1
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Ito Y, Yoshidome D, Hidaka M, Araki Y, Ito K, Kosono S, Nishiyama M. Improvement of the nitrogenase activity in Escherichia coli that expresses the nitrogen fixation-related genes from Azotobacter vinelandii. Biochem Biophys Res Commun 2024; 728:150345. [PMID: 38971001 DOI: 10.1016/j.bbrc.2024.150345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The transfer of nitrogen fixation (nif) genes from diazotrophs to non-diazotrophic hosts is of increasing interest for engineering biological nitrogen fixation. A recombinant Escherichia coli strain expressing Azotobacter vinelandii 18 nif genes (nifHDKBUSVQENXYWZMF, nifiscA, and nafU) were previously constructed and showed nitrogenase activity. In the present study, we constructed several E. coli strain derivatives in which all or some of the 18 nif genes were additionally integrated into the fliK locus of the chromosome in various combinations. E. coli derivatives with the chromosomal integration of nifiscA, nifU, and nifS, which are involved in the biosynthesis of the [4Fe-4S] cluster of dinitrogenase reductase, exhibited enhanced nitrogenase activity. We also revealed that overexpression of E. coli fldA and ydbK, which encode flavodoxin and flavodoxin-reducing enzyme, respectively, enhanced nitrogenase activity, likely by facilitating electron transfer to dinitrogenase reductase. The additional expression of nifM, putatively involved in maturation of dinitrogenase reductase, further enhanced nitrogenase activity and the amount of soluble NifH. By combining these factors, we successfully improved nitrogenase activity 10-fold.
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Affiliation(s)
- Yusuke Ito
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Daisuke Yoshidome
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Makoto Hidaka
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yasuko Araki
- Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Kotaro Ito
- Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Saori Kosono
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Nishiyama
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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2
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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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3
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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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4
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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. [PMID: 38696373 DOI: 10.1111/febs.17148] [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: 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 - $$ {\mathrm{AlF}}_4^{-} $$ 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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5
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Vallières C, Benoit O, Guittet O, Huang ME, Lepoivre M, Golinelli-Cohen MP, Vernis L. Iron-sulfur protein odyssey: exploring their cluster functional versatility and challenging identification. Metallomics 2024; 16:mfae025. [PMID: 38744662 PMCID: PMC11138216 DOI: 10.1093/mtomcs/mfae025] [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: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Iron-sulfur (Fe-S) clusters are an essential and ubiquitous class of protein-bound prosthetic centers that are involved in a broad range of biological processes (e.g. respiration, photosynthesis, DNA replication and repair and gene regulation) performing a wide range of functions including electron transfer, enzyme catalysis, and sensing. In a general manner, Fe-S clusters can gain or lose electrons through redox reactions, and are highly sensitive to oxidation, notably by small molecules such as oxygen and nitric oxide. The [2Fe-2S] and [4Fe-4S] clusters, the most common Fe-S cofactors, are typically coordinated by four amino acid side chains from the protein, usually cysteine thiolates, but other residues (e.g. histidine, aspartic acid) can also be found. While diversity in cluster coordination ensures the functional variety of the Fe-S clusters, the lack of conserved motifs makes new Fe-S protein identification challenging especially when the Fe-S cluster is also shared between two proteins as observed in several dimeric transcriptional regulators and in the mitoribosome. Thanks to the recent development of in cellulo, in vitro, and in silico approaches, new Fe-S proteins are still regularly identified, highlighting the functional diversity of this class of proteins. In this review, we will present three main functions of the Fe-S clusters and explain the difficulties encountered to identify Fe-S proteins and methods that have been employed to overcome these issues.
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Affiliation(s)
- Cindy Vallières
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Orane Benoit
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Olivier Guittet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Meng-Er Huang
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Michel Lepoivre
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Marie-Pierre Golinelli-Cohen
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Laurence Vernis
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
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6
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Zhai H, Larsson HR, Lee S, Cui ZH, Zhu T, Sun C, Peng L, Peng R, Liao K, Tölle J, Yang J, Li S, Chan GKL. Block2: A comprehensive open source framework to develop and apply state-of-the-art DMRG algorithms in electronic structure and beyond. J Chem Phys 2023; 159:234801. [PMID: 38108484 DOI: 10.1063/5.0180424] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
block2 is an open source framework to implement and perform density matrix renormalization group and matrix product state algorithms. Out-of-the-box it supports the eigenstate, time-dependent, response, and finite-temperature algorithms. In addition, it carries special optimizations for ab initio electronic structure Hamiltonians and implements many quantum chemistry extensions to the density matrix renormalization group, such as dynamical correlation theories. The code is designed with an emphasis on flexibility, extensibility, and efficiency and to support integration with external numerical packages. Here, we explain the design principles and currently supported features and present numerical examples in a range of applications.
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Affiliation(s)
- Huanchen Zhai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Henrik R Larsson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Zhi-Hao Cui
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Tianyu Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Chong Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Linqing Peng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Ruojing Peng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Ke Liao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Johannes Tölle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Junjie Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Shuoxue Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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7
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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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8
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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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9
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Einsle O. Catalysis and structure of nitrogenases. Curr Opin Struct Biol 2023; 83:102719. [PMID: 37802004 DOI: 10.1016/j.sbi.2023.102719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
In providing bioavailable nitrogen as building blocks for all classes of biomacromolecules, biological nitrogen fixation is an essential process for all organismic life. Only a single enzyme, nitrogenase, performs this task at ambient conditions and with ATP as an energy source. The assembly of the complex iron-sulfur enzyme nitrogenase and its catalytic mechanism remains a matter of intense study. Recent progress in the structural analysis of the three known isoforms of nitrogenase-differentiated primarily by the heterometal in their active site cofactor-has revealed a degree of structural plasticity of these clusters that suggest two distinct binding sites for substrates and reaction intermediates. A mechanistic proposal based on this finding integrates most of the available experimental data. Furthermore, the first applications of high-resolution cryo-electron microscopy have highlighted further dynamic conformational changes. Structures obtained under turnover conditions support the proposed alternating half-site reactivity in the C2-symmetric nitrogenase complex.
