anaerobic biochemistry and crystallography of oxygen-sensitive proteins. Manual control of the airlock allows for introduction of liquid cryogens into the tent. A custom vacuum port provides slow, continuous evacuation of the tent atmosphere to avoid accumulation of flammable vapors within the enclosed chamber. These methods allowed us to obtain high-resolution structures of both nitrogenase proteins using single-particle cryoEM. The procedures involved can be generally subdivided into a 4 d anaerobic sample generation procedure, and a 1 d anaerobic cryoEM sample preparation step, followed by conventional cryoEM imaging and processing steps. As nitrogen is a substrate for nitrogenase, the Schlenk lines and anaerobic chambers described in this procedure are operated under an argon atmosphere; however, the system and these procedures are compatible with other controlled gas environments.
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Affiliation(s)
- Rebeccah A Warmack
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
| | - Belinda B Wenke
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas Spatzal
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
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2
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Le LN, Joyce JP, Oyala PH, DeBeer S, Agapie T. Highly Activated Terminal Carbon Monoxide Ligand in an Iron-Sulfur Cluster Model of FeMco with Intermediate Local Spin State at Fe. J Am Chem Soc 2024; 146:5045-5050. [PMID: 38358932 PMCID: PMC10910499 DOI: 10.1021/jacs.3c12025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024]
Abstract
Nitrogenases, the enzymes that convert N2 to NH3, also catalyze the reductive coupling of CO to yield hydrocarbons. CO-coordinated species of nitrogenase clusters have been isolated and used to infer mechanistic information. However, synthetic FeS clusters displaying CO ligands remain rare, which limits benchmarking. Starting from a synthetic cluster that models a cubane portion of the FeMo cofactor (FeMoco), including a bridging carbyne ligand, we report a heterometallic tungsten-iron-sulfur cluster with a single terminal CO coordination in two oxidation states with a high level of CO activation (νCO = 1851 and 1751 cm-1). The local Fe coordination environment (2S, 1C, 1CO) is identical to that in the protein making this system a suitable benchmark. Computational studies find an unusual intermediate spin electronic configuration at the Fe sites promoted by the presence the carbyne ligand. This electronic feature is partly responsible for the high degree of CO activation in the reduced cluster.
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Affiliation(s)
- Linh N.
V. Le
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Justin P. Joyce
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Paul H. Oyala
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Theodor Agapie
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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3
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Einsle O. On the Shoulders of Giants-Reaching for Nitrogenase. Molecules 2023; 28:7959. [PMID: 38138449 PMCID: PMC10745432 DOI: 10.3390/molecules28247959] [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: 10/08/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Only a single enzyme system-nitrogenase-carries out the conversion of atmospheric N2 into bioavailable ammonium, an essential prerequisite for all organismic life. The reduction of this inert substrate at ambient conditions poses unique catalytic challenges that strain our mechanistic understanding even after decades of intense research. Structural biology has added its part to this greater tapestry, and in this review, I provide a personal (and highly biased) summary of the parts of the story to which I had the privilege to contribute. It focuses on the crystallographic analysis of the three isoforms of nitrogenases at high resolution and the binding of ligands and inhibitors to the active-site cofactors of the enzyme. In conjunction with the wealth of available biochemical, biophysical, and spectroscopic data on the protein, this has led us to a mechanistic hypothesis based on an elementary mechanism of repetitive hydride formation and insertion.
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Affiliation(s)
- Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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4
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Einsle O. Catalysis and structure of nitrogenases. Curr Opin Struct Biol 2023; 83:102719. [PMID: 37802004 DOI: 10.1016/j.sbi.2023.102719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
In providing bioavailable nitrogen as building blocks for all classes of biomacromolecules, biological nitrogen fixation is an essential process for all organismic life. Only a single enzyme, nitrogenase, performs this task at ambient conditions and with ATP as an energy source. The assembly of the complex iron-sulfur enzyme nitrogenase and its catalytic mechanism remains a matter of intense study. Recent progress in the structural analysis of the three known isoforms of nitrogenase-differentiated primarily by the heterometal in their active site cofactor-has revealed a degree of structural plasticity of these clusters that suggest two distinct binding sites for substrates and reaction intermediates. A mechanistic proposal based on this finding integrates most of the available experimental data. Furthermore, the first applications of high-resolution cryo-electron microscopy have highlighted further dynamic conformational changes. Structures obtained under turnover conditions support the proposed alternating half-site reactivity in the C2-symmetric nitrogenase complex.
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Affiliation(s)
- Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.
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5
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Brown AC, Suess DLM. An Iron-Sulfur Cluster with a Highly Pyramidalized Three-Coordinate Iron Center and a Negligible Affinity for Dinitrogen. J Am Chem Soc 2023; 145:20088-20096. [PMID: 37656961 PMCID: PMC10824254 DOI: 10.1021/jacs.3c07677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Attempts to generate open coordination sites for N2 binding at synthetic Fe-S clusters often instead result in cluster oligomerization. Recently, it was shown for Mo-Fe-S clusters that such oligomerization reactions can be prevented through the use of sterically protective supporting ligands, thereby enabling N2 complex formation. Here, this strategy is extended to Fe-only Fe-S clusters. One-electron reduction of (IMes)3Fe4S4Cl (IMes = 1,3-dimesitylimidazol-2-ylidene) forms the transiently stable edge-bridged double cubane (IMes)6Fe8S8, which loses two IMes ligands to form the face-bridged double-cubane, (IMes)4Fe8S8. The finding that the three supporting IMes ligands do not confer sufficient protection to curtail cluster oligomerization prompted the design of a new N-heterocyclic carbene, SIArMe,iPr (1,3-bis(3,5-diisopropyl-2,6-dimethylphenyl)-2-imidazolidinylidene; abbreviated as SIAr), that features bulky groups strategically placed in remote positions. When the reduction of (SIAr)3Fe4S4Cl or [(SIAr)3Fe4S4(THF)]+ is conducted in the presence of SIAr, the formation of (SIAr)4Fe8S8 is indeed suppressed, permitting characterization of the reduced [Fe4S4]0 product. Surprisingly, rather than being an N2 complex, the product is simply (SIAr)3Fe4S4: a cluster with a three-coordinate Fe site that adopts an unusually pyramidalized geometry. Although (SIAr)3Fe4S4 does not coordinate N2 to any appreciable extent under the surveyed conditions, it does bind CO to form (SIAr)3Fe4S4(CO). This finding demonstates that the binding pocket at the unique Fe is not too small for N2; instead, the exceptionally weak affinity for N2 can be attributed to weak Fe-N2 bonding. The differences in the N2 coordination chemistry between sterically protected Mo-Fe-S clusters and Fe-only Fe-S clusters are discussed.
