1
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Yu L, Tian C. Electron spin resonance analysis of photoenzymatic catalysis. Natl Sci Rev 2024; 11:nwae095. [PMID: 39144745 PMCID: PMC11321245 DOI: 10.1093/nsr/nwae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 08/16/2024] Open
Abstract
This Perspective highlights recent research progress and prospects in elucidating the catalytic mechanism of photoenzymes using ESR (electron spin resonance) spectroscopy, which is emerging as a unique and crucial method for identifying radical intermediates, illustrating electron transfer events and the underlying mechanisms of photoenzymatic catalysis.
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Affiliation(s)
- Lu Yu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, China
| | - Changlin Tian
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, China
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2
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Oka Y, Inoue K. Time-resolved EPR observation of blue-light-induced radical ion pairs in a flavin-Trp dyad. Phys Chem Chem Phys 2024; 26:16444-16448. [PMID: 38808575 DOI: 10.1039/d3cp06219h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
A dyad of flavin and Trp bridged by a p-phenylamide linker was synthesized as an artificial model system to investigate molecular-based magnetic-field sensors relevant to blue-light photoreceptor proteins. The results demonstrated that intramolecular electron transfer generates a radical pair, only the triplet-born one of which has a microsecond lifetime at room temperature.
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Affiliation(s)
- Yoshimi Oka
- Frontier Research Core for Life Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
- Research Promotion Institute, Oita University, 700 Dannoharu, Oita 870-1192, Japan
- Graduate School of Advanced Science and Engineering, Chirality Research Center (CResCent), and International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima 739-8526, Japan.
| | - Katsuya Inoue
- Graduate School of Advanced Science and Engineering, Chirality Research Center (CResCent), and International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima 739-8526, Japan.
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3
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Zhan T, Jacoby C, Jede M, Knapp B, Ferlaino S, Günter A, Drepper F, Müller M, Weber S, Boll M. Bacterial stigmasterol degradation involving radical flavin delta-24 desaturase and molybdenum-dependent C26 hydroxylase. J Biol Chem 2024; 300:107243. [PMID: 38556086 PMCID: PMC11061730 DOI: 10.1016/j.jbc.2024.107243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/20/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024] Open
Abstract
Sterols are ubiquitous membrane constituents that persist to a large extent in the environment due to their water insolubility and chemical inertness. Recently, an oxygenase-independent sterol degradation pathway was discovered in a cholesterol-grown denitrifying bacterium Sterolibacterium (S.) denitrificans. It achieves hydroxylation of the unactivated primary C26 of the isoprenoid side chain to an allylic alcohol via a phosphorylated intermediate in a four-step ATP-dependent enzyme cascade. However, this pathway is incompatible with the degradation of widely distributed steroids containing a double bond at C22 in the isoprenoid side chain such as the plant sterol stigmasterol. Here, we have enriched a prototypical delta-24 desaturase from S. denitrificans, which catalyzes the electron acceptor-dependent oxidation of the intermediate stigmast-1,4-diene-3-one to a conjugated (22,24)-diene. We suggest an α4β4 architecture of the 440 kDa enzyme, with each subunit covalently binding an flavin mononucleotide cofactor to a histidyl residue. As isolated, both flavins are present as red semiquinone radicals, which can be reduced by stigmast-1,4-diene-3-one but cannot be oxidized even with strong oxidizing agents. We propose a mechanism involving an allylic radical intermediate in which two flavin semiquinones each abstract one hydrogen atom from the substrate. The conjugated delta-22,24 moiety formed allows for the subsequent hydroxylation of the terminal C26 with water by a heterologously produced molybdenum-dependent steroid C26 dehydrogenase 2. In conclusion, the pathway elucidated for delta-22 steroids achieves oxygen-independent hydroxylation of the isoprenoid side chain by bypassing the ATP-dependent formation of a phosphorylated intermediate.
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Affiliation(s)
- Tingyi Zhan
- Faculty of Biology, Department of Microbiology, University of Freiburg, Freiburg, Germany
| | - Christian Jacoby
- Faculty of Biology, Department of Microbiology, University of Freiburg, Freiburg, Germany
| | - Martin Jede
- Faculty of Biology, Department of Microbiology, University of Freiburg, Freiburg, Germany
| | - Bettina Knapp
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, Freiburg, Germany
| | - Sascha Ferlaino
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Andreas Günter
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Matthias Boll
- Faculty of Biology, Department of Microbiology, University of Freiburg, Freiburg, Germany.