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Affiliation(s)
- Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.
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10
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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: 2] [Impact Index Per Article: 2.0] [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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11
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Vansuch G, Mulder DW, Chica B, Ruzicka JL, Yang ZY, Pellows LM, Willis MA, Brown KA, Seefeldt LC, Peters JW, Dukovic G, King PW. Cryo-annealing of Photoreduced CdS Quantum Dot-Nitrogenase MoFe Protein Complexes Reveals the Kinetic Stability of the E 4(2N2H) Intermediate. J Am Chem Soc 2023; 145:21165-21169. [PMID: 37729189 PMCID: PMC10557137 DOI: 10.1021/jacs.3c06832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Indexed: 09/22/2023]
Abstract
A critical step in the mechanism of N2 reduction to 2NH3 catalyzed by the enzyme nitrogenase is the reaction of the four-electron/four-proton reduced intermediate state of the active-site FeMo-cofactor (E4(4H)). This state is a junction in the catalytic mechanism, either relaxing by the reaction of a metal bound Fe-hydride with a proton forming H2 or going forward with N2 binding coupled to the reductive elimination (re) of two Fe-hydrides as H2 to form the E4(2N2H) state. E4(2N2H) can relax to E4(4H) by the oxidative addition (oa) of H2 and release of N2 or can be further reduced in a series of catalytic steps to release 2NH3. If the H2 re/oa mechanism is correct, it requires that oa of H2 be associative with E4(2N2H). In this report, we have taken advantage of CdS quantum dots in complex with MoFe protein to achieve photodriven electron delivery in the frozen state, with cryo-annealing in the dark, to reveal details of the E-state species and to test the stability of E4(2N2H). Illumination of frozen CdS:MoFe protein complexes led to formation of a population of reduced intermediates. Electron paramagnetic resonance spectroscopy identified E-state signals including E2 and E4(2N2H), as well as signals suggesting the formation of E6 or E8. It is shown that in the frozen state when pN2 is much greater than pH2, the E4(2N2H) state is kinetically stable, with very limited forward or reverse reaction rates. These results establish that the oa of H2 to the E4(2N2H) state follows an associative reaction mechanism.
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Affiliation(s)
- Gregory
E. Vansuch
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W. Mulder
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Bryant Chica
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jesse L. Ruzicka
- Department
of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Zhi-Yong Yang
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322, United States
| | - 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
| | - Katherine A. Brown
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Lance C. Seefeldt
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322, 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
| | - 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, University
of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Paul W. King
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80303, United States
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12
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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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13
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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14
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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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15
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Xuan J, He L, Wen W, Feng Y. Hydrogenase and Nitrogenase: Key Catalysts in Biohydrogen Production. Molecules 2023; 28:molecules28031392. [PMID: 36771068 PMCID: PMC9919214 DOI: 10.3390/molecules28031392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Hydrogen with high energy content is considered to be a promising alternative clean energy source. Biohydrogen production through microbes provides a renewable and immense hydrogen supply by utilizing raw materials such as inexhaustible natural sunlight, water, and even organic waste, which is supposed to solve the two problems of "energy supply and environment protection" at the same time. Hydrogenases and nitrogenases are two classes of key enzymes involved in biohydrogen production and can be applied under different biological conditions. Both the research on enzymatic catalytic mechanisms and the innovations of enzymatic techniques are important and necessary for the application of biohydrogen production. In this review, we introduce the enzymatic structures related to biohydrogen production, summarize recent enzymatic and genetic engineering works to enhance hydrogen production, and describe the chemical efforts of novel synthetic artificial enzymes inspired by the two biocatalysts. Continual studies on the two types of enzymes in the future will further improve the efficiency of biohydrogen production and contribute to the economic feasibility of biohydrogen as an energy source.
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Affiliation(s)
- Jinsong Xuan
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
- Correspondence: (J.X.); (Y.F.)
| | - Lingling He
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Wen Wen
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.X.); (Y.F.)
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16
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Ke N, Kumka JE, Fang M, Weaver B, Burstyn JN, Bauer CE. RedB, a Member of the CRP/FNR Family, Functions as a Transcriptional Redox Brake. Microbiol Spectr 2022; 10:e0235322. [PMID: 36106751 PMCID: PMC9603854 DOI: 10.1128/spectrum.02353-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023] Open
Abstract
Phylogenetic and sequence similarity network analyses of the CRP (cyclic AMP receptor protein)/FNR (fumarate and nitrate reductase regulatory protein) family of transcription factors indicate the presence of numerous subgroups, many of which have not been analyzed. Five homologs of the CRP/FNR family are present in the Rhodobacter capsulatus genome. One is a member of a broadly disseminated, previously uncharacterized CRP/FNR family subgroup encoded by the gene rcc01561. In this study, we utilize mutational disruption, transcriptome sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) to determine the role of RCC01561 in regulating R. capsulatus physiology. This analysis shows that a mutant strain disrupted for rcc01561 exhibits altered expression of 451 genes anaerobically. A detailed analysis of the affected loci shows that RCC01561 represses photosynthesis and favors catabolism over anabolism and the use of the Entner-Doudoroff shunt and glycolysis over that of the tricarboxylic acid (TCA) cycle to limit NADH and ATP formation. This newly characterized CRP/FNR family member with a predominant role in reducing the production of reducing potential and ATP is given the nomenclature RedB as it functions as an energy and redox brake. Beyond limiting energy production, RedB also represses the expression of numerous genes involved in protein synthesis, including those involved in translation initiation, tRNA synthesis and charging, and amino acid biosynthesis. IMPORTANCE CRP and FNR are well-characterized members of the CRP/FNR family of regulatory proteins that function to maximize cellular energy production. In this study, we identify several new subgroups of the CRP/FNR family, many of which have not yet been characterized. Using Rhodobacter capsulatus as a model, we have mutationally disrupted the gene rcc01561, which codes for a transcription factor that is a member of a unique subgroup of the CRP/FNR family. Transcriptomic analysis shows that the disruption of rcc01561 leads to the altered expression of 451 genes anaerobically. Analysis of these regulated genes indicates that RCC01561 has a novel role in limiting cellular energy production. To our knowledge, this is first example of a member of the CRP/FNR family that functions as a brake on cellular energy production.