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Affiliation(s)
- Alexandra C Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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6
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Cesari C, Bortoluzzi M, Funaioli T, Femoni C, Iapalucci MC, Zacchini S. Highly Reduced Ruthenium Carbide Carbonyl Clusters: Synthesis, Molecular Structure, Reactivity, Electrochemistry, and Computational Investigation of [Ru 6C(CO) 15] 4. Inorg Chem 2023; 62:14590-14603. [PMID: 37646082 PMCID: PMC10498495 DOI: 10.1021/acs.inorgchem.3c01711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Indexed: 09/01/2023]
Abstract
The reaction of [Ru6C(CO)16]2- (1) with NaOH in DMSO resulted in the formation of a highly reduced [Ru6C(CO)15]4- (2), which was readily protonated by acids, such as HBF4·Et2O, to [HRu6C(CO)15]3- (3). Oxidation of 2 with [Cp2Fe][PF6] or [C7H7][BF4] in CH3CN resulted in [Ru6C(CO)15(CH3CN)]2- (5), which was quantitatively converted into 1 after exposure to CO atmosphere. The reaction of 2 with a mild methylating agent such as CH3,I afforded the purported [Ru6C(CO)14(COCH3)]3- (6). By employing a stronger reagent, that is, CF3SO3CH3, a mixture of [HRu6C(CO)16]- (4), [H3Ru6C(CO)15]- (7), and [Ru6C(CO)15(CH3CNCH3)]- (8) was obtained. The molecular structures of 2-5, 7, and 8 were determined by single-crystal X-ray diffraction as their [NEt4]4[2]·CH3CN, [NEt4]3[3], [NEt4][4], [NEt4]2[5], [NEt4][7], and [NEt4][8]·solv salts. The carbyne-carbide cluster 6 was partially characterized by IR spectroscopy and ESI-MS, and its structure was computationally predicted using DFT methods. The redox behavior of 2 and 3 was investigated by electrochemical and IR spectroelectrochemical methods. Computational studies were performed in order to unravel structural and thermodynamic aspects of these octahedral Ru-carbide carbonyl clusters displaying miscellaneous ligands and charges in comparison with related iron derivatives.
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Affiliation(s)
- Cristiana Cesari
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale Risorgimento 4, 40136 Bologna. Italy
| | - Marco Bortoluzzi
- Dipartimento
di Scienze Molecolari e Nanosistemi, Ca’
Foscari University of Venice, Via Torino 155, 30175 Mestre (Ve), Italy
| | - Tiziana Funaioli
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi
13, 56124 Pisa, Italy
| | - Cristina Femoni
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale Risorgimento 4, 40136 Bologna. Italy
| | - Maria Carmela Iapalucci
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale Risorgimento 4, 40136 Bologna. Italy
| | - Stefano Zacchini
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale Risorgimento 4, 40136 Bologna. Italy
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7
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Abstract
The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Joseph B. Solomon
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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8
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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9
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Lycus P, Einsle O, Zhang L. Structural biology of proteins involved in nitrogen cycling. Curr Opin Chem Biol 2023; 74:102278. [PMID: 36889028 DOI: 10.1016/j.cbpa.2023.102278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.
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Affiliation(s)
- Pawel Lycus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
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10
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Dance I. The binding of reducible N 2 in the reaction domain of nitrogenase. Dalton Trans 2023; 52:2013-2026. [PMID: 36691966 DOI: 10.1039/d2dt03599e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The binding of N2 to FeMo-co, the catalytic site of the enzyme nitrogenase, is central to the conversion to NH3, but also has a separate role in promoting the N2-dependent HD reaction (D2 + 2H+ + 2e- → 2HD). The protein surrounding FeMo-co contains a clear channel for ingress of N2, directly towards the exo-coordination position of Fe2, a position which is outside the catalytic reaction domain. This led to the hypothesis [I. Dance, Dalton Trans., 2022, 51, 12717] of 'promotional' N2 bound at exo-Fe2, and a second 'reducible' N2 bound in the reaction domain, specifically the endo-coordination position of Fe2 or Fe6. The range of possibilities for the binding of reducible N2 in the presence of bound promotional N2 is described here, using density functional simulations with a 486 atom model of the active site and surrounding protein. The pathway for ingress of the second N2 through protein, past the first N2 at exo-Fe2, and tumbling into the binding domain between Fe2 and Fe6, is described. The calculations explore 24 structures involving 6 different forms of hydrogenated FeMo-co, including structures with S2BH unhooked from Fe2 but tethered to Fe6. The calculations use the most probable electronic states. End-on (η1) binding of N2 at the endo position of either Fe2 or Fe6 is almost invariably exothermic, with binding potential energies ranging up to -18 kcal mol-1. Many structures have binding energies in the range -6 to -14 kcal mol-1. The relevant entropic penalty for N2 binding from a diffusible position within the protein is estimated to be 4 kcal mol-1, and so the binding free energies for reducible N2 are suitably negative. N2 binding at endo-Fe2 is stronger than at endo-Fe6 in three of the six structure categories. In many cases the reaction domain containing reducible N2 is expanded. These results inform computational simulation of the subsequent steps in which surrounding H atoms transfer to reducible N2.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Australia.
