1
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Abdullin D, Hett T, Fleck N, Kopp K, Cassidy S, Richert S, Schiemann O. Magneto-Structural Correlations in a Mixed Porphyrin(Cu 2+ )/Trityl Spin System: Magnitude, Sign, and Distribution of the Exchange Coupling Constant. Chemistry 2023; 29:e202203148. [PMID: 36519664 DOI: 10.1002/chem.202203148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Tetrathiatriarylmethyl radicals (TAM or trityl) are receiving increasing attention in various fields of magnetic resonance such as imaging, dynamic nuclear polarization, spin labeling, and, more recently, molecular magnetism and quantum information technology. Here, a trityl radical attached via a phenyl bridge to a copper(II)tetraphenylporphyrin was synthesized, and its magnetic properties studied by multi-frequency continuous-wave electron paramagnetic resonance (EPR) spectroscopy and magnetic measurements. EPR revealed that the electron spin-spin coupling constant J between the trityl and Cu2+ spin centers is ferromagnetic with a magnitude of -2.3 GHz (-0.077 cm-1 , + J S → 1 S → 2 ${+J{\vec{S}}_{1}{\vec{S}}_{2}}$ convention) and a distribution width of 1.2 GHz (0.040 cm-1 ). With the help of density functional theory (DFT) calculations, the obtained ferromagnetic exchange coupling, which is unusual for para-substituted phenyl-bridged biradicals, could be related to the almost perpendicular orientation of the phenyl linker with respect to the porphyrin and trityl ring planes in the energy minimum, while the J distribution was rationalized by the temperature weighted rotation of the phenyl bridge about the molecular axis connecting both spin centers. This study exemplifies the importance of molecular dynamics for the homogeneity (or heterogeneity) of the magnetic properties of trityl-based systems.
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Affiliation(s)
- Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Tobias Hett
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Nico Fleck
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.,Merck KGaA, Q20/001, Frankfurterstr. 250, 64293, Darmstadt, Germany
| | - Kevin Kopp
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Simon Cassidy
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Sabine Richert
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.,Department of Chemical and Biological Physics, Weizmann Institute of Science, 761001, Rehovot, Israel
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2
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Joutsuka T, Nanasawa R, Igarashi K, Horie K, Sugishima M, Hagiwara Y, Wada K, Fukuyama K, Yano N, Mori S, Ostermann A, Kusaka K, Unno M. Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states. J Biol Chem 2022; 299:102763. [PMID: 36463961 PMCID: PMC9800206 DOI: 10.1016/j.jbc.2022.102763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/16/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
PcyA, a ferredoxin-dependent bilin pigment reductase, catalyzes the site-specific reduction of the two vinyl groups of biliverdin (BV), producing phycocyanobilin. Previous neutron crystallography detected both the neutral BV and its protonated form (BVH+) in the wildtype (WT) PcyA-BV complex, and a nearby catalytic residue Asp105 was found to have two conformations (protonated and deprotonated). Semiempirical calculations have suggested that the protonation states of BV are reflected in the absorption spectrum of the WT PcyA-BV complex. In the previously determined absorption spectra of the PcyA D105N and I86D mutants, complexed with BV, a peak at 730 nm, observed in the WT, disappeared and increased, respectively. Here, we performed neutron crystallography and quantum chemical analysis of the D105N-BV and I86D-BV complexes to determine the protonation states of BV and the surrounding residues and study the correlation between the absorption spectra and protonation states around BV. Neutron structures elucidated that BV in the D105N mutant is in a neutral state, whereas that in the I86D mutant is dominantly in a protonated state. Glu76 and His88 showed different hydrogen bonding with surrounding residues compared with WT PcyA, further explaining why D105N and I86D have much lower activities for phycocyanobilin synthesis than the WT PcyA. Our quantum mechanics/molecular mechanics calculations of the absorption spectra showed that the spectral change in D105N arises from Glu76 deprotonation, consistent with the neutron structure. Collectively, our findings reveal more mechanistic details of bilin pigment biosynthesis.