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Affiliation(s)
- Nijia Ke
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Joseph E. Kumka
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Mingxu Fang
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Brian Weaver
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Carl E. Bauer
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
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17
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Cao J, Yin W, Zhang Q, Yao Y, Cao J, Wei X. Intrinsic anion vacancy of Mo6X6 (X = S, Se, Te) nanowires as a promising nitrogen fixation catalysis: A first-principles study. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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19
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He J, Wei J, Xu G, Chen XD. Stepwise Construction of Mo-Fe-S Clusters Using a LEGO Strategy. Inorg Chem 2022; 61:4150-4158. [PMID: 35200007 DOI: 10.1021/acs.inorgchem.1c03998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rational synthesis of iron-sulfur clusters with excellent control of the core ligands has been a significant challenge in biomimetic chemistry. In this work, the rational construction of versatile Mo-Fe-S cubane clusters was realized using a LEGO strategy. (LEGO is a line of plastic construction toys consisting of various interlocking plastic bricks which can be assembled and connected in different ways to construct versatile objects. Herein we use "LEGO strategy" as an analogy for the stepwise synthetic methodology, and we use "brick" to represent a corner atom of the cubane structure.) Through careful synthetic control, the ⟨Fe⟩, ⟨S⟩, and ⟨Cl⟩ bricks were mounted piece-by-piece onto the basic ⟨MoS3⟩ frame to stepwise construct the incomplete cubane core ⟨MoFe2S3Cl⟩ and the complete cubane core ⟨MoFe3S3Cl⟩. The significantly elongated Fe-Cl bonds for the bridging chlorides in the ⟨MoFe2S3Cl⟩ and ⟨MoFe3S3Cl⟩ cores permit ligand metatheses to introduce 2p donors at the bridging sites, which used to be a challenge in traditional iron-sulfur chemistry. Therefore, in subsequent controlled reactions, the bridging ⟨Cl⟩ bricks of the ⟨MoFe2S3Cl⟩ and ⟨MoFe3S3Cl⟩ frames could be easily replaced by ⟨N⟩ , ⟨O⟩, or ⟨S⟩ bricks to generate the ⟨MoFe2S3N⟩, ⟨MoFe2S3O⟩, ⟨MoFe3S3N⟩, and ⟨MoFe3S4⟩ cluster cores, demonstrating more choices for the LEGO synthetic strategy. The series of Mo-Fe-S clusters and their derivatives, together with related synthetic strategies, offers a good platform and methodology for biomimetic chemistry in relation to nitrogenase, especially the FeMo cofactor.
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Affiliation(s)
- Juan He
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Jia Wei
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Gan Xu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xu-Dong Chen
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, Jiangsu, China.,State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093, Jiangsu, China
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20
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Liu H, Wang P, Jiang J, Cheng G, Wu T, Zhang Y. Construction of stable Mo xS y/CeO 2 heterostructures for the electrocatalytic hydrogen evolution reaction. Phys Chem Chem Phys 2022; 24:4891-4898. [PMID: 35137755 DOI: 10.1039/d1cp05466j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unique structures of polynuclear MoxSy clusters make it possible to maximize the number of their active sites and for them to be good candidates for HER catalysts. An appropriate support is highly necessary not only to avoid the desorption of MoxSy clusters in a working environment, but also to improve their HER activity. Our work here shows that the CeO2 support could provide strong support for interaction with various MoxSy clusters and the formed MoxSy/CeO2 hetero-structures also have modest ΔGH* for the HER. The electronic features of MoxSy clusters are regulated by the CeO2 support, which leads to charge redistribution on edge atoms and plays a key role in H adsorption. Our studies provide instructive predictions on efficient candidates of molybdenum-sulfur based catalysts for the HER.
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Affiliation(s)
- Hongxian Liu
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, China.
| | - Pai Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, China.
| | - Jinxiu Jiang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, China.
| | - Gang Cheng
- Institute of Energy Research, Jiangxi Academy of Sciences, Nanchang, P. R. China
| | - Tongwei Wu
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, China.
| | - Yanning Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, China.
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21
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Silva PJ, Cheng Q. An Alternative Proposal for the Reaction Mechanism of Light-Dependent Protochlorophyllide Oxidoreductase. ACS Catal 2022; 12:2589-2605. [PMID: 36568346 PMCID: PMC9778109 DOI: 10.1021/acscatal.1c05351] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Light-dependent protochlorophyllide oxidoreductase is one of the few known enzymes that require a quantum of light to start their catalytic cycle. Upon excitation, it uses NADPH to reduce the C17-C18 in its substrate (protochlorophyllide) through a complex mechanism that has heretofore eluded precise determination. Isotopic labeling experiments have shown that the hydride-transfer step is very fast, with a small barrier close to 9 kcal mol-1, and is followed by a proton-transfer step, which has been postulated to be the protonation of the product by the strictly conserved Tyr189 residue. Since the structure of the enzyme-substrate complex has not yet been experimentally determined, we first used modeling techniques to discover the actual substrate binding mode. Two possible binding modes were found, both yielding stable binding (as ascertained through molecular dynamics simulations) but only one of which placed the critical C17=C18 bond consistently close to the NADPH pro-S hydrogen and to Tyr189. This binding pose was then used as a starting point for the testing of previous mechanistic proposals using time-dependent density functional theory. The quantum-chemical computations clearly showed that such mechanisms have prohibitively high activation energies. Instead, these computations showed the feasibility of an alternative mechanism initiated by excited-state electron transfer from the key Tyr189 to the substrate. This mechanism appears to agree with the extant experimental data and reinterprets the final protonation step as a proton transfer to the active site itself rather than to the product, aiming at regenerating it for another round of catalysis.
