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Yang D, Wang B, Qu J. Construction and Function of Thiolate-Bridged Diiron N xH y Nitrogenase Model Complexes. Acc Chem Res 2024; 57:1761-1776. [PMID: 38861704 DOI: 10.1021/acs.accounts.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
ConspectusBiological nitrogen fixation mediated by nitrogenases has garnered significant research interest due to its critical importance to the development of efficient catalysts for mild ammonia synthesis. Although the active center of the most studied FeMo-nitrogenases has been determined to be a complicated [Fe7S9MoC] hetero-multinuclear metal-sulfur cluster known as the FeMo-cofactor, the exact binding site and reduction pathway of N2 remain a subject of debate. Over the past decades, the majority of studies have focused on mononuclear molybdenum or iron centers as potential reaction sites. In stark contrast, cooperative activation of N2 through bi- or multimetallic centers has been largely overlooked and underexplored, despite the renewed interest sparked by recent biochemical and computational studies. Consequently, constructing bioinspired bi- or multinuclear metallic model complexes presents an intriguing yet challenging prospect. In this Account, we detail our long-standing research on the design and synthesis of novel thiolate-bridged diiron complexes as nitrogenase models and their application to chemical simulations of potential biological N2 reduction pathways.Inspired by the structural and electronic features of the potential diiron active center in the belt region of the FeMo-cofactor, we have designed and synthesized a series of new thiolate-bridged diiron nitrogenase model complexes, wherein iron centers with +2 or +3 oxidation states are coordinated by Cp* as carbon-based donors and thiolate ligands as sulfur donors. Through the synergistic interaction between the two iron centers, unstable diazene (NH═NH) species can be trapped to generate the first example of a [Fe2S2]-type complex bearing a cis-μ-η1:η1-NH═NH subunit. Significantly, this species can not only catalyze the reductive N-N bond cleavage of hydrazine to ammonia but also trigger a stepwise reduction sequence NH═NH → [NH2-NH]- → [NH]2-(+NH3) → [NH2]- → NH3. Furthermore, an unprecedented thiolate-bridged diiron μ-nitride featuring a bent Fe-N-Fe moiety was successfully isolated and structurally characterized. Importantly, this diiron μ-nitride can undergo successive proton-coupled electron transfer processes to efficiently release ammonia in the presence of separate protons and electrons and can even be directly hydrogenated using H2 as a combination of protons and electrons for high-yield ammonia formation. Based on combined experimental and computational studies, we proposed two distinct reductive transformation sequences on the diiron centers, which involve a series of crucial NxHy intermediates. Moreover, we also achieved catalytic N2 reduction to silylamines with [Fe2S2]-type complexes by ligand modulation.Our bioinspired diiron cooperative scaffold may provide a suitable model for probing the potential N2 stepwise reduction pathways from the molecular level. Different from the traditional alternating and distal pathways dominated by mononuclear iron or molybdenum complexes, our proposed alternating transformation route based on the diiron centers may not involve the N2H4 intermediate, and the convergence point of the alternating and terminal pathways is imide, not amide. Our research strategy could inform the design and development of new types of bioinspired catalysts for mild and efficient nitrogen reduction in the future.
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Affiliation(s)
- Dawei Yang
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, P. R. China
| | - Baomin Wang
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, P. R. China
| | - Jingping Qu
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, P. R. China
- State Key Laboratory of Bioreactor Engineering, Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
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Lee CC, Górecki K, Stang M, Ribbe MW, Hu Y. Cofactor maturase NifEN: A prototype ancient nitrogenase? SCIENCE ADVANCES 2024; 10:eado6169. [PMID: 38865457 PMCID: PMC11168457 DOI: 10.1126/sciadv.ado6169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Nitrogenase plays a key role in the global nitrogen cycle; yet, the evolutionary history of nitrogenase and, particularly, the sequence of appearance between the homologous, yet distinct NifDK (the catalytic component) and NifEN (the cofactor maturase) of the extant molybdenum nitrogenase, remains elusive. Here, we report the ability of NifEN to reduce N2 at its surface-exposed L-cluster ([Fe8S9C]), a structural/functional homolog of the M-cluster (or cofactor; [(R-homocitrate)MoFe7S9C]) of NifDK. Furthermore, we demonstrate the ability of the L-cluster-bound NifDK to mimic its NifEN counterpart and enable N2 reduction. These observations, coupled with phylogenetic, ecological, and mechanistic considerations, lead to the proposal of a NifEN-like, L-cluster-carrying protein as an ancient nitrogenase, the exploration of which could shed crucial light on the evolutionary origin of nitrogenase and related enzymes.
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Affiliation(s)
- Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
| | - Martin Stang
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
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3
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Sohraby F, Nunes-Alves A. Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase. J Chem Inf Model 2024; 64:4193-4203. [PMID: 38728115 PMCID: PMC11134402 DOI: 10.1021/acs.jcim.4c00187] [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: 02/02/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
[NiFe] hydrogenases can act as efficient catalysts for hydrogen oxidation and biofuel production. However, some [NiFe] hydrogenases are inhibited by gas molecules present in the environment, such as O2 and CO. One strategy to engineer [NiFe] hydrogenases and achieve O2- and CO-tolerant enzymes is by introducing point mutations to block the access of inhibitors to the catalytic site. In this work, we characterized the unbinding pathways of CO in the complex with the wild-type and 10 different mutants of [NiFe] hydrogenase from Desulfovibrio fructosovorans using τ-random accelerated molecular dynamics (τRAMD) to enhance the sampling of unbinding events. The ranking provided by the relative residence times computed with τRAMD is in agreement with experiments. Extensive data analysis of the simulations revealed that from the two bottlenecks proposed in previous studies for the transit of gas molecules (residues 74 and 122 and residues 74 and 476), only one of them (residues 74 and 122) effectively modulates diffusion and residence times for CO. We also computed pathway probabilities for the unbinding of CO, O2, and H2 from the wild-type [NiFe] hydrogenase, and we observed that while the most probable pathways are the same, the secondary pathways are different. We propose that introducing mutations to block the most probable paths, in combination with mutations to open the main secondary path used by H2, can be a feasible strategy to achieve CO and O2 resistance in the [NiFe] hydrogenase from Desulfovibrio fructosovorans.
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Affiliation(s)
- Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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4
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Gong Z, Wang L, Xu Y, Xie D, Qi X, Nam W, Guo M. Enhanced Reactivities of Iron(IV)-Oxo Porphyrin Species in Oxidation Reactions Promoted by Intramolecular Hydrogen-Bonding. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310333. [PMID: 38477431 PMCID: PMC11109629 DOI: 10.1002/advs.202310333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/19/2024] [Indexed: 03/14/2024]
Abstract
High-valent iron-oxo species are one of the common intermediates in both biological and biomimetic catalytic oxidation reactions. Recently, hydrogen-bonding (H-bonding) has been proved to be critical in determining the selectivity and reactivity. However, few examples have been established for mechanistic insights into the H-bonding effect. Moreover, intramolecular H-bonding effect on both C-H activation and oxygen atom transfer (OAT) reactions in synthetic porphyrin model system has not been investigated yet. In this study, a series of heme-containing iron(IV)-oxo porphyrin species with or without intramolecular H-bonding are synthesized and characterized. Kinetic studies revealed that intramolecular H-bonding can significantly enhance the reactivity of iron(IV)-oxo species in OAT, C-H activation, and electron-transfer reactions. This unprecedented unified H-bonding effect is elucidated by theoretical calculations, which showed that intramolecular H-bonding interactions lower the energy of the anti-bonding orbital of iron(IV)-oxo porphyrin species, resulting in the enhanced reactivities in oxidation reactions irrespective of the reaction type. To the best of the knowledge, this is the first extensive investigation on the intramolecular H-bonding effect in heme system. The results show that H-bonding interactions have a unified effect with iron(IV)-oxo porphyrin species in all three investigated reactions.
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Affiliation(s)
- Zhe Gong
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Liwei Wang
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Yiran Xu
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Duanfeng Xie
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Xiaotian Qi
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Wonwoo Nam
- Department of Chemistry and Nano ScienceEwha Womans UniversitySeoul03760South Korea
| | - Mian Guo
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
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Hooper RX, Wertz AE, Shafaat HS, Holland PL. Evaluating Diazene to N 2 Interconversion at Iron-Sulfur Complexes. Chemistry 2024; 30:e202304072. [PMID: 38376370 PMCID: PMC11045311 DOI: 10.1002/chem.202304072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
Biological N2 reduction occurs at sulfur-rich multiiron sites, and an interesting potential pathway is concerted double reduction/ protonation of bridging N2 through PCET. Here, we test the feasibility of using synthetic sulfur-supported diiron complexes to mimic this pathway. Oxidative proton transfer from μ-η1 : η1-diazene (HN=NH) is the microscopic reverse of the proposed N2 fixation pathway, revealing the energetics of the process. Previously, Sellmann assigned the purple metastable product from two-electron oxidation of [{Fe2+(PPr3)L1}2(μ-η1 : η1-N2H2)] (L1=tetradentate SSSS ligand) at -78 °C as [{Fe2+(PPr3)L1}2(μ-η1 : η1-N2)]2+, which would come from double PCET from diazene to sulfur atoms of the supporting ligands. Using resonance Raman, Mössbauer, NMR, and EPR spectroscopies in conjunction with DFT calculations, we show that the product is not an N2 complex. Instead, the data are most consistent with the spectroscopically observed species being the mononuclear iron(III) diazene complex [{Fe(PPr3)L1}(η2-N2H2)]+. Calculations indicate that the proposed double PCET has a barrier that is too high for proton transfer at the reaction temperature. Also, PCET from the bridging diazene is highly exergonic as a result of the high Fe3+/2+ redox potential, indicating that the reverse N2 protonation would be too endergonic to proceed. This system establishes the "ground rules" for designing reversible N2/N2H2 interconversion through PCET, such as tuning the redox potentials of the metal sites.
