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Liu B, Lin B, Su H, Sheng X. Quantum chemical studies of the reaction mechanisms of enzymatic CO 2 conversion. Phys Chem Chem Phys 2024; 26:26677-26692. [PMID: 39347748 DOI: 10.1039/d4cp03049d] [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: 10/01/2024]
Abstract
Enzymatic capture and conversion of carbon dioxide (CO2) into value-added chemicals are of great interest in the field of biocatalysis and have a positive impact on climate change. The quantum chemical methods, recognized as valuable tools for studying reaction mechanisms, have been widely employed in investigating the reaction mechanisms of the enzymes involved in CO2 utilization. In this perspective, we review the mechanistic studies of representative enzymes that are either currently used or have the potential for converting CO2, utilizing the quantum chemical cluster approach and the quantum mechanical/molecular mechanical (QM/MM) method. We begin by summarizing current trends in enzymatic CO2 conversion, followed by a brief description of the computational details of quantum chemical methods. Then, a series of representative examples of the computational modeling of biocatalytic CO2 conversion are presented, including the reduction of CO2 to C1 species (carbon monoxide and formate), and the fixation of CO2 to form aliphatic and aromatic carboxylic acids. The microscopic views of reaction mechanisms obtained from these studies are helpful in guiding the rational design of current enzymes and the discovery of novel enzymes with enhanced performance in converting CO2. Additionally, they provide key information for the de novo design of new-to-nature enzymes. To conclude, we present a perspective on the potential combination of machine learning with quantum description in the study of enzymatic conversion of CO2.
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Affiliation(s)
- Baoyan Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Beibei Lin
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Hao Su
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Xiang Sheng
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
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Niks D, Hakopian S, Canchola A, Lin YH, Hille R. Mechanism of Action of Formate Dehydrogenases. J Am Chem Soc 2024; 146:28601-28604. [PMID: 39382156 PMCID: PMC11503769 DOI: 10.1021/jacs.4c07376] [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: 05/30/2024] [Revised: 09/27/2024] [Accepted: 09/30/2024] [Indexed: 10/10/2024]
Abstract
The molybdenum- and tungsten-containing formate dehydrogenases from a variety of microorganisms catalyze the reversible interconversion of formate and CO2; several, in fact, function as CO2 reductases in the reverse direction under physiological conditions. CO2 reduction catalyzed by these enzymes occurs under mild temperature and pressure rather than the elevated conditions required for current industrial processes. Given the contemporary importance of remediation of atmospheric CO2 to address global warming, there has been considerable interest in the application of these enzymes in bioreactors. Equally important, understanding the detailed means by which these biological catalysts convert CO2 to formate, a useful and easily transported feedstock chemical, might also inspire the development of a new generation of highly efficient, biomimetic synthetic catalysts. Here we have examined the ability of the FdsDABG formate dehydrogenase from Cupriavidus necator to catalyze the exchange of solvent oxygen into product CO2 during the course of formate oxidation under single-turnover conditions. Negligible incorporation of 18O is observed when the experiment is performed in H218O, indicating that bicarbonate cannot be the immediate product of the enzyme-catalyzed reaction, as previously concluded. These results, in conjunction with the observation that the reductive half-reaction exhibits mildly acid-catalyzed rather than base-catalyzed chemistry, are consistent with a reaction mechanism involving direct hydride transfer from formate to the enzyme's molybdenum center, directly yielding CO2. Our results are inconsistent with any mechanism in which the initial product formed on oxidation of formate is bicarbonate.
