1
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Kass D, Larson VA, Corona T, Kuhlmann U, Hildebrandt P, Lohmiller T, Bill E, Lehnert N, Ray K. Trapping of a phenoxyl radical at a non-haem high-spin iron(II) centre. Nat Chem 2024; 16:658-665. [PMID: 38216752 DOI: 10.1038/s41557-023-01405-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 11/17/2023] [Indexed: 01/14/2024]
Abstract
The activation of dioxygen at haem and non-haem metal centres, and subsequent functionalization of unactivated C‒H bonds, has been a focal point of much research. In iron-mediated oxidation reactions, O2 binding at an iron(II) centre is often accompanied by an oxidation of the iron centre. Here we demonstrate dioxygen activation by sodium tetraphenylborate and protons in the presence of an iron(II) complex to form a reactive radical species, whereby the iron oxidation state remains unaltered in the presence of a highly oxidizing phenoxyl radical and O2. This complex, containing an unusual iron(II)-phenoxyl radical motif, represents an elusive example of a spectroscopically characterized oxygen-derived iron(II)-reactive intermediate during chemical and biological dioxygen activation at haem and non-haem iron active centres. The present report opens up strategies for the stabilization of a phenoxyl radical cofactor, with its full oxidizing capabilities, to act as an independent redox centre next to an iron(II) site during substrate oxidation reactions.
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Affiliation(s)
- Dustin Kass
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Virginia A Larson
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Teresa Corona
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Uwe Kuhlmann
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Thomas Lohmiller
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
- EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, Germany
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
| | - Kallol Ray
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany.
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2
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Ussembayev Y, Beunis F, Oorlynck L, Bahrami M, Strubbe F, Neyts K. Single Elementary Charge Fluctuations on Nanoparticles in Aqueous Solution. ACS NANO 2023; 17:22952-22959. [PMID: 37787115 DOI: 10.1021/acsnano.3c08161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
100 years ago, in 1923, the Nobel prize in physics was awarded for measurement of the unit charge. In addition to a profound impact on contemporary physics, this discovery has reshaped our understanding of charge-based interactions in chemistry and biology, ranging from oxidation and ionization to protein folding and metabolism. In a liquid, the discrete nature of the electric charge becomes prominent at the nanoscale when a charge carrier is exchanged between a molecule or a nanoparticle and the surrounding medium. However, our ability to observe the dynamics of such interactions at the level of a single elementary charge is limited due to the abundance of ions in water. Here, we report on the observation of single binding-unbinding events with elementary charge resolution at the surface of a nanoparticle suspended in water. Discrete steps in the electrical charge are revealed by analyzing the motion of optically trapped nanoparticles under the influence of an applied sinusoidal electric field. The measurements are sufficiently fast and long to observe individual (dis)charging events that occur on average every 3 s. Our results offer prospective routes for studying the dynamics of diverse chemical and biological phenomena on the nanoscale with elementary charge resolution.
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Affiliation(s)
- Yera Ussembayev
- LCP Research Group, Ghent University, Technologiepark 126, 9052 Gent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Technologiepark 126, 9052 Gent, Belgium
| | - Filip Beunis
- LCP Research Group, Ghent University, Technologiepark 126, 9052 Gent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Technologiepark 126, 9052 Gent, Belgium
| | - Lucas Oorlynck
- LCP Research Group, Ghent University, Technologiepark 126, 9052 Gent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Technologiepark 126, 9052 Gent, Belgium
| | - Mohammadreza Bahrami
- LCP Research Group, Ghent University, Technologiepark 126, 9052 Gent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Technologiepark 126, 9052 Gent, Belgium
| | - Filip Strubbe
- LCP Research Group, Ghent University, Technologiepark 126, 9052 Gent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Technologiepark 126, 9052 Gent, Belgium
| | - Kristiaan Neyts
- LCP Research Group, Ghent University, Technologiepark 126, 9052 Gent, Belgium
- Center for Nano- and Biophotonics, Ghent University, Technologiepark 126, 9052 Gent, Belgium
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3
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Tsybizova A, Fritsche L, Miloglyadova L, Kräutler B, Chen P. Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B 12 Derivatives? J Am Chem Soc 2023; 145:19561-19570. [PMID: 37656981 PMCID: PMC10510309 DOI: 10.1021/jacs.3c03001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 09/03/2023]
Abstract
Aryl corrins represent a novel class of designed B12 derivatives with biological properties of "antivitamins B12". In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born-Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both "static" DFT calculations and "dynamic" BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made.
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Affiliation(s)
- Alexandra Tsybizova
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Lukas Fritsche
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Larisa Miloglyadova
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Bernhard Kräutler
- Institute
of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Peter Chen
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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4
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Zhang Z, Feng J, Yang C, Cui H, Harrison W, Zhong D, Wang B, Zhao H. Photoenzymatic Enantioselective Intermolecular Radical Hydroamination. Nat Catal 2023; 6:687-694. [PMID: 38501052 PMCID: PMC10948044 DOI: 10.1038/s41929-023-00994-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/30/2023] [Indexed: 03/20/2024]
Abstract
Since the discovery of Hofmann-Löffler-Freytag reaction more than 130 years ago, nitrogen-centered radicals have been widely studied in both structures and reactivities1-2. Nevertheless, catalytic enantioselective intermolecular radical hydroamination remains a challenge due to the existence of side reactions, short lifetime of nitrogen-centered radicals, and lack of understanding of the fundamental catalytic steps. In chemistry, nitrogen-centered radicals are produced with radical initiators, photocatalysts, or electrocatalysts. On the other hand, the generation and reaction of nitrogen-centered radicals are unknown in nature. Here we report a pure biocatalytic system by successfully repurposing an ene-reductase through directed evolution for the photoenzymatic production of nitrogen-centered radicals and enantioselective intermolecular radical hydroaminations. These reactions progress efficiently at room temperature under visible light without any external photocatalysts and exhibit excellent enantioselectivities. Detailed mechanistic study reveals that the enantioselectivity originates from the radical-addition step while the reactivity originates from the ultrafast photoinduced electron transfer (ET) from reduced flavin mononucleotide (FMNH-) to nitrogen-containing substrates.
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Affiliation(s)
- Zhengyi Zhang
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- These authors contributed equally
| | - Jianqiang Feng
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- These authors contributed equally
| | - Chao Yang
- Department of Physics, Programs of Biophysics, Chemical Physics and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Haiyang Cui
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- NSF Molecular Maker Lab Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wesley Harrison
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dongping Zhong
- Department of Physics, Programs of Biophysics, Chemical Physics and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Binju Wang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Huimin Zhao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- NSF Molecular Maker Lab Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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5
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Abstract
Radical S-adenosylmethionine (SAM) enzymes use a site-differentiated [4Fe-4S] cluster and SAM to initiate radical reactions through liberation of the 5'-deoxyadenosyl (5'-dAdo•) radical. They form the largest enzyme superfamily, with more than 700,000 unique sequences currently, and their numbers continue to grow as a result of ongoing bioinformatics efforts. The range of extremely diverse, highly regio- and stereo-specific reactions known to be catalyzed by radical SAM superfamily members is remarkable. The common mechanism of radical initiation in the radical SAM superfamily is the focus of this review. Most surprising is the presence of an organometallic intermediate, Ω, exhibiting an Fe-C5'-adenosyl bond. Regioselective reductive cleavage of the SAM S-C5' bond produces 5'-dAdo• to form Ω, with the regioselectivity originating in the Jahn-Teller effect. Ω liberates the free 5'-dAdo• as the catalytically active intermediate through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12, which was once viewed as biology's choice of radical generator.