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11
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Yogendra S, Wilson DWN, Hahn AW, Weyhermüller T, Van Stappen C, Holland P, DeBeer S. Sulfur-Ligated [2Fe-2C] Clusters as Synthetic Model Systems for Nitrogenase. Inorg Chem 2023; 62:2663-2671. [PMID: 36715662 PMCID: PMC9930126 DOI: 10.1021/acs.inorgchem.2c03693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 01/31/2023]
Abstract
Metal clusters featuring carbon and sulfur donors have coordination environments comparable to the active site of nitrogenase enzymes. Here, we report a series of di-iron clusters supported by the dianionic yldiide ligands, in which the Fe sites are bridged by two μ2-C atoms and four pendant S donors.The [L2Fe2] (L = {[Ph2P(S)]2C}2-) cluster is isolable in two oxidation levels, all-ferrous Fe2II and mixed-valence FeIIFeIII. The mixed-valence cluster displays two peaks in the Mössbauer spectra, indicating slow electron transfer between the two sites. The addition of the Lewis base 4-dimethylaminopyridine to the Fe2II cluster results in coordination with only one of the two Fe sites, even in the presence of an excess base. Conversely, the cluster reacts with 8 equiv of isocyanide tBuNC to give a monometallic complex featuring a new C-C bond between the ligand backbone and the isocyanide. The electronic structure descriptions of these complexes are further supported by X-ray absorption and resonant X-ray emission spectroscopies.
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Affiliation(s)
- Sivathmeehan Yogendra
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Daniel W. N. Wilson
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Anselm W. Hahn
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Thomas Weyhermüller
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Casey Van Stappen
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Patrick Holland
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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12
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Dance I. The HD Reaction of Nitrogenase: a Detailed Mechanism. Chemistry 2023; 29:e202202502. [PMID: 36274057 PMCID: PMC10099629 DOI: 10.1002/chem.202202502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 11/06/2022]
Abstract
Nitrogenase is the enzyme that converts N2 to NH3 under ambient conditions. The chemical mechanism of this catalysis at the active site FeMo-co [Fe7 S9 CMo(homocitrate)] is unknown. An obligatory co-product is H2 , while exogenous H2 is a competitive inhibitor. Isotopic substitution using exogenous D2 revealed the N2 -dependent reaction D2 +2H+ +2e- →2HD (the 'HD reaction'), together with a collection of additional experimental characteristics and requirements. This paper describes a detailed mechanism for the HD reaction, developed and elaborated using density functional simulations with a 486-atom model of the active site and surrounding protein. First D2 binds at one Fe atom (endo-Fe6 coordination position), where it is flanked by H-Fe6 (exo position) and H-Fe2 (endo position). Then there is synchronous transfer of these two H atoms to bound D2 , forming one HD bound to Fe2 and a second HD bound to Fe6. These two HD dissociate sequentially. The final phase is recovery of the two flanking H atoms. These H atoms are generated, sequentially, by translocation of a proton from the protein surface to S3B of FeMo-co and combination with introduced electrons. The first H atom migrates from S3B to exo-Fe6 and the second from S3B to endo-Fe2. Reaction energies and kinetic barriers are reported for all steps. This mechanism accounts for the experimental data: (a) stoichiometry; (b) the N2 -dependence results from promotional N2 bound at exo-Fe2; (c) different N2 binding Km for the HD reaction and the NH3 formation reaction results from involvement of two different sites; (d) inhibition by CO; (e) the non-occurrence of 2HD→H2 +D2 results from the synchronicity of the two transfers of H to D2 ; (f) inhibition of HD production at high pN2 is by competitive binding of N2 at endo-Fe6; (g) the non-leakage of D to solvent follows from the hydrophobic environment and irreversibility of proton introduction.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW, Sydney, Australia
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13
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Molecular Fe, CO and Ni carbide carbonyl clusters and Nanoclusters†. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2022.121235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Threatt SD, Rees DC. Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system. FEBS Lett 2023; 597:45-58. [PMID: 36344435 PMCID: PMC10100503 DOI: 10.1002/1873-3468.14534] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
Abstract
Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH3 ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH3 , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.
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Affiliation(s)
- Stephanie D Threatt
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
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15
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Lukoyanov DA, Yang ZY, Pérez-González A, Raugei S, Dean DR, Seefeldt LC, Hoffman BM. 13C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe 6 Core Is a Stabilizing "Heart of Steel". J Am Chem Soc 2022; 144:18315-18328. [PMID: 36166637 DOI: 10.1021/jacs.2c06149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe-9S-C-Mo-homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe-C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. This report compares 13CFe6 ENDOR measurements for (i) the wild-type protein resting state (E0; α-Val70) to those of (ii) α-Ile70, (iii) α-Ala70-substituted proteins; (iv) crystallographically characterized CO-inhibited "hi-CO" state; (v) E4(4H) Janus intermediate, activated for N2 binding/reduction by accumulation of 4[e-/H+]; (vi) E4(2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13C isotropic hyperfine coupling constants, Ca = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe-C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe-C bonding of the CFe6 core indicate that it does not provide a functionally dynamic (hemilabile) "beating heart"─instead it acts as "a heart of steel", stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.
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Affiliation(s)
- Dmitriy A Lukoyanov
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois60208, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah84322, United States
| | - Ana Pérez-González
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah84322, United States
| | - Brian M Hoffman
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois60208, United States
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16
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Decamps L, Rice DB, DeBeer S. An Fe 6 C Core in All Nitrogenase Cofactors. Angew Chem Int Ed Engl 2022; 61:e202209190. [PMID: 35975943 PMCID: PMC9826452 DOI: 10.1002/anie.202209190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Indexed: 01/11/2023]
Abstract
The biological process of dinitrogen reduction to ammonium occurs at the cofactors of nitrogenases, the only enzymes that catalyze this challenging chemical reaction. Three types of nitrogenases have been described, named according to the heterometal in their cofactor: molybdenum, vanadium or iron nitrogenases. Spectroscopic and structural characterization allowed the unambiguous identification of the cofactors of molybdenum and vanadium nitrogenases and revealed a central μ6 -carbide in both of them. Although genetic studies suggested that the cofactor of the iron nitrogenase contains a similar Fe6 C core, this has not been experimentally demonstrated. Here we report Valence-to-Core X-ray Emission Spectroscopy providing experimental evidence that this cofactor contains a carbide, thereby making the Fe6 C core a feature of all nitrogenase cofactors.