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Affiliation(s)
- Dimitri Niks
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Sheron Hakopian
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Alexa Canchola
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Ying-Hsuan Lin
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Russ Hille
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
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3
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Trevino RE, Fuller JT, Reid DJ, Laureanti JA, Ginovska B, Linehan JC, Shaw WJ. Understanding the role of negative charge in the scaffold of an artificial enzyme for CO 2 hydrogenation on catalysis. J Biol Inorg Chem 2024; 29:625-638. [PMID: 39207604 DOI: 10.1007/s00775-024-02070-0] [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: 04/26/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024]
Abstract
We have approached the construction of an artificial enzyme by employing a robust protein scaffold, lactococcal multidrug resistance regulator, LmrR, providing a structured secondary and outer coordination spheres around a molecular rhodium complex, [RhI(PEt2NglyPEt2)2]-. Previously, we demonstrated a 2-3 fold increase in activity for one Rh-LmrR construct by introducing positive charge in the secondary coordination sphere. In this study, a series of variants was made through site-directed mutagenesis where the negative charge is located in the secondary sphere or outer coordination sphere, with additional variants made with increasingly negative charge in the outer coordination sphere while keeping a positive charge in the secondary sphere. Placing a negative charge in the secondary or outer coordination sphere demonstrates decreased activity by a factor of two compared to the wild-type Rh-LmrR. Interestingly, addition of positive charge in the secondary sphere, with the negatively charged outer coordination sphere restores activity. Vibrational and NMR spectroscopy suggest minimal changes to the electronic density at the rhodium center, regardless of inclusion of a negative or positive charge in the secondary sphere, suggesting another mechanism is impacting catalytic activity, explored in the discussion.
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Affiliation(s)
- Regina E Trevino
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - Jack T Fuller
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - Deseree J Reid
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - Joseph A Laureanti
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
- Admiral Instruments, Tempe, AZ, 85281, USA
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - John C Linehan
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA
| | - Wendy J Shaw
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN J7-10, PO Box 999, Richland, WA, 99352, USA.
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4
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Vilela-Alves G, Manuel RR, Viegas A, Carpentier P, Biaso F, Guigliarelli B, Pereira IAC, Romão MJ, Mota C. Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement. Chem Sci 2024; 15:13090-13101. [PMID: 39148770 PMCID: PMC11323313 DOI: 10.1039/d4sc02394c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/16/2024] [Indexed: 08/17/2024] Open
Abstract
Metal-dependent formate dehydrogenases are very promising targets for enzyme optimization and design of bio-inspired catalysts for CO2 reduction, towards innovative strategies for climate change mitigation. For effective application of these enzymes, the catalytic mechanism must be better understood, and the molecular determinants clarified. Despite numerous studies, several doubts persist, namely regarding the role played by the possible dissociation of the SeCys ligand from the Mo/W active site. Additionally, the oxygen sensitivity of these enzymes must also be understood as it poses an important obstacle for biotechnological applications. This work presents a combined biochemical, spectroscopic, and structural characterization of Desulfovibrio vulgaris FdhAB (DvFdhAB) when exposed to oxygen in the presence of a substrate (formate or CO2). This study reveals that O2 inactivation is promoted by the presence of either substrate and involves forming a different species in the active site, captured in the crystal structures, where the SeCys ligand is displaced from tungsten coordination and replaced by a dioxygen or peroxide molecule. This form was reproducibly obtained and supports the conclusion that, although W-DvFdhAB can catalyse the oxidation of formate in the presence of oxygen for some minutes, it gets irreversibly inactivated after prolonged O2 exposure in the presence of either substrate.
