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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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2
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Schleicher E, Rein S, Illarionov B, Lehmann A, Al Said T, Kacprzak S, Bittl R, Bacher A, Fischer M, Weber S. Selective 13C labelling reveals the electronic structure of flavocoenzyme radicals. Sci Rep 2021; 11:18234. [PMID: 34521887 PMCID: PMC8440535 DOI: 10.1038/s41598-021-97588-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Flavocoenzymes are nearly ubiquitous cofactors that are involved in the catalysis and regulation of a wide range of biological processes including some light-induced ones, such as the photolyase-mediated DNA repair, magnetoreception of migratory birds, and the blue-light driven phototropism in plants. One of the factors that enable versatile flavin-coenzyme biochemistry and biophysics is the fine-tuning of the cofactor's frontier orbital by interactions with the protein environment. Probing the singly-occupied molecular orbital (SOMO) of the intermediate radical state of flavins is therefore a prerequisite for a thorough understanding of the diverse functions of the flavoprotein family. This may be ultimately achieved by unravelling the hyperfine structure of a flavin by electron paramagnetic resonance. In this contribution we present a rigorous approach to obtaining a hyperfine map of the flavin's chromophoric 7,8-dimethyl isoalloxazine unit at an as yet unprecedented level of resolution and accuracy. We combine powerful high-microwave-frequency/high-magnetic-field electron-nuclear double resonance (ENDOR) with 13C isotopologue editing as well as spectral simulations and density functional theory calculations to measure and analyse 13C hyperfine couplings of the flavin cofactor in DNA photolyase. Our data will provide the basis for electronic structure considerations for a number of flavin radical intermediates occurring in blue-light photoreceptor proteins.
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Affiliation(s)
- Erik Schleicher
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Stephan Rein
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Boris Illarionov
- grid.9026.d0000 0001 2287 2617Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Ariane Lehmann
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Tarek Al Said
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Sylwia Kacprzak
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany ,grid.423218.ePresent Address: Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Robert Bittl
- grid.14095.390000 0000 9116 4836Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Adelbert Bacher
- grid.6936.a0000000123222966Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Markus Fischer
- grid.9026.d0000 0001 2287 2617Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Stefan Weber
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
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3
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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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4
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Nohr D, Weber S, Schleicher E. EPR spectroscopy on flavin radicals in flavoproteins. Methods Enzymol 2019; 620:251-275. [PMID: 31072489 DOI: 10.1016/bs.mie.2019.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Flavin semiquinone redox states are important intermediates in a broad variety of reactions catalyzed by flavoproteins. As paramagnetic states they can be favorably probed by EPR spectroscopy in all its flavors. This review summarizes recent results in the characterization of flavin radicals. On the one hand, flavin radical states, e.g., trapped as reaction intermediates, can be characterized using modern pulsed EPR methods to unravel their electronic structure and to gain information about the surrounding environment and its changes on protein action. On the other hand, short-lived intermediate flavin radical states generated, e.g., photochemically, can be followed by time-resolved EPR, which allows a direct tracking of flavin-dependent reactions with a temporal resolution reaching nanoseconds.
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Affiliation(s)
- Daniel Nohr
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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5
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Rostas A, Einholz C, Illarionov B, Heidinger L, Said TA, Bauss A, Fischer M, Bacher A, Weber S, Schleicher E. Long-Lived Hydrated FMN Radicals: EPR Characterization and Implications for Catalytic Variability in Flavoproteins. J Am Chem Soc 2018; 140:16521-16527. [PMID: 30412389 DOI: 10.1021/jacs.8b07544] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Until now, FMN/FAD radicals could not be stabilized in aqueous solution or other protic solvents because of rapid and efficient dismutation reactions. In this contribution, a novel system for stabilizing flavin radicals in aqueous solution is reported. Subsequent to trapping FMN in an agarose matrix, light-generated FMN radicals could be produced that were stable for days even under aerobic conditions, and their concentrations were high enough for extensive EPR characterization. All large hyperfine couplings could be extracted by using a combination of continuous-wave EPR and low-temperature ENDOR spectroscopy. To map differences in the electronic structure of flavin radicals, two exemplary proton hyperfine couplings were compared with published values from various neutral and anionic flavoprotein radicals: C(6)H and C(8α)H 3. It turned out that FMN•- in an aqueous environment shows the largest hyperfine couplings, whereas for FMNH• under similar conditions, hyperfine couplings are at the lower end and the values of both vary by up to 30%. This finding demonstrates that protein-cofactor interactions in neutral and anionic flavoprotein radicals can alter their electron spin density in different directions. With this aqueous system that allows the characterization of flavin radicals without protein interactions and that can be extended by using selective isotope labeling, a powerful tool is now at hand to quantify interactions in flavin radicals that modulate the reactivity in different flavoproteins.