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Affiliation(s)
- Pedro J. Silva
- FP-I3ID/Fac.
de Ciências da Saúde, Universidade
Fernando Pessoa, 4200-150 Porto, Portugal,UCIBIO@REQUIMTE,
BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal,
| | - Qi Cheng
- Department
of Biochemistry, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071000, China,State
Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei 071000, China,
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22
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A theoretical study on molybdenum and sulfur co-doped graphene for electrocatalytic nitrogen reduction. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2021.112048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Bigness A, Vaddypally S, Zdilla MJ, Mendoza-Cortes JL. Ubiquity of cubanes in bioinorganic relevant compounds. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Meirovich MM, Bachar O, Nandi R, Amdursky N, Yehezkeli O. Tailoring Quantum Dot Sizes for Optimal Photoinduced Catalytic Activation of Nitrogenase. CHEMSUSCHEM 2021; 14:5410-5416. [PMID: 34612599 DOI: 10.1002/cssc.202101676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Many efforts have been directed towards elucidating the nitrogenase structure, its biocatalytic activity, and methods to artificially activate it by external stimuli. Here, we investigated how semiconductor nanoparticles (NPs) with sizes ranging between 2.3-3.5 nm form nano-biohybrids with the nitrogenase enzyme and enable its photoinduced biocatalytic activity. We examined two homogenously synthesized quantum dots (QDs), CdS, CdSe, and two nitrogenase variants, the wild-type and a cysteine-mutated. We show that the cysteine-mutated variant does not enhance the hydrogen generation amounts, as compared with the wild type. Nevertheless, we show that the 2.3 nm-sized CdSe NPs facilitate an eightfold increase compared with larger CdSe NPs. The obtained results were investigated using electrochemical techniques, transmission electron microscopy, and further confirmed by time-resolved spectroscopic measurements, which allow us to determine the electron tranfer rate constant (kET ) of the different configurations.
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Affiliation(s)
- Matan M Meirovich
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Oren Bachar
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Ramesh Nandi
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Nadav Amdursky
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Omer Yehezkeli
- Department 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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25
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Martín-Fernández C, Harvey JN. On the Use of Normalized Metrics for Density Sensitivity Analysis in DFT. J Phys Chem A 2021; 125:4639-4652. [PMID: 34018759 DOI: 10.1021/acs.jpca.1c01290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the past years, there has been a discussion about how the errors in density functional theory might be related to errors in the self-consistent densities obtained from different density functional approximations. This, in turn, brings up the discussion about the different ways in which we can measure such errors and develop metrics that assess the sensitivity of calculated energies to changes in the density. It is important to realize that there cannot be a unique metric in order to look at this density sensitivity, simultaneously needing size-extensive and size-intensive metrics. In this study, we report two metrics that are widely applicable to any density functional approximation. We also show how they can be used to classify different chemical systems of interest with respect to their sensitivity to small variations in the density.
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Affiliation(s)
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan, 200F 3001 Leuven, Belgium
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26
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Xue L, Xu G, Wang Z, Chen XD. Nitride-incorporated W-Fe-S double cubane clusters: terminal ligand substitutions and redox behaviors. Dalton Trans 2021; 50:6840-6847. [PMID: 33912872 DOI: 10.1039/d1dt00414j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural mimicking of the nitrogenase FeMo cofactor has long been a challenge in synthetic inorganic chemistry and bioinorganic chemistry. This already very tough task had become even harder after the discovery of an interstitial light atom, which was later evidenced to be carbide. From a synthetic point of view, to introduce such a 2p atom into the core of a Fe-S cluster would have to overcome the coordination competition from overwhelming sulfide ligands. Recently, we have reported a controlled synthetic strategy named redox metathesis based on template-assisted structure design, and have successfully synthesized a couple of nitride-incorporated edge-bridged double cubane (N-EBDC) W-Fe-S clusters. In this work, we have systematically studied the terminal ligand substitutions of heteroleptic N-EBDC clusters, utilizing ethanethiolate, thiophenolate, p-thiocresolate, azide, and methoxide to replace the terminally bound chloride ligands. Structural analysis of this family of N-EBDC clusters reveals that different terminal ligands affect the fine structures of the cluster cores at different levels. Further studies by cyclic voltammetry indicate that these N-EBDC clusters with distinct terminal ligands exhibit different redox behaviors, furnishing in-depth information on the electronic structure of these clusters potentially related to their reactivity. This study provided useful information for the investigation of nitrogenase related Fe-S clusters toward structural and functional mimicking of the nitrogenase FeMo cofactor.
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Affiliation(s)
- Lian Xue
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, Jiangsu, China.