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Affiliation(s)
- Guilherme Vilela-Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Rita R Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
| | - Aldino Viegas
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Philippe Carpentier
- European Synchrotron Radiation Facility Grenoble France
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM), Université Grenoble Alpes, CNRS, CEA Grenoble France
| | - Frédéric Biaso
- Aix Marseille Univ, CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines Marseille 13402 France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines Marseille 13402 France
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
| | - Maria João Romão
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
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5
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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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6
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Contreras-Martínez OI, Angulo-Ortíz A, Santafé-Patiño G, Aviña-Padilla K, Velasco-Pareja MC, Yasnot MF. Transcriptional Reprogramming of Candida tropicalis in Response to Isoespintanol Treatment. J Fungi (Basel) 2023; 9:1199. [PMID: 38132799 PMCID: PMC10744401 DOI: 10.3390/jof9121199] [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: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Candida tropicalis, an opportunistic pathogen, ranks among the primary culprits of invasive candidiasis, a condition notorious for its resistance to conventional antifungal drugs. The urgency to combat these drug-resistant infections has spurred the quest for novel therapeutic compounds, with a particular focus on those of natural origin. In this study, we set out to evaluate the impact of isoespintanol (ISO), a monoterpene derived from Oxandra xylopioides, on the transcriptome of C. tropicalis. Leveraging transcriptomics, our research aimed to unravel the intricate transcriptional changes induced by ISO within this pathogen. Our differential gene expression analysis unveiled 186 differentially expressed genes (DEGs) in response to ISO, with a striking 85% of these genes experiencing upregulation. These findings shed light on the multifaceted nature of ISO's influence on C. tropicalis, spanning a spectrum of physiological, structural, and metabolic adaptations. The upregulated DEGs predominantly pertained to crucial processes, including ergosterol biosynthesis, protein folding, response to DNA damage, cell wall integrity, mitochondrial activity modulation, and cellular responses to organic compounds. Simultaneously, 27 genes were observed to be repressed, affecting functions such as cytoplasmic translation, DNA damage checkpoints, membrane proteins, and metabolic pathways like trans-methylation, trans-sulfuration, and trans-propylamine. These results underscore the complexity of ISO's antifungal mechanism, suggesting that it targets multiple vital pathways within C. tropicalis. Such complexity potentially reduces the likelihood of the pathogen developing rapid resistance to ISO, making it an attractive candidate for further exploration as a therapeutic agent. In conclusion, our study provides a comprehensive overview of the transcriptional responses of C. tropicalis to ISO exposure. The identified molecular targets and pathways offer promising avenues for future research and the development of innovative antifungal therapies to combat infections caused by this pathogenic yeast.
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Affiliation(s)
| | - Alberto Angulo-Ortíz
- Chemistry Department, Faculty of Basic Sciences, University of Córdoba, Montería 230002, Colombia; (A.A.-O.); (G.S.-P.)
| | - Gilmar Santafé-Patiño
- Chemistry Department, Faculty of Basic Sciences, University of Córdoba, Montería 230002, Colombia; (A.A.-O.); (G.S.-P.)
| | - Katia Aviña-Padilla
- Center for Research and Advanced Studies of the I.P.N. Unit Irapuato, Irapuato 36821, Mexico;
| | - María Camila Velasco-Pareja
- Bacteriology Department, Faculty of Health Sciences, University of Córdoba, Montería 230002, Colombia; (M.C.V.-P.); (M.F.Y.)
| | - María Fernanda Yasnot
- Bacteriology Department, Faculty of Health Sciences, University of Córdoba, Montería 230002, Colombia; (M.C.V.-P.); (M.F.Y.)
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7
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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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8
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Chaudière J. Biological and Catalytic Properties of Selenoproteins. Int J Mol Sci 2023; 24:10109. [PMID: 37373256 DOI: 10.3390/ijms241210109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Selenocysteine is a catalytic residue at the active site of all selenoenzymes in bacteria and mammals, and it is incorporated into the polypeptide backbone by a co-translational process that relies on the recoding of a UGA termination codon into a serine/selenocysteine codon. The best-characterized selenoproteins from mammalian species and bacteria are discussed with emphasis on their biological function and catalytic mechanisms. A total of 25 genes coding for selenoproteins have been identified in the genome of mammals. Unlike the selenoenzymes of anaerobic bacteria, most mammalian selenoenzymes work as antioxidants and as redox regulators of cell metabolism and functions. Selenoprotein P contains several selenocysteine residues and serves as a selenocysteine reservoir for other selenoproteins in mammals. Although extensively studied, glutathione peroxidases are incompletely understood in terms of local and time-dependent distribution, and regulatory functions. Selenoenzymes take advantage of the nucleophilic reactivity of the selenolate form of selenocysteine. It is used with peroxides and their by-products such as disulfides and sulfoxides, but also with iodine in iodinated phenolic substrates. This results in the formation of Se-X bonds (X = O, S, N, or I) from which a selenenylsulfide intermediate is invariably produced. The initial selenolate group is then recycled by thiol addition. In bacterial glycine reductase and D-proline reductase, an unusual catalytic rupture of selenium-carbon bonds is observed. The exchange of selenium for sulfur in selenoproteins, and information obtained from model reactions, suggest that a generic advantage of selenium compared with sulfur relies on faster kinetics and better reversibility of its oxidation reactions.