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Affiliation(s)
- Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA;
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA;
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6
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Julizan N, Ishmayana S, Zainuddin A, Van Hung P, Kurnia D. Potential of Syzygnium polyanthum as Natural Food Preservative: A Review. Foods 2023; 12:2275. [PMID: 37372486 DOI: 10.3390/foods12122275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/25/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Food preservation is one of the strategies taken to maintain the level of public health. Oxidation activity and microbial contamination are the primary causes of food spoilage. For health reasons, people prefer natural preservatives over synthetic ones. Syzygnium polyanthum is widely spread throughout Asia and is utilized as a spice by the community. S. polyanthum has been found to be rich in phenols, hydroquinones, tannins, and flavonoids, which are potential antioxidants and antimicrobial agents. Consequently, S. polyanthum presents a tremendous opportunity as a natural preservative. This paper reviews recent articles about S. polyanthum dating back to the year 2000. This review summarizes the findings of natural compounds presented in S. polyanthum and their functional properties as antioxidants, antimicrobial agents, and natural preservatives in various types of food.
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Affiliation(s)
- Nur Julizan
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Safri Ishmayana
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Achmad Zainuddin
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Pham Van Hung
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 721400, Vietnam
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia
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7
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Zhou Y, He G, Jiang H, Pan K, Liu W. Nanoplastics induces oxidative stress and triggers lysosome-associated immune-defensive cell death in the earthworm Eisenia fetida. ENVIRONMENT INTERNATIONAL 2023; 174:107899. [PMID: 37054650 DOI: 10.1016/j.envint.2023.107899] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/03/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Nanoplastics (NPs) are increasingly perceived as an emerging threat to terrestrial environments, but the adverse impacts of NPs on soil fauna and the mechanisms behind these negative outcomes remain elusive. Here, a risk assessment of NPs was conducted on model organism (earthworm) from tissue to cell. Using palladium-doped polystyrene NPs, we quantitatively measured nanoplastic accumulation in earthworm and investigated its toxic effects by combining physiological assessment with RNA-Seq transcriptomic analyses. After a 42-day exposure, earthworm accumulated up to 15.9 and 143.3 mg kg-1 of NPs for the low (0.3 mg kg-1) and high (3 mg kg-1) dose groups, respectively. NPs retention led to the decrease of antioxidant enzyme activity and the accumulation of reactive oxygen species (O2- and H2O2), which reduced growth rate by 21.3 %-50.8 % and caused pathological abnormalities. These adverse effects were enhanced by the positively charged NPs. Furthermore, we observed that irrespective of surface charge, after 2 h of exposure, NPs were gradually internalized by earthworm coelomocytes (∼0.12 μg per cell) and mainly amassed at lysosomes. Those agglomerations stimulated lysosomal membranes to lose stability and even rupture, resulting in impeded autophagy process and cellular clearance, and eventually coelomocyte death. In comparison with negatively charged nanoplastics, the positively charged NPs exerted 83 % higher cytotoxicity. Our findings provide a better understanding of how NPs posed harmful effects on soil fauna and have important implications for evaluating the ecological risk of NPs.
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Affiliation(s)
- Yanfei Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China; Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Gang He
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hao Jiang
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
| | - Wenzhi Liu
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, China.
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8
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Gruber K, Csitkovits V, Łyskowski A, Kratky C, Kräutler B. Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues. Angew Chem Int Ed Engl 2022; 61:e202208295. [PMID: 35793207 PMCID: PMC9545868 DOI: 10.1002/anie.202208295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 12/04/2022]
Abstract
Catalysis by radical enzymes dependent on coenzyme B12 (AdoCbl) relies on the reactive primary 5'-deoxy-5'adenosyl radical, which originates from reversible Co-C bond homolysis of AdoCbl. This bond homolysis is accelerated roughly 1012 -fold upon binding the enzyme substrate. The structural basis for this activation is still strikingly enigmatic. As revealed here, a displaced firm adenosine binding cavity in substrate-loaded glutamate mutase (GM) causes a structural misfit for intact AdoCbl that is relieved by the homolytic Co-C bond cleavage. Strategically interacting adjacent adenosine- and substrate-binding protein cavities provide a tight caged radical reaction space, controlling the entire radical path. The GM active site is perfectly structured for promoting radical catalysis, including "negative catalysis", a paradigm for AdoCbl-dependent mutases.
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Affiliation(s)
- Karl Gruber
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- BioTechMed-Graz8010GrazAustria
- Field of Excellence “BioHealth”University of Graz8010GrazAustria
| | - Vanessa Csitkovits
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Andrzej Łyskowski
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- Present address: Department of Biotechnology and BioinformaticsRzeszów University of Technologyal. Powstańców Warszawy 1235-959RzeszówPoland
| | - Christoph Kratky
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Bernhard Kräutler
- Institute of Organic ChemistryUniversity of InnsbruckInnrain 80/826020InnsbruckAustria
- Center of Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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9
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Gruber K, Csitkovits V, Łyskowski A, Kratky C, Kräutler B. Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202208295. [PMID: 38505740 PMCID: PMC10947579 DOI: 10.1002/ange.202208295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 03/21/2024]
Abstract
Catalysis by radical enzymes dependent on coenzyme B12 (AdoCbl) relies on the reactive primary 5'-deoxy-5'adenosyl radical, which originates from reversible Co-C bond homolysis of AdoCbl. This bond homolysis is accelerated roughly 1012-fold upon binding the enzyme substrate. The structural basis for this activation is still strikingly enigmatic. As revealed here, a displaced firm adenosine binding cavity in substrate-loaded glutamate mutase (GM) causes a structural misfit for intact AdoCbl that is relieved by the homolytic Co-C bond cleavage. Strategically interacting adjacent adenosine- and substrate-binding protein cavities provide a tight caged radical reaction space, controlling the entire radical path. The GM active site is perfectly structured for promoting radical catalysis, including "negative catalysis", a paradigm for AdoCbl-dependent mutases.
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Affiliation(s)
- Karl Gruber
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- BioTechMed-Graz8010GrazAustria
- Field of Excellence “BioHealth”University of Graz8010GrazAustria
| | - Vanessa Csitkovits
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Andrzej Łyskowski
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
- Present address: Department of Biotechnology and BioinformaticsRzeszów University of Technologyal. Powstańców Warszawy 1235-959RzeszówPoland
| | - Christoph Kratky
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Bernhard Kräutler
- Institute of Organic ChemistryUniversity of InnsbruckInnrain 80/826020InnsbruckAustria
- Center of Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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10
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Maity AN, Chen JR, Ke SC. Exploring the mechanism of action of lysine 5,6-aminomutase using EPR and ENDOR spectroscopies. Methods Enzymol 2022; 669:197-228. [PMID: 35644172 DOI: 10.1016/bs.mie.2021.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Radical enzymes orchestrate challenging chemical transformations by devising strategies to tame the highly reactive radical intermediates. Electron paramagnetic resonance (EPR) spectroscopy is the most suitable technique to study various aspects of the radical enzymes. Lysine 5,6-aminomutase (5,6-LAM) is one such radical enzyme and employs coenzyme B12 and pyridoxal 5'-phosphate (PLP) to catalyze the 1,2-amino shift reaction through a radical mechanism. 5,6-LAM accepts either d-lysine or l-β-lysine as the substrate. EPR and electron nuclear double resonance (ENDOR) spectroscopies have played major roles in deciphering the mechanism of action of 5,6-LAM, while density functional theoretical (DFT) computation and synthetic isotopologues have played supporting roles. This comprehensive toolkit has revealed that 5,6-LAM undergoes large-scale conformational movement to bring PLP and coenzyme B12 close together, which allows the reaction to progress. The conformational change also closes the active site, which protects the radical intermediates and enables their transformation to product without unwanted side reactions. The substrate-related radical (S•), which is spin-coupled with Co2+ generated from homolysis of the CoC bond in coenzyme B12, was unequivocally characterized when a substrate analog, 4-thia-l-lysine, and isotopologues of it were reacted with 5,6-LAM. Studies with substrate analogs revealed a unique "odd-even" correlation with opening of the closed state. Moreover, mutagenesis studies identified the contributions that conserved residues in 5,6-LAM make toward binding of the substrate. Further studies with a cofactor analog, PLP-N-oxide, have shed light on various aspects of the mechanism of action of 5,6-LAM.