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Affiliation(s)
- Tatsuya Joutsuka
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan,For correspondence: Tatsuya Joutsuka; Masaki Unno
| | - Ryota Nanasawa
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan
| | - Keisuke Igarashi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan
| | - Kazuki Horie
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Yoshinori Hagiwara
- Department of Biochemistry and Applied Chemistry, National Institute of Technology, Kurume College, Kurume, Fukuoka, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Keiichi Fukuyama
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Naomine Yano
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan
| | - Seiji Mori
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technical University Munich, Garching, Germany
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan,For correspondence: Tatsuya Joutsuka; Masaki Unno
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3
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Rao G, Chen N, Marchiori DA, Wang LP, Britt RD. Accumulation and Pulse Electron Paramagnetic Resonance Spectroscopic Investigation of the 4-Oxidobenzyl Radical Generated in the Radical S-Adenosyl-l-methionine Enzyme HydG. Biochemistry 2022; 61:107-116. [PMID: 34989236 DOI: 10.1021/acs.biochem.1c00619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The radical S-adenosyl-l-methionine (SAM) enzyme HydG cleaves tyrosine to generate CO and CN- ligands of the [FeFe] hydrogenase H-cluster, accompanied by the formation of a 4-oxidobenzyl radical (4-OB•), which is the precursor to the HydG p-cresol byproduct. Native HydG only generates a small amount of 4-OB•, limiting detailed electron paramagnetic resonance (EPR) spectral characterization beyond our initial EPR lineshape study employing various tyrosine isotopologues. Here, we show that the concentration of trapped 4-OB• is significantly increased in reactions using HydG variants, in which the "dangler Fe" to which CO and CN- bind is missing or substituted by a redox-inert Zn2+ ion. This allows for the detailed characterization of 4-OB• using high-field EPR and electron nuclear double resonance spectroscopy to extract its g-values and 1H/13C hyperfine couplings. These results are compared to density functional theory-predicted values of several 4-OB• models with different sizes and protonation states, with a best fit to the deprotonated radical anion configuration of 4-OB•. Overall, our results depict a clearer electronic structure of the transient 4-OB• radical and provide new insights into the radical SAM chemistry of HydG.
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Affiliation(s)
- Guodong Rao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Nanhao Chen
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - David A Marchiori
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
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4
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Montoya EJO, Dorion S, Atehortua-Garcés L, Rivoal J. Phycobilin heterologous production from the Rhodophyta Porphyridium cruentum. J Biotechnol 2021; 341:30-42. [PMID: 34500003 DOI: 10.1016/j.jbiotec.2021.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/19/2022]
Abstract
Phycobiliproteins are colored, active molecules with potential use in different industries. They are the union of proteins and bilins (Chromophores). The primary source of phycobiliproteins is algae; however, the traditional algae culture has production restrictions. The production in bacterial models can be a more efficient alternative to produce these molecules. However, the lack of knowledge in some steps of the phycobiliprotein metabolic pathway limits this alternative. Porphyridium cruentum is a single cell red alga with a high phycobiliprotein content. Its protein sequences were the basis for phycobilin production in this study. In this study, we cloned and characterized enzymes presumably involved in the chromophore production of P. cruentum. Using sequences obtained from its transcriptome, we characterized two cDNA sequences predicted to code respectively for a ferredoxin-dependent bilin reductase and a bilin lyase-isomerase. We expressed these enzymes in Escherichia coli to obtain in vivo evidence of their enzymatic activity on the substrate biliverdin IXα. Lastly, we analyzed them using thin-layer chromatography, spectrophotometry, and fluorescence spectroscopy. These experiments provided evidence of bilin modification. The expressed bilin lyase-isomerase did not show significant activity over the biliverdin molecule. On the contrary, the expressed ferredoxin-dependent bilin reductase showed activity over the biliverdin.
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Affiliation(s)
- Erika Juliana Obando Montoya
- Laboratorio de Biotecnología, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Carrera 53 # 61 - 30 - SIU. Torre 1 Laboratorio de 210, Medellín 050010, Colombia.
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Lucía Atehortua-Garcés
- Laboratorio de Biotecnología, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Carrera 53 # 61 - 30 - SIU. Torre 1 Laboratorio de 210, Medellín 050010, Colombia
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
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5
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Witwicki M, Lewińska A, Ozarowski A. o-Semiquinone radical anion isolated as an amorphous porous solid. Phys Chem Chem Phys 2021; 23:17408-17419. [PMID: 34351330 DOI: 10.1039/d1cp01596f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of metal cations is a commonly applied strategy to create S > 1/2 stable molecular systems containing semiquinone radicals. Persistent mono-semiquinonato complexes of diamagnetic metal ions (S = 1/2) have been hitherto less common and mostly limited to the complexes of heavy metal ions. In this work, a mono-semiquinonato complex of aluminum, derived from 1,2-dihydroxybenzene, is obtained using a surprisingly short and uncomplicated procedure. The isolated product is an amorphous and porous solid that exhibits very good stability under ambient conditions. To characterise its molecular and electronic structure, 9.7, 34 and 406 GHz EPR spectroscopy was used in concert with computational techniques (DFT and DLPNO-CCSD). It was revealed that the radical complex is composed of two chemically equivalent aluminum cations and two catechol-like ligands with the unpaired electron uniformly distributed between the two organic molecules. The good stability and porous structure make this complex applicable in heterogeneous aerobic reactions.