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Affiliation(s)
- Reagan X Hooper
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT-06511
| | - Ashlee E Wertz
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, OH-43210
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, OH-43210
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA-90095
| | - Patrick L Holland
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT-06511
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6
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Fasano A, Fourmond V, Léger C. Outer-sphere effects on the O 2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases. Chem Sci 2024; 15:5418-5433. [PMID: 38638217 PMCID: PMC11023054 DOI: 10.1039/d4sc00691g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
The comparison of homologous metalloenzymes, in which the same inorganic active site is surrounded by a variable protein matrix, has demonstrated that residues that are remote from the active site may have a great influence on catalytic properties. In this review, we summarise recent findings on the diverse molecular mechanisms by which the protein matrix may define the oxygen tolerance, catalytic directionality and catalytic reversibility of hydrogenases, enzymes that catalyse the oxidation and evolution of H2. These mechanisms involve residues in the second coordination sphere of the active site metal ion, more distant residues affecting protein flexibility through their side chains, residues lining the gas channel and even accessory subunits. Such long-distance effects, which contribute to making enzymes efficient, robust and different from one another, are a source of wonder for biochemists and a challenge for synthetic bioinorganic chemists.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281 Marseille France
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7
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Yang G, Wang D, Wang Y, Hu W, Hu S, Jiang J, Huang J, Jiang HL. Modulating the Primary and Secondary Coordination Spheres of Single Ni(II) Sites in Metal-Organic Frameworks for Boosting Photocatalysis. J Am Chem Soc 2024; 146:10798-10805. [PMID: 38579304 DOI: 10.1021/jacs.4c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
Though the coordination environment of single metal sites has been recognized to be of great importance in promoting catalysis, the influence of simultaneous precise modulation of primary and secondary coordination spheres on catalysis remains largely unknown. Herein, a series of single Ni(II) sites with altered primary and secondary coordination spheres have been installed onto metal-organic frameworks (MOFs) with UiO-67 skeleton, affording UiO-Ni-X-Y (X = S, O; Y = H, Cl, CF3) with X and Y on the primary and secondary coordination spheres, respectively. Upon deposition with CdS nanoparticles, the resulting composites present high photocatalytic H2 production rates, in which the optimized CdS/UiO-Ni-S-CF3 exhibits an excellent activity of 13.44 mmol g-1, ∼500 folds of the pristine catalyst (29.6 μmol g-1 for CdS/UiO), in 8 h, highlighting the key role of microenvironment modulation around Ni sites. Charge kinetic analysis and theoretical calculation results demonstrate that the charge transfer dynamics and reaction energy barrier are closely correlated with their coordination spheres. This work manifests the advantages of MOFs in the fabrication of structurally precise catalysts and the elucidation of particular influences of microenvironment modulation around single metal sites on the catalytic performance.
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Affiliation(s)
- Ge Yang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Denan Wang
- Department of Chemistry and Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Yang Wang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Wenhui Hu
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - Shuaishuai Hu
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jun Jiang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jier Huang
- Department of Chemistry and Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Hai-Long Jiang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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8
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Chatterjee S, Fellner M, Rankin J, Thomas MG, J S Rifayee SB, Christov CZ, Hu J, Hausinger RP. Structural, Spectroscopic, and Computational Insights from Canavanine-Bound and Two Catalytically Compromised Variants of the Ethylene-Forming Enzyme. Biochemistry 2024; 63:1038-1050. [PMID: 38577885 PMCID: PMC11025135 DOI: 10.1021/acs.biochem.4c00031] [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: 01/19/2024] [Revised: 03/16/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
The ethylene-forming enzyme (EFE) is an Fe(II), 2-oxoglutarate (2OG), and l-arginine (l-Arg)-dependent oxygenase that either forms ethylene and three CO2/bicarbonate from 2OG or couples the decarboxylation of 2OG to C5 hydroxylation of l-Arg. l-Arg binds with C5 toward the metal center, causing 2OG to change from monodentate to chelate metal interaction and OD1 to OD2 switch of D191 metal coordination. We applied anaerobic UV-visible spectroscopy, X-ray crystallography, and computational approaches to three EFE systems with high-resolution structures. The ineffective l-Arg analogue l-canavanine binds to the EFE with O5 pointing away from the metal center while promoting chelate formation by 2OG but fails to switch the D191 metal coordination from OD1 to OD2. Substituting alanine for R171 that interacts with 2OG and l-Arg inactivates the protein, prevents metal chelation by 2OG, and weakens l-Arg binding. The R171A EFE had electron density at the 2OG binding site that was identified by mass spectrometry as benzoic acid. The substitution by alanine of Y306 in the EFE, a residue 12 Å away from the catalytic metal center, generates an interior cavity that leads to multiple local and distal structural changes that reduce l-Arg binding and significantly reduce the enzyme activity. Flexibility analyses revealed correlated and anticorrelated motions in each system, with important distinctions from the wild-type enzyme. In combination, the results are congruent with the currently proposed enzyme mechanism, reinforce the importance of metal coordination by OD2 of D191, and highlight the importance of the second coordination sphere and longer range interactions in promoting EFE activity.
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Affiliation(s)
- Shramana Chatterjee
- Department
of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Matthias Fellner
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - JoelA. Rankin
- Department
of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Midhun G. Thomas
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Jian Hu
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Robert P. Hausinger
- Department
of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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9
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Duffus BR, Gauglitz M, Teutloff C, Leimkühler S. Redox potentials elucidate the electron transfer pathway of NAD +-dependent formate dehydrogenases. J Inorg Biochem 2024; 253:112487. [PMID: 38306887 DOI: 10.1016/j.jinorgbio.2024.112487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/04/2024]
Abstract
Metal-dependent, nicotine adenine dinucleotide (NAD+)-dependent formate dehydrogenases (FDHs) are complex metalloenzymes coupling biochemical transformations through intricate electron transfer pathways. Rhodobacter capsulatus FDH is a model enzyme for understanding coupled catalysis, in that reversible CO2 reduction and formate oxidation are linked to a flavin mononuclotide (FMN)-bound diaphorase module via seven iron-sulfur (FeS) clusters as a dimer of heterotetramers. Catalysis occurs at a bis-metal-binding pterin (Mo) binding two molybdopterin guanine dinucleotides (bis-MGD), a protein-based Cys residue and a participatory sulfido ligand. Insights regarding the proposed electron transfer mechanism between the bis-MGD and the FMN have been complicated by the discovery that an alternative pathway might occur via intersubunit electron transfer between two [4Fe4S] clusters within electron transfer distance. To clarify this difference, the redox potentials of the bis-MGD and the FeS clusters were determined via redox titration by EPR spectroscopy. Redox potentials for the bis-MGD cofactor and five of the seven FeS clusters could be assigned. Furthermore, substitution of the active site residue Lys295 with Ala resulted in altered enzyme kinetics, primarily due to a more negative redox potential of the A1 [4Fe4S] cluster. Finally, characterization of the monomeric FdsGBAD heterotetramer exhibited slightly decreased formate oxidation activity and similar iron-sulfur clusters reduced relative to the dimeric heterotetramer. Comparison of the measured redox potentials relative to structurally defined FeS clusters support a mechanism by which electron transfer occurs within a heterotetrameric unit, with the interfacial [4Fe4S] cluster serving as a structural component toward the integrity of the heterodimeric structure to drive efficient catalysis.