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Affiliation(s)
| | - Jun-Ru Chen
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Shyue-Chu Ke
- Department of Physics, National Dong Hwa University, Hualien, Taiwan.
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11
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Maity AN, Chen JR, Li QY, Ke SC. The Nitrogen Atom of Vitamin B 6 Is Essential for the Catalysis of Radical Aminomutases. Int J Mol Sci 2022; 23:ijms23095210. [PMID: 35563602 PMCID: PMC9105233 DOI: 10.3390/ijms23095210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Radical aminomutases are pyridoxal 5'-phosphate (PLP, a B6 vitamer)-dependent enzymes that require the generation of a 5'-deoxyadenosyl radical to initiate the catalytic cycle, to perform a 1,2 amino group shift reaction. The role of the nitrogen atom of PLP in radical aminomutases has not been investigated extensively yet. We report an alternative synthetic procedure to provide easy access to 1-deazaPLP (dAPLP), an isosteric analog of PLP which acts as a probe for studying the role of the nitrogen atom. Our results revealed that lysine 5,6-aminomutase (5,6-LAM), a radical aminomutase, reconstituted with dAPLP cannot turn over a substrate, demonstrating that the nitrogen atom is essential for radical aminomutases. In contrast, biochemical and spectroscopic studies on the S238A variant reconstituted with PLP revealed a minuscule loss of activity. This apparent anomaly can be explained by a water-mediated rescue of activity in S238A, as if mimicking the active site of lysine 2,3-aminomutase. This study leads to a better comprehension of how enzymes harness the optimum capability of PLP to realize catalysis.
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12
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Chen JR, Ke TX, Frey PA, Ke SC. Electron Spin Echo Envelope Modulation Spectroscopy Reveals How Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase Positions the Radical Pair Intermediates and Modulates Their Stabilities for Efficient Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-Ru Chen
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Ting-Xi Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53726, United States
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
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13
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Moghadam B, Ashouri M, Roohi H, Karimi-Jafari MH. Computational evidence of new putative allosteric sites in the acetylcholinesterase receptor. J Mol Graph Model 2021; 107:107981. [PMID: 34246109 DOI: 10.1016/j.jmgm.2021.107981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/27/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
Acetylcholinesterase (AChE), with a rigid structure and buried active site at the end of a deep narrow gorge, is interesting enough to solve the paradox between high catalytic activity and unavailability of the active site in treatment of Alzheimer's disease (AD). In this way, the blind docking process is performed on an ensemble of AChE structures created with molecular dynamics (MD) simulations to survey the whole space of AChE to find multiple access pathways to the active site and ranking them based on their affinity scores. Our results show that there are other allosteric binding sites in the protein structure whose inhibition, can affect protein function by disrupting the release of the Acetylcholine (AC) degradation products. In this study, inhibitory activities of Hybride14 and two natural compounds (Papaverine and Palmatine) were evaluated for all possible allosteric sites via docking method. The results confirmed the non-competitive inhibition mechanism. The best binding mode for these inhibitors and efficacy of hydrogen bonds and hydrophobic interactions on inhibitory activities of ligands were also disclosed. Furthermore, our studies provide significant molecular insight for AChE inhibition that could aid in the development of new drugs for AD's treatment.
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Affiliation(s)
- Behnaz Moghadam
- Department of Chemistry, Faculty of Science, University of Guilan, Iran
| | - Mitra Ashouri
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Hossein Roohi
- Department of Chemistry, Faculty of Science, University of Guilan, Iran.
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14
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Wu XD, Ding LF, Chen B, Li XN, Peng LY, Zhao QS. Cunlanceloic acids A–D: unprecedented labdane diterpenoid dimers with AChE inhibitory and cytotoxic activities from Cunninghamia lanceolata. Org Chem Front 2021. [DOI: 10.1039/d1qo00999k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four unprecedented labdane diterpenoid dimers with new carbon skeletons, cunlanceloic acids A–D (1–4), were isolated from the cones of Cunninghamia lanceolata.
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Affiliation(s)
- Xing-De Wu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Lin-Fen Ding
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, People's Republic of China
| | - Bin Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Xiao-Nian Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Li-Yan Peng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Qin-Shi Zhao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
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15
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Abstract
The recently delineated structure- and reactivity-based concept of antivitamins B12 has begun to bear fruit by the generation, and study, of a range of such B12 -dummies, either vitamin B12 -derived, or transition metal analogues that also represent potential antivitamins B12 or specific B12 -antimetabolites. As reviewed here, this has opened up new research avenues in organometallic B12 -chemistry and bioinorganic coordination chemistry. Exploratory studies with antivitamins B12 have, furthermore, revealed some of their potential, as pharmacologically interesting compounds, for inducing B12 -deficiency in a range of organisms, from hospital resistant bacteria to laboratory mice. The derived capacity of antivitamins B12 to induce functional B12 -deficiency in mammalian cells and organs also suggest their valuable potential as growth inhibitors of cancerous human and animal cells.
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Affiliation(s)
- Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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16
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Kieninger C, Wurst K, Podewitz M, Stanley M, Deery E, Lawrence AD, Liedl KR, Warren MJ, Kräutler B. Replacement of the Cobalt Center of Vitamin B
12
by Nickel: Nibalamin and Nibyric Acid Prepared from Metal‐Free B
12
Ligands Hydrogenobalamin and Hydrogenobyric Acid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry University of Innsbruck 6020 Innsbruck Austria
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| | - Klaus Wurst
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Maren Podewitz
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Maria Stanley
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
| | - Evelyne Deery
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
| | | | - Klaus R. Liedl
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Martin J. Warren
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
- Quadram Institute Bioscience Norwich Science Park Norwich NR4 7UQ UK
| | - Bernhard Kräutler
- Institute of Organic Chemistry University of Innsbruck 6020 Innsbruck Austria
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
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17
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Kieninger C, Wurst K, Podewitz M, Stanley M, Deery E, Lawrence AD, Liedl KR, Warren MJ, Kräutler B. Replacement of the Cobalt Center of Vitamin B 12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal-Free B 12 Ligands Hydrogenobalamin and Hydrogenobyric Acid. Angew Chem Int Ed Engl 2020; 59:20129-20136. [PMID: 32686888 PMCID: PMC7693184 DOI: 10.1002/anie.202008407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Indexed: 12/18/2022]
Abstract
The (formal) replacement of Co in cobalamin (Cbl) by NiII generates nibalamin (Nibl), a new transition-metal analogue of vitamin B12 . Described here is Nibl, synthesized by incorporation of a NiII ion into the metal-free B12 ligand hydrogenobalamin (Hbl), itself prepared from hydrogenobyric acid (Hby). The related NiII corrin nibyric acid (Niby) was similarly synthesized from Hby, the metal-free cobyric acid ligand. The solution structures of Hbl, and Niby and Nibl, were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby. X-ray analysis of Niby shows the structural adaptation of the corrin ligand to NiII ions and the coordination behavior of NiII . The diamagnetic Niby and Nibl, and corresponding isoelectronic CoI corrins, were deduced to be isostructural. Nibl is a structural mimic of four-coordinate base-off Cbls, as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase.