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27
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Stennett CR, Fettinger JC, Power PP. Low-Coordinate Iron Chalcogenolates and Their Complexes with Diethyl Ether and Ammonia. Inorg Chem 2021; 60:6712-6720. [PMID: 33848423 DOI: 10.1021/acs.inorgchem.1c00539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Treatment of Fe{N(SiMe3)2}2 with 2 equiv of the appropriate phenol or thiol affords the dimers {Fe(OC6H2-2,6-But2-4-Me)2}2 (1) and {Fe(OC6H3-2,6-But2)2}2 (2) or the monomeric Fe{SC6H3-2,6-(C6H3-2,6-Pri2)2}2 (3) in moderate to excellent yields. Recrystallization of 1 and 2 from diethyl ether gives the corresponding three-coordinate ether complexes Fe(OC6H3-2,6-But2-4-Me)2(OEt2) (4) and Fe(OC6H3-2,6-But2)2(OEt2) (5). In contrast, no diethyl ether complex is formed by the dithiolate 3. The 1H NMR spectra of 4 and 5 show equilibria between the ether complexes and the base-free dimers. A comparison of these spectra with those of the dimeric 1 and 2 allows an unambiguous assignment of the paramagnetically shifted signals. Treatment of 1 with excess ammonia gives the tetrahedral diammine Fe(OC6H2-2,6-But2-4-Me)2(NH3)2 (6). Ammonia is strongly coordinated in 6, with no apparent loss of ammine ligand either in solution or upon heating under low pressure. In contrast, significantly weaker ammonia coordination is observed when dithiolate 3 is treated with excess ammonia, which gives the diammine Fe{SC6H3-2,6-(2,6-Pri2-C6H3)2}2(NH3)2 (7). Complex 7 readily loses ammonia either in solution or under reduced pressure to give the monoammine complex Fe{SC6H3-2,6-(2,6-Pri2-C6H3)2}2(NH3) (8). The weak binding of ammonia by iron thiolate 7 reflects the likely behavior of the proposed iron-sulfur active site in nitrogenases, where release of ammonia is required to close the catalytic cycle.
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Affiliation(s)
- Cary R Stennett
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - James C Fettinger
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Philip P Power
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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28
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Mechanical coupling in the nitrogenase complex. PLoS Comput Biol 2021; 17:e1008719. [PMID: 33661889 PMCID: PMC7963043 DOI: 10.1371/journal.pcbi.1008719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 03/16/2021] [Accepted: 01/18/2021] [Indexed: 11/19/2022] Open
Abstract
The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.
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29
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Aasfar A, Bargaz A, Yaakoubi K, Hilali A, Bennis I, Zeroual Y, Meftah Kadmiri I. Nitrogen Fixing Azotobacter Species as Potential Soil Biological Enhancers for Crop Nutrition and Yield Stability. Front Microbiol 2021; 12:628379. [PMID: 33717018 PMCID: PMC7947814 DOI: 10.3389/fmicb.2021.628379] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Biological nitrogen fixation (BNF) refers to a microbial mediated process based upon an enzymatic "Nitrogenase" conversion of atmospheric nitrogen (N2) into ammonium readily absorbable by roots. N2-fixing microorganisms collectively termed as "diazotrophs" are able to fix biologically N2 in association with plant roots. Specifically, the symbiotic rhizobacteria induce structural and physiological modifications of bacterial cells and plant roots into specialized structures called nodules. Other N2-fixing bacteria are free-living fixers that are highly diverse and globally widespread in cropland. They represent key natural source of nitrogen (N) in natural and agricultural ecosystems lacking symbiotic N fixation (SNF). In this review, the importance of Azotobacter species was highlighted as both important free-living N2-fixing bacteria and potential bacterial biofertilizer with proven efficacy for plant nutrition and biological soil fertility. In addition, we described Azotobacter beneficial plant promoting traits (e.g., nutrient use efficiency, protection against phytopathogens, phytohormone biosynthesis, etc.). We shed light also on the agronomic features of Azotobacter that are likely an effective component of integrated plant nutrition strategy, which contributes positively to sustainable agricultural production. We pointed out Azotobacter based-biofertilizers, which possess unique characteristics such as cyst formation conferring resistance to environmental stresses. Such beneficial traits can be explored profoundly for the utmost aim to research and develop specific formulations based on inoculant Azotobacter cysts. Furthermore, Azotobacter species still need to be wisely exploited in order to address specific agricultural challenges (e.g., nutrient deficiencies, biotic and abiotic constraints) taking into consideration several variables including their biological functions, synergies and multi-trophic interactions, and biogeography and abundance distribution.
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Affiliation(s)
- Abderrahim Aasfar
- Green Biotechnology Laboratory, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Centre, Rabat, Morocco.,Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Adnane Bargaz
- AgroBioSciences-Microbiome, Laboratory of Plant-Microbe Interactions, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Kaoutar Yaakoubi
- Green Biotechnology Laboratory, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Centre, Rabat, Morocco
| | - Abderraouf Hilali
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Iman Bennis
- Green Biotechnology Laboratory, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Centre, Rabat, Morocco
| | | | - Issam Meftah Kadmiri
- Green Biotechnology Laboratory, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Centre, Rabat, Morocco.,AgroBioSciences-Microbiome, Laboratory of Plant-Microbe Interactions, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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30
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Parison K, Gies-Elterlein J, Trncik C, Einsle O. Expression, Isolation, and Characterization of Vanadium Nitrogenase from Azotobacter vinelandii. Methods Mol Biol 2021; 2353:97-121. [PMID: 34292546 DOI: 10.1007/978-1-0716-1605-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitrogenases are the sole enzymes known to mediate biological nitrogen fixation, an essential process for sustaining life on earth. Among the three known variants, molybdenum nitrogenase is the best-studied to date. Recent work on the alternative vanadium nitrogenase provided important insights into the mechanism of nitrogen fixation since this enzyme differs from its molybdenum counterpart in some important aspects. Here, we present a protocol to obtain unmodified vanadium nitrogenase in high yield and purity from the paradigmatic diazotroph Azotobacter vinelandii, including procedures for cell cultivation, purification, and protein characterization.
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Affiliation(s)
- Katharina Parison
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | - Christian Trncik
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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31
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Zhai DD, Xie SJ, Xia Y, Fang HY, Shi ZJ. Silylamido supported dinitrogen heterobimetallic complexes: syntheses and their catalytic ability. Natl Sci Rev 2020; 8:nwaa290. [PMID: 34987834 PMCID: PMC8694672 DOI: 10.1093/nsr/nwaa290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 11/13/2022] Open
Abstract
Molybdenum dinitrogen complexes supported by monodentate arylsilylamido ligand, [Ar(Me3Si)N]3MoN2Mg(THF)2[N(SiMe3)Ar] (5) and [Ar(Me3Si)N]3MoN2SiMe3 (6) (Ar = 3,5-Me2C6H3) were synthesized and structurally characterized, and proved to be effective catalysts for the disproportionation of cyclohexadienes and isomerization of terminal alkenes. The 1H NMR spectrum suggested that the bridging nitrogen ligand remains intact during the catalytic reaction, indicating possible catalytic ability of the Mo-N=N motif.