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Affiliation(s)
- Benjamin R Duffus
- Institute for Biochemistry and Biology, Molecular Enzymology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Marcel Gauglitz
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Teutloff
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Silke Leimkühler
- Institute for Biochemistry and Biology, Molecular Enzymology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
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10
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Kim SM, Kang SH, Lee J, Heo Y, Poloniataki EG, Kang J, Yoon HJ, Kong SY, Yun Y, Kim H, Ryu J, Lee HH, Kim YH. Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity. Nat Commun 2024; 15:2732. [PMID: 38548760 PMCID: PMC10979024 DOI: 10.1038/s41467-024-46909-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Fe‒S cluster-harboring enzymes, such as carbon monoxide dehydrogenases (CODH), employ sophisticated artificial electron mediators like viologens to serve as potent biocatalysts capable of cleaning-up industrial off-gases at stunning reaction rates. Unraveling the interplay between these enzymes and their associated mediators is essential for improving the efficiency of CODHs. Here we show the electron mediator-interaction site on ChCODHs (Ch, Carboxydothermus hydrogenoformans) using a systematic approach that leverages the viologen-reactive characteristics of superficial aromatic residues. By enhancing mediator-interaction (R57G/N59L) near the D-cluster, the strategically tailored variants exhibit a ten-fold increase in ethyl viologen affinity relative to the wild-type without sacrificing the turn-over rate (kcat). Viologen-complexed structures reveal the pivotal positions of surface phenylalanine residues, serving as external conduits for the D-cluster to/from viologen. One variant (R57G/N59L/A559W) can treat a broad spectrum of waste gases (from steel-process and plastic-gasification) containing O2. Decoding mediator interactions will facilitate the development of industrially high-efficient biocatalysts encompassing gas-utilizing enzymes.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Jinhee Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Yoonyoung Heo
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eleni G Poloniataki
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Jingu Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - So Yeon Kong
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yaejin Yun
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyunwoo Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Jungki Ryu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea.
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea.
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11
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Isegawa M. Metal- and ligand-substitution-induced changes in the kinetics and thermodynamics of hydrogen activation and hydricity in a dinuclear metal complex. Dalton Trans 2024; 53:5966-5978. [PMID: 38462977 DOI: 10.1039/d4dt00361f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Catalytic function in organometallic complexes is achieved by carefully selecting their central metals and ligands. In this study, the effects of a metal and a ligand on the kinetics and thermodynamics of hydrogen activation, hydricity degree of the hydride complex, and susceptibility to electronic oxidation in bioinspired NiFe complexes, [NiIIX FeII(Cl)(CO)Y]+ ([NiFe(Cl)(CO)]+; X = N,N'-diethyl-3,7-diazanonane-1,9-dithiolato and Y = 1,2-bis(diphenylphosphino)ethane), were investigated. The density functional theory calculations revealed that the following order thermodynamically favored hydrogen activation: [NiFe(CO)]2+ > [NiRu(CO)]2+ > [NiFe(CNMe)]2+ ∼ [PdRu(CO)]2+ ∼ [PdFe(CO)]2+ ≫ [NiFe(NCS)]+. Moreover, the reverse order thermodynamically favored the hydricity degree.
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Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
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12
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Xiao Y, Xie F, Zhang HT, Zhang MT. Bioinspired Binickel Catalyst for Carbon Dioxide Reduction: The Importance of Metal-ligand Cooperation. JACS AU 2024; 4:1207-1218. [PMID: 38559717 PMCID: PMC10976602 DOI: 10.1021/jacsau.4c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 04/04/2024]
Abstract
Catalyst design for the efficient CO2 reduction reaction (CO2RR) remains a crucial challenge for the conversion of CO2 to fuels. Natural Ni-Fe carbon monoxide dehydrogenase (NiFe-CODH) achieves reversible conversion of CO2 and CO at nearly thermodynamic equilibrium potential, which provides a template for developing CO2RR catalysts. However, compared with the natural enzyme, most biomimetic synthetic Ni-Fe complexes exhibit negligible CO2RR catalytic activities, which emphasizes the significance of effective bimetallic cooperation for CO2 activation. Enlightened by bimetallic synergy, we herein report a dinickel complex, NiIINiII(bphpp)(AcO)2 (where NiNi(bphpp) is derived from H2bphpp = 2,9-bis(5-tert-butyl-2-hydroxy-3-pyridylphenyl)-1,10-phenanthroline) for electrocatalytic reduction of CO2 to CO, which exhibits a remarkable reactivity approximately 5 times higher than that of the mononuclear Ni catalyst. Electrochemical and computational studies have revealed that the redox-active phenanthroline moiety effectively modulates the electron injection and transfer akin to the [Fe3S4] cluster in NiFe-CODH, and the secondary Ni site facilitates the C-O bond activation and cleavage through electron mediation and Lewis acid characteristics. Our work underscores the significant role of bimetallic cooperation in CO2 reduction catalysis and provides valuable guidance for the rational design of CO2RR catalysts.
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Affiliation(s)
- Yao Xiao
- Center of Basic Molecular
Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Fei Xie
- Center of Basic Molecular
Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Hong-Tao Zhang
- Center of Basic Molecular
Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ming-Tian Zhang
- Center of Basic Molecular
Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
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13
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Russell SJ, Garcia AK, Kaçar B. A CRISPR interference system for engineering biological nitrogen fixation. mSystems 2024; 9:e0015524. [PMID: 38376168 PMCID: PMC10949490 DOI: 10.1128/msystems.00155-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
A grand challenge for the next century is in facing a changing climate through bioengineering solutions. Biological nitrogen fixation, the globally consequential, nitrogenase-catalyzed reduction of atmospheric nitrogen to bioavailable ammonia, is a vital area of focus. Nitrogen fixation engineering relies upon extensive understanding of underlying genetics in microbial models, including the broadly utilized gammaproteobacterium, Azotobacter vinelandii (A. vinelandii). Here, we report the first CRISPR interference (CRISPRi) system for targeted gene silencing in A. vinelandii that integrates genomically via site-specific transposon insertion. We demonstrate that CRISPRi can repress transcription of an essential nitrogen fixation gene by ~60%. Further, we show that nitrogenase genes are suitably expressed from the transposon insertion site, indicating that CRISPRi and engineered nitrogen fixation genes can be co-integrated for combinatorial studies of gene expression and engineering. Our established CRISPRi system fills an important gap for engineering microbial nitrogen fixation for desired purposes.IMPORTANCEAll life on Earth requires nitrogen to survive. About 78% of the atmosphere alone is nitrogen, yet humans cannot use it directly. Instead, we obtain the nitrogen we need for our survival through the food we eat. For more than 100 years, a substantial portion of agricultural productivity has relied on industrial methods for nitrogen fertilizer synthesis, which consumes significant amounts of nonrenewable energy resources and exacerbates environmental degradation and human-induced climate change. Promising alternatives to these industrial methods rely on engineering the only biological pathway for generating bioaccessible nitrogen: microbial nitrogen fixation. Bioengineering strategies require an extensive understanding of underlying genetics in nitrogen-fixing microbes, but genetic tools for this critical goal remain lacking. The CRISPRi gene silencing system that we report, developed in the broadly utilized nitrogen-fixing bacterial model, Azotobacter vinelandii, is an important step toward elucidating the complexity of nitrogen fixation genetics and enabling their manipulation.
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Affiliation(s)
- Steven J. Russell
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amanda K. Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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14
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Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
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15
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Aguado S, García-Álvarez P, Cabeza JA, Casarrubios L, Sierra MA. A cross-metathesis approach for polymetallic [FeFe]-hydrogenase mimics. Dalton Trans 2024; 53:3756-3764. [PMID: 38304983 DOI: 10.1039/d3dt04197b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
A method has been developed for synthesizing [FeFe]-H2ase mimics with diverse structures and properties, employing cross-metathesis of olefins. Vinylmetallocenes (5 and 6) and vinyl half-sandwich complexes (10 and 11) have been used as cross-metathesis partners with [FeFe]-H2ase mimics (4, 8, and 9) bearing a double bond in the moiety attached to the ADT-bridge nitrogen. Electrochemical studies of these complexes, encompassing metallocene-type (7a-b, 12a-b, and 13a-b) as well as half-sandwich derivatives (12c and 13c-d), have demonstrated that the introduction of a redox unit has a marginal impact on the reduction potential of these [FeFe]-H2ase mimics. The application of this cross-metathesis approach has allowed the synthesis of [FeFe]-H2ase mimics featuring an Ir(III) electrochemical antenna (16-18) as well as systems having an electron-donor-photosensitizer structure (ED-PS) (23). The electrocatalytic properties of these complexes have been elucidated through electrochemical studies.
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Affiliation(s)
- Sergio Aguado
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
- Centro de Innovación en Química Avanzada, (ORFEO-CINQA), Spain
| | - Pablo García-Álvarez
- Departamento de Química Orgánica e Inorgánica. Facultad de Química, Universidad de Oviedo, 33071 Oviedo, Spain
- Centro de Innovación en Química Avanzada, (ORFEO-CINQA), Spain
| | - Javier A Cabeza
- Departamento de Química Orgánica e Inorgánica. Facultad de Química, Universidad de Oviedo, 33071 Oviedo, Spain
- Centro de Innovación en Química Avanzada, (ORFEO-CINQA), Spain
| | - Luis Casarrubios
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
- Centro de Innovación en Química Avanzada, (ORFEO-CINQA), Spain
| | - Miguel A Sierra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
- Centro de Innovación en Química Avanzada, (ORFEO-CINQA), Spain
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16
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Cobb SJ, Rodríguez-Jiménez S, Reisner E. Connecting Biological and Synthetic Approaches for Electrocatalytic CO 2 Reduction. Angew Chem Int Ed Engl 2024; 63:e202310547. [PMID: 37983571 DOI: 10.1002/anie.202310547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
Electrocatalytic CO2 reduction has developed into a broad field, spanning fundamental studies of enzymatic 'model' catalysts to synthetic molecular catalysts and heterogeneous gas diffusion electrodes producing commercially relevant quantities of product. This diversification has resulted in apparent differences and a disconnect between seemingly related approaches when using different types of catalysts. Enzymes possess discrete and well understood active sites that can perform reactions with high selectivity and activities at their thermodynamic limit. Synthetic small molecule catalysts can be designed with desired active site composition but do not yet display enzyme-like performance. These properties of the biological and small molecule catalysts contrast with heterogeneous materials, which can contain multiple, often poorly understood active sites with distinct reactivity and therefore introducing significant complexity in understanding their activities. As these systems are being better understood and the continuously improving performance of their heterogeneous active sites closes the gap with enzymatic activity, this performance difference between heterogeneous and enzymatic systems begins to close. This convergence removes the barriers between using different types of catalysts and future challenges can be addressed without multiple efforts as a unified picture for the biological-synthetic catalyst spectrum emerges.
