1
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Rogers CJ, Bogdanov A, Seal M, Thornton ME, Su XC, Natrajan LS, Goldfarb D, Bowen AM. Frequency swept pulses for the enhanced resolution of ENDOR spectra detecting on higher spin transitions of Gd(III). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 351:107447. [PMID: 37119743 DOI: 10.1016/j.jmr.2023.107447] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 05/29/2023]
Abstract
Half-Integer High Spin (HIHS) systems with zero-field splitting (ZFS) parameters below 1 GHz are generally dominated by the spin |─1/2>→|+1/2 > central transition (CT). Accordingly, most pulsed Electron Paramagnetic Resonance (EPR) experiments are performed at this position for maximum sensitivity. However, in certain cases it can be desirable to detect higher spin transitions away from the CT in such systems. Here, we describe the use of frequency swept Wideband, Uniform Rate, Smooth Truncation (WURST) pulses for transferring spin population from the CT, and other transitions, of Gd(III) to the neighbouring higher spin transition |─3/2>→|─1/2 > at Q- and W-band frequencies. Specifically, we demonstrate this approach to enhance the sensitivity of 1H Mims Electron-Nuclear Double Resonance (ENDOR) measurements on two model Gd(III) aryl substituted 1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (DO3A) complexes, focusing on transitions other than the CT. We show that an enhancement factor greater than 2 is obtained for both complexes at Q- and W-band frequencies by the application of two polarising pulses prior to the ENDOR sequence. This is in agreement with simulations of the spin dynamics of the system during WURST pulse excitation. The technique demonstrated here should allow more sensitive experiments to be measured away from the CT at higher operating temperatures, and be combined with any relevant pulse sequence.
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Affiliation(s)
- Ciarán J Rogers
- Department of Chemistry, Photon Science Institute and the National Research Facility for Electron Paramagnetic Resonance, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK
| | - Alexey Bogdanov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Matthew E Thornton
- Department of Chemistry, Photon Science Institute and the National Research Facility for Electron Paramagnetic Resonance, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition College of Chemistry, Nankai University, Tianjin 300071, China
| | - Louise S Natrajan
- Department of Chemistry, Photon Science Institute and the National Research Facility for Electron Paramagnetic Resonance, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Alice M Bowen
- Department of Chemistry, Photon Science Institute and the National Research Facility for Electron Paramagnetic Resonance, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK.
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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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Paulus B, Illarionov B, Nohr D, Roellinger G, Kacprzak S, Fischer M, Weber S, Bacher A, Schleicher E. One Protein, Two Chromophores: Comparative Spectroscopic Characterization of 6,7-Dimethyl-8-ribityllumazine and Riboflavin Bound to Lumazine Protein. J Phys Chem B 2014; 118:13092-105. [DOI: 10.1021/jp507618f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Bernd Paulus
- Institute
of Physical Chemistry, Albert-Ludwigs-University Freiburg, Albertstrasse
21, 79104 Freiburg, Germany
| | - Boris Illarionov
- Institute for Biochemistry & Food Chemistry, University of Hamburg, Bundesstrasse 45, 20146 Hamburg, Germany
| | - Daniel Nohr
- Institute
of Physical Chemistry, Albert-Ludwigs-University Freiburg, Albertstrasse
21, 79104 Freiburg, Germany
| | - Guillaume Roellinger
- Institute
of Physical Chemistry, Albert-Ludwigs-University Freiburg, Albertstrasse
21, 79104 Freiburg, Germany
| | - Sylwia Kacprzak
- Institute
of Physical Chemistry, Albert-Ludwigs-University Freiburg, Albertstrasse
21, 79104 Freiburg, Germany
| | - Markus Fischer
- Institute for Biochemistry & Food Chemistry, University of Hamburg, Bundesstrasse 45, 20146 Hamburg, Germany
| | - Stefan Weber
- Institute
of Physical Chemistry, Albert-Ludwigs-University Freiburg, Albertstrasse
21, 79104 Freiburg, Germany
| | - Adelbert Bacher
- Institute for Biochemistry & Food Chemistry, University of Hamburg, Bundesstrasse 45, 20146 Hamburg, Germany
- Chemistry
Department, Technical University Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Erik Schleicher
- Institute
of Physical Chemistry, Albert-Ludwigs-University Freiburg, Albertstrasse
21, 79104 Freiburg, Germany
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6
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Abstract
Flavoproteins often employ radical mechanisms in their enzymatic reactions. This involves paramagnetic species, which can ideally be investigated with electron paramagnetic resonance (EPR) spectroscopy. In this chapter we focus on the example of flavin-based photoreceptors and discuss, how different EPR methods have been used to extract information about the flavin radical's electronic state, its binding pocket, electron-transfer pathways, and about the protein's tertiary and quaternary structure.