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Affiliation(s)
- Dan-Dan Zhai
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Si-Jun Xie
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yi Xia
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Hua-Yi Fang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zhang-Jie Shi
- Department of Chemistry, Fudan University, Shanghai 200433, China
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32
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Arnett CH, Bogacz I, Chatterjee R, Yano J, Oyala PH, Agapie T. Mixed-Valent Diiron μ-Carbyne, μ-Hydride Complexes: Implications for Nitrogenase. J Am Chem Soc 2020; 142:18795-18813. [PMID: 32976708 DOI: 10.1021/jacs.0c05920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Binding of N2 by the FeMo-cofactor of nitrogenase is believed to occur after transfer of 4 e- and 4 H+ equivalents to the active site. Although pulse EPR studies indicate the presence of two Fe-(μ-H)-Fe moieties, the structural and electronic features of this mixed valent intermediate remain poorly understood. Toward an improved understanding of this bioorganometallic cluster, we report herein that diiron μ-carbyne complex (P6ArC)Fe2(μ-H) can be oxidized and reduced, allowing for the first time spectral characterization of two EPR-active Fe(μ-C)(μ-H)Fe model complexes linked by a 2 e- transfer which bear some resemblance to a pair of En and En+2 states of nitrogenase. Both species populate S = 1/2 states at low temperatures, and the influence of valence (de)localization on the spectroscopic signature of the μ-hydride ligand was evaluated by pulse EPR studies. Compared to analogous data for the {Fe2(μ-H)}2 state of FeMoco (E4(4H)), the data and analysis presented herein suggest that the hydride ligands in E4(4H) bridge isovalent (most probably FeIII) metal centers. Although electron transfer involves metal-localized orbitals, investigations of [(P6ArC)Fe2(μ-H)]+1 and [(P6ArC)Fe2(μ-H)]-1 by pulse EPR revealed that redox chemistry induces significant changes in Fe-C covalency (-50% upon 2 e- reduction), a conclusion further supported by X-ray absorption spectroscopy, 57Fe Mössbauer studies, and DFT calculations. Combined, our studies demonstrate that changes in covalency buffer against the accumulation of excess charge density on the metals by partially redistributing it to the bridging carbon, thereby facilitating multielectron transformations.
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Affiliation(s)
- Charles H Arnett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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33
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Rohde M, Grunau K, Einsle O. Bindung von CO am FeV‐Cofaktor der CO‐reduzierenden Vanadium‐Nitrogenase bei atomarer Auflösung. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael Rohde
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
| | - Katharina Grunau
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
| | - Oliver Einsle
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
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34
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Rohde M, Grunau K, Einsle O. CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution. Angew Chem Int Ed Engl 2020; 59:23626-23630. [PMID: 32915491 PMCID: PMC7756900 DOI: 10.1002/anie.202010790] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Indexed: 11/24/2022]
Abstract
Nitrogenases reduce N2, the most abundant element in Earth's atmosphere that is otherwise resistant to chemical conversions due to its stable triple bond. Vanadium nitrogenase stands out in that it additionally processes carbon monoxide, a known inhibitor of the reduction of all substrates other than H+. The reduction of CO leads to the formation of hydrocarbon products, holding the potential for biotechnological applications in analogy to the industrial Fischer–Tropsch process. Here we report the most highly resolved structure of vanadium nitrogenase to date at 1.0 Å resolution, with CO bound to the active site cofactor after catalytic turnover. CO bridges iron ions Fe2 and Fe6, replacing sulfide S2B, in a binding mode that is in line with previous reports on the CO complex of molybdenum nitrogenase. We discuss the structural consequences of continued turnover when CO is removed, which involve the replacement of CO possibly by OH−, the movement of Q176D and K361D, the return of sulfide and the emergence of two additional water molecules that are absent in the CO‐bound state.
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Affiliation(s)
- Michael Rohde
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
| | - Katharina Grunau
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
| | - Oliver Einsle
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
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35
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Rapson TD, Gregg CM, Allen RS, Ju H, Doherty CM, Mulet X, Giddey S, Wood CC. Insights into Nitrogenase Bioelectrocatalysis for Green Ammonia Production. CHEMSUSCHEM 2020; 13:4856-4865. [PMID: 32696610 DOI: 10.1002/cssc.202001433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/20/2020] [Indexed: 05/26/2023]
Abstract
There is a growing interest in using ammonia as a liquid carrier of hydrogen for energy applications. Currently, ammonia is produced industrially by the Haber-Bosch process, which requires high temperature and high pressure. In contrast, bacteria have naturally evolved an enzyme known as nitrogenase, that is capable of producing ammonia and hydrogen at ambient temperature and pressure. Therefore, nitrogenases are attractive as a potentially more efficient means to produce ammonia via harnessing the unique properties of this enzyme. In recent years, exciting progress has been made in bioelectrocatalysis using nitrogenases to produce ammonia. Here, the prospects for developing biological ammonia production are outlined, key advances in bioelectrocatalysis by nitrogenases are highlighted, and possible solutions to the obstacles faced in realising this goal are discussed.