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Affiliation(s)
- Samuel J Cobb
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | | | - Erwin Reisner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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17
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Plummer SM, Plummer MA, Merkel PA, Waidner LA. Using directed evolution to improve hydrogen production in chimeric hydrogenases from algal species. Enzyme Microb Technol 2024; 173:110349. [PMID: 37984199 DOI: 10.1016/j.enzmictec.2023.110349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Abstract
Algae generate hydrogen from sunlight and water utilizing high-energy electrons generated during photosynthesis. The amount of hydrogen produced in heterologous expression of the wild-type hydrogenase is currently insufficient for industrial applications. One approach to improve hydrogen yields is through directed evolution of the DNA of the native hydrogenase. Here, we created 113 chimeric algal hydrogenase gene variants derived from combining segments of three parent hydrogenases, two from Chlamydomonas reinhardtii (CrHydA1 and CrHydA2) and one from Scenedesmus obliquus (HydA1). To generate chimeras, there were seven segments into which each of the parent hydrogenase genes was divided and recombined in a variety of combinations. The chimeric and parental hydrogenase sequences were cloned for heterologous expression in Escherichia coli, and 40 of the resultant enzymes expressed were assayed for H2 production. Chimeric clones that resulted in equal or greater production obtained with the cloned CrHydA1 parent hydrogenase were those comprised of CrHydA1 sequence in segments #1, 2, 3, and/or 4. These best-performing chimeras all contained one common region, segment #2, the part of the sequence known to contain important amino acids involved in proton transfer or hydrogen cluster coordination. The amino acid sequence distances among all chimeric clones to that of the CrHydA1 parent were determined, and the relationship between sequence distances and experimentally-derived H2 production was evaluated. An additional model determined the correlation between electrostatic potential energy surface area ratios and H2 production. The model yielded several algal mutants with predicted hydrogen productions in a range of two to three times that of the wild-type hydrogenase. The mutant data and the model can now be used to predict which specific mutant sequences may result in even higher hydrogen yields. Overall, results provide more precise details in planning future directed evolution to functionally improve algal hydrogenases.
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Affiliation(s)
| | | | - Patricia A Merkel
- H2OPE Biofuels LLC, Greenwood Village, CO, USA; Children's Hospital, 3123 East 16th Avenue, B518, Aurora, CO, USA
| | - Lisa A Waidner
- H2OPE Biofuels LLC, Greenwood Village, CO, USA; University of West Florida, Pensacola, FL USA.
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18
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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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19
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Ocampo MVL, Murray LJ. Metal-Tuned Ligand Reactivity Enables CX 2 (X = O, S) Homocoupling with Spectator Cu Centers. J Am Chem Soc 2024; 146:1019-1025. [PMID: 38165085 DOI: 10.1021/jacs.3c11928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Ligand non-innocence is ubiquitous in catalysis with ligands in synthetic complexes contributing as electron reservoirs or co-sites for substrate activation. The latter chemical non-innocence is manifested in H+ storage or relay at sites beyond the metal primary coordination sphere. Reaction of a competent CO2-to-oxalate reduction catalyst, namely, [K(THF)3](Cu3SL), where L3- is a tris(β-diketiminate) cyclophane, with CS2 affords tetrathiooxalate at long reaction times or at high CS2 concentrations, where otherwise an equilibrium is established between the starting species and a complex-CS2 adduct in which the CS2 is bound to the C atom on the ligand backbone. X-ray diffraction analysis of this adduct reveals no apparent metal participation, suggesting an entirely ligand-based reaction controlled by the charge state of the cluster. Thermodynamic parameters for the formation of the aforementioned Cligand-CS2 bond were experimentally determined, and trends with cation Lewis acidity were studied, where more acidic cations shift the equilibrium toward the adduct. Relevance of such an adduct in the reduction of CO2 to oxalate by this complex is supported by DFT studies, similar effects of countercation Lewis acidity on product formation, and the homocoupled heterocumulene product speciation as determined by isotopic labeling studies. Taken together, this system extends chemical non-innocence beyond H+ to effect catalytic transformations involving C-C bond formation and represents the rarest example of metal-ligand cooperativity, that is, spectator metal ion(s) and the ligand as the reaction center.
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Affiliation(s)
- M Victoria Lorenzo Ocampo
- Center for Catalysis, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Leslie J Murray
- Center for Catalysis, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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20
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Oliveira AR, Mota C, Vilela-Alves G, Manuel RR, Pedrosa N, Fourmond V, Klymanska K, Léger C, Guigliarelli B, Romão MJ, Cardoso Pereira IA. An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Nat Chem Biol 2024; 20:111-119. [PMID: 37985883 DOI: 10.1038/s41589-023-01484-2] [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: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Guilherme Vilela-Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vincent Fourmond
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Kateryna Klymanska
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Christophe Léger
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Bruno Guigliarelli
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Maria João Romão
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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21
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Yong WW, Zhang HT, Guo YH, Xie F, Zhang MT. Redox-Active Ligand Assisted Multielectron Catalysis: A Case of Electrocatalyzed CO 2-to-CO Conversion. ACS ORGANIC & INORGANIC AU 2023; 3:384-392. [PMID: 38075450 PMCID: PMC10704577 DOI: 10.1021/acsorginorgau.3c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 03/16/2024]
Abstract
The selective reduction of carbon dioxide remains a significant challenge due to the complex multielectron/proton transfer process, which results in a high kinetic barrier and the production of diverse products. Inspired by the electrostatic and H-bonding interactions observed in the second sphere of the [NiFe]-CODH enzyme, researchers have extensively explored these interactions to regulate proton transfer, stabilize intermediates, and ultimately improve the performance of catalytic CO2 reduction. In this work, a series of cobalt(II) tetraphenylporphyrins with varying numbers of redox-active nitro groups were synthesized and evaluated as CO2 reduction electrocatalysts. Analyses of the redox properties of these complexes revealed a consistent relationship between the number of nitro groups and the corresponding accepted electron number of the ligand at -1.59 V vs. Fc+/0. Among the catalysts tested, TNPPCo with four nitro groups exhibited the most efficient catalytic activity with a turnover frequency of 4.9 × 104 s-1 and a catalytic onset potential 820 mV more positive than that of the parent TPPCo. Furthermore, the turnover frequencies of the catalysts increased with a higher number of nitro groups. These results demonstrate the promising design strategy of incorporating multielectron redox-active ligands into CO2 reduction catalysts to enhance catalytic performance.
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Affiliation(s)
- Wen-Wen Yong
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
- Institute
of Materials, China Academy of Engineering Physics (CAEP), Jiangyou 621908, China
| | - Hong-Tao Zhang
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu-Hua Guo
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Fei Xie
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ming-Tian Zhang
- Center
of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
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22
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Duan J, Veliju A, Lampret O, Liu L, Yadav S, Apfel UP, Armstrong FA, Hemschemeier A, Hofmann E. Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases. J Am Chem Soc 2023; 145:26068-26074. [PMID: 37983562 DOI: 10.1021/jacs.3c07800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
[FeFe]-hydrogenases are efficient H2 converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor's amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules.
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Affiliation(s)
- Jifu Duan
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Astrit Veliju
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Oliver Lampret
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lingling Liu
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Shanika Yadav
- Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Energy, Electrosynthesis Group, Fraunhofer UMSICHT, 46047 Oberhausen, Germany
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Anja Hemschemeier
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
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23
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Woern C, Grossmann L. Microbial gas fermentation technology for sustainable food protein production. Biotechnol Adv 2023; 69:108240. [PMID: 37647973 DOI: 10.1016/j.biotechadv.2023.108240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.
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Affiliation(s)
- Carlos Woern
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Lutz Grossmann
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA.