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Affiliation(s)
- Laure Decamps
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
| | - Derek B. Rice
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
| | - Serena DeBeer
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an derRuhrGermany
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17
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Tanifuji K, Jasniewski AJ, Lee CC, Solomon JB, Nagasawa T, Ohki Y, Tatsumi K, Hedman B, Hodgson KO, Hu Y, Ribbe MW. Incorporation of an Asymmetric Mo-Fe-S Cluster as an Artificial Cofactor into Nitrogenase. Chembiochem 2022; 23:e202200384. [PMID: 35925843 PMCID: PMC9547968 DOI: 10.1002/cbic.202200384] [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: 07/07/2022] [Revised: 08/03/2022] [Indexed: 11/07/2022]
Abstract
Nitrogenase employs a sophisticated electron transfer system and a Mo-Fe-S-C cofactor, designated the M-cluster [(cit)MoFe7 S9 C]), to reduce atmospheric N2 to bioaccessible NH3 . Previously, we have shown that the cofactor-free form of nitrogenase can be repurposed as a protein scaffold for the incorporation of a synthetic Fe-S cluster [Fe6 S9 (SEt)2 ]4- . Here, we demonstrate the utility of an asymmetric Mo-Fe-S cluster [Cp*MoFe5 S9 (SH)]3- as an alternative artificial cofactor upon incorporation into the cofactor-free nitrogenase scaffold. The resultant semi-artificial enzyme catalytically reduces C2 H2 to C2 H4 , and CN- into short-chain hydrocarbons, yet it is clearly distinct in activity from its [Fe6 S9 (SEt)2 ]4- -reconstituted counterpart, pointing to the possibility to employ molecular design and cluster synthesis strategies to further develop semi-artificial or artificial systems with desired catalytic activities.
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Affiliation(s)
- Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Joseph B Solomon
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697-2025, USA
| | - Takayuki Nagasawa
- Department of Chemistry Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yasuhiro Ohki
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Kazuyuki Tatsumi
- Department of Chemistry Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho Chikusa-ku, Nagoya, 464-8602, Japan
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697-2025, USA
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18
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Dance I. Calculating the chemical mechanism of nitrogenase: new working hypotheses. Dalton Trans 2022; 51:12717-12728. [PMID: 35946501 DOI: 10.1039/d2dt01920e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enzyme nitrogenase converts N2 to NH3 with stoichiometry N2 + 8H+ + 8e- → 2NH3 + H2. The mechanism is chemically complex with multiple steps that must be consistent with much accumulated experimental information, including exchange of H2 and N2 and the N2-dependent hydrogenation of D2 to HD. Previous investigations have developed a collection of working hypotheses that guide ongoing density functional investigations of mechanistic steps and sequences. These include (i) hypotheses about the serial provision of protons and their conversion to H atoms bonded to S and Fe atoms of the FeMo-co catalytic site, (ii) the migration of H atoms over the surface of FeMo-co, (iii) the roles of His195, (iv) identification of three protein channels, one for the ingress of N2, a separate pathway for the passage of exogenous H2 (D2) and product H2 (HD), and a hydrophilic pathway for egress of product NH3. Two additional working hypotheses are described in this paper. N2 passing along the N2 channel approaches and binds end-on to the exo coordination position of Fe2, with favourable energetics when FeMo-co is pre-hydrogenated. This exo-Fe2-N2 is apparently not reduced but has a promotional role by expanding the reaction zone. A second N2 can enter via the N2 ingress channel and bind at the endo-Fe6 position, where it is surrounded by H atom donors suitable for the N2 → NH3 conversion. It is proposed that this endo-Fe6 position is also the binding site for H2 (generated or exogenous), accounting for the competitive inhibition of N2 reduction by H2. The HD reaction occurs at the endo-Fe6 site, promoted by N2 at the exo-Fe2 site. The second hypothesis concerns the most stable electronic states of FeMo-co with ligands bound at Fe2 and Fe6, and provides a protocol for management of electronic states in mechanism calculations.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2051, Australia.
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19
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Decamps L, Rice D, DeBeer S. An Fe6C Core in All Nitrogenase Cofactors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laure Decamps
- Max-Planck-Institute for Chemical Energy Conversion: Max-Planck-Institut fur chemische Energiekonversion Inorganic Spectroscopy GERMANY
| | - Derek Rice
- Max-Planck-Institute for Chemical Energy Conversion: Max-Planck-Institut fur chemische Energiekonversion Inorganic Spectroscopy GERMANY
| | - Serena DeBeer
- MPI CEC Molecular Theory and Spectroscopy Stidtstr. 34-36 45470 Muelheim an der Ruhr GERMANY
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20
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Buscagan TM, Kaiser JT, Rees DC. Selenocyanate derived Se-incorporation into the Nitrogenase Fe protein cluster. eLife 2022; 11:79311. [PMID: 35904245 PMCID: PMC9462850 DOI: 10.7554/elife.79311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/28/2022] [Indexed: 11/15/2022] Open
Abstract
The nitrogenase Fe protein mediates ATP-dependent electron transfer to the nitrogenase MoFe protein during nitrogen fixation, in addition to catalyzing MoFe protein-independent substrate (CO2) reduction and facilitating MoFe protein metallocluster biosynthesis. The precise role(s) of the Fe protein Fe4S4 cluster in some of these processes remains ill-defined. Herein, we report crystallographic data demonstrating ATP-dependent chalcogenide exchange at the Fe4S4 cluster of the nitrogenase Fe protein when potassium selenocyanate is used as the selenium source, an unexpected result as the Fe protein cluster is not traditionally perceived as a site of substrate binding within nitrogenase. The observed chalcogenide exchange illustrates that this Fe4S4 cluster is capable of core substitution reactions under certain conditions, adding to the Fe protein’s repertoire of unique properties. Many of the molecules that form the building blocks of life contain nitrogen. This element makes up most of the gas in the atmosphere, but in this form, it does not easily react, and most organisms cannot incorporate atmospheric nitrogen into biological molecules. To get around this problem, some species of bacteria produce an enzyme complex called nitrogenase that can transform nitrogen from the air into ammonia. This process is called nitrogen fixation, and it converts nitrogen into a form that can be used to sustain life. The nitrogenase complex is made up of two proteins: the MoFe protein, which contains the active site that binds nitrogen, turning it into ammonia; and the Fe protein, which drives the reaction. Besides the nitrogen fixation reaction, the Fe protein is involved in other biological processes, but it was not thought to bind directly to nitrogen, or to any of the other small molecules that the nitrogenase complex acts on. The Fe protein contains a cluster of iron and sulfur ions that is required to drive the nitrogen fixation reaction, but the role of this cluster in the other reactions performed by the Fe protein remains unclear. To better understand the role of this iron sulfur cluster, Buscagan, Kaiser and Rees used X-ray crystallography, a technique that can determine the structure of molecules. This approach revealed for the first time that when nitrogenase reacts with a small molecule called selenocyanate, the selenium in this molecule can replace the sulfur ions of the iron sulfur cluster in the Fe protein. Buscagan, Kaiser and Rees also demonstrated that the Fe protein could still incorporate selenium ions in the absence of the MoFe protein, which has traditionally been thought to provide the site essential for transforming small molecules. These results indicate that the iron sulfur cluster in the Fe protein may bind directly to small molecules that react with nitrogenase. In the future, these findings could lead to the development of new molecules that artificially produce ammonia from nitrogen, an important process for fertilizer manufacturing. In addition, the iron sulfur cluster found in the Fe protein is also present in many other proteins, so Buscagan, Kaiser and Rees’ experiments may shed light on the factors that control other biological reactions.
