1
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Deng Y, Wang JX, Ghosh B, Lu Y. Enzymatic CO 2 reduction catalyzed by natural and artificial Metalloenzymes. J Inorg Biochem 2024; 259:112669. [PMID: 39059175 DOI: 10.1016/j.jinorgbio.2024.112669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/04/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
The continuously increasing level of atmospheric CO2 in the atmosphere has led to global warming. Converting CO2 into other carbon compounds could mitigate its atmospheric levels and produce valuable products, as CO2 also serves as a plentiful and inexpensive carbon feedstock. However, the inert nature of CO2 poses a major challenge for its reduction. To meet the challenge, nature has evolved metalloenzymes using transition metal ions like Fe, Ni, Mo, and W, as well as electron-transfer partners for their functions. Mimicking these enzymes, artificial metalloenzymes (ArMs) have been designed using alternative protein scaffolds and various metallocofactors like Ni, Co, Re, Rh, and FeS clusters. Both the catalytic efficiency and the scope of CO2-reduction product of these ArMs have been improved over the past decade. This review first focuses on the natural metalloenzymes that directly reduce CO2 by discussing their structures and active sites, as well as the proposed reaction mechanisms. It then introduces the common strategies for electrochemical, photochemical, or photoelectrochemical utilization of these native enzymes for CO2 reduction and highlights the most recent advancements from the past five years. We also summarize principles of protein design for bio-inspired ArMs, comparing them with native enzymatic systems and outlining challenges and opportunities in enzymatic CO2 reduction.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Jing-Xiang Wang
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Barshali Ghosh
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America.
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2
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Tanabe Y, Nishibayashi Y. Catalytic Nitrogen Fixation Using Well-Defined Molecular Catalysts under Ambient or Mild Reaction Conditions. Angew Chem Int Ed Engl 2024; 63:e202406404. [PMID: 38781115 DOI: 10.1002/anie.202406404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Ammonia (NH3) is industrially produced from dinitrogen (N2) and dihydrogen (H2) by the Haber-Bosch process, although H2 is prepared from fossil fuels, and the reaction requires harsh conditions. On the other hand, microorganisms have fixed nitrogen under ambient reaction conditions. Recently, well-defined molecular transition metal complexes have been found to work as catalyst to convert N2 into NH3 by reactions with chemical reductants and proton sources under ambient reaction conditions. Among them, involvement of both N2-splitting pathway and proton-coupled electron transfer is found to be very effective for high catalytic activity. Furthermore, direct electrocatalytic and photocatalytic conversions of N2 into NH3 have been recently achieved. In addition to catalytic formation of NH3, selective catalytic conversion of N2 into hydrazine (NH2NH2) and catalytic silylation of N2 into silylamines have been reported. Catalytic C-N bond formation has been more recently established to afford cyanate anion (NCO-) under ambient reaction conditions. Further development of direct conversion of N2 into nitrogen-containing compounds as well as green ammonia synthesis leading to the use of ammonia as an energy carrier is expected.
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Affiliation(s)
- Yoshiaki Tanabe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshiaki Nishibayashi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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3
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Maslać N, Cadoux C, Bolte P, Murken F, Gu W, Milton RD, Wagner T. Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales. FEBS J 2024; 291:3454-3480. [PMID: 38696373 DOI: 10.1111/febs.17148] [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: 08/16/2023] [Revised: 01/17/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
The nitrogenase reductase NifH catalyses ATP-dependent electron delivery to the Mo-nitrogenase, a reaction central to biological dinitrogen (N2) fixation. While NifHs have been extensively studied in bacteria, structural information about their archaeal counterparts is limited. Archaeal NifHs are considered more ancient, particularly those from Methanococcales, a group of marine hydrogenotrophic methanogens, which includes diazotrophs growing at temperatures near 92 °C. Here, we structurally and biochemically analyse NifHs from three Methanococcales, offering the X-ray crystal structures from meso-, thermo-, and hyperthermophilic methanogens. While NifH from Methanococcus maripaludis (37 °C) was obtained through heterologous recombinant expression, the proteins from Methanothermococcus thermolithotrophicus (65 °C) and Methanocaldococcus infernus (85 °C) were natively purified from the diazotrophic archaea. The structures from M. thermolithotrophicus crystallised as isolated exhibit high flexibility. In contrast, the complexes of NifH with MgADP obtained from the three methanogens are superposable, more rigid, and present remarkable structural conservation with their homologues. They retain key structural features of P-loop NTPases and share similar electrostatic profiles with the counterpart from the bacterial model organism Azotobacter vinelandii. In comparison to the NifH from the phylogenetically distant Methanosarcina acetivorans, these reductases do not cross-react significantly with Mo-nitrogenase from A. vinelandii. However, they associate with bacterial nitrogenase when ADP·AlF 4 - is added to mimic a transient reactive state. Accordingly, detailed surface analyses suggest that subtle substitutions would affect optimal binding during the catalytic cycle between the NifH from Methanococcales and the bacterial nitrogenase, implying differences in the N2-machinery from these ancient archaea.
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Affiliation(s)
- Nevena Maslać
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cécile Cadoux
- Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Switzerland
| | - Pauline Bolte
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Fenja Murken
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wenyu Gu
- Laboratory of Microbial Physiology and Resource Biorecovery, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédéral de Lausanne, Switzerland
| | - Ross D Milton
- Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Switzerland
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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4
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Cook BD, Narehood SM, McGuire KL, Li Y, Tezcan FA, Herzik MA. Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604374. [PMID: 39091810 PMCID: PMC11291078 DOI: 10.1101/2024.07.19.604374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
High-quality grid preparation for single-particle cryogenic electron microscopy (cryoEM) remains a bottleneck for routinely obtaining high-resolution structures. The issues that arise from traditional grid preparation workflows are particularly exacerbated for oxygen-sensitive proteins, including metalloproteins, whereby oxygen-induced damage and alteration of oxidation states can result in protein inactivation, denaturation, and/or aggregation. Indeed, 99% of the current structures in the EMBD were prepared aerobically and limited successes for anaerobic cryoEM grid preparation exist. Current practices for anaerobic grid preparation involve a vitrification device located in an anoxic chamber, which presents significant challenges including temperature and humidity control, optimization of freezing conditions, costs for purchase and operation, as well as accessibility. Here, we present a streamlined approach that allows for the (an)aerobic vitrification of oxygen-sensitive proteins using an automated aerobic blot-free grid vitrification device - the SPT Labtech chameleon. This robust workflow allows for high-resolution structure determination of dynamic, oxygen-sensitive proteins, of varying complexity and molecular weight.
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Affiliation(s)
- Brian D. Cook
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Sarah M. Narehood
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Kelly L. McGuire
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Yizhou Li
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
| | - Mark A. Herzik
- Department of Chemistry and Biochemistry, University of California, San Diego, California, USA
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5
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Harris DF, Rucker HR, Garcia AK, Yang ZY, Chang SD, Feinsilber H, Kaçar B, Seefeldt LC. Ancient nitrogenases are ATP dependent. mBio 2024; 15:e0127124. [PMID: 38869277 PMCID: PMC11253609 DOI: 10.1128/mbio.01271-24] [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: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 06/14/2024] Open
Abstract
Life depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent metal ion such as Mg2+, can be hydrolyzed to support numerous cellular and molecular processes. Despite its centrality to extant biochemistry, it is unclear whether ATP supported the function of ancient enzymes. We investigate the evolutionary necessity of ATP by experimentally reconstructing an ancestral variant of the N2-reducing enzyme nitrogenase. The Proterozoic ancestor is predicted to be ~540-2,300 million years old, post-dating the Great Oxidation Event. Growth rates under nitrogen-fixing conditions are ~80% of those of wild type in Azotobacter vinelandii. In the extant enzyme, the hydrolysis of two MgATP is coupled to electron transfer to support substrate reduction. The ancestor has a strict requirement for ATP with no other nucleotide triphosphate analogs (GTP, ITP, and UTP) supporting activity. Alternative divalent metal ions (Fe2+, Co2+, and Mn2+) support activity with ATP but with diminished activities compared to Mg2+, similar to the extant enzyme. Additionally, it is shown that the ancestor has an identical efficiency in ATP hydrolyzed per electron transferred to the extant of two. Our results provide direct laboratory evidence of ATP usage by an ancient enzyme.IMPORTANCELife depends on energy-carrying molecules to power many sustaining processes. There is evidence that these molecules may predate the rise of life on Earth, but how and when these dependencies formed is unknown. The resurrection of ancient enzymes provides a unique tool to probe the enzyme's function and usage of energy-carrying molecules, shedding light on their biochemical origins. Through experimental reconstruction, this research investigates the ancestral dependence of a nitrogen-fixing enzyme on the energy carrier ATP, a requirement for function in the modern enzyme. We show that the resurrected ancestor does not have generalist nucleotide specificity. Rather, the ancestor has a strict requirement for ATP, like the modern enzyme, with similar function and efficiency. The findings elucidate the early-evolved necessity of energy-yielding molecules, delineating their role in ancient biochemical processes. Ultimately, these insights contribute to unraveling the intricate tapestry of evolutionary biology and the origins of life-sustaining dependencies.