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24
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Li Y, Chen JY, Zhang X, Peng Z, Miao Q, Chen W, Xie F, Liao RZ, Ye S, Tung CH, Wang W. Electrocatalytic Interconversions of CO 2 and Formate on a Versatile Iron-Thiolate Platform. J Am Chem Soc 2023. [PMID: 38019775 DOI: 10.1021/jacs.3c09824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Exploring bidirectional CO2/HCO2- catalysis holds significant potential in constructing integrated (photo)electrochemical formate fuel cells for energy storage and applications. Herein, we report selective CO2/HCO2- electrochemical interconversion by exploiting the flexible coordination modes and rich redox properties of a versatile iron-thiolate platform, Cp*Fe(II)L (L = 1,2-Ph2PC6H4S-). Upon oxidation, this iron complex undergoes formate binding to generate a diferric formate complex, [(L-)2Fe(III)(μ-HCO2)Fe(III)]+, which exhibits remarkable electrocatalytic performance for the HCO2--to-CO2 transformation with a maximum turnover frequency (TOFmax) ∼103 s-1 and a Faraday efficiency (FE) ∼92(±4)%. Conversely, this iron system also allows for reduction at -1.85 V (vs Fc+/0) and exhibits an impressive FE ∼93 (±3)% for the CO2-to-HCO2- conversion. Mechanism studies revealed that the HCO2--to-CO2 electrocatalysis passes through dicationic [(L2)-•Fe(III)(μ-HCO2)Fe(III)]2+ generated by unconventional oxidation of the diferric formate species taking place at ligand L, while the CO2-to-HCO2- reduction involves a critical intermediate of [Fe(II)-H]- that was independently synthesized and structurally characterized.
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Affiliation(s)
- Yongxian Li
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jia-Yi Chen
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xinchao Zhang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqiang Peng
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiyi Miao
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wang Chen
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Xie
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Rong-Zhen Liao
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Wenguang Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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25
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Quechol R, Solomon JB, Liu YA, Lee CC, Jasniewski AJ, Górecki K, Oyala P, Hedman B, Hodgson KO, Ribbe MW, Hu Y. Heterologous synthesis of the complex homometallic cores of nitrogenase P- and M-clusters in Escherichia coli. Proc Natl Acad Sci U S A 2023; 120:e2314788120. [PMID: 37871225 PMCID: PMC10622910 DOI: 10.1073/pnas.2314788120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/28/2023] [Indexed: 10/25/2023] Open
Abstract
Nitrogenase is an active target of heterologous expression because of its importance for areas related to agronomy, energy, and environment. One major hurdle for expressing an active Mo-nitrogenase in Escherichia coli is to generate the complex metalloclusters (P- and M-clusters) within this enzyme, which involves some highly unique bioinorganic chemistry/metalloenzyme biochemistry that is not generally dealt with in the heterologous expression of proteins via synthetic biology; in particular, the heterologous synthesis of the homometallic P-cluster ([Fe8S7]) and M-cluster core (or L-cluster; [Fe8S9C]) on their respective protein scaffolds, which represents two crucial checkpoints along the biosynthetic pathway of a complete nitrogenase, has yet to be demonstrated by biochemical and spectroscopic analyses of purified metalloproteins. Here, we report the heterologous formation of a P-cluster-containing NifDK protein upon coexpression of Azotobacter vinelandii nifD, nifK, nifH, nifM, and nifZ genes, and that of an L-cluster-containing NifB protein upon coexpression of Methanosarcina acetivorans nifB, nifS, and nifU genes alongside the A. vinelandii fdxN gene, in E. coli. Our metal content, activity, EPR, and XAS/EXAFS data provide conclusive evidence for the successful synthesis of P- and L-clusters in a nondiazotrophic host, thereby highlighting the effectiveness of our metallocentric, divide-and-conquer approach that individually tackles the key events of nitrogenase biosynthesis prior to piecing them together into a complete pathway for the heterologous expression of nitrogenase. As such, this work paves the way for the transgenic expression of an active nitrogenase while providing an effective tool for further tackling the biosynthetic mechanism of this important metalloenzyme.
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Affiliation(s)
- Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Joseph B. Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
- Department of Chemistry, University of California, Irvine, CA92697-2025
| | - Yiling A. Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Andrew J. Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
| | - Paul Oyala
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
| | - Keith O. Hodgson
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
- Department of Chemistry, University of California, Irvine, CA92697-2025
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697-3900
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26
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Kalimuthu P, Hakopian S, Niks D, Hille R, Bernhardt PV. The Reversible Electrochemical Interconversion of Formate and CO 2 by Formate Dehydrogenase from Cupriavidus necator. J Phys Chem B 2023; 127:8382-8392. [PMID: 37728992 DOI: 10.1021/acs.jpcb.3c04652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The bacterial molybdenum (Mo)-containing formate dehydrogenase (FdsDABG) from Cupriavidus necator is a soluble NAD+-dependent enzyme belonging to the DMSO reductase family. The holoenzyme is complex and possesses nine redox-active cofactors including a bis(molybdopterin guanine dinucleotide) (bis-MGD) active site, seven iron-sulfur clusters, and 1 equiv of flavin mononucleotide (FMN). FdsDABG catalyzes the two-electron oxidation of HCOO- (formate) to CO2 and reversibly reduces CO2 to HCOO- under physiological conditions close to its thermodynamic redox potential. Here we develop an electrocatalytically active formate oxidation/CO2 reduction system by immobilizing FdsDABG on a glassy carbon electrode in the presence of coadsorbents such as chitosan and glutaraldehyde. The reversible enzymatic interconversion between HCOO- and CO2 by FdsDABG has been realized with cyclic voltammetry using a range of artificial electron transfer mediators, with methylene blue (MB) and phenazine methosulfate (PMS) being particularly effective as electron acceptors for FdsDABG in formate oxidation. Methyl viologen (MV) acts as both an electron acceptor (MV2+) in formate oxidation and an electron donor (MV+•) for CO2 reduction. The catalytic voltammetry was reproduced by electrochemical simulation across a range of sweep rates and concentrations of formate and mediators to provide new insights into the kinetics of the FdsDABG catalytic mechanism.
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Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Sheron Hakopian
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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27
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Fasano A, Guendon C, Jacq-Bailly A, Kpebe A, Wozniak J, Baffert C, Barrio MD, Fourmond V, Brugna M, Léger C. A Chimeric NiFe Hydrogenase Heterodimer to Assess the Role of the Electron Transfer Chain in Tuning the Enzyme's Catalytic Bias and Oxygen Tolerance. J Am Chem Soc 2023; 145:20021-20030. [PMID: 37657413 DOI: 10.1021/jacs.3c06895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
The observation that some homologous enzymes have the same active site but very different catalytic properties demonstrates the importance of long-range effects in enzyme catalysis, but these effects are often difficult to rationalize. The NiFe hydrogenases 1 and 2 (Hyd 1 and Hyd 2) from E. coli both consist of a large catalytic subunit that embeds the same dinuclear active site and a small electron-transfer subunit with a chain of three FeS clusters. Hyd 1 is mostly active in H2 oxidation and resistant to inhibitors, whereas Hyd 2 also catalyzes H2 production and is strongly inhibited by O2 and CO. Based on structural and site-directed mutagenesis data, it is currently believed that the catalytic bias and tolerance to O2 of Hyd 1 are defined by the distal and proximal FeS clusters, respectively. To test these hypotheses, we produced and characterized a hybrid enzyme made of the catalytic subunit of Hyd 1 and the electron transfer subunit of Hyd 2. We conclude that catalytic bias and sensitivity to CO are set by the catalytic subunit rather than by the electron transfer chain. We confirm the importance of the proximal cluster in making the enzyme Hyd 1 resist long-term exposure to O2, but we show that other structural determinants, in both subunits, contribute to O2 tolerance. A similar strategy based on the design of chimeric heterodimers could be used in the future to elucidate various structure-function relationships in hydrogenases and other multimeric metalloenzymes and to engineer useful hydrogenases that combine the desirable properties of distinct, homologous enzymes.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Chloé Guendon
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Aurore Jacq-Bailly
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Arlette Kpebe
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Jérémy Wozniak
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Carole Baffert
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Melisa Del Barrio
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, 28040 Madrid, Spain
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Myriam Brugna
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
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28
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Brown AC, Suess DLM. An Iron-Sulfur Cluster with a Highly Pyramidalized Three-Coordinate Iron Center and a Negligible Affinity for Dinitrogen. J Am Chem Soc 2023; 145:20088-20096. [PMID: 37656961 PMCID: PMC10824254 DOI: 10.1021/jacs.3c07677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Attempts to generate open coordination sites for N2 binding at synthetic Fe-S clusters often instead result in cluster oligomerization. Recently, it was shown for Mo-Fe-S clusters that such oligomerization reactions can be prevented through the use of sterically protective supporting ligands, thereby enabling N2 complex formation. Here, this strategy is extended to Fe-only Fe-S clusters. One-electron reduction of (IMes)3Fe4S4Cl (IMes = 1,3-dimesitylimidazol-2-ylidene) forms the transiently stable edge-bridged double cubane (IMes)6Fe8S8, which loses two IMes ligands to form the face-bridged double-cubane, (IMes)4Fe8S8. The finding that the three supporting IMes ligands do not confer sufficient protection to curtail cluster oligomerization prompted the design of a new N-heterocyclic carbene, SIArMe,iPr (1,3-bis(3,5-diisopropyl-2,6-dimethylphenyl)-2-imidazolidinylidene; abbreviated as SIAr), that features bulky groups strategically placed in remote positions. When the reduction of (SIAr)3Fe4S4Cl or [(SIAr)3Fe4S4(THF)]+ is conducted in the presence of SIAr, the formation of (SIAr)4Fe8S8 is indeed suppressed, permitting characterization of the reduced [Fe4S4]0 product. Surprisingly, rather than being an N2 complex, the product is simply (SIAr)3Fe4S4: a cluster with a three-coordinate Fe site that adopts an unusually pyramidalized geometry. Although (SIAr)3Fe4S4 does not coordinate N2 to any appreciable extent under the surveyed conditions, it does bind CO to form (SIAr)3Fe4S4(CO). This finding demonstates that the binding pocket at the unique Fe is not too small for N2; instead, the exceptionally weak affinity for N2 can be attributed to weak Fe-N2 bonding. The differences in the N2 coordination chemistry between sterically protected Mo-Fe-S clusters and Fe-only Fe-S clusters are discussed.