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Affiliation(s)
- Trixia M Buscagan
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - Jens T Kaiser
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
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21
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McSkimming A, Thompson NB. Four-Coordinate Fe N 2 and Imido Complexes Supported by a Hemilabile NNC Heteroscorpionate Ligand. Inorg Chem 2022; 61:12318-12326. [PMID: 35895990 PMCID: PMC9367695 DOI: 10.1021/acs.inorgchem.2c01656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Inspired by mechanistic proposals for N2 reduction
at
the nitrogenase FeMo cofactor, we report herein a new, strongly σ-donating
heteroscorpionate ligand featuring two weak-field pyrazoles and an
alkyl donor. This ligand supports four-coordinate Fe(I)-N2, Fe(II)-Cl, and Fe(III)-imido complexes, which we have characterized
using a variety of spectroscopic and computational methods. Structural
and quantum mechanical analysis reveal the nature of the Fe–C
bonds to be essentially invariant between the complexes, with conversion
between the (formally) low-valent Fe-N2 and high-valent
Fe-imido complexes mediated by pyrazole hemilability. This presents
a useful strategy for substrate reduction at such low-coordinate centers
and suggests a mechanism by which FeMoco might accommodate the binding
of both π-acidic and π-basic nitrogenous substrates. We report a new, strongly σ-donating
NNC heteroscorpionate
ligand and its Fe(I)-N2, Fe(II)-Cl and Fe(III)-imido complexes.
Conversion between the low-valent Fe-N2 and high-valent
Fe-imido complexes is mediated by pyrazole hemilability, presenting
a useful strategy for substrate reduction at such low-coordinate centers.
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Affiliation(s)
- Alex McSkimming
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Niklas B Thompson
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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22
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Gee LB, Myers WK, Nack-Lehman PA, Scott AD, Yan L, George SJ, Dong W, Dapper CH, Newton WE, Cramer SP. Nitrogenase Chemistry at 10 Kelvin─Phototautomerization and Recombination of CO-Inhibited α-H195Q Enzyme. Inorg Chem 2022; 61:11509-11513. [PMID: 35856737 DOI: 10.1021/acs.inorgchem.2c00818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CO-bound forms of nitrogenase are N2-reduction inhibited and likely intermediates in Fischer-Tropsch chemistry. Visible-light photolysis at 7 K was used to interrogate all three known CO-related EPR-active forms as exhibited by the α-H195Q variant of Azotobacter vinelandii nitrogenase MoFe protein. The hi(5)-CO EPR signal converted to the hi-CO EPR signal, which reverted at 10 K. FT-IR monitoring revealed an exquisitely light-sensitive "Hi-2" species with bands at 1932 and 1866 cm-1 that yielded "Hi-1" with bands at 1969 and 1692 cm-1, which reverted to "Hi-2". The similarities of photochemical behavior and recombination kinetics showed, for the first time, that hi-CO EPR and "Hi-1" IR signals arise from one chemical species. hi(5)-CO EPR and "Hi-2" IR signals are from a second species, and lo-CO EPR and "Lo-2" IR signals, formed after prolonged illumination, are from a third species. Comparing FT-IR data with CO-inhibited MoFe-protein crystal structures allowed assignment of CO-bonding geometries in these species.
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Affiliation(s)
- Leland B Gee
- Department of Chemistry, University of California, Davis, California 95616, United States.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - William K Myers
- Department of Chemistry, University of Oxford, Oxford 3QR OX1, United Kingdom
| | - Patrick A Nack-Lehman
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Aubrey D Scott
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Lifen Yan
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Simon J George
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Weibing Dong
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Christie H Dapper
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - William E Newton
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, California 95616, United States.,SETI Institute, Mountain View, California 94043, United States
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23
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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24
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Gopalasingam CC, Hasnain SS. Frontiers in metalloprotein crystallography and cryogenic electron microscopy. Curr Opin Struct Biol 2022; 75:102420. [PMID: 35841747 DOI: 10.1016/j.sbi.2022.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/03/2022]
Abstract
Metalloproteins comprise at least a third of all proteins that utilize redox properties of transition metals on their own or as parts of cofactors. The development of third generation storage ring sources and X-ray free-electron lasers with femtosecond pulses in the first decade of the 21st century has transformed metalloprotein crystallography. In the past decade, cryogenic-electron microscopy single-particle analysis, which does not require crystallization of biological samples has been extensively utilized, particularly for membrane-bound metalloprotein systems. Here, we explore recent frontiers in metalloprotein crystallography and cryogenic electron microscopy, organized for convenience under three metalloprotein-centered biological cycles, focusing on contributions from each technique, their synergy and the ability to preserve metals' redox states when subjected to a particular probe.