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Affiliation(s)
- Christoph Kieninger
- Institute of Organic ChemistryUniversity of Innsbruck6020InnsbruckAustria
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| | - Klaus Wurst
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Maren Podewitz
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Maria Stanley
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
| | - Evelyne Deery
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
| | | | - Klaus R. Liedl
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Martin J. Warren
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
- Quadram Institute BioscienceNorwich Science ParkNorwichNR4 7UQUK
| | - Bernhard Kräutler
- Institute of Organic ChemistryUniversity of Innsbruck6020InnsbruckAustria
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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18
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Oshita H, Shimazaki Y. Recent Advances in One-Electron-Oxidized Cu II -Diphenoxide Complexes as Models of Galactose Oxidase: Importance of the Structural Flexibility in the Active Site. Chemistry 2020; 26:8324-8340. [PMID: 32056294 DOI: 10.1002/chem.201905877] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Indexed: 11/09/2022]
Abstract
The phenoxyl radical plays important roles in biological systems as cofactors in some metalloenzymes, such as galactose oxidase (GO) catalyzing oxidation of primary alcohols to give the corresponding aldehydes. Many metal(II)-phenoxyl radical complexes have hitherto been studied for understanding the detailed properties and reactivities of GO, and thus the nature of GO has gradually become clearer. However, the effects of the subtle geometric and electronic structural changes at the active site of GO, especially the structural change in the catalytic cycle and the effect of the second coordination sphere, have not been fully discussed yet. In this Review, we focus on further details of the model studies of GO and discuss the importance of the structural change at the active site of GO.
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Affiliation(s)
- Hiromi Oshita
- Faculty of Chemistry of Functional Molecules, Konan University, Higashinada-ku, Kobe, 658-8501, Japan
| | - Yuichi Shimazaki
- Graduate School of Science and Engineering, Ibaraki University, Bunkyo, Mito, 310-8512, Japan
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19
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Liu ZQ. Bridging free radical chemistry with drug discovery: A promising way for finding novel drugs efficiently. Eur J Med Chem 2019; 189:112020. [PMID: 32006794 DOI: 10.1016/j.ejmech.2019.112020] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/06/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023]
Abstract
Many diseases have been regarded to correlate with the in vivo oxidative damages, which are caused by overproduced free radicals from metabolic process or reactive oxygen species (ROS). This background motivates chemists to explore free radical reactions and to design a number of antioxidants, but whether free radical chemistry can be applied to accelerate the efficacy of the drug discovery is still underrepresented. Herein, in light of recent findings as well as kinetics on free radical reaction, the discipline of free radical chemistry is introduced to be a novel tool for finding potential drugs from antioxidant libraries accumulated during the study on free radical chemistry. These antioxidants provide with such abundant types of structural skeleton that might be employed to inhibit oxidations in different biological microenvironments. Although the in vitro characterization on the antioxidative property exerts a potential role of an antioxidant as a prodrug, the in vivo investigation on the property for quenching free radicals will make a final decision for the antioxidant whether it is worthy to be further explored pharmacologically. Therefore, it is reasonable to expect that bridging free radical chemistry with the pharmacological research will provide with a succinct way for finding novel drugs efficiently.
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Affiliation(s)
- Zai-Qun Liu
- Department of Organic Chemistry, College of Chemistry, Jilin University, No.2519 Jiefang Road, Changchun, 130021, People's Republic of China.
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20
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Yang H, McDaniel EC, Impano S, Byer AS, Jodts RJ, Yokoyama K, Broderick WE, Broderick JB, Hoffman BM. The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by Electron Paramagnetic Resonance and Electron Nuclear Double Resonance Spectroscopies. J Am Chem Soc 2019; 141:12139-12146. [PMID: 31274303 DOI: 10.1021/jacs.9b05926] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The 5'-deoxyadenosyl radical (5'-dAdo·) abstracts a substrate H atom as the first step in radical-based transformations catalyzed by adenosylcobalamin-dependent and radical S-adenosyl-l-methionine (RS) enzymes. Notwithstanding its central biological role, 5'-dAdo· has eluded characterization despite efforts spanning more than a half-century. Here, we report generation of 5'-dAdo· in a RS enzyme active site at 12 K using a novel approach involving cryogenic photoinduced electron transfer from the [4Fe-4S]+ cluster to the coordinated S-adenosylmethionine (SAM) to induce homolytic S-C5' bond cleavage. We unequivocally reveal the structure of this long-sought radical species through the use of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopies with isotopic labeling, complemented by density-functional computations: a planar C5' (2pπ) radical (∼70% spin occupancy); the C5'(H)2 plane is rotated by ∼37° (experiment)/39° (DFT) relative to the C5'-C4'-(C4'-H) plane, placing a C5'-H antiperiplanar to the ribose-ring oxygen, which helps stabilize the radical against elimination of the 4'-H. The agreement between φ from experiment and in vacuo DFT indicates that the conformation is intrinsic to 5-dAdo· itself, and not determined by its environment.
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Affiliation(s)
- Hao Yang
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Elizabeth C McDaniel
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Stella Impano
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Richard J Jodts
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Kenichi Yokoyama
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States
| | - William E Broderick
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Brian M Hoffman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
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21
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Liu Y, Wang QL, Chen Z, Zhou CS, Xiong BQ, Zhang PL, Yang CA, Zhou Q. Oxidative radical ring-opening/cyclization of cyclopropane derivatives. Beilstein J Org Chem 2019; 15:256-278. [PMID: 30800176 PMCID: PMC6369981 DOI: 10.3762/bjoc.15.23] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/04/2019] [Indexed: 01/21/2023] Open
Abstract
The ring-opening/cyclization of cyclopropane derivatives has drawn great attention in the past several decades. In this review, recent efforts in the development of oxidative radical ring-opening/cyclization of cyclopropane derivatives, including methylenecyclopropanes, cyclopropyl olefins and cyclopropanols, are described. We hope this review will be of sufficient interest for the scientific community to further advance the application of oxidative radical strategies in the ring-opening/cyclization of cyclopropane derivatives.