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4
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Anghel L, Rada S, Erhan RV. Structural Factors and Electron Transfer Mechanisms in Flavoenzymes. ANAL LETT 2023. [DOI: 10.1080/00032719.2023.2174131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Lilia Anghel
- Laboratory Physical and Quantum Chemistry, Institute of Chemistry, Chisinau, Republic of Moldova
| | - Simona Rada
- INCDTIM Cluj-Napoca, Cluj-Napoca, Romania
- Technical University of Cluj-Napoca, Cluj-Napoca, Romania
| | - Raul-Victor Erhan
- Department of Nuclear Physics, Horia Hulubei National Institute for R&D in Physics and Nuclear Engineering, Magurele-Ilfov, Romania
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5
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Deviers J, Cailliez F, Gutiérrez BZ, Kattnig DR, de la Lande A. Ab initio derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome. Phys Chem Chem Phys 2022; 24:16784-16798. [PMID: 35775941 DOI: 10.1039/d1cp05804e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations.
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Affiliation(s)
- Jean Deviers
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK.,Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Fabien Cailliez
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Bernardo Zúñiga Gutiérrez
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, C. P. 44430, Guadalajara Jal, Mexico
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
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6
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Pompe N, Illarionov B, Fischer M, Bacher A, Weber S. Completing the Picture: Determination of 13C Hyperfine Coupling Constants of Flavin Semiquinone Radicals by Photochemically Induced Dynamic Nuclear Polarization Spectroscopy. J Phys Chem Lett 2022; 13:5160-5167. [PMID: 35658481 DOI: 10.1021/acs.jpclett.2c00919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We investigate the electronic structure of flavin semiquinone radicals in terms of their 13C hyperfine coupling constants. Photochemically induced dynamic nuclear polarization (photo-CIDNP) spectroscopy was used to study both the neutral and anionic radical species of flavin mononucleotide (FMN) in bulk aqueous solution. Apart from universally 13C-labeled FMN, partially labeled isotopologues are used to increase sensitivity for nuclei exhibiting very small hyperfine couplings and to cope with spectral overlap. In addition, experimental findings are supported by quantum chemical calculations, and implications for the spin density distribution in free flavin radicals are discussed.
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Affiliation(s)
- Nils Pompe
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Boris Illarionov
- Hamburg School of Food Science, University of Hamburg, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, University of Hamburg, 20146 Hamburg, Germany
| | - Adelbert Bacher
- Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg im Breisgau, Germany
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7
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Understanding flavin electronic structure and spectra. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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8
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Caux C, Guigliarelli B, Vivès C, Biaso F, Horeau M, Hassoune H, Petit-Hartlein I, Juillan-Binard C, Torelli S, Fieschi F, Nivière V. Membrane-Bound Flavocytochrome MsrQ Is a Substrate of the Flavin Reductase Fre in Escherichia coli. ACS Chem Biol 2021; 16:2547-2559. [PMID: 34550690 DOI: 10.1021/acschembio.1c00613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
MsrPQ is a new type of methionine sulfoxide reductase (Msr) system found in bacteria. It is specifically involved in the repair of periplasmic methionine residues that are oxidized by hypochlorous acid. MsrP is a periplasmic molybdoenzyme that carries out the Msr activity, whereas MsrQ, an integral membrane-bound hemoprotein, acts as the physiological partner of MsrP to provide electrons for catalysis. Although MsrQ (YedZ) was associated since long with a protein superfamily named FRD (ferric reductase domain), including the eukaryotic NADPH oxidases and STEAP proteins, its biochemical properties are still sparsely documented. Here, we have investigated the cofactor content of the E. coli MsrQ and its mechanism of reduction by the flavin reductase Fre. We showed by electron paramagnetic resonance (EPR) spectroscopy that MsrQ contains a single highly anisotropic low-spin (HALS) b-type heme located on the periplasmic side of the membrane. We further demonstrated that MsrQ holds a flavin mononucleotide (FMN) cofactor that occupies the site where a second heme binds in other members of the FDR superfamily on the cytosolic side of the membrane. EPR spectroscopy indicates that the FMN cofactor can accommodate a radical semiquinone species. The cytosolic flavin reductase Fre was previously shown to reduce the MsrQ heme. Here, we demonstrated that Fre uses the FMN MsrQ cofactor as a substrate to catalyze the electron transfer from cytosolic NADH to the heme. Formation of a specific complex between MsrQ and Fre could favor this unprecedented mechanism, which most likely involves transfer of the reduced FMN cofactor from the Fre active site to MsrQ.