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Affiliation(s)
- Chai C Gopalasingam
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK; Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan. https://twitter.com/@Chai_Gopal
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
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25
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Brown AC, Thompson NB, Suess DLM. Evidence for Low-Valent Electronic Configurations in Iron-Sulfur Clusters. J Am Chem Soc 2022; 144:9066-9073. [PMID: 35575703 DOI: 10.1021/jacs.2c01872] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Although biological iron-sulfur (Fe-S) clusters perform some of the most difficult redox reactions in nature, they are thought to be composed exclusively of Fe2+ and Fe3+ ions, as well as mixed-valent pairs with average oxidation states of Fe2.5+. We herein show that Fe-S clusters formally composed of these valences can access a wider range of electronic configurations─in particular, those featuring low-valent Fe1+ centers. We demonstrate that CO binding to a synthetic [Fe4S4]0 cluster supported by N-heterocyclic carbene ligands induces the generation of Fe1+ centers via intracluster electron transfer, wherein a neighboring pair of Fe2+ sites reduces the CO-bound site to a low-valent Fe1+ state. Similarly, CO binding to an [Fe4S4]+ cluster induces electron delocalization with a neighboring Fe site to form a mixed-valent Fe1.5+Fe2.5+ pair in which the CO-bound site adopts partial low-valent character. These low-valent configurations engender remarkable C-O bond activation without having to traverse highly negative and physiologically inaccessible [Fe4S4]0/[Fe4S4]- redox couples.
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Affiliation(s)
- Alexandra C Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Niklas B Thompson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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26
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Kuriyama S, Kato T, Tanaka H, Konomi A, Yoshizawa K, Nishibayashi Y. Catalytic Reduction of Dinitrogen to Ammonia and Hydrazine Using Iron–Dinitrogen Complexes Bearing Anionic Benzene-Based PCP-type Pincer Ligands. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shogo Kuriyama
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656
| | - Takeru Kato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656
| | - Hiromasa Tanaka
- School of Liberal Arts and Sciences, Daido University, Minami-ku, Nagoya 457-8530
| | - Asuka Konomi
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395
| | - Yoshiaki Nishibayashi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656
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27
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Gee LB, Scott AD, Dapper CH, Newton WE, Cramer SP. Carbon monoxide binding to α-R277H Mo-nitrogenase – Evidence for multiple pH-dependent species from IR-monitored photolysis. J Inorg Biochem 2022; 232:111806. [DOI: 10.1016/j.jinorgbio.2022.111806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
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28
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Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Kim J. Metal complexes containing
silicon‐based
pincer ligands: Reactivity and application in small molecule activation. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jin Kim
- Department of Chemistry Sunchon National University Suncheon Jeollanam‐do Republic of Korea
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30
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Yuan C, Jin WT, Zhou ZH. Comparisons of bond valences and distances for CO- and N 2-bound clusters of FeMo-cofactors. NEW J CHEM 2022. [DOI: 10.1039/d2nj00754a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By comparisons of N2 and isoelectronic substrate CO bound FeMo-cofactors (FeMo-cos) in nitrogenases, we have used a classical bond valence method to calculate the oxidation states of the iron and molybdenum atoms in FeMo-cos.
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Affiliation(s)
- Chang Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Wan-Ting Jin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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31
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Yuan C, Jin WT, Zhou ZH. Statistical analysis of PN clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures. RSC Adv 2022; 12:5214-5224. [PMID: 35425536 PMCID: PMC8981338 DOI: 10.1039/d1ra08507g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022] Open
Abstract
Iron valences of 129 P-clusters from FeMo/V proteins were analyzed using a bond valence method, supposing the existence of Fe3+ in a generally considered all-ferrous PN cluster in solution with excess reducing agent.
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Affiliation(s)
- Chang Yuan
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Wan-Ting Jin
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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32
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Dance I. Structures and reaction dynamics of N 2 and H 2 binding at FeMo-co, the active site of nitrogenase. Dalton Trans 2021; 50:18212-18237. [PMID: 34860237 DOI: 10.1039/d1dt03548g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The chemical reactions occurring at the Fe7MoS9C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N2 → NH3), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N2 and H2, each with more than one type of reactivity. This paper reports investigations of the binding of H2 and N2 at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H2 and/or N2 bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H2/N2 are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H2 or N2, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol-1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N2 structures and three H2 structures have negative binding free energies, which include the estimated entropy penalties for binding of N2, H2 from proximal protein. These favoured structures have N2 bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H2 bound at the endo-Fe2 position. Various postulated structures with N2 bridging Fe2 and Fe6 revert to end-on-N2 at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H2 range from 1 to 20 kcal mol-1 and barriers to dissociation of H2 range from 3 to 18 kcal mol-1. Barriers to the binding of N2, in either side-on or end-on mode, range from 2 to 18 kcal mol-1, while dissociation of bound N2 encounters barriers of 3 to 8 kcal mol-1 for side-on bonding and 7 to 18 kcal mol-1 for end-on bonding. These results allow formulation of mechanisms for the H2/N2 exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2051, Australia.