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Affiliation(s)
- Jean Chaudière
- CBMN (CNRS, UMR 5248), University of Bordeaux, 33600 Pessac, France
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9
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Meneghello M, Uzel A, Broc M, Manuel RR, Magalon A, Léger C, Pereira IAC, Walburger A, Fourmond V. Electrochemical Kinetics Support a Second Coordination Sphere Mechanism in Metal-Based Formate Dehydrogenase. Angew Chem Int Ed Engl 2023; 62:e202212224. [PMID: 36465058 PMCID: PMC10107981 DOI: 10.1002/anie.202212224] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/28/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022]
Abstract
Metal-based formate dehydrogenases are molybdenum or tungsten-dependent enzymes that catalyze the interconversion between formate and CO2 . According to the current consensus, the metal ion of the catalytic center in its active form is coordinated by 6 S (or 5 S and 1 Se) atoms, leaving no free coordination sites to which formate could bind to the metal. Some authors have proposed that one of the active site ligands decoordinates during turnover to allow formate binding. Another proposal is that the oxidation of formate takes place in the second coordination sphere of the metal. Here, we have used electrochemical steady-state kinetics to elucidate the order of the steps in the catalytic cycle of two formate dehydrogenases. Our results strongly support the "second coordination sphere" hypothesis.
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Affiliation(s)
- Marta Meneghello
- CNRSAix Marseille UniversitéBIPIMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Alexandre Uzel
- CNRSAix Marseille UniversitéBIPIMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
- Aix Marseille UniversitéCNRSLaboratoire de Chimie Bactérienne (UMR7283)IMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Marianne Broc
- Aix Marseille UniversitéCNRSLaboratoire de Chimie Bactérienne (UMR7283)IMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Rita R. Manuel
- Instituto de Tecnologia Quimica e Biologica Antonio Xavier (ITQB NOVA)Universidade Nova de LisboaOeirasPortugal
| | - Axel Magalon
- Aix Marseille UniversitéCNRSLaboratoire de Chimie Bactérienne (UMR7283)IMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Christophe Léger
- CNRSAix Marseille UniversitéBIPIMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Inês A. C. Pereira
- Instituto de Tecnologia Quimica e Biologica Antonio Xavier (ITQB NOVA)Universidade Nova de LisboaOeirasPortugal
| | - Anne Walburger
- Aix Marseille UniversitéCNRSLaboratoire de Chimie Bactérienne (UMR7283)IMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
| | - Vincent Fourmond
- CNRSAix Marseille UniversitéBIPIMMIM2B31 Chemin J. Aiguier13009MarseilleFrance
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10
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Vilela-Alves G, Manuel RR, Oliveira AR, Pereira IC, Romão MJ, Mota C. Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation. Int J Mol Sci 2022; 24:ijms24010476. [PMID: 36613918 PMCID: PMC9820355 DOI: 10.3390/ijms24010476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO2 to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we report a time-resolved characterization by X-ray crystallography of the Desulfovibrio vulgaris Hildenborough SeCys/W-Fdh during formate oxidation. The results allowed us to model five different intermediate structures and to chronologically map the changes occurring during enzyme reduction. Formate molecules were assigned for the first time to populate the catalytic pocket of a Fdh. Finally, the redox reversibility of DvFdhAB in crystals was confirmed by reduction and reoxidation structural studies.
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Affiliation(s)
- Guilherme Vilela-Alves
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Inês Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria João Romão
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Correspondence:
| | - Cristiano Mota
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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11
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Laun K, Duffus BR, Wahlefeld S, Katz S, Belger D, Hildebrandt P, Mroginski MA, Leimkühler S, Zebger I. Infrared Spectroscopy Elucidates the Inhibitor Binding Sites in a Metal-Dependent Formate Dehydrogenase. Chemistry 2022; 28:e202201091. [PMID: 35662280 PMCID: PMC9804402 DOI: 10.1002/chem.202201091] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Indexed: 01/05/2023]
Abstract
Biological carbon dioxide (CO2 ) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.