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Affiliation(s)
- Alexandra C Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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29
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Rivier AJ, Myers KS, Garcia AK, Sobol MS, Kaçar B. Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii. Microbiol Spectr 2023; 11:e0281523. [PMID: 37702481 PMCID: PMC10581106 DOI: 10.1128/spectrum.02815-23] [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: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 09/14/2023] Open
Abstract
Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs. IMPORTANCE Azotobacter vinelandii is a key model bacterium for the study of biological nitrogen fixation, an important metabolic process catalyzed by nitrogenase enzymes. Here, we demonstrate that compatibilities between engineered A. vinelandii strains and nitrogenase variants can be modulated at the regulatory level. The engineered strain studied here responds by adjusting the expression of proteins involved in cellular processes adjacent to nitrogen fixation, rather than that of nitrogenase proteins themselves. These insights can inform future strategies to transfer nitrogenase variants to non-native hosts.
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Affiliation(s)
- Alex J. Rivier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin S. Myers
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amanda K. Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Morgan S. Sobol
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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30
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Hiromoto T, Nishikawa K, Inoue S, Ogata H, Hori Y, Kusaka K, Hirano Y, Kurihara K, Shigeta Y, Tamada T, Higuchi Y. New insights into the oxidation process from neutron and X-ray crystal structures of an O 2-sensitive [NiFe]-hydrogenase. Chem Sci 2023; 14:9306-9315. [PMID: 37712026 PMCID: PMC10498676 DOI: 10.1039/d3sc02156d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
[NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F is an O2-sensitive enzyme that is inactivated in the presence of O2 but the oxidized enzyme can recover its catalytic activity by reacting with H2 under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O2, as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17S thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19S with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster.
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Affiliation(s)
- Takeshi Hiromoto
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
| | - Koji Nishikawa
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
| | - Seiya Inoue
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
| | - Hideaki Ogata
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
| | - Yuta Hori
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Katsuhiro Kusaka
- Neutron Industrial Application Promotion Center, Comprehensive Research Organization for Science and Society 162-1 Shirakata, Tokai Ibaraki 319-1106 Japan
| | - Yu Hirano
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University 1-33 Yayoi, Inage Chiba 263-8522 Japan
| | - Kazuo Kurihara
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
| | - Yasuteru Shigeta
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University 1-33 Yayoi, Inage Chiba 263-8522 Japan
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
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31
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Kobayashi A, Taketa M, Sowa K, Kano K, Higuchi Y, Ogata H. Structure and function relationship of formate dehydrogenases: an overview of recent progress. IUCRJ 2023; 10:544-554. [PMID: 37668215 PMCID: PMC10478512 DOI: 10.1107/s2052252523006437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/24/2023] [Indexed: 09/06/2023]
Abstract
Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. FDHs can be divided into several groups depending on their subunit composition and active-site metal ions. Metal-dependent (Mo- or W-containing) FDHs from prokaryotic organisms belong to the superfamily of molybdenum enzymes and are members of the dimethylsulfoxide reductase family. In this short review, recent progress in the structural analysis of FDHs together with their potential biotechnological applications are summarized.
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Affiliation(s)
- Ami Kobayashi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Midori Taketa
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
| | - Keisei Sowa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kenji Kano
- Office of Society Academia Collaboration for Innovation, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hideaki Ogata
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
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32
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Cabotaje P, Walter K, Zamader A, Huang P, Ho F, Land H, Senger M, Berggren G. Probing Substrate Transport Effects on Enzymatic Hydrogen Catalysis: An Alternative Proton Transfer Pathway in Putatively Sensory [FeFe] Hydrogenase. ACS Catal 2023; 13:10435-10446. [PMID: 37560193 PMCID: PMC10407848 DOI: 10.1021/acscatal.3c02314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/04/2023] [Indexed: 08/11/2023]
Abstract
[FeFe] hydrogenases, metalloenzymes catalyzing proton/dihydrogen interconversion, have attracted intense attention due to their remarkable catalytic properties and (bio-)technological potential for a future hydrogen economy. In order to unravel the factors enabling their efficient catalysis, both their unique organometallic cofactors and protein structural features, i.e., "outer-coordination sphere" effects have been intensively studied. These structurally diverse enzymes are divided into distinct phylogenetic groups, denoted as Group A-D. Prototypical Group A hydrogenases display high turnover rates (104-105 s-1). Conversely, the sole characterized Group D representative, Thermoanaerobacter mathranii HydS (TamHydS), shows relatively low catalytic activity (specific activity 10-1 μmol H2 mg-1 min-1) and has been proposed to serve a H2-sensory function. The various groups of [FeFe] hydrogenase share the same catalytic cofactor, the H-cluster, and the structural factors causing the diverging reactivities of Group A and D remain to be elucidated. In the case of the highly active Group A enzymes, a well-defined proton transfer pathway (PTP) has been identified, which shuttles H+ between the enzyme surface and the active site. In Group D hydrogenases, this conserved pathway is absent. Here, we report on the identification of highly conserved amino acid residues in Group D hydrogenases that constitute a possible alternative PTP. We varied two proposed key amino acid residues of this pathway (E252 and E289, TamHydS numbering) via site-directed mutagenesis and analyzed the resulting variants via biochemical and spectroscopic methods. All variants displayed significantly decreased H2-evolution and -oxidation activities. Additionally, the variants showed two redox states that were not characterized previously. These findings provide initial evidence that these amino acid residues are central to the putative PTP of Group D [FeFe] hydrogenase. Since the identified residues are highly conserved in Group D exclusively, our results support the notion that the PTP is not universal for different phylogenetic groups in [FeFe] hydrogenases.
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Affiliation(s)
| | | | - Afridi Zamader
- Molecular Biomimetics, Department
of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Ping Huang
- Molecular Biomimetics, Department
of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Felix Ho
- Molecular Biomimetics, Department
of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Henrik Land
- Molecular Biomimetics, Department
of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Moritz Senger
- Molecular Biomimetics, Department
of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Gustav Berggren
- Molecular Biomimetics, Department
of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
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Ahmad MG, Balamurali MM, Chanda K. Click-derived multifunctional metal complexes for diverse applications. Chem Soc Rev 2023; 52:5051-5087. [PMID: 37431583 DOI: 10.1039/d3cs00343d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The Click reaction that involves Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) serves as the most potent and highly dependable tool for the development of many complex architectures. It has paved the way for the synthesis of numerous drug molecules with enhanced synthetic flexibility, reliability, specificity and modularity. It is all about bringing two different molecular entities together to achieve the required molecular properties. The utilization of Click chemistry has been well demonstrated in organic synthesis, particularly in reactions that involve biocompatible precursors. In pharmaceutical research, Click chemistry is extensively utilized for drug delivery applications. The exhibited bio-compatibility and dormancy towards other biological components under cellular environments makes Click chemistry an identified boon in bio-medical research. In this review, various click-derived transition metal complexes are discussed in terms of their applications and uniqueness. The scope of this chemistry towards other streams of applied sciences is also discussed.
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Affiliation(s)
- Md Gulzar Ahmad
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
| | - M M Balamurali
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Chennai 600127, Tamilnadu, India.
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
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Leimkühler S. Metal-Containing Formate Dehydrogenases, a Personal View. Molecules 2023; 28:5338. [PMID: 37513211 PMCID: PMC10385643 DOI: 10.3390/molecules28145338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/04/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Mo/W-containing formate dehydrogenases (FDH) catalyzes the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active sites. The metal-containing FDHs are members of the dimethylsulfoxide reductase family of mononuclear molybdenum cofactor (Moco)- or tungsten cofactor (Wco)-containing enzymes. In these enzymes, the active site in the oxidized state comprises a Mo or W atom present in the bis-Moco, which is coordinated by the two dithiolene groups from the two MGD moieties, a protein-derived SeCys or Cys, and a sixth ligand that is now accepted as being a sulfido group. SeCys-containing enzymes have a generally higher turnover number than Cys-containing enzymes. The analogous chemical properties of W and Mo, the similar active sites of W- and Mo-containing enzymes, and the fact that W can replace Mo in some enzymes have led to the conclusion that Mo- and W-containing FDHs have the same reaction mechanism. Details of the catalytic mechanism of metal-containing formate dehydrogenases are still not completely understood and have been discussed here.