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Affiliation(s)
- Derek F. Harris
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Holly R. Rucker
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Amanda K. Garcia
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Scott D. Chang
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Hannah Feinsilber
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
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6
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Mrnjavac N, Degli Esposti M, Mizrahi I, Martin WF, Allen JF. Three enzymes governed the rise of O 2 on Earth. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149495. [PMID: 39004113 DOI: 10.1016/j.bbabio.2024.149495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
Current views of O2 accumulation in Earth history depict three phases: The onset of O2 production by ∼2.4 billion years ago; 2 billion years of stasis at ∼1 % of modern atmospheric levels; and a rising phase, starting about 500 million years ago, in which oxygen eventually reached modern values. Purely geochemical mechanisms have been proposed to account for this tripartite time course of Earth oxygenation. In particular the second phase, the long period of stasis between the advent of O2 and the late rise to modern levels, has posed a puzzle. Proposed solutions involve Earth processes (geochemical, ecosystem, day length). Here we suggest that Earth oxygenation was not determined by geochemical processes. Rather it resulted from emergent biological innovations associated with photosynthesis and the activity of only three enzymes: 1) The oxygen evolving complex of cyanobacteria that makes O2; 2) Nitrogenase, with its inhibition by O2 causing two billion years of oxygen level stasis; 3) Cellulose synthase of land plants, which caused mass deposition and burial of carbon, thus removing an oxygen sink and therefore increasing atmospheric O2. These three enzymes are endogenously produced by, and contained within, cells that have the capacity for exponential growth. The catalytic properties of these three enzymes paved the path of Earth's atmospheric oxygenation, requiring no help from Earth other than the provision of water, CO2, salts, colonizable habitats, and sunlight.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK.
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7
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Fritz G, Kroneck PMH, Steuber J. The power supply for biological nitrogen fixation. Nat Chem Biol 2024:10.1038/s41589-024-01663-9. [PMID: 38987384 DOI: 10.1038/s41589-024-01663-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Affiliation(s)
- Günter Fritz
- Department of Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Peter M H Kroneck
- Department of Biology, Faculty of Sciences, University of Konstanz, Konstanz, Germany
| | - Julia Steuber
- Department of Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
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8
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M Meirovich M, Bachar O, Shemesh M, Cohen Y, Popik A, Yehezkeli O. Light-driven, bias-free nitrogenase-based bioelectrochemical cell for ammonia generation. Biosens Bioelectron 2024; 255:116254. [PMID: 38569252 DOI: 10.1016/j.bios.2024.116254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Nitrogen fixation is a key process that sustains life on Earth. Nitrogenase is the sole enzyme capable of fixing nitrogen under ambient conditions. Extensive research efforts have been dedicated to elucidating the enzyme mechanism and its artificial activation through high applied voltage, photochemistry, or strong reducing agents. Harnessing light irradiation to minimize the required external bias can lower the process's high energy investment. Herein, we present the development of photo-bioelectrochemical cells (PBECs) utilizing BiVO4/CoP or CdS/NiO photoanodes for nitrogenase activation toward N2 fixation. The constructed PBEC based on BiVO4/CoP photoanode requires minimal external bias (200 mV) and suppresses O2 generation that allows efficient activation of the nitrogenase enzyme, using glucose as an electron donor. In a second developed PBEC configuration, CdS/NiO photoanode was used, enabling bias-free activation of the nitrogenase-based cathode to produce 100 μM of ammonia at a faradaic efficiency (FE) of 12%. The ammonia production was determined by a commonly used fluorescence probe and further validated using 1H-NMR spectroscopy. The presented PBECs lay the foundation for biotic-abiotic systems to directly activate enzymes toward value-added chemicals by light-driven reactions.
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Affiliation(s)
- Matan M Meirovich
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel
| | - Oren Bachar
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel
| | - Mor Shemesh
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel
| | - Yifat Cohen
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel
| | - Alice Popik
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel
| | - Omer Yehezkeli
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel; Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, 3200003, Haifa, Israel; The Nancy and Stephen Grand Technion Energy Program, Technion - Israel Institute of Technology, 3200003, Haifa, Israel.
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9
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Vazquez Ramos J, Kulka-Peschke CJ, Bechtel DF, Zebger I, Pierik AJ, Layer G. Characterization of the iron-sulfur clusters in the nitrogenase-like reductase CfbC/D required for coenzyme F 430 biosynthesis. FEBS J 2024; 291:3233-3248. [PMID: 38588274 DOI: 10.1111/febs.17134] [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: 11/17/2023] [Revised: 02/14/2024] [Accepted: 03/28/2024] [Indexed: 04/10/2024]
Abstract
Coenzyme F430 is a nickel-containing tetrapyrrole, serving as the prosthetic group of methyl-coenzyme M reductase in methanogenic and methanotrophic archaea. During coenzyme F430 biosynthesis, the tetrapyrrole macrocycle is reduced by the nitrogenase-like CfbC/D system consisting of the reductase component CfbC and the catalytic component CfbD. Both components are homodimeric proteins, each carrying a [4Fe-4S] cluster. Here, the ligands of the [4Fe-4S] clusters of CfbC2 and CfbD2 were identified revealing an all cysteine ligation of both clusters. Moreover, the midpoint potentials of the [4Fe-4S] clusters were determined to be -256 mV for CfbC2 and -407 mV for CfbD2. These midpoint potentials indicate that the consecutive thermodynamically unfavorable 6 individual "up-hill" electron transfers to the organic moiety of the Ni2+-sirohydrochlorin a,c-diamide substrate require an intricate interplay of ATP-binding, hydrolysis, protein complex formation and release to drive product formation, which is a common theme in nitrogenase-like systems.
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Affiliation(s)
- José Vazquez Ramos
- Pharmazeutische Biologie, Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Germany
| | | | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Germany
| | | | - Gunhild Layer
- Pharmazeutische Biologie, Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Germany
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10
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Fan J, Zhang X, Tan W, Feng Z, Li K. Bioinspired Surface Ligand Engineering Regulates Electron Transfers in Gold Clusterzymes to Enhance the Catalytic Activity for Improving Sensing Performance. NANO LETTERS 2024; 24:7800-7808. [PMID: 38870391 DOI: 10.1021/acs.nanolett.4c02175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Metal nanoclusters feature a hierarchical structure, facilitating their ability to mimic enzyme-catalyzed reactions. However, the lack of true catalytic centers, compounded by tightly bound surface ligands hindering electron transfers to substrates, underscores the need for universal rational design methodologies to emulate the structure and mechanisms of natural enzymes. Motivated by the electron transfer in active centers with specific chemical structures, by integrating the peroxidase cofactor Fe-TCPP onto the surface of glutathione-stabilized gold nanoclusters (AuSG), we engineered AuSG-Fe-TCPP clusterzymes with a remarkable 39.6-fold enhancement in peroxidase-like activity compared to AuSG. Fe-TCPP not only mimics the active center structure, enhancing affinity to H2O2, but also facilitates the electron transfer process, enabling efficient H2O2 activation. By exemplifying the establishment of a detecting platform for trace H2O2 produced by ultrasonic cleaners, we substantiate that the bioinspired surface-ligand-engineered electron transfer can improve sensing performance with a wider linear range and lower detection limit.
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Affiliation(s)
- Jinsong Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Xiyue Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Wenlong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhenzhen Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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11
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Zhang L, Einsle O. Architecture of the RNF1 complex that drives biological nitrogen fixation. Nat Chem Biol 2024:10.1038/s41589-024-01641-1. [PMID: 38890433 DOI: 10.1038/s41589-024-01641-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotroph Azotobacter vinelandii transfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryogenic electron microscopy structure of the nitrogenase-associated RNF complex of A. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron-sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling.
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Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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12
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Lee CC, Górecki K, Stang M, Ribbe MW, Hu Y. Cofactor maturase NifEN: A prototype ancient nitrogenase? SCIENCE ADVANCES 2024; 10:eado6169. [PMID: 38865457 PMCID: PMC11168457 DOI: 10.1126/sciadv.ado6169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Nitrogenase plays a key role in the global nitrogen cycle; yet, the evolutionary history of nitrogenase and, particularly, the sequence of appearance between the homologous, yet distinct NifDK (the catalytic component) and NifEN (the cofactor maturase) of the extant molybdenum nitrogenase, remains elusive. Here, we report the ability of NifEN to reduce N2 at its surface-exposed L-cluster ([Fe8S9C]), a structural/functional homolog of the M-cluster (or cofactor; [(R-homocitrate)MoFe7S9C]) of NifDK. Furthermore, we demonstrate the ability of the L-cluster-bound NifDK to mimic its NifEN counterpart and enable N2 reduction. These observations, coupled with phylogenetic, ecological, and mechanistic considerations, lead to the proposal of a NifEN-like, L-cluster-carrying protein as an ancient nitrogenase, the exploration of which could shed crucial light on the evolutionary origin of nitrogenase and related enzymes.