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Affiliation(s)
- Konstantin Laun
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Benjamin R. Duffus
- Institut für Biochemie und BiologieMolekulare EnzymologieUniversität PotsdamKarl-Liebknecht-Strasse 24–2514476PotsdamGermany
| | - Stefan Wahlefeld
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
- Institut für Technische BiokatalyseTechnische Universität HamburgDenickestr. 1521073HamburgGermany
| | - Sagie Katz
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Dennis Belger
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Peter Hildebrandt
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Maria Andrea Mroginski
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Silke Leimkühler
- Institut für Biochemie und BiologieMolekulare EnzymologieUniversität PotsdamKarl-Liebknecht-Strasse 24–2514476PotsdamGermany
| | - Ingo Zebger
- Institut für ChemieMax-Volmer-Laboratorium für Biophysikalische ChemiePC14Technische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
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12
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
- Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan
- Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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13
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Oliveira AR, Mota C, Klymanska K, Biaso F, Romão MJ, Guigliarelli B, Pereira IC. Spectroscopic and Structural Characterization of Reduced Desulfovibrio vulgaris Hildenborough W-FdhAB Reveals Stable Metal Coordination during Catalysis. ACS Chem Biol 2022; 17:1901-1909. [PMID: 35766974 PMCID: PMC9774666 DOI: 10.1021/acschembio.2c00336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO2 reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from Desulfovibrio vulgaris Hildenborough is a good example displaying high activity, simple composition, and a notable structural and catalytic robustness. Here, we report the first spectroscopic redox characterization of FdhAB metal centers by EPR. Titration with dithionite or formate leads to reduction of three [4Fe-4S]1+ clusters, and full reduction requires Ti(III)-citrate. The redox potentials of the four [4Fe-4S]1+ centers range between -250 and -530 mV. Two distinct WV signals were detected, WDV and WFV, which differ in only the g2-value. This difference can be explained by small variations in the twist angle of the two pyranopterins, as determined through DFT calculations of model compounds. The redox potential of WVI/V was determined to be -370 mV when reduced by dithionite and -340 mV when reduced by formate. The crystal structure of dithionite-reduced FdhAB was determined at high resolution (1.5 Å), revealing the same structural alterations as reported for the formate-reduced structure. These results corroborate a stable six-ligand W coordination in the catalytic intermediate WV state of FdhAB.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cristiano Mota
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Kateryna Klymanska
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Frédéric Biaso
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, Aix Marseille Univ, CNRS, BIP, Marseille 13402, France
| | - Maria João Romão
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,UCIBIO,
Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA
School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal,
| | - Bruno Guigliarelli
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, Aix Marseille Univ, CNRS, BIP, Marseille 13402, France,
| | - Inês Cardoso Pereira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal,
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14
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Membrane-anchored HDCR nanowires drive hydrogen-powered CO 2 fixation. Nature 2022; 607:823-830. [PMID: 35859174 DOI: 10.1038/s41586-022-04971-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 06/13/2022] [Indexed: 01/11/2023]
Abstract
Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive1. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO2 fixation-hydrogen-dependent CO2 reductase (HDCR)2,3-which directly converts H2 and CO2 into formic acid. HDCR reduces CO2 with a higher activity than any other known biological or chemical catalyst4,5, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO2. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.
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15
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Nazemi A, Steeves AH, Kastner DW, Kulik HJ. Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase. J Phys Chem B 2022; 126:4069-4079. [PMID: 35609244 DOI: 10.1021/acs.jpcb.2c02260] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Mo/W-containing metalloenzyme formate dehydrogenase (FDH) is an efficient and selective natural catalyst that reversibly converts CO2 to formate under ambient conditions. In this study, we investigate the impact of the greater protein environment on the electrostatic potential (ESP) of the active site. To model the enzyme environment, we used a combination of classical molecular dynamics and multiscale quantum-mechanical (QM)/molecular-mechanical (MM) simulations. We leverage charge shift analysis to systematically construct QM regions and analyze the electronic environment of the active site by evaluating the degree of charge transfer between the core active site and the protein environment. The contribution of the terminal chalcogen ligand to the ESP of the metal center is substantial and dependent on the chalcogen identity, with similar, less negative ESPs for Se and S terminal chalcogens in comparison to O regardless of whether the metal is Mo or W. The orientation of the side chains and conformations of the cofactor also affect the ESP, highlighting the importance of sampling dynamic fluctuations in the protein. Overall, our observations suggest that the terminal chalcogen ligand identity plays an important role in the enzymatic activity of FDH, suggesting opportunities for a rational bioinspired catalyst design.