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Affiliation(s)
- Richard Brosi
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany,
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7
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Collins HF, Biedendieck R, Leech HK, Gray M, Escalante-Semerena JC, McLean KJ, Munro AW, Rigby SEJ, Warren MJ, Lawrence AD. Bacillus megaterium has both a functional BluB protein required for DMB synthesis and a related flavoprotein that forms a stable radical species. PLoS One 2013; 8:e55708. [PMID: 23457476 PMCID: PMC3573010 DOI: 10.1371/journal.pone.0055708] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 12/29/2012] [Indexed: 01/05/2023] Open
Abstract
Despite the extensive study of the biosynthesis of the complex molecule B12 (cobalamin), the mechanism by which the lower ligand 5,6-dimethylbenzimidazole (DMB) is formed has remained something of a mystery. However, recent work has identified and characterized a DMB-synthase (BluB) responsible for the oxygen-dependent, single enzyme conversion of FMN to DMB. In this work, we have identified BluB homologs from the aerobic purple, nonsulfur, photosynthetic bacterium Rhodobacter capsulatus and the aerobic soil bacterium Bacillus megaterium and have demonstrated DMB synthesis by the use of a novel complementation assay in which a B12 deficient strain, substituted with the precursor cobinamide is recovered either by the addition of DMB or by the recombinant expression of a bluB gene. The DMB-synthetic activity of the purified recombinant BluB enzymes was further confirmed in vitro by providing the enzyme with FMNH2 and oxygen and observing the formation of DMB by HPLC. The formation of a 4a-peroxyflavin intermediate, the first step in the oxygen dependent mechanism of DMB biosynthesis, is reported here and is the first intermediate in the enzyme catalysed reaction to be demonstrated experimentally to date. The identification and characterization of an FMN-binding protein found on the cobI operon of B. megaterium, CbiY, is also detailed, revealing an FMN-containing enzyme which is able to stabilize a blue flavin semiquinone upon reduction with a 1-electron donor.
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Affiliation(s)
- Hannah F. Collins
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Rebekka Biedendieck
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Helen K. Leech
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Michael Gray
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | | | - Kirsty J. McLean
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Andrew W. Munro
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Stephen E. J. Rigby
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Martin J. Warren
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Andrew D. Lawrence
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
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8
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Maly T, Cui D, Griffin RG, Miller AF. 1H dynamic nuclear polarization based on an endogenous radical. J Phys Chem B 2012; 116:7055-65. [PMID: 22472179 DOI: 10.1021/jp300539j] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate a 15-fold enhancement of solid-state NMR signals via dynamic nuclear polarization (DNP) based on a stable, naturally occurring radical in a protein: the flavin mononucleotide (FMN) semiquinone of flavodoxin. The line width of flavodoxin's EPR signal suggests that the dominant DNP mechanism is the solid effect, consistent with the field-dependent DNP enhancement profile. The magnitude of the enhancement as well as the bulk-polarization build-up time constant (τ(B)) with which it develops are dependent on the isotopic composition of the protein. Deuteration of the protein to 85% increased the nuclear longitudinal relaxation time T(1n) and τ(B) by factors of five and seven, respectively. Slowed dissipation of polarization can explain the 2-fold higher maximal enhancement than that obtained in proteated protein, based on the endogenous semiquinone. In contrast, the long τ(B) of TOTAPOL-based DNP in nonglassy samples was not accompanied by a similarly important long T(1n), and in this case the enhancement was greatly reduced. The low concentrations of radicals occurring naturally in biological systems limit the magnitude of DNP enhancement that is attainable by this means. However, our enhancement factors of up to 15 can nonetheless make an important difference to the feasibility of applying solid-state NMR to biochemical systems. We speculate that DNP based on endogenous radicals may facilitate MAS NMR characterization of biochemical complexes and even organelles, and could also serve as a source of additional structural and physiological information.