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Affiliation(s)
- Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
| | - Martin Stang
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
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13
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Kang W, Mu L, Hu X. Marine Colloids Boost Nitrogen Fixation in Trichodesmium erythraeum by Photoelectrophy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9236-9249. [PMID: 38748855 DOI: 10.1021/acs.est.4c01849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Nitrogen fixation by the diazotrophic cyanobacterium Trichodesmium contributes up to 50% of the bioavailable nitrogen in the ocean. N2 fixation by Trichodesmium is limited by the availability of nutrients, such as iron (Fe) and phosphorus (P). Although colloids are ubiquitous in the ocean, the effects of Fe limitation on nitrogen fixation by marine colloids (MC) and the related mechanisms are largely unexplored. In this study, we found that MC exhibit photoelectrochemical properties that boost nitrogen fixation by photoelectrophy in Trichodesmium erythraeum. MC efficiently promote photosynthesis in T. erythraeum, thus enhancing its growth. Photoexcited electrons from MC are directly transferred to the photosynthetic electron transport chain and contribute to nitrogen fixation and ammonia assimilation. Transcriptomic analysis revealed that MC significantly upregulates genes related to the electron transport chain, photosystem, and photosynthesis, which is consistent with elevated photosynthetic capacities (e.g., Fv/Fm and carboxysomes). As a result, MC increase the N2 fixation rate by 67.5-89.3%. Our findings highlight a proof-of-concept electron transfer pathway by which MC boost nitrogen fixation, broadening our knowledge on the role of ubiquitous colloids in marine nitrogen biogeochemistry.
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Affiliation(s)
- Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Carbon Neutrality Interdisciplinary Science Centre, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-Environment and Product Safety, Key Laboratory for Environmental Factors Controlling Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Carbon Neutrality Interdisciplinary Science Centre, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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14
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Lee CC, Stang M, Ribbe MW, Hu Y. ATP-Independent Turnover of Dinitrogen Intermediates Captured on the Nitrogenase Cofactor. Angew Chem Int Ed Engl 2024; 63:e202400273. [PMID: 38527309 DOI: 10.1002/anie.202400273] [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: 01/04/2024] [Revised: 03/17/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Nitrogenase reduces N2 to NH3 at its active-site cofactor. Previous studies of an N2-bound Mo-nitrogenase from Azotobacter vinelandii suggest binding of three N2 species via asymmetric belt-sulfur displacements in the two cofactors of its catalytic component (designated Av1*), leading to the proposal of stepwise N2 reduction involving all cofactor belt-sulfur sites; yet, the evidence for the existence of multiple N2 species on Av1* remains elusive. Here we report a study of ATP-independent, EuII/SO3 2--driven turnover of Av1* using GC-MS and frequency-selective pulse NMR techniques. Our data demonstrate incorporation of D2-derived D by Av1* into the products of C2H2- and H+-reduction, and decreased formation of NH3 by Av1* concomitant with the release of N2 under H2; moreover, they reveal a strict dependence of these activities on SO3 2-. These observations point to the presence of distinct N2 species on Av1*, thereby providing strong support for our proposed mechanism of stepwise reduction of N2 via belt-sulfur mobilization.
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Affiliation(s)
- Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Martin Stang
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
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15
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Heidinger L, Perez K, Spatzal T, Einsle O, Weber S, Rees DC, Schleicher E. Analysis of early intermediate states of the nitrogenase reaction by regularization of EPR spectra. Nat Commun 2024; 15:4041. [PMID: 38740794 DOI: 10.1038/s41467-024-48271-8] [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] [Received: 06/28/2023] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Due to the complexity of the catalytic FeMo cofactor site in nitrogenases that mediates the reduction of molecular nitrogen to ammonium, mechanistic details of this reaction remain under debate. In this study, selenium- and sulfur-incorporated FeMo cofactors of the catalytic MoFe protein component from Azotobacter vinelandii are prepared under turnover conditions and investigated by using different EPR methods. Complex signal patterns are observed in the continuous wave EPR spectra of selenium-incorporated samples, which are analyzed by Tikhonov regularization, a method that has not yet been applied to high spin systems of transition metal cofactors, and by an already established grid-of-error approach. Both methods yield similar probability distributions that reveal the presence of at least four other species with different electronic structures in addition to the ground state E0. Two of these species were preliminary assigned to hydrogenated E2 states. In addition, advanced pulsed-EPR experiments are utilized to verify the incorporation of sulfur and selenium into the FeMo cofactor, and to assign hyperfine couplings of 33S and 77Se that directly couple to the FeMo cluster. With this analysis, we report selenium incorporation under turnover conditions as a straightforward approach to stabilize and analyze early intermediate states of the FeMo cofactor.
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Affiliation(s)
- Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Kathryn Perez
- Howard Hughes Medical Institute (HHMI), California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
| | - Thomas Spatzal
- Howard Hughes Medical Institute (HHMI), California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Douglas C Rees
- Howard Hughes Medical Institute (HHMI), California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA.
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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16
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Dance I. What triggers the coupling of proton transfer and electron transfer at the active site of nitrogenase? Dalton Trans 2024; 53:7996-8004. [PMID: 38651170 DOI: 10.1039/d4dt00474d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In converting N2 to NH3 the enzyme nitrogenase utilises 8 electrons and 8 protons in the complete catalytic cycle. The source of the electrons is an Fe4S4 reductase protein (Fe-protein) which temporarily docks with the MoFe-protein that contains the catalytic active cofactor, FeMo-co, and an electron transfer cluster called the P cluster. The overall mechanism involves 8 repetitions of a cycle in which reduced Fe-protein docks with the MoFe-protein, one electron transfers to the P-cluster, and then to FeMo-co, followed by dissociation of the two proteins and re-reduction of the Fe-protein. Protons are supplied serially to FeMo-co by a Grotthuss proton translocation mechanism from the protein surface along a conserved chain of water molecules (a proton wire) that terminates near S atoms of the FeMo-co cluster [CFe7S9Mo(homocitrate)] where the multiple steps of the chemical conversions are effected. It is assumed that the chemical mechanisms use proton-coupled electron-transfer (PCET) and that H atoms (e- + H+) are involved in each of the hydrogenation steps. However there is neither evidence for, or mechanism proposed, for this coupling. Here I report calculations of cluster charge distribution upon electron addition, revealing that the added negative charge is on the S atoms of FeMo-co, which thereby become more basic, and able to trigger proton transfer from H3O+ waiting at the near end of the proton wire. This mechanism is supported by calculations of the dynamics of the proton transfer step, in which the barrier is reduced by ca. 3.5 kcal mol-1 and the product stabilised by ca. 7 kcal mol-1 upon electron addition. H tunneling is probable in this step. In nitrogenase it is electron transfer that triggers proton transfer.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2052, Australia.
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17
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Lewis NM, Kisgeropoulos EC, Lubner CE, Fixen KR. Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe4S] Fd activity. J Inorg Biochem 2024; 254:112521. [PMID: 38471286 DOI: 10.1016/j.jinorgbio.2024.112521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1T11I). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1T11I. Electrochemical characterization revealed both Fer1 and Fer1T11I have similar redox transitions (-480 mV and - 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron‑sulfur (FeS) cluster of Fer1. Additionally, disruption of hydrogen bonding around an FeS cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1T11I. Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1T11I, which indicate changes to the high spin states and/or spin-spin coupling between the FeS clusters of Fer1. Our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.
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Affiliation(s)
- Nathan M Lewis
- Department of Plant and Microbial Biology and the Biotechnology Institute, University of Minnesota, Minneapolis, MN, United States of America
| | | | - Carolyn E Lubner
- National Renewable Energy Laboratory, Golden, CO, United States of America.
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology and the Biotechnology Institute, University of Minnesota, Minneapolis, MN, United States of America.