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Affiliation(s)
- Azadeh Nazemi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam H Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David W Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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16
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Wiedner ES, Appel AM, Raugei S, Shaw WJ, Bullock RM. Molecular Catalysts with Diphosphine Ligands Containing Pendant Amines. Chem Rev 2022; 122:12427-12474. [PMID: 35640056 DOI: 10.1021/acs.chemrev.1c01001] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Pendant amines play an invaluable role in chemical reactivity, especially for molecular catalysts based on earth-abundant metals. As inspired by [FeFe]-hydrogenases, which contain a pendant amine positioned for cooperative bifunctionality, synthetic catalysts have been developed to emulate this multifunctionality through incorporation of a pendant amine in the second coordination sphere. Cyclic diphosphine ligands containing two amines serve as the basis for a class of catalysts that have been extensively studied and used to demonstrate the impact of a pendant base. These 1,5-diaza-3,7-diphosphacyclooctanes, now often referred to as "P2N2" ligands, have profound effects on the reactivity of many catalysts. The resulting [Ni(PR2NR'2)2]2+ complexes are electrocatalysts for both the oxidation and production of H2. Achieving the optimal benefit of the pendant amine requires that it has suitable basicity and is properly positioned relative to the metal center. In addition to the catalytic efficacy demonstrated with [Ni(PR2NR'2)2]2+ complexes for the oxidation and production of H2, catalysts with diphosphine ligands containing pendant amines have also been demonstrated for several metals for many different reactions, both in solution and immobilized on surfaces. The impact of pendant amines in catalyst design continues to expand.
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17
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Succinylated isoniazid potential prodrug: Design of Experiments (DoE) for synthesis optimization and computational study of the reaction mechanism by DFT calculations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Siegbahn PEM. Energetics for CO 2 Reduction by Molybdenum-Containing Formate Dehydrogenase. J Phys Chem B 2022; 126:1728-1733. [PMID: 35192765 PMCID: PMC8900120 DOI: 10.1021/acs.jpcb.2c00151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/12/2022] [Indexed: 11/28/2022]
Abstract
The level of carbon dioxide in the atmosphere has increased in a dangerous way during the past century. Methods to decrease this level are therefore of high interest at present. Inspiration to do so in an efficient way could come from biological systems. Molybdenum-containing formate dehydrogenase (Mo-FDH) is one of the most interesting enzymes in this respect. For example, the reduction potential required is not very low. The normal reaction catalyzed by Mo-FDH is actually the opposite one of oxidizing formate to CO2. However, recent electrochemical studies have shown that the reaction can be reversed by a moderate lowering of the reduction potential. The goal of the present study has been to study the full mechanism of Mo-FDH, particularly in the most interesting direction of reducing CO2, which has not been done before. The methods used are the same as those that have been shown to give excellent results for redox enzymes in all cases they have been tested. The results obtained for Mo-FDH are also in excellent agreement with the experimental results.