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Affiliation(s)
- Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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35
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T Waffo AF, Lorent C, Katz S, Schoknecht J, Lenz O, Zebger I, Caserta G. Structural Determinants of the Catalytic Ni a-L Intermediate of [NiFe]-Hydrogenase. J Am Chem Soc 2023. [PMID: 37328284 DOI: 10.1021/jacs.3c01625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
[NiFe]-hydrogenases catalyze the reversible cleavage of H2 into two protons and two electrons at the inorganic heterobimetallic NiFe center of the enzyme. Their catalytic cycle involves at least four intermediates, some of which are still under debate. While the core reaction, including H2/H- binding, takes place at the inorganic cofactor, a major challenge lies in identifying those amino acid residues that contribute to the reactivity and how they stabilize (short-lived) intermediate states. Using cryogenic infrared and electron paramagnetic resonance spectroscopy on the regulatory [NiFe]-hydrogenase from Cupriavidus necator, a model enzyme for the analysis of catalytic intermediates, we deciphered the structural basis of the hitherto elusive Nia-L intermediates. We unveiled the protonation states of a proton-accepting glutamate and a Ni-bound cysteine residue in the Nia-L1, Nia-L2, and the hydride-binding Nia-C intermediates as well as previously unknown conformational changes of amino acid residues in proximity of the bimetallic active site. As such, this study unravels the complexity of the Nia-L intermediate and reveals the importance of the protein scaffold in fine-tuning proton and electron dynamics in [NiFe]-hydrogenase.
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Affiliation(s)
- Armel F T Waffo
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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Labidi RJ, Faivre B, Carpentier P, Veronesi G, Solé-Daura A, Bjornsson R, Léger C, Gotico P, Li Y, Atta M, Fontecave M. Light-Driven Hydrogen Evolution Reaction Catalyzed by a Molybdenum-Copper Artificial Hydrogenase. J Am Chem Soc 2023. [PMID: 37307141 DOI: 10.1021/jacs.3c01350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Orange protein (Orp) is a small bacterial metalloprotein of unknown function that harbors a unique molybdenum/copper (Mo/Cu) heterometallic cluster, [S2MoS2CuS2MoS2]3-. In this paper, the performance of Orp as a catalyst for the photocatalytic reduction of protons into H2 has been investigated under visible light irradiation. We report the complete biochemical and spectroscopic characterization of holo-Orp containing the [S2MoS2CuS2MoS2]3- cluster, with docking and molecular dynamics simulations suggesting a positively charged Arg, Lys-containing pocket as the binding site. Holo-Orp exhibits excellent photocatalytic activity, in the presence of ascorbate as the sacrificial electron donor and [Ru(bpy)3]Cl2 as the photosensitizer, for hydrogen evolution with a maximum turnover number of 890 after 4 h irradiation. Density functional theory (DFT) calculations were used to propose a consistent reaction mechanism in which the terminal sulfur atoms are playing a key role in promoting H2 formation. A series of dinuclear [S2MS2M'S2MS2](4n)- clusters, with M = MoVI, WVI and M'(n+) = CuI, FeI, NiI, CoI, ZnII, CdII were assembled in Orp, leading to different M/M'-Orp versions which are shown to display catalytic activity, with the Mo/Fe-Orp catalyst giving a remarkable turnover number (TON) of 1150 after 2.5 h reaction and an initial turnover frequency (TOF°) of 800 h-1 establishing a record among previously reported artificial hydrogenases.
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Affiliation(s)
- Raphaël J Labidi
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11 place Marcellin-Berthelot, 75231 Paris, France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11 place Marcellin-Berthelot, 75231 Paris, France
| | - Philippe Carpentier
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 rue des Martyrs, 38000 Grenoble, France
| | - Giulia Veronesi
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 rue des Martyrs, 38000 Grenoble, France
| | - Albert Solé-Daura
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11 place Marcellin-Berthelot, 75231 Paris, France
| | - Ragnar Bjornsson
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 rue des Martyrs, 38000 Grenoble, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, 13009 Marseille, France
| | - Philipp Gotico
- Laboratoire des Mécanismes Fondamentaux de la Bioénergétique, DRF/JOLIOT/SB2SM, UMR 9198 CEA/CNRS/I2BC, 91191 Gif Sur Yvette, France
| | - Yun Li
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11 place Marcellin-Berthelot, 75231 Paris, France
| | - Mohamed Atta
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11 place Marcellin-Berthelot, 75231 Paris, France
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 rue des Martyrs, 38000 Grenoble, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11 place Marcellin-Berthelot, 75231 Paris, France
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37
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Dent MR, Weaver BR, Roberts MG, Burstyn JN. Carbon Monoxide-Sensing Transcription Factors: Regulators of Microbial Carbon Monoxide Oxidation Pathway Gene Expression. J Bacteriol 2023; 205:e0033222. [PMID: 37154694 PMCID: PMC10210986 DOI: 10.1128/jb.00332-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Carbon monoxide (CO) serves as a source of energy and carbon for a diverse set of microbes found in anaerobic and aerobic environments. The enzymes that bacteria and archaea use to oxidize CO depend upon complex metallocofactors that require accessory proteins for assembly and proper function. This complexity comes at a high energetic cost and necessitates strict regulation of CO metabolic pathways in facultative CO metabolizers to ensure that gene expression occurs only when CO concentrations and redox conditions are appropriate. In this review, we examine two known heme-dependent transcription factors, CooA and RcoM, that regulate inducible CO metabolism pathways in anaerobic and aerobic microorganisms. We provide an analysis of the known physiological and genomic contexts of these sensors and employ this analysis to contextualize known biochemical properties. In addition, we describe a growing list of putative transcription factors associated with CO metabolism that potentially use cofactors other than heme to sense CO.
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Affiliation(s)
- Matthew R. Dent
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian R. Weaver
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Madeleine G. Roberts
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
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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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39
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Chalopin Y, Cramer SP, Arragain S. Phonon-assisted electron-proton transfer in [FeFe] hydrogenases: Topological role of clusters. Biophys J 2023; 122:1557-1567. [PMID: 36960530 PMCID: PMC10147833 DOI: 10.1016/j.bpj.2023.03.027] [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: 11/01/2022] [Revised: 02/27/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023] Open
Abstract
[FeFe] hydrogenases are enzymes that have acquired a unique capacity to synthesize or consume molecular hydrogen (H2). This function relies on a complex catalytic mechanism involving the active site and two distinct electron and proton transfer networks working in concert. By an analysis based on terahertz vibrations of [FeFe] hydrogenase structure, we are able to predict and identify the existence of rate-promoting vibrations at the catalytic site and the coupling with functional residues involved in reported electron and proton transfer networks. Our findings suggest that the positioning of the cluster is influenced by the response of the scaffold to thermal fluctuations, which in turn drives the formation of networks for electron transfer through phonon-assisted mechanisms. Thus, we address the problem of linking the molecular structure to the catalytic function through picosecond dynamics, while raising the functional gain brought by the cofactors or clusters, using the concept of fold-encoded localized vibrations.
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Affiliation(s)
- Yann Chalopin
- Laboratoire d'Energétique Macroscopique et Moléculaire, Combustion (EM2C), CNRS/CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France.
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40
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Beagan DM, Kiernicki JJ, Zeller M, Szymczak NK. A Bidentate Ligand Featuring Ditopic Lewis Acids in the Second Sphere for Selective Substrate Capture and Activation. Angew Chem Int Ed Engl 2023; 62:e202218907. [PMID: 36720708 PMCID: PMC10023486 DOI: 10.1002/anie.202218907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023]
Abstract
We present a ligand platform featuring appended ditopic Lewis acids to facilitate capture/activation of diatomic substrates. We show that incorporation of two 9-borabicyclo[3.3.1]nonane (9-BBN) units on a single carbon tethered to a pyridine pyrazole scaffold maintains a set of unquenched nitrogen donors available to coordinate FeII , ZnII , and NiII . Using hydride ion affinity and competition experiments, we establish an additive effect for ditopic secondary sphere boranes, compared to the monotopic analogue. These effects are exploited to achieve high selectivity for binding NO2 - in the presence of competitive anions such as F- and NO3 - . Finally, we demonstrate hydrazine capture within the second-sphere of metal complexes, followed by unique activation pathways to generate hydrazido and diazene ligands on Zn and Fe, respectively.
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Affiliation(s)
- Daniel M Beagan
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
| | - John J Kiernicki
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
- Present address: Drury University, Department of Chemistry and Physics, 900 North Benton Ave., Springfield, MO 65802, USA
| | - Matthias Zeller
- H.C. Brown Laboratory, Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Nathaniel K Szymczak
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
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41
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Sidabras JW, Stripp ST. A personal account on 25 years of scientific literature on [FeFe]-hydrogenase. J Biol Inorg Chem 2023; 28:355-378. [PMID: 36856864 DOI: 10.1007/s00775-023-01992-5] [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: 11/19/2022] [Accepted: 01/25/2023] [Indexed: 03/02/2023]
Abstract
[FeFe]-hydrogenases are gas-processing metalloenzymes that catalyze H2 oxidation and proton reduction (H2 release) in microorganisms. Their high turnover frequencies and lack of electrical overpotential in the hydrogen conversion reaction has inspired generations of biologists, chemists, and physicists to explore the inner workings of [FeFe]-hydrogenase. Here, we revisit 25 years of scientific literature on [FeFe]-hydrogenase and propose a personal account on 'must-read' research papers and review article that will allow interested scientists to follow the recent discussions on catalytic mechanism, O2 sensitivity, and the in vivo synthesis of the active site cofactor with its biologically uncommon ligands carbon monoxide and cyanide. Focused on-but not restricted to-structural biology and molecular biophysics, we highlight future directions that may inspire young investigators to pursue a career in the exciting and competitive field of [FeFe]-hydrogenase research.