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18
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Hooper RX, Wertz AE, Shafaat HS, Holland PL. Evaluating Diazene to N 2 Interconversion at Iron-Sulfur Complexes. Chemistry 2024; 30:e202304072. [PMID: 38376370 PMCID: PMC11045311 DOI: 10.1002/chem.202304072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
Biological N2 reduction occurs at sulfur-rich multiiron sites, and an interesting potential pathway is concerted double reduction/ protonation of bridging N2 through PCET. Here, we test the feasibility of using synthetic sulfur-supported diiron complexes to mimic this pathway. Oxidative proton transfer from μ-η1 : η1-diazene (HN=NH) is the microscopic reverse of the proposed N2 fixation pathway, revealing the energetics of the process. Previously, Sellmann assigned the purple metastable product from two-electron oxidation of [{Fe2+(PPr3)L1}2(μ-η1 : η1-N2H2)] (L1=tetradentate SSSS ligand) at -78 °C as [{Fe2+(PPr3)L1}2(μ-η1 : η1-N2)]2+, which would come from double PCET from diazene to sulfur atoms of the supporting ligands. Using resonance Raman, Mössbauer, NMR, and EPR spectroscopies in conjunction with DFT calculations, we show that the product is not an N2 complex. Instead, the data are most consistent with the spectroscopically observed species being the mononuclear iron(III) diazene complex [{Fe(PPr3)L1}(η2-N2H2)]+. Calculations indicate that the proposed double PCET has a barrier that is too high for proton transfer at the reaction temperature. Also, PCET from the bridging diazene is highly exergonic as a result of the high Fe3+/2+ redox potential, indicating that the reverse N2 protonation would be too endergonic to proceed. This system establishes the "ground rules" for designing reversible N2/N2H2 interconversion through PCET, such as tuning the redox potentials of the metal sites.
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Affiliation(s)
- Reagan X Hooper
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT-06511
| | - Ashlee E Wertz
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, OH-43210
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, OH-43210
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA-90095
| | - Patrick L Holland
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT-06511
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19
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Grunwald L, Abbott DF, Mougel V. Gauging Iron-Sulfur Cubane Reactivity from Covalency: Trends with Oxidation State. JACS AU 2024; 4:1315-1322. [PMID: 38665672 PMCID: PMC11040707 DOI: 10.1021/jacsau.4c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
We investigated room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge position provides a qualitative but convenient alternative to the traditional spectroscopic descriptors used to identify oxidation states in these systems, which we demonstrate by providing a calibration curve based on two analytic methods. Furthermore, high energy resolution fluorescence detected XAS (HERFD-XAS) at the S K-edge was used to measure Fe-S bond covalencies and record their variation with the average valence of the Fe atoms. While the Fe-S(thiolate) covalency evolves linearly, gaining 11 ± 0.4% per bond and hole, the Fe-S(μ3) covalency evolves asystematically, reflecting changes in the magnetic exchange mechanism. A strong discontinuity manifested for superoxidation to the all-ferric state, distinguishing its electronic structure and its potential (bio)chemical role from those of its redox congeners. We highlight the functional implications of these trends for the reactivity of iron-sulfur cubanes.
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Affiliation(s)
- Liam Grunwald
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Daniel F. Abbott
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Victor Mougel
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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20
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Xie ZL, Jin WT, Zhou ZH. Analyses of the electronic structures of FeFe-cofactors compared with those of FeMo- and FeV-cofactors and their P-clusters. Dalton Trans 2024; 53:6529-6536. [PMID: 38299993 DOI: 10.1039/d3dt04126c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The electronic structures of FeFe-cofactors (FeFe-cos) in resting and turnover states, together with their PN clusters from iron-only nitrogenases, have been calculated using the bond valence method, and their crystallographic data were reported recently and deposited in the Protein Data Bank (PDB codes: 8BOQ and 8OIE). The calculated results have also been compared with those of their homologous Mo- and V-nitrogenases. For FeFe-cos in the resting state, Fe1/2/4/5/6/7/8 atoms are prone to Fe3+, while the Fe3 atom shows different degrees of mixed valences. The results support that the Fe8 atom at the terminal positions of FeFe-cos possesses the same oxidation states as the Mo3+/V3+ atoms of FeMo-/FeV-cos. In the turnover state, the overall oxidation state of FeFe-co is slightly reduced than those in the resting species, and its electronic configuration is rearranged after the substitution of S2B with OH, compatible with those found in CO-bound FeV-co. Moreover, the calculations give the formal oxidation states of 6Fe2+-2Fe3+ for the electronic structures of PN clusters in Fe-nitrogenases. By the comparison of Mo-, V- and Fe-nitrogenases, the overall oxidation levels of 7Fe atoms (Fe1-Fe7) for both FeFe- and FeMo-cos in resting states are found to be higher than that of FeV-co. For the PN clusters in MoFe-, VFe- and FeFe-proteins, they all exhibit a strong reductive character.
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Affiliation(s)
- Zhen-Lang Xie
- State Key Laboratory of Physical Chemistry of Solid Surfaces and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Wan-Ting Jin
- College of Chemical and Material Engineering, Quzhou University, Quzhou, 324000, China
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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21
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Clinger A, Yang ZY, Pellows LM, King P, Mus F, Peters JW, Dukovic G, Seefeldt LC. Hole-scavenging in photo-driven N 2 reduction catalyzed by a CdS-nitrogenase MoFe protein biohybrid system. J Inorg Biochem 2024; 253:112484. [PMID: 38219407 DOI: 10.1016/j.jinorgbio.2024.112484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
The light-driven reduction of dinitrogen (N2) to ammonia (NH3) catalyzed by a cadmium sulfide (CdS) nanocrystal‑nitrogenase MoFe protein biohybrid is dependent on a range of different factors, including an appropriate hole-scavenging sacrificial electron donor (SED). Here, the impact of different SEDs on the overall rate of N2 reduction catalyzed by a CdS quantum dot (QD)-MoFe protein system was determined. The selection of SED was guided by several goals: (i) molecules with standard reduction potentials sufficient to reduce the oxidized CdS QD, (ii) molecules that do not absorb the excitation wavelength of the CdS QD, and (iii) molecules that could be readily reduced by sustainable processes. Earlier studies utilized buffer molecules or ascorbic acid as the SED. The effectiveness of ascorbic acid as SED was compared to dithionite (DT), triethanolamine (TEOA), and hydroquinone (HQ) across a range of concentrations in supporting N2 reduction to NH3 in a CdS QD-MoFe protein photocatalytic system. It was found that TEOA supported N2 reduction rates comparable to those observed for dithionite and ascorbic acid. HQ was found to support significantly higher rates of N2 reduction compared to the other SEDs at a concentration of 50 mM. A comparison of the rates of N2 reduction by the biohybrid complex to the standard reduction potential (Eo) of the SEDs reveals that Eo is not the only factor impacting the efficiency of hole-scavenging. These findings reveal the importance of the SED properties for improving the efficiency of hole-scavenging in the light-driven N2 reduction reaction catalyzed by a CdS QD-MoFe protein hybrid.
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Affiliation(s)
- Andrew Clinger
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States of America
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States of America
| | - Lauren M Pellows
- Department of Chemistry, University of Colorado Boulder, Boulder, CO 80309, United States of America
| | - Paul King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, United States of America
| | - Florence Mus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, United States of America
| | - John W Peters
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, United States of America
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado Boulder, Boulder, CO 80309, United States of America; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO 80303, United States of America; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO 80303, United States of America
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States of America.
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22
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Ouyang P, Yang J, Zhong Q, Yuan Y, Gao Y, Wang H, Yang ST. Toxicity of VO 2 micro/nanoparticles to nitrogen-fixing bacterium Azotobacter vinelandii. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133553. [PMID: 38266589 DOI: 10.1016/j.jhazmat.2024.133553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Vanadium dioxide (VO2) has been used in a variety of products due to its outstanding phase transition properties. However, as potential heavy metal contaminants, the environmental hazards and risks of VO2 should be systematically investigated. Biological nitrogen fixation is one of the most dominant processes in biogeochemical cycle, which is associated with nitrogen-fixing bacteria. In this study, we reported the environmental bio-effects of VO2 micro/nanoparticles on the nitrogen-fixing bacterium Azotobacter vinelandii. VO2 at 10 and 30 mg/L caused severe hazards to A. vinelandii, such as cell apoptosis, oxidative damage, physical damage, genotoxicity, and the loss of nitrogen fixation activity. The up-regulated differentially expressed genes of A. vinelandii were related to stress response, and the down-regulated genes were mainly related to energy metabolism. Surprisingly, VO2 of 10 mg/L decreased the nif gene expression but elevated the vnf gene expression, which enhanced the ability of A. vinelandii to reduce acetylene in anaerobic environment. In addition, under tested conditions, VO2 nanoparticles exhibited insignificantly higher toxicity than VO2 microparticles.
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Affiliation(s)
- Peng Ouyang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China; College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Jinwei Yang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Qinmei Zhong
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Yue Yuan
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Yanfeng Gao
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China.
| | - Sheng-Tao Yang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China.