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33
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Spiller N, Bjornsson R, DeBeer S, Neese F. Carbon Monoxide Binding to the Iron-Molybdenum Cofactor of Nitrogenase: a Detailed Quantum Mechanics/Molecular Mechanics Investigation. Inorg Chem 2021; 60:18031-18047. [PMID: 34767349 PMCID: PMC8653219 DOI: 10.1021/acs.inorgchem.1c02649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbon monoxide (CO) is a well-known inhibitor of nitrogenase activity. Under turnover conditions, CO binds to FeMoco, the active site of Mo nitrogenase. Time-resolved IR measurements suggest an initial terminal CO at 1904 cm-1 that converts to a bridging CO at 1715 cm-1, and an X-ray structure shows that CO can displace one of the bridging belt sulfides of FeMoco. However, the CO-binding redox state(s) of FeMoco (En) and the role of the protein environment in stabilizing specific CO-bound intermediates remain elusive. In this work, we carry out an in-depth analysis of the CO-FeMoco interaction based on quantum chemical calculations addressing different aspects of the electronic structure. (1) The local electronic structure of the Fe-CO bond is studied through diamagnetically substituted FeMoco. (2) A cluster model of FeMoco within a polarizable continuum illustrates how CO binding may affect the spin-coupling between the metal centers. (3) A QM/MM model incorporates the explicit influence of the amino acid residues surrounding FeMoco in the MoFe protein. The QM/MM model predicts both a terminal and a bridging CO in the E1 redox state. The scaled calculated CO frequencies (1922 and 1716 cm-1, respectively) are in good agreement with the experimentally observed IR bands supporting CO binding to the E1 state. Alternatively, an E2 state QM/MM model, which has the same atomic structure as the CO-bound X-ray structure, features a semi-bridging CO with a scaled calculated frequency (1718 cm-1) similar to the bridging CO in the E1 model.
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Affiliation(s)
- Nico Spiller
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- 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
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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34
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Thorhallsson AT, Bjornsson R. The E 2 state of FeMoco: Hydride Formation versus Fe Reduction and a Mechanism for H 2 Evolution. Chemistry 2021; 27:16788-16800. [PMID: 34541722 PMCID: PMC9293435 DOI: 10.1002/chem.202102730] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/27/2022]
Abstract
The iron‐molybdenum cofactor (FeMoco) is responsible for dinitrogen reduction in Mo nitrogenase. Unlike the resting state, E0, reduced states of FeMoco are much less well characterized. The E2 state has been proposed to contain a hydride but direct spectroscopic evidence is still lacking. The E2 state can, however, relax back the E0 state via a H2 side‐reaction, implying a hydride intermediate prior to H2 formation. This E2→E0 pathway is one of the primary mechanisms for H2 formation under low‐electron flux conditions. In this study we present an exploration of the energy surface of the E2 state. Utilizing both cluster‐continuum and QM/MM calculations, we explore various classes of E2 models: including terminal hydrides, bridging hydrides with a closed or open sulfide‐bridge, as well as models without. Importantly, we find the hemilability of a protonated belt‐sulfide to strongly influence the stability of hydrides. Surprisingly, non‐hydride models are found to be almost equally favorable as hydride models. While the cluster‐continuum calculations suggest multiple possibilities, QM/MM suggests only two models as contenders for the E2 state. These models feature either i) a bridging hydride between Fe2 and Fe6 and an open sulfide‐bridge with terminal SH on Fe6 (E2‐hyd) or ii) a double belt‐sulfide protonated, reduced cofactor without a hydride (E2‐nonhyd). We suggest both models as contenders for the E2 redox state and further calculate a mechanism for H2 evolution. The changes in electronic structure of FeMoco during the proposed redox‐state cycle, E0→E1→E2→E0, are discussed.
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Affiliation(s)
- Albert Th Thorhallsson
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.,Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.,Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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35
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Abstract
Carbide complexes remain a rare class of molecules. Their paucity does not reflect exceptional instability but is rather due to the generally narrow scope of synthetic procedures for constructing carbide complexes. The preparation of carbide complexes typically revolves around generating LnM-CEx fragments, followed by cleavage of the C-E bonds of the coordinated carbon-based ligands (the alternative being direct C atom transfer). Prime examples involve deoxygenation of carbonyl ligands and deprotonation of methyl ligands, but several other p-block fragments can be cleaved off to afford carbide ligands. This Review outlines synthetic strategies toward terminal carbide complexes, bridging carbide complexes, as well as carbide-carbonyl cluster complexes. It then surveys the reactivity of carbide complexes, covering stoichiometric reactions where the carbide ligands act as C1 reagents, engage in cross-coupling reactions, and enact Fischer-Tropsch-like chemistry; in addition, we discuss carbide complexes in the context of catalysis. Finally, we examine spectroscopic features of carbide complexes, which helps to establish the presence of the carbide functionality and address its electronic structure.
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Affiliation(s)
- Anders Reinholdt
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Jesper Bendix
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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36
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Oehlmann NN, Rebelein JG. The Conversion of Carbon Monoxide and Carbon Dioxide by Nitrogenases. Chembiochem 2021; 23:e202100453. [PMID: 34643977 PMCID: PMC9298215 DOI: 10.1002/cbic.202100453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/13/2021] [Indexed: 12/02/2022]
Abstract
Nitrogenases are the only known family of enzymes that catalyze the reduction of molecular nitrogen (N2) to ammonia (NH3). The N2 reduction drives biological nitrogen fixation and the global nitrogen cycle. Besides the conversion of N2, nitrogenases catalyze a whole range of other reductions, including the reduction of the small gaseous substrates carbon monoxide (CO) and carbon dioxide (CO2) to hydrocarbons. However, it remains an open question whether these ‘side reactivities’ play a role under environmental conditions. Nonetheless, these reactivities and particularly the formation of hydrocarbons have spurred the interest in nitrogenases for biotechnological applications. There are three different isozymes of nitrogenase: the molybdenum and the alternative vanadium and iron‐only nitrogenase. The isozymes differ in their metal content, structure, and substrate‐dependent activity, despite their homology. This minireview focuses on the conversion of CO and CO2 to methane and higher hydrocarbons and aims to specify the differences in activity between the three nitrogenase isozymes.