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Affiliation(s)
- Yu Liu
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, P. R. China
| | - Qiao-Lin Wang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, P. R. China
| | - Zan Chen
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, P. R. China
| | - Cong-Shan Zhou
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, P. R. China
| | - Bi-Quan Xiong
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, P. R. China
| | - Pan-Liang Zhang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, P. R. China
| | - Chang-An Yang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, P. R. China
| | - Quan Zhou
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, P. R. China
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22
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Robbins JM, Geng J, Barry BA, Gadda G, Bommarius AS. Photoirradiation Generates an Ultrastable 8-Formyl FAD Semiquinone Radical with Unusual Properties in Formate Oxidase. Biochemistry 2018; 57:5818-5826. [PMID: 30226367 DOI: 10.1021/acs.biochem.8b00571] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formate oxidase (FOX) was previously shown to contain a noncovalently bound 8-formyl FAD (8-fFAD) cofactor. However, both the absorption spectra and the kinetic parameters previously reported for FOX are inconsistent with more recent reports. The ultraviolet-visible (UV-vis) absorption spectrum reported in early studies closely resembles the spectra observed for protein-bound 8-formyl flavin semiquinone species, thus suggesting FOX may be photosensitive. Therefore, the properties of dark and light-exposed FOX were investigated using steady-state kinetics and site-directed mutagenesis analysis along with inductively coupled plasma optical emission spectroscopy, UV-vis absorption spectroscopy, circular dichroism spectroscopy, liquid chromatography and mass spectrometry, and electron paramagnetic resonance (EPR) spectroscopy. Surprisingly, these experimental results demonstrate that FOX is deactivated in the presence of light through generation of an oxygen stable, anionic (red) 8-fFAD semiquinone radical capable of persisting either in an aerobic environment for multiple weeks or in the presence of a strong reducing agent like sodium dithionite. Herein, we study the photoinduced formation of the 8-fFAD semiquinone radical in FOX and report the first EPR spectrum of this radical species. The stability of the 8-fFAD semiquinone radical suggests FOX to be a model enzyme for probing the structural and mechanistic features involved in stabilizing flavin semiquinone radicals. It is likely that the photoinduced formation of a stable 8-fFAD semiquinone radical is a defining characteristic of 8-formyl flavin-dependent enzymes. Additionally, a better understanding of the radical stabilization process may yield a FOX enzyme with more robust activity and broader industrial usefulness.
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Affiliation(s)
- John M Robbins
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.,Engineered Biosystems Building (EBB) , Georgia Institute of Technology , Atlanta , Georgia 30332-2000 , United States
| | - Jiafeng Geng
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
| | - Giovanni Gadda
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Center for Biotechnology and Drug Design , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Department of Biology , Georgia State University , Atlanta , Georgia 30302-3965 , United States
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.,Engineered Biosystems Building (EBB) , Georgia Institute of Technology , Atlanta , Georgia 30332-2000 , United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
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23
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Sulfur Radicals and Their Application. Top Curr Chem (Cham) 2018; 376:22. [DOI: 10.1007/s41061-018-0197-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/11/2018] [Indexed: 12/11/2022]
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24
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Chen JR, Ke SC. Magnetic field effects on coenzyme B12- and B6-dependent lysine 5,6-aminomutase: switching of the J-resonance through a kinetically competent radical-pair intermediate. Phys Chem Chem Phys 2018; 20:13068-13074. [DOI: 10.1039/c8cp01497c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
External magnetic fields interact with lysine 5,6-aminomutase, through an immobilized radical-pair with constant and large exchange interaction, to switch on J-resonance between singlet and triplet spin states, which have different reactive fates.
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Affiliation(s)
- Jun-Ru Chen
- Department of Physics
- National Dong Hwa University
- Hualien
- Taiwan
| | - Shyue-Chu Ke
- Department of Physics
- National Dong Hwa University
- Hualien
- Taiwan
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25
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Greene BL, Taguchi AT, Stubbe J, Nocera DG. Conformationally Dynamic Radical Transfer within Ribonucleotide Reductase. J Am Chem Soc 2017; 139:16657-16665. [PMID: 29037038 DOI: 10.1021/jacs.7b08192] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNR) catalyze the reduction of nucleotides to deoxynucleotides through a mechanism involving an essential cysteine based thiyl radical. In the E. coli class 1a RNR the thiyl radical (C439•) is a transient species generated by radical transfer (RT) from a stable diferric-tyrosyl radical cofactor located >35 Å away across the α2:β2 subunit interface. RT is facilitated by sequential proton-coupled electron transfer (PCET) steps along a pathway of redox active amino acids (Y122β ↔ [W48β?] ↔ Y356β ↔ Y731α ↔ Y730α ↔ C439α). The mutant R411A(α) disrupts the H-bonding environment and conformation of Y731, ostensibly breaking the RT pathway in α2. However, the R411A protein retains significant enzymatic activity, suggesting Y731 is conformationally dynamic on the time scale of turnover. Installation of the radical trap 3-amino tyrosine (NH2Y) by amber codon suppression at positions Y731 or Y730 and investigation of the NH2Y• trapped state in the active α2:β2 complex by HYSCORE spectroscopy validate that the perturbed conformation of Y731 in R411A-α2 is dynamic, reforming the H-bond between Y731 and Y730 to allow RT to propagate to Y730. Kinetic studies facilitated by photochemical radical generation reveal that Y731 changes conformation on the ns-μs time scale, significantly faster than the enzymatic kcat. Furthermore, the kinetics of RT across the subunit interface were directly assessed for the first time, demonstrating conformationally dependent RT rates that increase from 0.6 to 1.6 × 104 s-1 when comparing wild type to R411A-α2, respectively. These results illustrate the role of conformational flexibility in modulating RT kinetics by targeting the PCET pathway of radical transport.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Alexander T Taguchi
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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26
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Ghosh S, Cramer CJ, Truhlar DG, Gagliardi L. Generalized-active-space pair-density functional theory: an efficient method to study large, strongly correlated, conjugated systems. Chem Sci 2017; 8:2741-2750. [PMID: 28553509 PMCID: PMC5433034 DOI: 10.1039/c6sc05036k] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/16/2017] [Indexed: 12/16/2022] Open
Abstract
Predicting ground- and excited-state properties of open-shell organic molecules by electronic structure theory can be challenging because an accurate treatment has to correctly describe both static and dynamic electron correlation. Strongly correlated systems, i.e., systems with near-degeneracy correlation effects, are particularly troublesome. Multiconfigurational wave function methods based on an active space are adequate in principle, but it is impractical to capture most of the dynamic correlation in these methods for systems characterized by many active electrons. We recently developed a new method called multiconfiguration pair-density functional theory (MC-PDFT), that combines the advantages of wave function theory and density functional theory to provide a more practical treatment of strongly correlated systems. Here we present calculations of the singlet-triplet gaps in oligoacenes ranging from naphthalene to dodecacene. Calculations were performed for unprecedently large orbitally optimized active spaces of 50 electrons in 50 orbitals, and we test a range of active spaces and active space partitions, including four kinds of frontier orbital partitions. We show that MC-PDFT can predict the singlet-triplet splittings for oligoacenes consistent with the best available and much more expensive methods, and indeed MC-PDFT may constitute the benchmark against which those other models should be compared, given the absence of experimental data.
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Affiliation(s)
- Soumen Ghosh
- Department of Chemistry , Chemical Theory Center , Supercomputing Institute , University of Minnesota , 207 Pleasant Street SE , Minneapolis , MN 55455-0431 , USA . ; ;
| | - Christopher J Cramer
- Department of Chemistry , Chemical Theory Center , Supercomputing Institute , University of Minnesota , 207 Pleasant Street SE , Minneapolis , MN 55455-0431 , USA . ; ;
| | - Donald G Truhlar
- Department of Chemistry , Chemical Theory Center , Supercomputing Institute , University of Minnesota , 207 Pleasant Street SE , Minneapolis , MN 55455-0431 , USA . ; ;
| | - Laura Gagliardi
- Department of Chemistry , Chemical Theory Center , Supercomputing Institute , University of Minnesota , 207 Pleasant Street SE , Minneapolis , MN 55455-0431 , USA . ; ;
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27
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Zard SZ. Radicals in Action: A Festival of Radical Transformations. J Org Chem 2017; 82:2805. [DOI: 10.1021/acs.joc.7b00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samir Z. Zard
- Laboratoire de Synthèse Organique, UMR 7652 CNRS/Ecole Polytechnique
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28
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29
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Ding W, Ji X, Li Y, Zhang Q. Catalytic Promiscuity of the Radical S-adenosyl-L-methionine Enzyme NosL. Front Chem 2016; 4:27. [PMID: 27446906 PMCID: PMC4916742 DOI: 10.3389/fchem.2016.00027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
Catalytic promiscuity plays a key role in enzyme evolution and the acquisition of novel biological functions. Because of the high reactivity of radical species, in our view enzymes involving radical-mediated mechanisms could intrinsically be more prone to catalytic promiscuity. This mini-review summarizes the recent advances in the study of NosL, a radical S-adenosyl-L-methionine (SAM)-dependent L-tryptophan (L-Trp) lyase. We demonstrate here the interesting chemistry and remarkable catalytic promiscuity of NosL, and attempt to highlight the high evolvability of radical SAM enzymes and the potential to engineer these enzymes for novel and improved activities.