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Affiliation(s)
- Thorsten Maly
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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9
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10
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Pauwels E, Declerck R, Verstraelen T, De Sterck B, Kay CWM, Van Speybroeck V, Waroquier M. Influence of Protein Environment on the Electron Paramagnetic Resonance Properties of Flavoprotein Radicals: A QM/MM Study. J Phys Chem B 2010; 114:16655-65. [DOI: 10.1021/jp109763t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ewald Pauwels
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Reinout Declerck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Bart De Sterck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Christopher W. M. Kay
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Veronique Van Speybroeck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Michel Waroquier
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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11
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Stoll S, NejatyJahromy Y, Woodward JJ, Ozarowski A, Marletta MA, Britt RD. Nitric oxide synthase stabilizes the tetrahydrobiopterin cofactor radical by controlling its protonation state. J Am Chem Soc 2010; 132:11812-23. [PMID: 20669954 DOI: 10.1021/ja105372s] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitric oxide synthase (NOS), a homodimeric enzyme with a flavin reductase domain and a P450-type heme-containing oxygenase domain, catalyzes the formation of NO from L-arginine, NADPH, and O(2) in a two-step reaction sequence. In the first step, a tetrahydrobiopterin (H(4)B) cofactor bound near one of the heme propionate groups acts as an electron donor to the P450-type heme active site, yielding a one-electron oxidized radical that is subsequently re-reduced. In solution, H(4)B undergoes two-electron oxidation, showing that the enzyme significantly alters the proton- and electron-transfer properties of the cofactor. Multifrequency EPR and ENDOR spectroscopy were used to determine magnetic parameters, and from them the (de)protonation state of the H(4)B radical in the oxygenase domain dimer of inducible NO synthase that was trapped by rapid freeze quench. From 9.5 and 330-416 GHz EPR and from 34 GHz (1)H ENDOR spectroscopy, the g tensor of the radical and the hyperfine tensors of several N and H nuclei in the radical were obtained. Density functional theory calculations at the PBE0/EPR-II level for H(4)B radical models predict different spin density distributions and g and hyperfine tensors for different protonation states. Comparison of the predicted and experimental values leads to the conclusion that the radical is cationic H(4)B(*+), suggesting that NOS stabilizes this protonated form to utilize the cofactor in a unique dual one-electron redox role, where it can deliver an electron to the active site for reductive oxygen activation and also remove an electron from the active site to generate NO and not NO(-). The protein environment also prevents further oxidation and subsequent loss of function of the cofactor, thus enabling the enzyme to perform the unusual catalytic one-electron chemistry.
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Affiliation(s)
- Stefan Stoll
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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12
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Light-induced activation of class II cyclobutane pyrimidine dimer photolyases. DNA Repair (Amst) 2010; 9:495-505. [PMID: 20227927 DOI: 10.1016/j.dnarep.2010.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 01/16/2010] [Accepted: 01/19/2010] [Indexed: 11/23/2022]
Abstract
Light-induced activation of class II cyclobutane pyrimidine dimer (CPD) photolyases of Arabidopsis thaliana and Oryza sativa has been examined by UV/Vis and pulsed Davies-type electron-nuclear double resonance (ENDOR) spectroscopy, and the results compared with structure-known class I enzymes, CPD photolyase and (6-4) photolyase. By ENDOR spectroscopy, the local environment of the flavin adenine dinucleotide (FAD) cofactor is probed by virtue of proton hyperfine couplings that report on the electron-spin density at the positions of magnetic nuclei. Despite the amino-acid sequence dissimilarity as compared to class I enzymes, the results indicate similar binding motifs for FAD in the class II photolyases. Furthermore, the photoreduction kinetics starting from the FAD cofactor in the fully oxidized redox state, FAD(ox), have been probed by UV/Vis spectroscopy. In Escherichia coli (class I) CPD photolyase, light-induced generation of FADH from FAD(ox), and subsequently FADH(-) from FADH, proceeds in a step-wise fashion via a chain of tryptophan residues. These tryptophans are well conserved among the sequences and within all known structures of class I photolyases, but completely lacking from the equivalent positions of class II photolyase sequences. Nevertheless, class II photolyases show photoreduction kinetics similar to those of the class I enzymes. We propose that a different, but also effective, electron-transfer cascade is conserved among the class II photolyases. The existence of such electron transfer pathways is supported by the observation that the catalytically active fully reduced flavin state obtained by photoreduction is maintained even under oxidative conditions in all three classes of enzymes studied in this contribution.