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23
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Addison H, Glatter T, K. A. Hochberg G, Rebelein JG. Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in Rhodobacter capsulatus. mBio 2024; 15:e0331423. [PMID: 38377621 PMCID: PMC10936413 DOI: 10.1128/mbio.03314-23] [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: 12/07/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Nitrogenases are the only enzymes able to fix gaseous nitrogen into bioavailable ammonia and hence are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited: The electron transport to the iron (Fe)-nitrogenase has hardly been investigated. Here, we characterized the electron transfer pathway to the Fe-nitrogenase in Rhodobacter capsulatus via proteome analyses, genetic deletions, complementation studies, and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain, compared to non-nitrogen-fixing conditions. Based on these findings, R. capsulatus strains with deletions of ferredoxin (fdx) and flavodoxin (fld, nifF) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase. R. capsulatus deletion strains were characterized by monitoring diazotrophic growth and Fe-nitrogenase activity in vivo. Only deletions of fdxC or fdxN resulted in slower growth and reduced Fe-nitrogenase activity, whereas the double deletion of both fdxC and fdxN abolished diazotrophic growth. Differences in the proteomes of ∆fdxC and ∆fdxN strains, in conjunction with differing plasmid complementation behaviors of fdxC and fdxN, indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.IMPORTANCENitrogenases are essential for biological nitrogen fixation, converting atmospheric nitrogen gas to bioavailable ammonia. The production of ammonia by diazotrophic organisms, harboring nitrogenases, is essential for sustaining plant growth. Hence, there is a large scientific interest in understanding the cellular mechanisms for nitrogen fixation via nitrogenases. Nitrogenases rely on highly reduced electrons to power catalysis, although we lack knowledge as to which proteins shuttle the electrons to nitrogenases within cells. Here, we characterized the electron transport to the iron (Fe)-nitrogenase in the model diazotroph Rhodobacter capsulatus, showing that two distinct ferredoxins are very important for nitrogen fixation despite having different redox centers. In addition, our research expands upon the debate on whether ferredoxins have functional redundancy or perform distinct roles within cells. Here, we observe that both essential ferredoxins likely have distinct roles based on differential proteome shifts of deletion strains and different complementation behaviors.
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Affiliation(s)
- Holly Addison
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg K. A. Hochberg
- Evolutionary Biochemistry Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Johannes G. Rebelein
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
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24
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Willard D, Arellano JJ, Underdahl M, Lee TM, Ramaswamy AS, Fumes G, Kliman A, Wong EY, Owens CP. Mutational Analysis of the Nitrogenase Carbon Monoxide Protective Protein CowN Reveals That a Conserved C-Terminal Glutamic Acid Residue Is Necessary for Its Activity. Biochemistry 2024; 63:152-158. [PMID: 38091601 PMCID: PMC10765410 DOI: 10.1021/acs.biochem.3c00421] [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] [Received: 08/10/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN's protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work uncovers structural features in CowN that are required for its function and provides new insights into its nitrogenase binding and CO protection mechanism.
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Affiliation(s)
- Dustin
L. Willard
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Joshuah J. Arellano
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Mitch Underdahl
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Terrence M. Lee
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Avinash S. Ramaswamy
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Gabriella Fumes
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Agatha Kliman
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Emily Y. Wong
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Cedric P. Owens
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
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25
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Schmidt FV, Schulz L, Zarzycki J, Prinz S, Oehlmann NN, Erb TJ, Rebelein JG. Structural insights into the iron nitrogenase complex. Nat Struct Mol Biol 2024; 31:150-158. [PMID: 38062208 PMCID: PMC10803253 DOI: 10.1038/s41594-023-01124-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 01/24/2024]
Abstract
Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO2) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO2, but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF3-stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [Fe8S9C-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit 'communication' and thus the nitrogenase mechanism.
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Affiliation(s)
- Frederik V Schmidt
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Simone Prinz
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Niels N Oehlmann
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Johannes G Rebelein
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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26
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Solomon JB, Liu YA, Górecki K, Quechol R, Lee CC, Jasniewski AJ, Hu Y, Ribbe MW. Heterologous expression of a fully active Azotobacter vinelandii nitrogenase Fe protein in Escherichia coli. mBio 2023; 14:e0257223. [PMID: 37909748 PMCID: PMC10746259 DOI: 10.1128/mbio.02572-23] [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: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE The heterologous expression of a fully active Azotobacter vinelandii Fe protein (AvNifH) has never been accomplished. Given the functional importance of this protein in nitrogenase catalysis and assembly, the successful expression of AvNifH in Escherichia coli as reported herein supplies a key element for the further development of heterologous expression systems that explore the catalytic versatility of the Fe protein, either on its own or as a key component of nitrogenase, for nitrogenase-based biotechnological applications in the future. Moreover, the "clean" genetic background of the heterologous expression host allows for an unambiguous assessment of the effect of certain nif-encoded protein factors, such as AvNifM described in this work, in the maturation of AvNifH, highlighting the utility of this heterologous expression system in further advancing our understanding of the complex biosynthetic mechanism of nitrogenase.
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Affiliation(s)
- Joseph B. Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
- Department of Chemistry, University of California, Irvine, California, USA
| | - Yiling A. Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Andrew J. Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
- Department of Chemistry, University of California, Irvine, California, USA
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27
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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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28
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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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29
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Zhai H, Lee S, Cui ZH, Cao L, Ryde U, Chan GKL. Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters. J Phys Chem A 2023; 127:9974-9984. [PMID: 37967028 PMCID: PMC10694817 DOI: 10.1021/acs.jpca.3c06142] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023]
Abstract
Characterizing the electronic structure of the iron-sulfur clusters in nitrogenase is necessary to understand their role in the nitrogen fixation process. One challenging task is to determine the protonation state of the intermediates in the nitrogen fixing cycle. Here, we use a dimeric iron-sulfur model to study relative energies of protonation at C, S, or Fe. Using a composite method based on coupled cluster and density matrix renormalization group energetics, we converge the relative energies of four protonated configurations with respect to basis set and correlation level. We find that accurate relative energies require large basis sets as well as a proper treatment of multireference and relativistic effects. We have also tested ten density functional approximations for these systems. Most of them give large errors in their relative energies. The best performing functional in this system is B3LYP, which gives mean absolute and maximum deviations of only 10 and 13 kJ/mol with respect to our correlated wave function estimates, respectively, comparable to the uncertainty in our correlated estimates. Our work provides benchmark results for the calibration of new approximate electronic structure methods and density functionals for these problems.
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Affiliation(s)
- Huanchen Zhai
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Seunghoon Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Zhi-Hao Cui
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lili Cao
- Department
of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department
of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Garnet Kin-Lic Chan
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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30
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Cadoux C, Maslać N, Di Luzio L, Ratcliff D, Gu W, Wagner T, Milton RD. The Mononuclear Metal-Binding Site of Mo-Nitrogenase Is Not Required for Activity. JACS AU 2023; 3:2993-2999. [PMID: 38034976 PMCID: PMC10685413 DOI: 10.1021/jacsau.3c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023]
Abstract
The biological N2-fixation process is catalyzed exclusively by metallocofactor-containing nitrogenases. Structural and spectroscopic studies highlighted the presence of an additional mononuclear metal-binding (MMB) site, which can coordinate Fe in addition to the two metallocofactors required for the reaction. This MMB site is located 15-Å from the active site, at the interface of two NifK subunits. The enigmatic function of the MMB site and its implications for metallocofactor installation, catalysis, electron transfer, or structural stability are investigated in this work. The axial ligands coordinating the additional Fe are almost universally conserved in Mo-nitrogenases, but a detailed observation of the available structures indicates a variation in occupancy or a metal substitution. A nitrogenase variant in which the MMB is disrupted was generated and characterized by X-ray crystallography, biochemistry, and enzymology. The crystal structure refined to 1.55-Å revealed an unambiguous loss of the metal site, also confirmed by an absence of anomalous signal for Fe. The position of the surrounding side chains and the overall architecture are superposable with the wild-type structure. Accordingly, the biochemical and enzymatic properties of the variant are similar to those of the wild-type nitrogenase, indicating that the MMB does not impact nitrogenase's activity and stability in vitro.