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Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University Shanghai, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University Shanghai, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University Shanghai, China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai, China
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The Role of Biotin in Bacterial Physiology and Virulence: a Novel Antibiotic Target for
Mycobacterium tuberculosis. Microbiol Spectr 2016; 4. [DOI: 10.1128/microbiolspec.vmbf-0008-2015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
Biotin is an essential cofactor for enzymes present in key metabolic pathways such as fatty acid biosynthesis, replenishment of the tricarboxylic acid cycle, and amino acid metabolism. Biotin is synthesized
de novo
in microorganisms, plants, and fungi, but this metabolic activity is absent in mammals, making biotin biosynthesis an attractive target for antibiotic discovery. In particular, biotin biosynthesis plays important metabolic roles as the sole source of biotin in all stages of the
Mycobacterium tuberculosis
life cycle due to the lack of a transporter for scavenging exogenous biotin. Biotin is intimately associated with lipid synthesis where the products form key components of the mycobacterial cell membrane that are critical for bacterial survival and pathogenesis. In this review we discuss the central role of biotin in bacterial physiology and highlight studies that demonstrate the importance of its biosynthesis for virulence. The structural biology of the known biotin synthetic enzymes is described alongside studies using structure-guided design, phenotypic screening, and fragment-based approaches to drug discovery as routes to new antituberculosis agents.
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31
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Gruber K, Kräutler B. Coenzyme B12 Repurposed for Photoregulation of Gene Expression. Angew Chem Int Ed Engl 2016; 55:5638-40. [PMID: 27010518 DOI: 10.1002/anie.201601120] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Indexed: 12/22/2022]
Abstract
Old cofactor, new tricks: In enzymes, coenzyme B12 has a well-known function as a radical initiator through homolysis of the Co-C bond. It has recently been shown that nature has repurposed this cofactor as a photosensitive switch for the regulation of bacterial carotenoid biosynthesis. Co-C bond breakage is again the key event in this process, triggering huge conformational changes in the B12 -binding protein.
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Affiliation(s)
- Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010, Graz, Austria.
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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32
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Gruber K, Kräutler B. Coenzym B12- umfunktioniert für die Photoregulation der Genexpression. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Karl Gruber
- Institut für Molekulare Biowissenschaften; Universität Graz; Humboldtstraße 50 8010 Graz Österreich
| | - Bernhard Kräutler
- Institut für Organische Chemie und Zentrum für molekulare Biowissenschaften (CMBI); Universität Innsbruck; Innrain 80/82 6020 Innsbruck Österreich
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33
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Selvaraj B, Buckel W, Golding BT, Ullmann GM, Martins BM. Structure and Function of 4-Hydroxyphenylacetate Decarboxylase and Its Cognate Activating Enzyme. J Mol Microbiol Biotechnol 2016; 26:76-91. [DOI: 10.1159/000440882] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
4-Hydroxyphenylacetate decarboxylase (4Hpad) is the prototype of a new class of Fe-S cluster-dependent glycyl radical enzymes (Fe-S GREs) acting on aromatic compounds. The two-enzyme component system comprises a decarboxylase responsible for substrate conversion and a dedicated activating enzyme (4Hpad-AE). The decarboxylase uses a glycyl/thiyl radical dyad to convert 4-hydroxyphenylacetate into <i>p</i>-cresol (4-methylphenol) by a biologically unprecedented Kolbe-type decarboxylation. In addition to the radical dyad prosthetic group, the decarboxylase unit contains two [4Fe-4S] clusters coordinated by an extra small subunit of unknown function. 4Hpad-AE reductively cleaves S-adenosylmethionine (SAM or AdoMet) at a site-differentiated [4Fe-4S]<sup>2+/+</sup> cluster (RS cluster) generating a transient 5′-deoxyadenosyl radical that produces a stable glycyl radical in the decarboxylase by the abstraction of a hydrogen atom. 4Hpad-AE binds up to two auxiliary [4Fe-4S] clusters coordinated by a ferredoxin-like insert that is C-terminal to the RS cluster-binding motif. The ferredoxin-like domain with its two auxiliary clusters is not vital for SAM-dependent glycyl radical formation in the decarboxylase, but facilitates a longer lifetime for the radical. This review describes the 4Hpad and cognate AE families and focuses on the recent advances and open questions concerning the structure, function and mechanism of this novel Fe-S-dependent class of GREs.
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34
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Nohr D, Rodriguez R, Weber S, Schleicher E. How can EPR spectroscopy help to unravel molecular mechanisms of flavin-dependent photoreceptors? Front Mol Biosci 2015; 2:49. [PMID: 26389123 PMCID: PMC4555020 DOI: 10.3389/fmolb.2015.00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022] Open
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a well-established spectroscopic method for the examination of paramagnetic molecules. Proteins can contain paramagnetic moieties in form of stable cofactors, transiently formed intermediates, or spin labels artificially introduced to cysteine sites. The focus of this review is to evaluate potential scopes of application of EPR to the emerging field of optogenetics. The main objective for EPR spectroscopy in this context is to unravel the complex mechanisms of light-active proteins, from their primary photoreaction to downstream signal transduction. An overview of recent results from the family of flavin-containing, blue-light dependent photoreceptors is given. In detail, mechanistic similarities and differences are condensed from the three classes of flavoproteins, the cryptochromes, LOV (Light-oxygen-voltage), and BLUF (blue-light using FAD) domains. Additionally, a concept that includes spin-labeled proteins and examination using modern pulsed EPR is introduced, which allows for a precise mapping of light-induced conformational changes.