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Affiliation(s)
- Trevor D Rapson
- CSIRO Agriculture and Food, Black Mountain, ACT, 2601, Australia
| | | | - Robert S Allen
- CSIRO Agriculture and Food, Black Mountain, ACT, 2601, Australia
| | - HyungKuk Ju
- CSIRO Energy, Private Bag 10, Clayton South, 3169, Victoria, Australia
| | - Cara M Doherty
- CSIRO Manufacturing, Private Bag 10, Clayton South, 3169, Victoria, Australia
| | - Xavier Mulet
- CSIRO Manufacturing, Private Bag 10, Clayton South, 3169, Victoria, Australia
| | - Sarbjit Giddey
- CSIRO Energy, Private Bag 10, Clayton South, 3169, Victoria, Australia
| | - Craig C Wood
- CSIRO Agriculture and Food, Black Mountain, ACT, 2601, Australia
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36
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Abstract
Nitrogenase is the only enzyme capable of reducing N2 to NH3. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.
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Affiliation(s)
- Hannah L Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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37
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- 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
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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38
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Affiliation(s)
- Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena California 91125, United States
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39
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Rupnik K, Tanifuji K, Rettberg L, Ribbe MW, Hu Y, Hales BJ. Electron Paramagnetic Resonance and Magnetic Circular Dichroism Spectra of the Nitrogenase M Cluster Precursor Suggest Sulfur Migration upon Oxidation: A Proposal for Substrate and Inhibitor Binding. Chembiochem 2020; 21:1767-1772. [PMID: 31881119 PMCID: PMC7481019 DOI: 10.1002/cbic.201900681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 02/01/2023]
Abstract
The active site of the nitrogen-fixing enzyme Mo-nitrogenase is the M cluster ([MoFe7 S9 C⋅R-homocitrate]), also known as the FeMo cofactor or FeMoco. The biosynthesis of this highly complex metallocluster involves a series of proteins. Among them, NifB, a radical-SAM enzyme, is instrumental in the assembly of the L cluster ([Fe8 S9 C]), a precursor and all-iron core of the M cluster. In the absence of sulfite, NifB assembles a precursor form of the L cluster called the L* cluster ([Fe8 S8 C]), which lacks the final ninth sulfur. EPR and MCD spectroscopies are used to probe the electronic structures of the paramagnetic, oxidized forms of both the L and L* clusters, labeled LOx and [L*]Ox . This study shows that both LOx and [L*]Ox have nearly identical EPR and MCD spectra, thus suggesting that the two clusters have identical structures upon oxidation; in other words, a sulfur migrates away from LOx following oxidation, thereby rendering the cluster identical to [L*]Ox . It is proposed that a similar migration could occur to the M cluster upon oxidation, and that this is an instrumental part of both M cluster formation and nitrogenase substrate/inhibitor binding.
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Affiliation(s)
- Kresimir Rupnik
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Lee Rettberg
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Brian J Hales
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
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40
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Hu Y, Ribbe MW. Special Issue on Nitrogenases and Homologous Systems. Chembiochem 2020; 21:1668-1670. [PMID: 32426925 DOI: 10.1002/cbic.202000279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 12/16/2022]
Abstract
The nitrogenase superfamily comprises homologous enzyme systems that carry out fundamentally important processes, including the reduction of N2 and CO, and the biosynthesis of bacteriochlorophyll and coenzyme F430. This special issue provides a cross-disciplinary overview of the ongoing research in this highly diverse and unique research area of metalloprotein biochemistry.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.,Department Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
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41
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Miyagawa K, Shoji M, Isobe H, Yamanaka S, Kawakami T, Okumura M, Yamaguchi K. UNO(ULO) active space for multireference calculations on classical and quantum computers. Revisit to the iron-sulfur complexes. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Arnett CH, Agapie T. Activation of an Open Shell, Carbyne-Bridged Diiron Complex Toward Binding of Dinitrogen. J Am Chem Soc 2020; 142:10059-10068. [DOI: 10.1021/jacs.0c01896] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Charles H. Arnett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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43
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Jasniewski AJ, Lee CC, Ribbe MW, Hu Y. Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases. Chem Rev 2020; 120:5107-5157. [PMID: 32129988 DOI: 10.1021/acs.chemrev.9b00704] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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Abstract
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Nitrogenase harbors three distinct
metal prosthetic groups that
are required for its activity. The simplest one is a [4Fe-4S] cluster
located at the Fe protein nitrogenase component. The MoFe protein
component carries an [8Fe-7S] group called P-cluster and a [7Fe-9S-C-Mo-R-homocitrate] group called FeMo-co. Formation of nitrogenase
metalloclusters requires the participation of the structural nitrogenase
components and many accessory proteins, and occurs both in
situ, for the P-cluster, and in external assembly sites for
FeMo-co. The biosynthesis of FeMo-co is performed stepwise and involves
molecular scaffolds, metallochaperones, radical chemistry, and novel
and unique biosynthetic intermediates. This review provides a critical
overview of discoveries on nitrogenase cofactor structure, function,
and activity over the last four decades.