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Affiliation(s)
- Arpad Rostas
- Institut für Physikalische Chemie , Albert-Ludwigs-Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Christopher Einholz
- Institut für Physikalische Chemie , Albert-Ludwigs-Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Boris Illarionov
- Hamburg School of Food Science , 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
| | - Tarek Al Said
- Institut für Physikalische Chemie , Albert-Ludwigs-Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Anna Bauss
- Institut für Physikalische Chemie , Albert-Ludwigs-Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Markus Fischer
- Hamburg School of Food Science , Institut für Lebensmittelchemie, Universität Hamburg , Grindelallee 117 , 20146 Hamburg , Germany
| | - Adelbert Bacher
- Department of Chemistry , Technical University of Munich , Lichtenbergstr. 4 , 85747 Garching , Germany
| | - Stefan Weber
- Institut für Physikalische Chemie , Albert-Ludwigs-Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie , Albert-Ludwigs-Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
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6
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Martínez JI, Frago S, Lans I, Alonso PJ, García-Rubio I, Medina M. Spin Densities in Flavin Analogs within a Flavoprotein. Biophys J 2017; 110:561-571. [PMID: 26840722 DOI: 10.1016/j.bpj.2015.11.3525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/10/2015] [Accepted: 11/16/2015] [Indexed: 11/26/2022] Open
Abstract
Characterization by electron paramagnetic resonance techniques of several variants of Anabaena flavodoxin, where the naturally occurring FMN cofactor is substituted by different analogs, makes it possible to improve the details of the spin distribution map in the isoallosazine ring in its semiquinone state. The analyzed variants were selected to monitor the effects of intrinsic changes in the flavin ring electronic structure, as well as perturbations in the apoflavodoxin-flavin interaction, on the spin populations. When these effects were analyzed together with the functional properties of the different flavodoxin variants, a relationship between spin population and biochemical parameters, as the reduction potential, could be envisaged.
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Affiliation(s)
- Jesús Ignacio Martínez
- Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain.
| | - Susana Frago
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain; Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Isaías Lans
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Pablo Javier Alonso
- Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
| | - Inés García-Rubio
- Centro Universitario de la Defensa, Zaragoza, Spain; Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Switzerland
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
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7
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Martínez JI, Alonso PJ, García-Rubio I, Medina M. Methyl rotors in flavoproteins. Phys Chem Chem Phys 2014; 16:26203-12. [DOI: 10.1039/c4cp03115f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ENDOR evidence shows that methyl groups in flavin behave as quantum locked rotors.
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Affiliation(s)
- Jesús I. Martínez
- Instituto de Ciencia de Materiales de Aragón
- Universidad de Zaragoza-Consejo Superior de Investigaciones Científicas
- Facultad de Ciencias
- 50009 Zaragoza, Spain
| | - Pablo J. Alonso
- Instituto de Ciencia de Materiales de Aragón
- Universidad de Zaragoza-Consejo Superior de Investigaciones Científicas
- Facultad de Ciencias
- 50009 Zaragoza, Spain
| | - Inés García-Rubio
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zürich, Switzerland
- Centro Universitario de la Defensa
- 50090 Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)
- Universidad de Zaragoza
- 50009 Zaragoza, Spain
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8
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Kammler L, van Gastel M. Electronic structure of the lowest triplet state of flavin mononucleotide. J Phys Chem A 2012; 116:10090-8. [PMID: 22998491 DOI: 10.1021/jp305778v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The electronic structure of flavin mononucleotide (FMN), an organic cofactor that plays a role in many important enzymatic reactions, has been investigated by electron paramagnetic resonance (EPR) spectroscopy, optical spectroscopy, and quantum chemistry. In particular, the triplet state of FMN, which is paramagnetic (total spin S = 1), allows an investigation of the zero field splitting parameters D and E, which are directly related to the two singly occupied molecular orbitals. Triplet EPR spectra and optical absorption spectra at different pH values in combination with time dependent density functional theory (TDDFT) reveal that the highest occupied orbital (HOMO) and lowest unoccupied orbital (LUMO) of FMN are largely unaffected by changes in the protonation state of FMN. Rather, the orbital structure of the lower lying doubly occupied orbitals changes dramatically. Additional EPR experiments have been carried out in the presence of AgNO(3), which allows the formation of an Ag-FMN triplet state with different zero field splitting parameters and population and depopulation rates. Addition of AgNO(3) only induces small changes in the optical spectrum, indicating that the Ag(+) ion only contributes to the zero field splitting by second order spin-orbit coupling and leaves the orbital structure unaffected. By a combination of the three employed methods, the observed bands in the UV/vis spectra of FMN at different pH values are assigned to electronic transitions.
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Affiliation(s)
- Lydia Kammler
- Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn, Germany
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9
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Eaton SS, Eaton GR. The world as viewed by and with unpaired electrons. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:151-63. [PMID: 22975244 PMCID: PMC3496796 DOI: 10.1016/j.jmr.2012.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 06/01/2023]
Abstract
Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models.
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Affiliation(s)
- Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208, USA
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