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Affiliation(s)
- Daniel Nohr
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Ryan Rodriguez
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Stefan Weber
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Erik Schleicher
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
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35
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Jin L, Feng J, Lu G, Cai C. Di-tert-butyl Peroxide (DTBP)-Mediated Oxidative Cross- Coupling of Isochroman and Indole Derivatives. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500048] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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Maity AN, Lin HH, Chiang HS, Lo HH, Ke SC. Reaction of Pyridoxal-5′-phosphate-N-oxide with Lysine 5,6-Aminomutase: Enzyme Flexibility toward Cofactor Analog. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00671] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Hsin-Hua Lin
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
| | | | - Hsin-Hsi Lo
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
| | - Shyue-Chu Ke
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
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37
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Yu Y, Lv X, Li J, Zhou Q, Cui C, Hosseinzadeh P, Mukherjee A, Nilges MJ, Wang J, Lu Y. Defining the role of tyrosine and rational tuning of oxidase activity by genetic incorporation of unnatural tyrosine analogs. J Am Chem Soc 2015; 137:4594-7. [PMID: 25672571 PMCID: PMC4676419 DOI: 10.1021/ja5109936] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Indexed: 12/31/2022]
Abstract
While a conserved tyrosine (Tyr) is found in oxidases, the roles of phenol ring pKa and reduction potential in O2 reduction have not been defined despite many years of research on numerous oxidases and their models. These issues represent major challenges in our understanding of O2 reduction mechanism in bioenergetics. Through genetic incorporation of unnatural amino acid analogs of Tyr, with progressively decreasing pKa of the phenol ring and increasing reduction potential, in the active site of a functional model of oxidase in myoglobin, a linear dependence of both the O2 reduction activity and the fraction of H2O formation with the pKa of the phenol ring has been established. By using these unnatural amino acids as spectroscopic probe, we have provided conclusive evidence for the location of a Tyr radical generated during reaction with H2O2, by the distinctive hyperfine splitting patterns of the halogenated tyrosines and one of its deuterated derivatives incorporated at the 33 position of the protein. These results demonstrate for the first time that enhancing the proton donation ability of the Tyr enhances the oxidase activity, allowing the Tyr analogs to augment enzymatic activity beyond that of natural Tyr.
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Affiliation(s)
- Yang Yu
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Xiaoxuan Lv
- Laboratory
of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese
Academy of Sciences, Beijing 100049, P. R. China
| | - Jiasong Li
- Laboratory
of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese
Academy of Sciences, Beijing 100049, P. R. China
| | - Qing Zhou
- Laboratory
of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese
Academy of Sciences, Beijing 100049, P. R. China
| | - Chang Cui
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Arnab Mukherjee
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Mark J. Nilges
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jiangyun Wang
- Laboratory
of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, P. R. China
- University of Chinese
Academy of Sciences, Beijing 100049, P. R. China
| | - Yi Lu
- Center of Biophysics and Computational Biology, Department of Chemistry, Department of Biochemistry, Illinois EPR Research
Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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38
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Yang Y, Zhou Q, Wang L, Liu X, Zhang W, Hu M, Dong J, Li J, Xiaoxuan L, Ouyang H, Li H, Gao F, Gong W, Lu Y, Wang J. Significant Improvement of Oxidase Activity through the Genetic Incorporation of a Redox-active Unnatural Amino Acid. Chem Sci 2015; 6:3881-3885. [PMID: 26417427 PMCID: PMC4583198 DOI: 10.1039/c5sc01126d] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 04/13/2015] [Indexed: 12/19/2022] Open
Abstract
Incorporation of 3-methoxytyrosine boosts the oxidase activity of the myoglobin model of oxidase, stressing the importance of the redox potential tuning of tyrosine.
While nature employs various covalent and non-covalent strategies to modulate tyrosine (Y) redox potential and pKa in order to optimize enzyme activities, such approaches have not been systematically applied for the design of functional metalloproteins. Through the genetic incorporation of 3-methoxytyrosine (OMeY) into myoglobin, we replicated important features of cytochrome c oxidase (CcO) in this small soluble protein, which exhibits selective O2 reduction activity while generating a small amount of reactive oxygen species (ROS). These results demonstrate that the electron donating ability of a tyrosine residue in the active site is important for CcO function. Moreover, we elucidated the structural basis for the genetic incorporation of OMeY into proteins by solving the X-ray structure of OMeY specific aminoacyl-tRNA synthetase complexed with OMeY.
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Affiliation(s)
- Yu Yang
- Center of Biophysics and Computational Biology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Qing Zhou
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Li Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China ; Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Xiaohong Liu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Wei Zhang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Meirong Hu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jianshu Dong
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jiasong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China ; Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Lv Xiaoxuan
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Hanlin Ouyang
- Center of Biophysics and Computational Biology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Han Li
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Feng Gao
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Weimin Gong
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Yi Lu
- Center of Biophysics and Computational Biology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
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Fang X, Di YT, Zhang Y, Xu ZP, Lu Y, Chen QQ, Zheng QT, Hao XJ. Unprecedented Quassinoids with Promising Biological Activity fromHarrisonia perforata. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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Fang X, Di YT, Zhang Y, Xu ZP, Lu Y, Chen QQ, Zheng QT, Hao XJ. Unprecedented Quassinoids with Promising Biological Activity fromHarrisonia perforata. Angew Chem Int Ed Engl 2015; 54:5592-5. [DOI: 10.1002/anie.201412126] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/28/2015] [Indexed: 11/10/2022]
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41
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Salamone M, Basili F, Bietti M. Reactivity and selectivity patterns in hydrogen atom transfer from amino acid C-H bonds to the cumyloxyl radical: polar effects as a rationale for the preferential reaction at proline residues. J Org Chem 2015; 80:3643-50. [PMID: 25774567 DOI: 10.1021/acs.joc.5b00549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Absolute rate constants for hydrogen atom transfer (HAT) from the C-H bonds of N-Boc-protected amino acids to the cumyloxyl radical (CumO(•)) were measured by laser flash photolysis. With glycine, alanine, valine, norvaline, and tert-leucine, HAT occurs from the α-C-H bonds, and the stability of the α-carbon radical product plays a negligible role. With leucine, HAT from the α- and γ-C-H bonds was observed. The higher kH value measured for proline was explained in terms of polar effects, with HAT that predominantly occurs from the δ-C-H bonds, providing a rationale for the previous observation that proline residues represent favored HAT sites in the reactions of peptides and proteins with (•)OH. Preferential HAT from proline was also observed in the reactions of CumO(•) with the dipeptides N-BocProGlyOH and N-BocGlyGlyOH. The rate constants measured for CumO(•) were compared with the relative rates obtained previously for the corresponding reactions of different hydrogen-abstracting species. The behavior of CumO(•) falls between those observed for the highly reactive radicals Cl(•) and (•)OH and the significantly more stable Br(•). Taken together, these results provide a general framework for the description of the factors that govern reactivity and selectivity patterns in HAT reactions from amino acid C-H bonds.
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Affiliation(s)
- Michela Salamone
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Federica Basili
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Massimo Bietti
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
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42
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Synthesis, solution and crystal structure of the coenzyme B(12) analogue Co(β)-2'-fluoro-2',5'-dideoxyadenosylcobalamin. J Inorg Biochem 2015; 148:62-8. [PMID: 25726330 DOI: 10.1016/j.jinorgbio.2015.02.005] [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: 12/03/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 11/23/2022]
Abstract
Crystal structure analyses have helped to decipher the mode of binding of coenzyme B12 (AdoCbl) in the active site of AdoCbl-dependent enzymes. However, the question of how such enzymes perform their radical reactions is still incompletely answered. A pioneering study by Gruber and Kratky of AdoCbl-dependent glutamate mutase (GLM) laid out a path for the movement of the catalytically active 5'-deoxyadenosyl radical, in which H-bonds between the protein and the 2'- and 3'-OH groups of the protein bound AdoCbl would play a decisive role. Studies with correspondingly modified coenzyme B12-analogues are of interest to gain insights into cofactor binding and enzyme mechanism. Here we report the preparation of Coβ-2'-fluoro-2',5'-dideoxyadenosylcobalamin (2'FAdoCbl), which lacks the 2'-OH group critical for the interaction in enzymes. 2'FAdoCbl was prepared by alkylation of cob(I)alamin, obtained from the electrochemical reduction of aquocobalamin. Spectroscopic data and a single crystal X-ray analysis of 2'FAdoCbl established its structure, which was very similar to that one of coenzyme B12. 2'FAdoCbl is a (19)F NMR active mimic of coenzyme B12 that may help to gain insights into binding interactions of coenzyme B12 with AdoCbl-dependent enzymes, proteins of B12 transport and of AdoCbl-biosynthesis, as well as with B12-riboswitches.