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Affiliation(s)
- Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius
Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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19
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Liu M, Nazemi A, Taylor MG, Nandy A, Duan C, Steeves AH, Kulik HJ. Large-Scale Screening Reveals That Geometric Structure Matters More Than Electronic Structure in the Bioinspired Catalyst Design of Formate Dehydrogenase Mimics. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Mingjie Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Azadeh Nazemi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael G. Taylor
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chenru Duan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam H. Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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Abstract
The accumulation of carbon dioxide in the atmosphere as a result of human activities has caused a number of adverse circumstances in the world. For this reason, the proposed solutions lie within the aim of reducing carbon dioxide emissions have been quite valuable. However, as the human activity continues to increase on this planet, the possibility of reducing carbon dioxide emissions decreases with the use of conventional methods. The emergence of compounds than can be used in different fields by converting the released carbon dioxide into different chemicals will construct a fundamental solution to the problem. Although electro-catalysis or photolithography methods have emerged for this purpose, they have not been able to achieve successful results. Alternatively, another proposed solution are enzyme based systems. Among the enzyme-based systems, pyruvate decarboxylase, carbonic anhydrase and dehydrogenases have been the most studied enzymes. Pyruvate dehydrogenase and carbonic anhydrase have either been an expensive method or were incapable of producing the desired result due to the reaction cascade they catalyze. However, the studies reporting the production of industrial chemicals from carbon dioxide using dehydrogenases and in particular, the formate dehydrogenase enzyme, have been remarkable. Moreover, reported studies have shown the existence of more active and stable enzymes, especially the dehydrogenase family that can be identified from the biome. In addition to this, their redesign through protein engineering can have an immense contribution to the increased use of enzyme-based methods in CO2 reduction, resulting in an enormous expansion of the industrial capacity.
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21
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Ribeiro PMG, Fernandes HS, Maia LB, Sousa SF, Moura JJG, Cerqueira NMFSA. The complete catalytic mechanism of xanthine oxidase: a computational study. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01029d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this article, quantum mechanical/molecular mechanical (QM/MM) methods were used to study the full catalytic mechanism of xanthine oxidase (XO).
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Affiliation(s)
- Pedro M. G. Ribeiro
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - Henrique S. Fernandes
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - Luísa B. Maia
- LAQV
- REQUIMTE
- NOVA School of Science and Technology
- Campus de Caparica
- 2829-516 Caparica
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
| | - José J. G. Moura
- LAQV
- REQUIMTE
- NOVA School of Science and Technology
- Campus de Caparica
- 2829-516 Caparica
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina da Universidade do Porto
- Alameda Professor Hernâni Monteiro
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22
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Dong G, Lin LR, Xu LY, Li EM. Reaction mechanism of lysyl oxidase-like 2 (LOXL2) studied by computational methods. J Inorg Biochem 2020; 211:111204. [PMID: 32801097 DOI: 10.1016/j.jinorgbio.2020.111204] [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: 04/14/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 02/05/2023]
Abstract
Lysyl oxidase-like 2 (LOXL2) is a copper-dependent amine oxidase that catalyzes the oxidative deamination of the ε-amino group of lysines/hydroxylysines on substrate proteins (collagen and elastin) to form aldehyde groups. The generated aldehyde groups are of significance in crosslinking with the adjacent aldehyde or ε-amino group on proteins in extracellular matrix. In this paper, we have studied the reaction mechanism of LOXL2 by means of quantum mechanics (QM) and combined QM and molecular mechanics (QM/MM) methods. This study is divided into two parts, i.e. the biosynthesis of lysine tyrosylquinone (LTQ) cofactor and oxidative deamination of ε-amino group of lysine by LTQ. For the former part, the reaction is driven by a large exothermicity of about 284 kJ/mol. Dopaquinone radical (DPQr) is suggested to be an intermediate state in this reaction. In addition, His652 residue is predicted to serve as proton acceptor. The rate-determining step for the biosynthesis of LTQ is found to be hydrogen-atom abstraction from the benzene ring on substrate by Cu2+-hydroxide, which is a proton-coupled electron transfer (PCET) process with an energy barrier of 84 kJ/mol. For the latter part, the reaction is exothermic by about 145 kJ/mol, and the copper ion is proposed to play a role of redox catalyst in the last step to generate the product of aldehyde. However, the copper ion might not be indispensable for the latter part, which is consistent with the previous study.
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Affiliation(s)
- Geng Dong
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, PR China; Medical Informatics Research Center, Shantou University Medical College, Shantou 515041, PR China.
| | - Li-Rui Lin
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, PR China; Medical Informatics Research Center, Shantou University Medical College, Shantou 515041, PR China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, PR China; Cancer Research Center, Shantou University Medical College, Shantou 515041, PR China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, PR China; Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, PR China.