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13
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Schleicher E, Wenzel R, Ahmad M, Batschauer A, Essen LO, Hitomi K, Getzoff ED, Bittl R, Weber S, Okafuji A. The Electronic State of Flavoproteins: Investigations with Proton Electron-Nuclear Double Resonance. APPLIED MAGNETIC RESONANCE 2010; 37:339-352. [PMID: 26089595 PMCID: PMC4469238 DOI: 10.1007/s00723-009-0101-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Electron-nuclear double resonance (ENDOR) spectroscopy provides useful information on hyperfine interactions between nuclear magnetic moments and the magnetic moment of an unpaired electron spin. Because the hyperfine coupling constant reacts quite sensitively to polarity changes in the direct vicinity of the nucleus under consideration, ENDOR spectroscopy can be favorably used for the detection of subtle protein-cofactor interactions. A number of pulsed ENDOR studies on flavoproteins have been published during the past few years; most of them were designed to characterize the flavin cofactor by means of its protonation state, or to detect individual protein-cofactor interactions. The aim of this study is to compare the pulsed ENDOR spectra from different flavoproteins in terms of variations of characteristic proton hyperfine values. The general concept is to observe limits of possible influences on the cofactor's electronic state by surrounding amino acids. Furthermore, we compare ENDOR data obtained from in vivo experiments with in vitro data to emphasize the potential of the method for gaining molecular information in complex media.
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Affiliation(s)
- Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
| | - Ringo Wenzel
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Alfred Batschauer
- Fachbereich Biologie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Kenichi Hitomi
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elizabeth D Getzoff
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Bittl
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
| | - Asako Okafuji
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
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Schleicher E, Bittl R, Weber S. New roles of flavoproteins in molecular cell biology: Blue-light active flavoproteins studied by electron paramagnetic resonance. FEBS J 2009; 276:4290-303. [DOI: 10.1111/j.1742-4658.2009.07141.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Weber S, Bittl R. Studies of Organic Protein Cofactors Using Electron Paramagnetic Resonance. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Schleicher E, Hitomi K, Kay CWM, Getzoff ED, Todo T, Weber S. Electron nuclear double resonance differentiates complementary roles for active site histidines in (6-4) photolyase. J Biol Chem 2006; 282:4738-4747. [PMID: 17164245 DOI: 10.1074/jbc.m604734200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
(6-4) photolyase catalyzes the light-dependent repair of UV-damaged DNA containing (6-4) photoproducts. Blue light excitation of the enzyme generates the neutral FAD radical, FADH., which is believed to be transiently formed during the enzymatic DNA repair. Here (6-4) photolyase has been examined by optical spectroscopy, electron paramagnetic resonance, and pulsed electron nuclear double resonance spectroscopy. Characterization of selected proton hyperfine couplings of FADH., namely those of H(8alpha) and H(1'), yields information on the micropolarity at the site where the DNA substrate is expected to bind. Shifts in the hyperfine couplings as a function of structural modifications induced by point mutations and pH changes distinguish the protonation states of two highly conserved histidines, His(354) and His(358), in Xenopus laevis (6-4) photolyase. These are proposed to catalyze formation of the oxetane intermediate that precedes light-initiated DNA repair. The results show that at pH 9.5, where the enzymatic repair activity is highest, His(358) is deprotonated, whereas His(354) is protonated. Hence, the latter is likely the proton donor that initiates oxetane formation from the (6-4) photoproduct.
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Affiliation(s)
- Erik Schleicher
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Kenichi Hitomi
- Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Christopher W M Kay
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany; Department of Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom, and the
| | - Elizabeth D Getzoff
- Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Takeshi Todo
- Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyoku, Kyoto 606-8501, Japan
| | - Stefan Weber
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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Schnegg A, Kay CWM, Schleicher E, Hitomi K, Todo T, Möbius K, Weber∗ S. The g-tensor of the flavin cofactor in (6–4) photolyase: a 360 GHz/12.8 T electron paramagnetic resonance study. Mol Phys 2006. [DOI: 10.1080/00268970600593108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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