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Affiliation(s)
- Jason W Sidabras
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI, USA, 53226.
| | - Sven T Stripp
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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42
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Garcia AK, Harris DF, Rivier AJ, Carruthers BM, Pinochet-Barros A, Seefeldt LC, Kaçar B. Nitrogenase resurrection and the evolution of a singular enzymatic mechanism. eLife 2023; 12:e85003. [PMID: 36799917 PMCID: PMC9977276 DOI: 10.7554/elife.85003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/16/2023] [Indexed: 02/18/2023] Open
Abstract
The planetary biosphere is powered by a suite of key metabolic innovations that emerged early in the history of life. However, it is unknown whether life has always followed the same set of strategies for performing these critical tasks. Today, microbes access atmospheric sources of bioessential nitrogen through the activities of just one family of enzymes, nitrogenases. Here, we show that the only dinitrogen reduction mechanism known to date is an ancient feature conserved from nitrogenase ancestors. We designed a paleomolecular engineering approach wherein ancestral nitrogenase genes were phylogenetically reconstructed and inserted into the genome of the diazotrophic bacterial model, Azotobacter vinelandii, enabling an integrated assessment of both in vivo functionality and purified nitrogenase biochemistry. Nitrogenase ancestors are active and robust to variable incorporation of one or more ancestral protein subunits. Further, we find that all ancestors exhibit the reversible enzymatic mechanism for dinitrogen reduction, specifically evidenced by hydrogen inhibition, which is also exhibited by extant A. vinelandii nitrogenase isozymes. Our results suggest that life may have been constrained in its sampling of protein sequence space to catalyze one of the most energetically challenging biochemical reactions in nature. The experimental framework established here is essential for probing how nitrogenase functionality has been shaped within a dynamic, cellular context to sustain a globally consequential metabolism.
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Affiliation(s)
- Amanda K Garcia
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | - Derek F Harris
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUnited States
| | - Alex J Rivier
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | - Brooke M Carruthers
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | | | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUnited States
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
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43
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Torres A, Vicent DJ, Collado A, Gómez-Gallego M, de Arellano CR, Sierra MA. Phosphite Bearing [(μ-ADT) RFe 2(CO) 6] (ADT = Azadithiolate) Moieties: A Tool for the Building of Multimetallic [FeFe]-Hydrogenase Mimics. Organometallics 2023. [DOI: 10.1021/acs.organomet.2c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- Alejandro Torres
- Departamento de Química Orgánica, Facultad de Química Universidad Complutense, 28040 Madrid, Spain
| | - Diego J. Vicent
- Departamento de Química Orgánica, Facultad de Química Universidad Complutense, 28040 Madrid, Spain
| | - Alba Collado
- Departamento de Química Inorgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Mar Gómez-Gallego
- Departamento de Química Orgánica, Facultad de Química Universidad Complutense, 28040 Madrid, Spain
| | | | - Miguel A. Sierra
- Departamento de Química Orgánica, Facultad de Química Universidad Complutense, 28040 Madrid, Spain
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44
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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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Chattopadhyay S, Samanta S, Sarkar A, Bhattacharya A, Patra S, Dey A. Silver nanostructure-modified graphite electrode for in-operando SERRS investigation of iron porphyrins during high-potential electrocatalysis. J Chem Phys 2023; 158:044201. [PMID: 36725507 DOI: 10.1063/5.0136333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In-operando spectroscopic observation of the intermediates formed during various electrocatalytic oxidation and reduction reactions is crucial to propose the mechanism of the corresponding reaction. Surface-enhanced resonance Raman spectroscopy coupled to rotating disk electrochemistry (SERRS-RDE), developed about a decade ago, proved to be an excellent spectroscopic tool to investigate the mechanism of heterogeneous oxygen reduction reaction (ORR) catalyzed by synthetic iron porphyrin complexes under steady-state conditions in water. The information about the formation of the intermediates accumulated during the course of the reaction at the electrode interface helped to develop better ORR catalysts with second sphere residues in the porphyrin rings. To date, the application of this SERRS-RDE setup is limited to ORR only because the thiol self-assembled monolayer (SAM)-modified Ag electrode, used as the working electrode in these experiments, suffers from stability issues at more cathodic and anodic potential, where H2O oxidation, CO2 reduction, and H+ reduction reactions occur. The current investigation shows the development of a second-generation SERRS-RDE setup consisting of an Ag nanostructure (AgNS)-modified graphite electrode as the working electrode. These electrodes show higher stability (compared to the conventional thiol SAM-modified Ag electrode) upon exposure to very high cathodic and anodic potential with a good signal-to-noise ratio in the Raman spectra. The behavior of this modified electrode toward ORR is found to be the same as the SAM-modified Ag electrode, and the same ORR intermediates are observed during electrochemical ORR. At higher cathodic potential, the signatures of Fe(0) porphyrin, an important intermediate in H+ and CO2 reduction reactions, was observed at the electrode-water interface.
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Affiliation(s)
- Samir Chattopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Soumya Samanta
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ankita Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Aishik Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Suman Patra
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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Zamader A, Reuillard B, Marcasuzaa P, Bousquet A, Billon L, Espí Gallart JJ, Berggren G, Artero V. Electrode Integration of Synthetic Hydrogenase as Bioinspired and Noble Metal-Free Cathodes for Hydrogen Evolution. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Afridi Zamader
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, Grenoble, Cedex F-38054, France
- Department of Chemistry─Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-75120, Sweden
| | - Bertrand Reuillard
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, Grenoble, Cedex F-38054, France
| | - Pierre Marcasuzaa
- Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
- Bio-inspired Materials Group: Functionalities & Self-Assembly, Universite de Pau et des Pays de l’Adour, E2S UPPA, Pau 64053, France
| | - Antoine Bousquet
- Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Laurent Billon
- Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
- Bio-inspired Materials Group: Functionalities & Self-Assembly, Universite de Pau et des Pays de l’Adour, E2S UPPA, Pau 64053, France
| | - Jose Jorge Espí Gallart
- Eurecat, Centre Tecnologic de Catalunya, Waste, Energy and Environmental Impact Unit, Manresa 08243, Spain
| | - Gustav Berggren
- Department of Chemistry─Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-75120, Sweden
| | - Vincent Artero
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, Grenoble, Cedex F-38054, France
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Begum MS, Das D, Zangrando E, Rahman S, Alodhayb A, Begum MK, Sheikh CM, Miyatake R, Howlader MBH, Karim MR, Chowdhury MB. A dithiocarbazate N,S Schiff base ligand with a long alkyl chain: Synthesis, characterization, DFT study and antimicrobial activity of its Ni(II) complex. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Aguado S, Vicent DJ, Casarrubios L, Ramírez de Arellano C, Sierra MA. Two Complementary Approaches to Silicon-Supported Soluble [FeFe]-Hydrogenase Mimics. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sergio Aguado
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
- Centro de Innovación en Química Avanzada (ORFEO−CINQA), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Diego J. Vicent
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
- Centro de Innovación en Química Avanzada (ORFEO−CINQA), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Luis Casarrubios
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
- Centro de Innovación en Química Avanzada (ORFEO−CINQA), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Carmen Ramírez de Arellano
- Departamento de Química Orgánica, Universidad de Valencia, 46100 Valencia, Spain
- Centro de Innovación en Química Avanzada (ORFEO−CINQA), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Miguel A. Sierra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
- Centro de Innovación en Química Avanzada (ORFEO−CINQA), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
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Patel A, Mulder DW, Söll D, Krahn N. Harnessing selenocysteine to enhance microbial cell factories for hydrogen production. FRONTIERS IN CATALYSIS 2022; 2. [PMID: 36844461 PMCID: PMC9961374 DOI: 10.3389/fctls.2022.1089176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hydrogen is a clean, renewable energy source, that when combined with oxygen, produces heat and electricity with only water vapor as a biproduct. Furthermore, it has the highest energy content by weight of all known fuels. As a result, various strategies have engineered methods to produce hydrogen efficiently and in quantities that are of interest to the economy. To approach the notion of producing hydrogen from a biological perspective, we take our attention to hydrogenases which are naturally produced in microbes. These organisms have the machinery to produce hydrogen, which when cleverly engineered, could be useful in cell factories resulting in large production of hydrogen. Not all hydrogenases are efficient at hydrogen production, and those that are, tend to be oxygen sensitive. Therefore, we provide a new perspective on introducing selenocysteine, a highly reactive proteinogenic amino acid, as a strategy towards engineering hydrogenases with enhanced hydrogen production, or increased oxygen tolerance.
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Affiliation(s)
- Armaan Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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