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23
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Ren S, Wang Z, Bilal M, Feng Y, Jiang Y, Jia S, Cui J. Co-immobilization multienzyme nanoreactor with co-factor regeneration for conversion of CO2. Int J Biol Macromol 2020; 155:110-118. [DOI: 10.1016/j.ijbiomac.2020.03.177] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 01/13/2023]
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24
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Laureanti JA, Ginovska B, Buchko GW, Schenter GK, Hebert M, Zadvornyy OA, Peters JW, Shaw WJ. A Positive Charge in the Outer Coordination Sphere of an Artificial Enzyme Increases CO2 Hydrogenation. Organometallics 2020. [DOI: 10.1021/acs.organomet.9b00843] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph A. Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bojana Ginovska
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Gregory K. Schenter
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Margaret Hebert
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - John W. Peters
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Wendy J. Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Oliveira AR, Mota C, Mourato C, Domingos RM, Santos MFA, Gesto D, Guigliarelli B, Santos-Silva T, Romão MJ, Cardoso Pereira IA. Toward the Mechanistic Understanding of Enzymatic CO2 Reduction. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00086] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Cristiano Mota
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Cláudia Mourato
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Renato M. Domingos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Marino F. A. Santos
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Diana Gesto
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Bruno Guigliarelli
- Aix Marseille Université, CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Teresa Santos-Silva
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria João Romão
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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Fernandes HS, Teixeira CSS, Sousa SF, Cerqueira NMFSA. Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:E2462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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Affiliation(s)
- Henrique S Fernandes
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
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Cordas CM, Campaniço M, Baptista R, Maia LB, Moura I, Moura JJG. Direct electrochemical reduction of carbon dioxide by a molybdenum-containing formate dehydrogenase. J Inorg Biochem 2019; 196:110694. [PMID: 31005821 DOI: 10.1016/j.jinorgbio.2019.110694] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/03/2019] [Accepted: 04/12/2019] [Indexed: 11/19/2022]
Abstract
Formate dehydrogenase enzymes catalyse the reversible two-electron oxidation of formate to carbon dioxide. The class of metal-dependent formate dehydrogenases comprises prokaryotic enzymes holding redox-active centres and a catalytic site, containing either molybdenum or tungsten ion, that mediates the formate/carbon dioxide interconversion. The carbon dioxide reduction is of a particular interest, since it may be a route for its atmospheric mitigation with the simultaneous production of added-value products, as formate-derived compounds. Recently, the periplasmic formate dehydrogenase from Desulfovibrio desulfuricans, a molybdenum-containing enzyme, was proven to be an efficient enzyme for the CO2 reduction to formate. In this work, the immobilized formate dehydrogenase isolated from Desulfovibrio desulfuricans direct electrochemical behaviour was attained in the presence and absence of substrates and the formal potentials associated with the catalytic centre transitions were determined in non-turnover conditions. The enzyme catalytic activity towards carbon dioxide reduction was observed using direct electrochemical methods.
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Affiliation(s)
- Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT NOVA), 2829-516 Caparica, Portugal.
| | - Mariana Campaniço
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT NOVA), 2829-516 Caparica, Portugal
| | - Rita Baptista
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT NOVA), 2829-516 Caparica, Portugal
| | - Luísa B Maia
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT NOVA), 2829-516 Caparica, Portugal
| | - Isabel Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT NOVA), 2829-516 Caparica, Portugal
| | - José J G Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT NOVA), 2829-516 Caparica, Portugal.
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Seo J, Shearer J, Williard PG, Kim E. Reactivity of a biomimetic W(iv) bis-dithiolene complex with CO2 leading to formate production and structural rearrangement. Dalton Trans 2019; 48:17441-17444. [DOI: 10.1039/c9dt03906f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mononuclear W(iv) bis-dithiolene complex reduces CO2 to formate while generating a dinuclear W(v) complex.
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Affiliation(s)
- Junhyeok Seo
- Department of Chemistry
- Gwangju Institute of Science and Technology
- Gwangju 61005
- Republic of Korea
| | - Jason Shearer
- Department of Chemistry
- Trinity University
- San Antonio
- USA
| | | | - Eunsuk Kim
- Department of Chemistry
- Brown University
- Providence
- USA
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