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Affiliation(s)
- Christelle Caux
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Bruno Guigliarelli
- CNRS, BIP-UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Univ., Marseille 13402, France
| | - Corinne Vivès
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Frédéric Biaso
- CNRS, BIP-UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Univ., Marseille 13402, France
| | - Marius Horeau
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Hawra Hassoune
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | | | - Céline Juillan-Binard
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Stephane Torelli
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Franck Fieschi
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Vincent Nivière
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
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9
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Chandrasekaran S, Schneps CM, Dunleavy R, Lin C, DeOliveira CC, Ganguly A, Crane BR. Tuning flavin environment to detect and control light-induced conformational switching in Drosophila cryptochrome. Commun Biol 2021; 4:249. [PMID: 33637846 PMCID: PMC7910608 DOI: 10.1038/s42003-021-01766-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Light-induction of an anionic semiquinone (SQ) flavin radical in Drosophila cryptochrome (dCRY) alters the dCRY conformation to promote binding and degradation of the circadian clock protein Timeless (TIM). Specific peptide ligation with sortase A attaches a nitroxide spin-probe to the dCRY C-terminal tail (CTT) while avoiding deleterious side reactions. Pulse dipolar electron-spin resonance spectroscopy from the CTT nitroxide to the SQ shows that flavin photoreduction shifts the CTT ~1 nm and increases its motion, without causing full displacement from the protein. dCRY engineered to form the neutral SQ serves as a dark-state proxy to reveal that the CTT remains docked when the flavin ring is reduced but uncharged. Substitutions of flavin-proximal His378 promote CTT undocking in the dark or diminish undocking in the light, consistent with molecular dynamics simulations and TIM degradation activity. The His378 variants inform on recognition motifs for dCRY cellular turnover and strategies for developing optogenetic tools. Chandrasekaran et al. engineered the Drosophila circadian clock protein Cryptochrome (dCRY) to form the neutral semiquinone, which serves as a dark-state proxy. They find that the C-terminal tail of dCRY remains docked when the flavin ring is reduced but uncharged. dCRY His378 variants provide insights into the recognition motifs for dCRY turnover and strategies for optogenetic tools.
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Affiliation(s)
| | - Connor M Schneps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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10
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Brosi R, Illarionov B, Heidinger L, Kim RR, Fischer M, Weber S, Bacher A, Bittl R, Schleicher E. Coupled Methyl Group Rotation in FMN Radicals Revealed by Selective Deuterium Labeling. J Phys Chem B 2020; 124:1678-1690. [PMID: 32011886 DOI: 10.1021/acs.jpcb.9b11331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavin semiquinones are common intermediate redox states in flavoproteins, and thus, knowledge of their electronic structure is essential for fully understanding their chemistry and chemical versatility. In this contribution, we use a combination of high-field electron nuclear double resonance spectroscopy and selective deuterium labeling of flavin mononucleotide (FMN) with subsequent incorporation as cofactor into a variant Avena sativa LOV domain to extract missing traits of the electronic structure of a protein-bound FMN radical. From these experiments, precise values of small proton hyperfine and deuterium nuclear quadrupole couplings could be extracted. Specifically, isotropic hyperfine couplings of -3.34, -0.11, and +0.91 MHz were obtained for the protons H(6), H(9), and H(7α), respectively. These values are discussed in the light of specific protein-cofactor interactions. Furthermore, the temperature behavior of the H(7α) methyl-group rotation elicited by its energy landscape was analyzed in greater detail. Pronounced interplay between the two methyl groups at C(7) and C(8) of FMN could be revealed. Most strikingly, this rotational behavior could be modulated by selective deuterium editing.
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Affiliation(s)
- Richard Brosi
- Fachbereich Physik, Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Ryu-Ryun Kim
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Adelbert Bacher
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany.,Fakultät für Chemie, Technische Universität München, Lichtenbergstr. 4, 80247 Garching, Germany
| | - Robert Bittl
- Fachbereich Physik, Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
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11
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Pompe N, Chen J, Illarionov B, Panter S, Fischer M, Bacher A, Weber S. Methyl groups matter: Photo-CIDNP characterizations of the semiquinone radicals of FMN and demethylated FMN analogs. J Chem Phys 2019; 151:235103. [PMID: 31864274 DOI: 10.1063/1.5130557] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this contribution, the relative hyperfine couplings are determined for the 1H nuclei of the flavin mononucleotide (FMN) radical in an aqueous environment. In addition, three structural analogs with different methylation patterns are characterized and the influence of the substituents at the isoalloxazine moiety on the electronic structure of the radicals is explored. By exploiting nuclear hyperpolarization generated via the photo-CIDNP (chemically induced dynamic nuclear polarization) effect, it is possible to study the short-lived radical species generated by in situ light excitation. Experimental data are extracted by least-squares fitting and supported by quantum chemical calculations and published values from electron paramagnetic resonance and electron-nuclear double resonance. Furthermore, mechanistic details of the photoreaction of the investigated flavin analogs with l-tryptophan are derived from the photo-CIDNP spectra recorded at different pH values. Thereby, the neutral and anionic radicals of FMN and three structural analogs are, for the first time, characterized in terms of their electronic structure in an aqueous environment.
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Affiliation(s)
- Nils Pompe
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Jing Chen
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Boris Illarionov
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Sabrina Panter
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Adelbert Bacher
- Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
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