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Affiliation(s)
- Stefan Burén
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Emilio Jiménez-Vicente
- Department of Biochemistry, Virginia Polytechnic Institute, Blacksburg, Virginia 24061, United States
| | - Carlos Echavarri-Erasun
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
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Okada S, Gregg CM, Allen RS, Menon A, Hussain D, Gillespie V, Johnston E, Byrne K, Colgrave ML, Wood CC. A Synthetic Biology Workflow Reveals Variation in Processing and Solubility of Nitrogenase Proteins Targeted to Plant Mitochondria, and Differing Tolerance of Targeting Sequences in a Bacterial Nitrogenase Assay. FRONTIERS IN PLANT SCIENCE 2020; 11:552160. [PMID: 33013970 PMCID: PMC7511584 DOI: 10.3389/fpls.2020.552160] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/21/2020] [Indexed: 05/13/2023]
Abstract
While industrial nitrogen fertilizer is intrinsic to modern agriculture, it is expensive and environmentally harmful. One approach to reduce fertilizer usage is to engineer the bacterial nitrogenase enzyme complex within plant mitochondria, a location that may support enzyme function. Our current strategy involves fusing a mitochondrial targeting peptide (MTP) to nitrogenase (Nif) proteins, enabling their import to the mitochondrial matrix. However, the process of import modifies the N-terminus of each Nif protein and may impact nitrogenase assembly and function. Here we present our workflow assessing the mitochondrial processing, solubility and relative abundance of 16 Klebsiella oxytoca Nif proteins targeted to the mitochondrial matrix in Nicotiana benthamiana leaf. We found that processing and abundance of MTP::Nif proteins varied considerably, despite using the same constitutive promoter and MTP across all Nif proteins tested. Assessment of the solubility for all MTP::Nif proteins when targeted to plant mitochondria found NifF, M, N, S, U, W, X, Y, and Z were soluble, while NifB, E, H, J, K, Q, and V were mostly insoluble. The functional consequence of the N-terminal modifications required for mitochondrial targeting of Nif proteins was tested using a bacterial nitrogenase assay. With the exception of NifM, the Nif proteins generally tolerated the N-terminal extension. Proteomic analysis of Nif proteins expressed in bacteria found that the relative abundance of NifM with an N-terminal extension was increased ~50-fold, while that of the other Nif proteins was not influenced by the N-terminal extension. Based on the solubility, processing and functional assessments, our workflow identified that K. oxytoca NifF, N, S, U, W, Y, and Z successfully met these criteria. For the remaining Nif proteins, their limitations will need to be addressed before proceeding towards assembly of a complete set of plant-ready Nif proteins for reconstituting nitrogenase in plant mitochondria.
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Affiliation(s)
- Shoko Okada
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Christina M. Gregg
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Robert Silas Allen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Amratha Menon
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Dawar Hussain
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Vanessa Gillespie
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Ema Johnston
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Keren Byrne
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, QLD, Australia
| | - Michelle Lisa Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Queensland Biosciences Precinct, St. Lucia, QLD, Australia
| | - Craig C. Wood
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
- *Correspondence: Craig C. Wood,
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part V. Nitrogenases. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Liu X, Li F, Peng P, Licht G, Licht S. Efficient Electrocatalytic Synthesis of Ammonia from Water and Air in a Membrane‐Free Cell: Confining the Iron Oxide Catalyst to the Cathode. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Xinye Liu
- Department of Chemistry The George Washington University Washington DC 20052 USA
| | - Fang‐Fang Li
- Department of Chemistry The George Washington University Washington DC 20052 USA
| | - Ping Peng
- Department of Chemistry The George Washington University Washington DC 20052 USA
| | - Gad Licht
- Department of Chemistry The George Washington University Washington DC 20052 USA
| | - Stuart Licht
- Department of Chemistry The George Washington University Washington DC 20052 USA
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48
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Kowalska JK, Henthorn JT, Van Stappen C, Trncik C, Einsle O, Keavney D, DeBeer S. X-ray Magnetic Circular Dichroism Spectroscopy Applied to Nitrogenase and Related Models: Experimental Evidence for a Spin-Coupled Molybdenum(III) Center. Angew Chem Int Ed Engl 2019; 58:9373-9377. [PMID: 31119827 PMCID: PMC6772009 DOI: 10.1002/anie.201901899] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/17/2019] [Indexed: 11/23/2022]
Abstract
Nitrogenase enzymes catalyze the reduction of atmospheric dinitrogen to ammonia utilizing a Mo‐7Fe‐9S‐C active site, the so‐called FeMoco cluster. FeMoco and an analogous small‐molecule (Et4N)[(Tp)MoFe3S4Cl3] cubane have both been proposed to contain unusual spin‐coupled MoIII sites with an S(Mo)=1/2 non‐Hund configuration at the Mo atom. Herein, we present Fe and Mo L3‐edge X‐ray magnetic circular dichroism (XMCD) spectroscopy of the (Et4N)[(Tp)MoFe3S4Cl3] cubane and Fe L2,3‐edge XMCD spectroscopy of the MoFe protein (containing both FeMoco and the 8Fe‐7S P‐cluster active sites). As the P‐clusters of MoFe protein have an S=0 total spin, these are effectively XMCD‐silent at low temperature and high magnetic field, allowing for FeMoco to be selectively probed by Fe L2,3‐edge XMCD within the intact MoFe protein. Further, Mo L3‐edge XMCD spectroscopy of the cubane model has provided experimental support for a local S(Mo)=1/2 configuration, demonstrating the power and selectivity of XMCD.
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Affiliation(s)
- Joanna K Kowalska
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Justin T Henthorn
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Casey Van Stappen
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Christian Trncik
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Einsle
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert Ludwigs University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - David Keavney
- Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Serena DeBeer
- Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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49
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Kowalska JK, Henthorn JT, Van Stappen C, Trncik C, Einsle O, Keavney D, DeBeer S. X‐ray Magnetic Circular Dichroism Spectroscopy Applied to Nitrogenase and Related Models: Experimental Evidence for a Spin‐Coupled Molybdenum(III) Center. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Joanna K. Kowalska
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Justin T. Henthorn
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Casey Van Stappen
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Christian Trncik
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies Albert Ludwigs University of Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Oliver Einsle
- Institute for Biochemistry and BIOSS Centre for Biological Signalling Studies Albert Ludwigs University of Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - David Keavney
- Argonne National Laboratory 9700 S. Cass Ave Argonne IL 60439 USA
| | - Serena DeBeer
- Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
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Abstract
Biological nitrogen fixation, the conversion of dinitrogen (N2) into ammonia (NH3), stands as a particularly challenging chemical process. As the entry point into a bioavailable form of nitrogen, biological nitrogen fixation is a critical step in the global nitrogen cycle. In Nature, only one enzyme, nitrogenase, is competent in performing this reaction. Study of this complex metalloenzyme has revealed a potent substrate reduction system that utilizes some of the most sophisticated metalloclusters known. This chapter discusses the structure and function of nitrogenase, covers methods that have proven useful in the elucidation of enzyme properties, and provides an overview of the three known nitrogenase variants.
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