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Affiliation(s)
- Cécile Cadoux
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Nevena Maslać
- Max Planck
Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Léa Di Luzio
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Daniel Ratcliff
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Wenyu Gu
- Laboratory
of Microbial Physiology and Resource Biorecovery, School of Architecture,
Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tristan Wagner
- Max Planck
Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Ross D. Milton
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
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31
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Pellows LM, Willis MA, Ruzicka JL, Jagilinki BP, Mulder DW, Yang ZY, Seefeldt LC, King PW, Dukovic G, Peters JW. High Affinity Electrostatic Interactions Support the Formation of CdS Quantum Dot:Nitrogenase MoFe Protein Complexes. NANO LETTERS 2023; 23:10466-10472. [PMID: 37930772 DOI: 10.1021/acs.nanolett.3c03205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Nitrogenase MoFe protein can be coupled with CdS nanocrystals (NCs) to enable photocatalytic N2 reduction. The nature of interactions that support complex formation is of paramount importance in intermolecular electron transfer that supports catalysis. In this work we have employed microscale thermophoresis to examine binding interactions between 3-mercaptopropionate capped CdS quantum dots (QDs) and MoFe protein over a range of QD diameters (3.4-4.3 nm). The results indicate that the interactions are largely electrostatic, with the strength of interactions similar to that observed for the physiological electron donor. In addition, the strength of interactions is sensitive to the QD diameter, and the binding interactions are significantly stronger for QDs with smaller diameters. The ability to quantitatively assess NC protein interactions in biohybrid systems supports strategies for understanding properties and reaction parameters that are important for obtaining optimal rates of catalysis in biohybrid systems.
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Affiliation(s)
- Lauren M Pellows
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Mark A Willis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Jesse L Ruzicka
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Bhanu P Jagilinki
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Materials Science and Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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32
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Tokmina-Lukaszewska M, Huang Q, Berry L, Kallas H, Peters JW, Seefeldt LC, Raugei S, Bothner B. Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner. Commun Chem 2023; 6:254. [PMID: 37980448 PMCID: PMC10657360 DOI: 10.1038/s42004-023-01046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.
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Affiliation(s)
| | - Qi Huang
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - John W Peters
- Institute of Biological Chemistry, The University of Oklahoma, Norman, OK, USA
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA.
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33
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Quechol R, Solomon JB, Liu YA, Lee CC, Jasniewski AJ, Górecki K, Oyala P, Hedman B, Hodgson KO, Ribbe MW, Hu Y. Heterologous synthesis of the complex homometallic cores of nitrogenase P- and M-clusters in Escherichia coli. Proc Natl Acad Sci U S A 2023; 120:e2314788120. [PMID: 37871225 PMCID: PMC10622910 DOI: 10.1073/pnas.2314788120] [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: 08/26/2023] [Accepted: 09/28/2023] [Indexed: 10/25/2023] Open
Abstract
Nitrogenase is an active target of heterologous expression because of its importance for areas related to agronomy, energy, and environment. One major hurdle for expressing an active Mo-nitrogenase in Escherichia coli is to generate the complex metalloclusters (P- and M-clusters) within this enzyme, which involves some highly unique bioinorganic chemistry/metalloenzyme biochemistry that is not generally dealt with in the heterologous expression of proteins via synthetic biology; in particular, the heterologous synthesis of the homometallic P-cluster ([Fe8S7]) and M-cluster core (or L-cluster; [Fe8S9C]) on their respective protein scaffolds, which represents two crucial checkpoints along the biosynthetic pathway of a complete nitrogenase, has yet to be demonstrated by biochemical and spectroscopic analyses of purified metalloproteins. Here, we report the heterologous formation of a P-cluster-containing NifDK protein upon coexpression of Azotobacter vinelandii nifD, nifK, nifH, nifM, and nifZ genes, and that of an L-cluster-containing NifB protein upon coexpression of Methanosarcina acetivorans nifB, nifS, and nifU genes alongside the A. vinelandii fdxN gene, in E. coli. Our metal content, activity, EPR, and XAS/EXAFS data provide conclusive evidence for the successful synthesis of P- and L-clusters in a nondiazotrophic host, thereby highlighting the effectiveness of our metallocentric, divide-and-conquer approach that individually tackles the key events of nitrogenase biosynthesis prior to piecing them together into a complete pathway for the heterologous expression of nitrogenase. As such, this work paves the way for the transgenic expression of an active nitrogenase while providing an effective tool for further tackling the biosynthetic mechanism of this important metalloenzyme.
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Affiliation(s)
- Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Joseph B. Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
- Department of Chemistry, University of California, Irvine, CA92697-2025
| | - Yiling A. Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Andrew J. Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Paul Oyala
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
| | - Keith O. Hodgson
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
- Department of Chemistry, University of California, Irvine, CA92697-2025
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
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34
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Ding Y, Lee CC, Hu Y, Ribbe MM, Nagpal P, Chatterjee A. Light-driven Transformation of Carbon Monoxide into Hydrocarbons using CdS@ZnS : VFe Protein Biohybrids. CHEMSUSCHEM 2023; 16:e202300981. [PMID: 37419863 DOI: 10.1002/cssc.202300981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/09/2023]
Abstract
Enzymatic Fisher-Tropsch (FT) process catalyzed by vanadium (V)-nitrogenase can convert carbon monoxide (CO) to longer-chain hydrocarbons (>C2) under ambient conditions, although this process requires high-cost reducing agent(s) and/or the ATP-dependent reductase as electron and energy sources. Using visible light-activated CdS@ZnS (CZS) core-shell quantum dots (QDs) as alternative reducing equivalent for the catalytic component (VFe protein) of V-nitrogenase, we first report a CZS : VFe biohybrid system that enables effective photo-enzymatic C-C coupling reactions, hydrogenating CO into hydrocarbon fuels (up to C4) that can be hardly achieved with conventional inorganic photocatalysts. Surface ligand engineering optimizes molecular and opto-electronic coupling between QDs and the VFe protein, realizing high efficiency (internal quantum yield >56 %), ATP-independent, photon-to-fuel production, achieving an electron turnover number of >900, that is 72 % compared to the natural ATP-coupled transformation of CO into hydrocarbons by V-nitrogenase. The selectivity of products can be controlled by irradiation conditions, with higher photon flux favoring (longer-chain) hydrocarbon generation. The CZS : VFe biohybrids not only can find applications in industrial CO removal for high-value-added chemical production by using the cheap, renewable solar energy, but also will inspire related research interests in understanding the molecular and electronic processes in photo-biocatalytic systems.
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Affiliation(s)
- Yuchen Ding
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Markus M Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, USA
| | - Prashant Nagpal
- Sachi Bio, Louisville, CO 80027, USA
- Antimicrobial Regeneration Consortium Labs, Louisville, CO 80027, USA
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
- Sachi Bio, Louisville, CO 80027, USA
- Antimicrobial Regeneration Consortium Labs, Louisville, CO 80027, USA
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35
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Kang W. Unveiling Nature's Nitrogen-Fixing Secrets. Mol Cells 2023; 46:535-537. [PMID: 37691259 PMCID: PMC10495689 DOI: 10.14348/molcells.2023.0086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 09/12/2023] Open
Affiliation(s)
- Wonchull Kang
- Department of Chemistry and Integrative Institute of Basic Science, College of Natural Sciences, Soongsil University, Seoul 06978, Korea
- Department of Green Chemistry and Materials Engineering, Soongsil University, Seoul 06978, Korea
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36
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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: 2] [Impact Index Per Article: 2.0] [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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37
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Pang Y, Bjornsson R. The E3 state of FeMoco: one hydride, two hydrides or dihydrogen? Phys Chem Chem Phys 2023; 25:21020-21036. [PMID: 37522223 DOI: 10.1039/d3cp01106b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Hydrides are present in the reduced states of the iron-molybdenum cofactor (FeMoco) of Mo nitrogenase and are believed to play a key mechanistic role in the dinitrogen reduction reaction catalyzed by the enzyme. Two hydrides are present in the E4 state according to 1H ENDOR and there is likely a single hydride in the E2 redox state. The 2-hydride E4 state has been experimentally observed to bind N2 and it has been speculated that E3 may bind N2 as well. However, the E3 state has not been directly observed and very little is known about its molecular and electronic structure or reactivity. In recent computational studies, we have explored the energy surfaces of the E2 and E4 by QM/MM modelling, and found that the most stable hydride isomers contain bridging or partially bridging hydrides with an open protonated belt sulfide-bridge. In this work we systematically explore the energy surface of the E3 redox state, comparing single hydride and two-hydride isomers with varying coordination and bridging vs. terminal sulfhydryl groups. We also include a model featuring a triply protonated carbide. The results are only mildly dependent on the QM-region size. The three most stable E3 isomers at the r2SCAN level of theory have in common: an open belt sulfide-bridge (terminal sulfhydryl group on Fe6) and either 2 bridging hydrides (between Fe2 and Fe6), 1 bridging-1-terminal hydride (around Fe2 and Fe6) or a dihydrogen ligand bound at the Fe2 site. Analyzing the functional dependency of the results, we find that functionals previously found to predict accurate structures of spin-coupled Fe/Mo dimers and FeMoco (TPSSh, B97-D3, r2SCAN, and B3LYP*) are in generally good agreement about the stability of these 3 E3 isomers. However, B3LYP*, similar to its parent B3LYP method, predicts a triply protonated carbide isomer as the most stable isomer, an unlikely scenario in view of the lack of experimental evidence for carbide protonation occurring in reduced FeMoco states. Distinguishing further between the 3 hydride isomers is difficult and this flexible coordination nature of hydrides suggests that multiple hydride isomers could be present during experimental conditions. N2 binding was explored and resulted in geometries with 2 bridging hydrides and N2 bound to either Fe2 or Fe6 with a local low-spin state on the Fe. N2 binding is predicted to be mildly endothermic, similar to the E2 state, and it seems unlikely that the E3 state is capable of binding N2.