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Affiliation(s)
- Niels N Oehlmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Johannes G Rebelein
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
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37
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McSkimming A, Suess DLM. Dinitrogen binding and activation at a molybdenum-iron-sulfur cluster. Nat Chem 2021; 13:666-670. [PMID: 34045715 DOI: 10.1038/s41557-021-00701-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
The Fe-S clusters of nitrogenases carry out the life-sustaining conversion of N2 to NH3. Although progress continues to be made in modelling the structural features of nitrogenase cofactors, no synthetic Fe-S cluster has been shown to form a well-defined coordination complex with N2. Here we report that embedding an [MoFe3S4] cluster in a protective ligand environment enables N2 binding at Fe. The bridging [MoFe3S4]2(μ-η1:η1-N2) complex thus prepared features a substantially weakened N-N bond despite the relatively high formal oxidation states of the metal centres. Substitution of one of the [MoFe3S4] cubanes with an electropositive Ti metalloradical induces additional charge transfer to the N2 ligand with generation of Fe-N multiple-bond character. Structural and spectroscopic analyses demonstrate that N2 activation is accompanied by shortened Fe-S distances and charge transfer from each Fe site, including those not directly bound to N2. These findings indicate that covalent interactions within the cluster play a critical role in N2 binding and activation.
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Affiliation(s)
- Alex McSkimming
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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38
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Pérez-González A, Yang ZY, Lukoyanov DA, Dean DR, Seefeldt LC, Hoffman BM. Exploring the Role of the Central Carbide of the Nitrogenase Active-Site FeMo-cofactor through Targeted 13C Labeling and ENDOR Spectroscopy. J Am Chem Soc 2021; 143:9183-9190. [PMID: 34110795 DOI: 10.1021/jacs.1c04152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mo-dependent nitrogenase is a major contributor to global biological N2 reduction, which sustains life on Earth. Its multi-metallic active-site FeMo-cofactor (Fe7MoS9C-homocitrate) contains a carbide (C4-) centered within a trigonal prismatic CFe6 core resembling the structural motif of the iron carbide, cementite. The role of the carbide in FeMo-cofactor binding and activation of substrates and inhibitors is unknown. To explore this role, the carbide has been in effect selectively enriched with 13C, which enables its detailed examination by ENDOR/ESEEM spectroscopies. 13C-carbide ENDOR of the S = 3/2 resting state (E0) is remarkable, with an extremely small isotropic hyperfine coupling constant, Ca = +0.86 MHz. Turnover under high CO partial pressure generates the S = 1/2 hi-CO state, with two CO molecules bound to FeMo-cofactor. This conversion surprisingly leaves the small magnitude of the 13C carbide isotropic hyperfine-coupling constant essentially unchanged, Ca = -1.30 MHz. This indicates that both the E0 and hi-CO states exhibit an exchange-coupling scheme with nearly cancelling contributions to Ca from three spin-up and three spin-down carbide-bound Fe ions. In contrast, the anisotropic hyperfine coupling constant undergoes a symmetry change upon conversion of E0 to hi-CO that may be associated with bonding and coordination changes at Fe ions. In combination with the negligible difference between CFe6 core structures of E0 and hi-CO, these results suggest that in CO-inhibited hi-CO the dominant role of the FeMo-cofactor carbide is to maintain the core structure, rather than to facilitate inhibitor binding through changes in Fe-carbide covalency or stretching/breaking of carbide-Fe bonds.
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Affiliation(s)
- Ana Pérez-González
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dmitriy A Lukoyanov
- Department of Chemistry Northwestern University, Evanston, Illinois 60208, United States
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Brian M Hoffman
- Department of Chemistry Northwestern University, Evanston, Illinois 60208, United States
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39
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Affiliation(s)
- Sven T. Stripp
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195 Berlin, Germany
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40
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Buscagan TM, Perez KA, Maggiolo AO, Rees DC, Spatzal T. Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site. Angew Chem Int Ed Engl 2021; 60:5704-5707. [PMID: 33320413 PMCID: PMC7920927 DOI: 10.1002/anie.202015751] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Indexed: 12/31/2022]
Abstract
As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the active-site FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer-Tropsch-type chemistry). The C-C bond forming capabilities of nitrogenase suggest that multiple CO or CO-derived ligands bind to the active site. Herein, we report a crystal structure with two CO ligands coordinated to the FeMo-cofactor of the molybdenum nitrogenase at 1.33 Å resolution. In addition to the previously observed bridging CO ligand between Fe2 and Fe6 of the FeMo-cofactor, a new ligand binding mode is revealed through a second CO ligand coordinated terminally to Fe6. While the relevance of this state to nitrogenase-catalyzed reactions remains to be established, it highlights the privileged roles for Fe2 and Fe6 in ligand binding, with multiple coordination modes available depending on the ligand and reaction conditions.
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Affiliation(s)
- Trixia M. Buscagan
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Howard Hughes Medical InstituteCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Kathryn A. Perez
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Present address: European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Ailiena O. Maggiolo
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Howard Hughes Medical InstituteCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Thomas Spatzal
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
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41
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Medina MS, Bretzing KO, Aviles RA, Chong KM, Espinoza A, Garcia CNG, Katz BB, Kharwa RN, Hernandez A, Lee JL, Lee TM, Lo Verde C, Strul MW, Wong EY, Owens CP. CowN sustains nitrogenase turnover in the presence of the inhibitor carbon monoxide. J Biol Chem 2021; 296:100501. [PMID: 33667548 PMCID: PMC8047169 DOI: 10.1016/j.jbc.2021.100501] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 01/28/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022] Open
Abstract
Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N2) to ammonia (NH3). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, CowN restores nearly full nitrogenase activity. Our results further indicate that CowN's protection mechanism involves decreasing the binding affinity of CO to nitrogenase's active site approximately tenfold without interrupting substrate turnover. Taken together, our work suggests CowN is an important auxiliary protein in nitrogen fixation that engenders CO tolerance to nitrogenase.
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Affiliation(s)
- Michael S Medina
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Kevin O Bretzing
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Richard A Aviles
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Kiersten M Chong
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Alejandro Espinoza
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Chloe Nicole G Garcia
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Benjamin B Katz
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Ruchita N Kharwa
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Andrea Hernandez
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Justin L Lee
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Terrence M Lee
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Christine Lo Verde
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Max W Strul
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Emily Y Wong
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Cedric P Owens
- Schmid College of Science and Technology, Chapman University, Orange, California, USA.
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