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43
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Lanz ND, Booker SJ. Auxiliary iron-sulfur cofactors in radical SAM enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1316-34. [PMID: 25597998 DOI: 10.1016/j.bbamcr.2015.01.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 11/19/2022]
Abstract
A vast number of enzymes are now known to belong to a superfamily known as radical SAM, which all contain a [4Fe-4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5'-deoxyadenosyl radical. The 5'-deoxyadenosyl radical then abstracts a target substrate hydrogen atom, initiating a wide variety of radical-based transformations. A subset of radical SAM enzymes contains one or more additional iron-sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of radical SAM enzymes that harbor auxiliary iron-sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
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Martínez-Cifuentes M, Salazar R, Escobar CA, Weiss-López BE, Santos LS, Araya-Maturana R. Correlating experimental electrochemistry and theoretical calculations in 2′-hydroxy chalcones: the role of the intramolecular hydrogen bond. RSC Adv 2015. [DOI: 10.1039/c5ra10140a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The molecular structure and electrochemical behaviour of a series of 2′-hydroxychalcones were studied. Results show the importance of the intramolecular hydrogen bond and the methoxy substituent pattern on the redox properties of these compounds.
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Affiliation(s)
| | - Ricardo Salazar
- Laboratorio de Electroquímica MedioAmbiental
- LEQMA
- Departamento de Química de los Materiales
- Facultad de Química y Biología
- Universidad de Santiago de Chile, USACh
| | - Carlos A. Escobar
- Departamento de Ciencias Químicas
- Universidad Andres Bello
- Santiago
- Chile
| | | | - Leonardo S. Santos
- Laboratorio de Síntesis Asimétrica
- Instituto de Química de los Recursos Naturales
- Universidad de Talca
- Talca
- Chile
| | - Ramiro Araya-Maturana
- Departamento de Química Orgánica y Fisicoquímica
- Facultad de Ciencias Químicas Y Farmacéuticas
- Universidad de Chile
- Santiago 1
- Chile
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45
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Nechab M, Mondal S, Bertrand MP. 1,n-Hydrogen-Atom Transfer (HAT) Reactions in Whichn≠5: An Updated Inventory. Chemistry 2014; 20:16034-59. [DOI: 10.1002/chem.201403951] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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46
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Buckel W, Kung JW, Boll M. The benzoyl-coenzyme a reductase and 2-hydroxyacyl-coenzyme a dehydratase radical enzyme family. Chembiochem 2014; 15:2188-94. [PMID: 25204868 DOI: 10.1002/cbic.201402270] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg (Germany)
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47
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Hashimoto T, Kawamata Y, Maruoka K. An organic thiyl radical catalyst for enantioselective cyclization. Nat Chem 2014; 6:702-5. [DOI: 10.1038/nchem.1998] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 06/06/2014] [Indexed: 01/09/2023]
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Maity AN, Chen YH, Ke SC. Large-scale domain motions and pyridoxal-5'-phosphate assisted radical catalysis in coenzyme B12-dependent aminomutases. Int J Mol Sci 2014; 15:3064-87. [PMID: 24562332 PMCID: PMC3958899 DOI: 10.3390/ijms15023064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/25/2013] [Accepted: 01/22/2014] [Indexed: 12/31/2022] Open
Abstract
Lysine 5,6-aminomutase (5,6-LAM) and ornithine 4,5-aminomutase (4,5-OAM) are two of the rare enzymes that use assistance of two vitamins as cofactors. These enzymes employ radical generating capability of coenzyme B12 (5'-deoxyadenosylcobalamin, dAdoCbl) and ability of pyridoxal-5'-phosphate (PLP, vitamin B6) to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. In spite of all the similarities, these enzymes differ in substrate specificities. 4,5-OAM is highly specific for D-ornithine as a substrate while 5,6-LAM can accept D-lysine and L-β-lysine. This review focuses on recent computational, spectroscopic and structural studies of these enzymes and their implications on the related enzymes. Additionally, we also discuss the potential biosynthetic application of 5,6-LAM.
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Affiliation(s)
| | - Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien 97401, Taiwan.
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 97401, Taiwan.
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Shimazaki Y. Properties of the one-electron oxidized copper(II) salen-type complexes: relationship between electronic structures and reactivities. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The Cu(II)-phenoxyl radical formed during the catalytic cycle of galactose oxidase (GO) attracted much attention, and the structures and properties of a number of metal-phenoxyl radical complexes have been studied. Some of the functional model systems of GO reported previously have shown that the Cu complexes oxidize primary alcohols to aldehydes and that the Cu(II)-phenoxyl radical species is formed in the catalytic cycle. Many Cu(II)-phenoxyl radical species have been produced by one-electron oxidation of the Cu(II)-phenolate complexes. On the other hand, one-electron oxidation of a Cu(II)-phenolate complex has the possibility to give different electronic structures, one of which is the Cu(III)-phenolate. From these points of view, this micro review is focused on the one-electron oxidized square-planar Cu(II) complexes of the salen-type ligands. Introduction of substituents into the phenolate moieties and conversion from a 5- to a 6-membered chelate backbone alter the electronic structure of the one-electron oxidized Cu(II) complexes and give rise to a different reactivity of benzyl alcohol oxidation. The relationship between the electronic structure and the reactivity is herein discussed.
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Román-Meléndez GD, von Glehn P, Harvey JN, Mulholland AJ, Marsh ENG. Role of active site residues in promoting cobalt-carbon bond homolysis in adenosylcobalamin-dependent mutases revealed through experiment and computation. Biochemistry 2014; 53:169-77. [PMID: 24341954 PMCID: PMC3928028 DOI: 10.1021/bi4012644] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Adenosylcobalamin (AdoCbl) serves as a source of reactive free radicals that are generated by homolytic scission of the coenzyme's cobalt-carbon bond. AdoCbl-dependent enzymes accelerate AdoCbl homolysis by ∼10(12)-fold, but the mechanism by which this is accomplished remains unclear. We have combined experimental and computational approaches to gain molecular-level insight into this process for glutamate mutase. Two residues, glutamate 330 and lysine 326, form hydrogen bonds with the adenosyl group of the coenzyme. A series of mutations that impair the enzyme's ability to catalyze coenzyme homolysis and tritium exchange with the substrate by 2-4 orders of magnitude were introduced at these positions. These mutations, together with the wild-type enzyme, were also characterized in silico by molecular dynamics simulations of the enzyme-AdoCbl-substrate complex with AdoCbl modeled in the associated (Co-C bond formed) or dissociated [adenosyl radical with cob(II)alamin] state. The simulations reveal that the number of hydrogen bonds between the adenosyl group and the protein side chains increases in the homolytically dissociated state, with respect to the associated state, for both the wild-type and mutant enzymes. The mutations also cause a progressive increase in the mean distance between the 5'-carbon of the adenosyl radical and the abstractable hydrogen of the substrate. Interestingly, the distance between the 5'-carbon and substrate hydrogen, determined computationally, was found to inversely correlate with the log k for tritium exchange (r = 0.93) determined experimentally. Taken together, these results point to a dual role for these residues: they both stabilize the homolytic state through electrostatic interactions between the protein and the dissociated coenzyme and correctly position the adenosyl radical to facilitate the abstraction of hydrogen from the substrate.
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Affiliation(s)
| | - Patrick von Glehn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Jeremy N. Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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