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Affiliation(s)
- Yunjie Pang
- College of Chemistry, Beijing Normal University, 100875, Beijing, China
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, F-38054 Grenoble, Cedex, France.
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38
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Alleman AB, Peters JW. Mechanisms for Generating Low Potential Electrons across the Metabolic Diversity of Nitrogen-Fixing Bacteria. Appl Environ Microbiol 2023; 89:e0037823. [PMID: 37154716 PMCID: PMC10231201 DOI: 10.1128/aem.00378-23] [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] [Indexed: 05/10/2023] Open
Abstract
The availability of fixed nitrogen is a limiting factor in the net primary production of all ecosystems. Diazotrophs overcome this limit through the conversion of atmospheric dinitrogen to ammonia. Diazotrophs are phylogenetically diverse bacteria and archaea that exhibit a wide range of lifestyles and metabolisms, including obligate anaerobes and aerobes that generate energy through heterotrophic or autotrophic metabolisms. Despite the diversity of metabolisms, all diazotrophs use the same enzyme, nitrogenase, to reduce N2. Nitrogenase is an O2-sensitive enzyme that requires a high amount of energy in the form of ATP and low potential electrons carried by ferredoxin (Fd) or flavodoxin (Fld). This review summarizes how the diverse metabolisms of diazotrophs utilize different enzymes to generate low potential reducing equivalents for nitrogenase catalysis. These enzymes include substrate-level Fd oxidoreductases, hydrogenases, photosystem I or other light-driven reaction centers, electron bifurcating Fix complexes, proton motive force-driven Rnf complexes, and Fd:NAD(P)H oxidoreductases. Each of these enzymes is critical for generating low potential electrons while simultaneously integrating the native metabolism to balance nitrogenase's overall energy needs. Understanding the diversity of electron transport systems to nitrogenase in various diazotrophs will be essential to guide future engineering strategies aimed at expanding the contributions of biological nitrogen fixation in agriculture.
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Affiliation(s)
- Alexander B. Alleman
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - John W. Peters
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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39
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Xu W, Zhong H, Wu Y, Qin Y, Jiao L, Sha M, Su R, Tang Y, Zheng L, Hu L, Zhang S, Beckman SP, Gu W, Yang Y, Guo S, Zhu C. Photoexcited Ru single-atomic sites for efficient biomimetic redox catalysis. Proc Natl Acad Sci U S A 2023; 120:e2220315120. [PMID: 37186847 PMCID: PMC10214184 DOI: 10.1073/pnas.2220315120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
The unsatisfactory catalytic activity of nanozymes owing to their inefficient electron transfer (ET) is the major challenge in biomimetic catalysis-related biomedical applications. Inspired by the photoelectron transfers in natural photoenzymes, we herein report a photonanozyme of single-atom Ru anchored on metal-organic frameworks (UiO-67-Ru) for achieving photoenhanced peroxidase (POD)-like activity. We demonstrate that the atomically dispersed Ru sites can realize high photoelectric conversion efficiency, superior POD-like activity (7.0-fold photoactivity enhancement relative to that of UiO-67), and good catalytic specificity. Both in situ experiments and theoretical calculations reveal that photoelectrons follow the cofactor-mediated ET process of enzymes to promote the production of active intermediates and the release of products, demonstrating more favorable thermodynamics and kinetics in H2O2 reduction. Taking advantage of the unique interaction of the Zr-O-P bond, we establish a UiO-67-Ru-based immunoassay platform for the photoenhanced detection of organophosphorus pesticides.
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Affiliation(s)
- Weiqing Xu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
| | - Hong Zhong
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA99164
| | - Yu Wu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
| | - Ying Qin
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
| | - Lei Jiao
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
| | - Meng Sha
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
| | - Rina Su
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
| | - Yinjun Tang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
| | - Lirong Zheng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing100049, P.R. China
| | - Liuyong Hu
- School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan430205, P.R. China
| | - Shipeng Zhang
- School of Materials Science and Engineering, Peking University, Beijing100871, P.R. China
| | - Scott P. Beckman
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA99164
| | - Wenling Gu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
| | - Yong Yang
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, Northwestern Polytechnical University, Xi’an710072, P.R. China
| | - Shaojun Guo
- School of Materials Science and Engineering, Peking University, Beijing100871, P.R. China
| | - Chengzhou Zhu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan430079, P.R. China
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40
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Cadoux C, Ratcliff D, Maslać N, Gu W, Tsakoumagkos I, Hoogendoorn S, Wagner T, Milton RD. Nitrogen Fixation and Hydrogen Evolution by Sterically Encumbered Mo-Nitrogenase. JACS AU 2023; 3:1521-1533. [PMID: 37234119 PMCID: PMC10207099 DOI: 10.1021/jacsau.3c00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
The substrate-reducing proteins of all nitrogenases (MoFe, VFe, and FeFe) are organized as α2ß2(γ2) multimers with two functional halves. While their dimeric organization could afford improved structural stability of nitrogenases in vivo, previous research has proposed both negative and positive cooperativity contributions with respect to enzymatic activity. Here, a 1.4 kDa peptide was covalently introduced in the proximity of the P cluster, corresponding to the Fe protein docking position. The Strep-tag carried by the added peptide simultaneously sterically inhibits electron delivery to the MoFe protein and allows the isolation of partially inhibited MoFe proteins (where the half-inhibited MoFe protein was targeted). We confirm that the partially functional MoFe protein retains its ability to reduce N2 to NH3, with no significant difference in selectivity over obligatory/parasitic H2 formation. Our experiment concludes that wild-type nitrogenase exhibits negative cooperativity during the steady state regarding H2 and NH3 formation (under Ar or N2), with one-half of the MoFe protein inhibiting turnover in the second half. This emphasizes the presence and importance of long-range (>95 Å) protein-protein communication in biological N2 fixation in Azotobacter vinelandii.
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Affiliation(s)
- Cécile Cadoux
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Daniel Ratcliff
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Nevena Maslać
- Max
Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Wenyu Gu
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ioannis Tsakoumagkos
- Department
of Organic Chemistry, National Center of Competence in Research (NCCR)
Chemical Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Sascha Hoogendoorn
- Department
of Organic Chemistry, National Center of Competence in Research (NCCR)
Chemical Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Tristan Wagner
- Max
Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Ross D. Milton
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
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41
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Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, Yang Z, Liang RR, Shi W, Zhou HC. Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis. Chem Rev 2023; 123:5347-5420. [PMID: 37043332 PMCID: PMC10853941 DOI: 10.1021/acs.chemrev.2c00879] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/13/2023]
Abstract
Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.
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Affiliation(s)
- Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Chuan Hsu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiandong Pang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- School
of Materials Science and Engineering, Tianjin Key Laboratory of Metal
and Molecule-Based Material Chemistry, Nankai
University, Tianjin 300350, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rong-Ran Liang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wei Shi
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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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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43
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Li J, Shi Y, Cheng T. Electronic coupling and electron transfer in hydrogen-bonded mixed-valence compounds. Phys Chem Chem Phys 2023. [PMID: 37158078 DOI: 10.1039/d3cp01337e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Electron transfer provided by hydrogen bonds represents a unique and highly significant area of research, as it has a crucial role to play in a wide variety of chemical and biological systems. The hydrogen-bonded mixed-valence system, in the form of donor-hydrogen bond-acceptor, provides an ideal platform for exploring thermally-induced electron transfer across this non-covalent unit. Over the past decades, ongoing progress has been made in this field. Here we critically assess some studies on the qualitative and quantitative evaluation of electronic coupling and thermal electron transfer across hydrogen bond interface. Additionally, selected experimental examples are discussed in terms of intervalence charge transfer, with particular attention paid to the proton-coupled and often overlooked proton-uncoupled electron transfer pathway in hydrogen-bonded mixed-valence systems. We further highlight the major limitations of this research area and suggest potential directions for future exploration.
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Affiliation(s)
- Juanjuan Li
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, P. R. China
| | - Yuqing Shi
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, P. R. China
| | - Tao Cheng
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, P. R. China
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Yu C, Yang W, Yang L, Ye L, Sun R, Gu T, Ying X, Wang M, Tang R, Fan S, Yao S. Synergistic Effect of Magneto-Mechanical Bioengineered Stem Cells and Magnetic Field to Alleviate Osteoporosis. ACS APPLIED MATERIALS & INTERFACES 2023; 15:19976-19988. [PMID: 37058439 DOI: 10.1021/acsami.3c01139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Therapeutic bioengineering based on stem cell therapy holds great promise in biomedical applications. However, the application of this treatment is limited in orthopedics because of their poor survival, weak localization, and low cell retention. In this work, magneto-mechanical bioengineered cells consisting of magnetic silica nanoparticles (MSNPs) and mesenchymal stem cells (MSCs) are prepared to alleviate osteoporosis. The magneto-mechanical bioengineered MSCs with spatial localization, cell retention, and directional tracking capabilities could be mediated by a guided magnetic field (MF) in vitro and in vivo. Furthermore, high uptake rates of the MSNPs ensure the efficient construction of magnetically controlled MSCs within 2 h. In conjunction with external MF, the magneto-mechanical bioengineered MSCs have the potential for the activation of the YAP/β-catenin signaling pathway, which could further promote osteogenesis, mineralization, and angiogenesis. The synergistic effects of MSNPs and guided MF could also decline bone resorption to rebalance bone metabolism in bone loss diseases. In vivo experiments confirm that the functional MSCs and guided MF could effectively alleviate postmenopausal osteoporosis, and the bone mass of the treated osteoporotic bones by using the bioengineered cells for 6 weeks is nearly identical to that of the healthy ones. Our results provide a new avenue for osteoporosis management and treatment, which contribute to the future advancement of magneto-mechanical bioengineering and treatment.
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Affiliation(s)
- Congcong Yu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
| | - Wentao Yang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
| | - Linjun Yang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
| | - Lin Ye
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
| | - Rongtai Sun
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
| | - Tianyuan Gu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
| | - Xiaozhang Ying
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
- Department of Orthopaedics, Zhejiang Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou 310003, Zhejiang, China
| | - Monian Wang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
| | - Ruikang Tang
- Center for Biomaterials and Biopathways, Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Shunwu Fan
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
| | - Shasha Yao
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration, Translational Research of Zhejiang Province, Hangzhou 310016, Zhejiang, China
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45
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Kokubo Y, Tsuzuki K, Sugiura H, Yomura S, Wasada-Tsutsui Y, Ozawa T, Yanagisawa S, Kubo M, Takeyama T, Yamaguchi T, Shimazaki Y, Kugimiya S, Masuda H, Kajita Y. Syntheses, Characterizations, Crystal Structures, and Protonation Reactions of Dinitrogen Chromium Complexes Supported with Triamidoamine Ligands. Inorg Chem 2023; 62:5320-5333. [PMID: 36972224 DOI: 10.1021/acs.inorgchem.2c01561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
A novel dinitrogen-dichromium complex, [{Cr(LBn)}2(μ-N2)] (1), has been prepared from reaction of CrCl3 with a lithiated triamidoamine ligand (Li3LBn) under dinitrogen. The X-ray crystal structure analysis of 1 revealed that it is composed of two independent dimeric Cr complexes bridged by N2 in the unit cell. The bridged N-N bond lengths (1.188(4) and 1.185(7) Å) were longer than the free dinitrogen molecule. The elongations of N-N bonds in 1 were also supported by the fact that the ν(N-N) stretching vibration at 1772 cm-1 observed in toluene is smaller than the free N2. Complex 1 was identified to be a 5-coordinated high spin Cr(IV) complex by Cr K-edge XANES measurement. The 1H NMR spectrum and temperature dependent magnetic susceptibility of 1 indicated that complex 1 is in the S = 1 ground state, in which two Cr(IV) ions and unpaired electron spins of the bridging N22- ligand are strongly antiferromagnetically coupled. Reaction of complex 1 with 2.3 equiv of Na or K gave chromium complexes with N2 between the Cr ion and the respective alkali metal ion, [{CrNa(LBn)(N2)(Et2O)}2] (2) and [{CrK(LBn)(N2)}4(Et2O)2] (3), respectively. Furthermore, the complexes 2 and 3 reacted with 15-crown-5 and 18-crown-6 to form the respective crown-ether adducts, [CrNa(LBn)(N2)(15-crown-5)] (4) and [CrK(LBn)(N2)(18-crown-6)] (5). The XANES measurements of complexes 2, 3, 4, and 5 revealed that they are high spin Cr(IV) complexes like complex 1. All complexes reacted with a reducing agent and a proton source to form NH3 and/or N2H4. The yields of these products in the presence of K+ were higher than those in the presence of Na+. The electronic structures and binding properties of 1, 2, 3, 4, and 5 were evaluated and discussed based on their DFT calculations.
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Yang ZY, Badalyan A, Hoffman BM, Dean DR, Seefeldt LC. The Fe Protein Cycle Associated with Nitrogenase Catalysis Requires the Hydrolysis of Two ATP for Each Single Electron Transfer Event. J Am Chem Soc 2023; 145:5637-5644. [PMID: 36857604 DOI: 10.1021/jacs.2c09576] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
A central feature of the current understanding of dinitrogen (N2) reduction by the enzyme nitrogenase is the proposed coupling of the hydrolysis of two ATP, forming two ADP and two Pi, to the transfer of one electron from the Fe protein component to the MoFe protein component, where substrates are reduced. A redox-active [4Fe-4S] cluster associated with the Fe protein is the agent of electron delivery, and it is well known to have a capacity to cycle between a one-electron-reduced [4Fe-4S]1+ state and an oxidized [4Fe-4S]2+ state. Recently, however, it has been shown that certain reducing agents can be used to further reduce the Fe protein [4Fe-4S] cluster to a super-reduced, all-ferrous [4Fe-4S]0 state that can be either diamagnetic (S = 0) or paramagnetic (S = 4). It has been proposed that the super-reduced state might fundamentally alter the existing model for nitrogenase energy utilization by the transfer of two electrons per Fe protein cycle linked to hydrolysis of only two ATP molecules. Here, we measure the number of ATP consumed for each electron transfer under steady-state catalysis while the Fe protein cluster is in the [4Fe-4S]1+ state and when it is in the [4Fe-4S]0 state. Both oxidation states of the Fe protein are found to operate by hydrolyzing two ATP for each single-electron transfer event. Thus, regardless of its initial redox state, the Fe protein transfers only one electron at a time to the MoFe protein in a process that requires the hydrolysis of two ATP.
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Affiliation(s)
- Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Artavazd Badalyan
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Brian M Hoffman
- Departments of Chemistry and Molecular Biosciences, 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
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Montoya-Castillo A, Markland TE. A derivation of the conditions under which bosonic operators exactly capture fermionic structure and dynamics. J Chem Phys 2023; 158:094112. [PMID: 36889969 DOI: 10.1063/5.0138664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The dynamics of many-body fermionic systems are important in problems ranging from catalytic reactions at electrochemical surfaces to transport through nanojunctions and offer a prime target for quantum computing applications. Here, we derive the set of conditions under which fermionic operators can be exactly replaced by bosonic operators that render the problem amenable to a large toolbox of dynamical methods while still capturing the correct dynamics of n-body operators. Importantly, our analysis offers a simple guide on how one can exploit these simple maps to calculate nonequilibrium and equilibrium single- and multi-time correlation functions essential in describing transport and spectroscopy. We use this to rigorously analyze and delineate the applicability of simple yet effective Cartesian maps that have been shown to correctly capture the correct fermionic dynamics in select models of nanoscopic transport. We illustrate our analytical results with exact simulations of the resonant level model. Our work provides new insights as to when one can leverage the simplicity of bosonic maps to simulate the dynamics of many-electron systems, especially those where an atomistic representation of nuclear interactions becomes essential.
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Affiliation(s)
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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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: 12] [Impact Index Per Article: 12.0] [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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Taut J, Chambron J, Kersting B. Fifty Years of Inorganic Biomimetic Chemistry: From the Complexation of Single Metal Cations to Polynuclear Metal Complexes by Multidentate Thiolate Ligands. Eur J Inorg Chem 2023. [DOI: 10.1002/ejic.202200739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Josef Taut
- Institut für Anorganische Chemie Universität Leipzig Johannisallee 29 04103 Leipzig Germany
- Institut de Chimie de Strasbourg UMR 7177 CNRS-Université de Strasbourg 1, rue Blaise Pascal 67008 Strasbourg France
| | - Jean‐Claude Chambron
- Institut de Chimie de Strasbourg UMR 7177 CNRS-Université de Strasbourg 1, rue Blaise Pascal 67008 Strasbourg France
| | - Berthold Kersting
- Institut für Anorganische Chemie Universität Leipzig Johannisallee 29 04103 Leipzig Germany
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50
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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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