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Affiliation(s)
- Maciej Witwicki
- Faculty of Chemistry, Wroclaw University, Joliot-Curie 14, 50-383 Wroclaw, Poland.
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6
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Pontes MS, Graciano DE, Antunes DR, Santos JS, Arruda GJ, Botero ER, Grillo R, Lima SM, Andrade LHC, Caires ARL, Santiago EF. In vitro and in vivo impact assessment of eco-designed CuO nanoparticles on non-target aquatic photoautotrophic organisms. JOURNAL OF HAZARDOUS MATERIALS 2020; 396:122484. [PMID: 32302886 DOI: 10.1016/j.jhazmat.2020.122484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 06/11/2023]
Abstract
This work has assessed the impact of copper oxide nanoparticles (CuONPs), designed via green route, toward photosynthetic apparatus on aquatic photoautotrophic organisms. In order to filling knowledge gaps, in vitro and in vivo assays were performed, using cyanobacterial phycocyanin (C-PC) from Arthrospira platensis and Lemna valdiviana plants (duckweed), respectively. Impairment in light energy transfer became evident in C-PC exposed to CuONPs, giving rise to an increase of light absorption and a suppression of fluorescence emission. Fourier transform infrared spectroscopy (FTIR) results showed that C-PC structures might be altered by the nanoparticles, also revealed that CuONPs preferably interacts with -NH functional groups. The data also revealed that CuONPs affected the chlorophyll a content in duckweed leaves. In addition, photosystem II (PSII) performance was significantly affected by CuONPs, negatively impacting the PSII photochemical network. In summary, the results point out that, even eco-friendly designed, CuONPs may negatively affect the photosynthetic process when accumulated by aquatic photoautotrophs.
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Affiliation(s)
- Montcharles S Pontes
- Natural Resources Program, Center for Natural Resources Studies (CERNA), Mato Grosso do Sul State University (UEMS), Dourados, Mato Grosso do Sul, 79804-970, Brazil
| | - Daniela E Graciano
- Applied Optics Group, Faculty of Science and Technology, Federal University of Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, 79804-970, Brazil
| | - Débora R Antunes
- Department of Physics and Chemistry, School of Engineering, São Paulo State University (UNESP), Ilha Solteira, São Paulo, 15385-000, Brazil
| | - Jaqueline S Santos
- Natural Resources Program, Center for Natural Resources Studies (CERNA), Mato Grosso do Sul State University (UEMS), Dourados, Mato Grosso do Sul, 79804-970, Brazil
| | - Gilberto J Arruda
- Natural Resources Program, Center for Natural Resources Studies (CERNA), Mato Grosso do Sul State University (UEMS), Dourados, Mato Grosso do Sul, 79804-970, Brazil
| | - Eriton R Botero
- Applied Optics Group, Faculty of Science and Technology, Federal University of Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, 79804-970, Brazil
| | - Renato Grillo
- Department of Physics and Chemistry, School of Engineering, São Paulo State University (UNESP), Ilha Solteira, São Paulo, 15385-000, Brazil
| | - Sandro M Lima
- Natural Resources Program, Center for Natural Resources Studies (CERNA), Mato Grosso do Sul State University (UEMS), Dourados, Mato Grosso do Sul, 79804-970, Brazil
| | - Luís H C Andrade
- Natural Resources Program, Center for Natural Resources Studies (CERNA), Mato Grosso do Sul State University (UEMS), Dourados, Mato Grosso do Sul, 79804-970, Brazil
| | - Anderson R L Caires
- Optics and Photonics Group, Institute of Physics, Federal University of Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, 79070-900, Brazil; School of Life Science, University of Essex, Colchester, CO4 3SQ, Essex, UK
| | - Etenaldo F Santiago
- Natural Resources Program, Center for Natural Resources Studies (CERNA), Mato Grosso do Sul State University (UEMS), Dourados, Mato Grosso do Sul, 79804-970, Brazil.
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7
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Yamamoto H, Mizoguchi T, Tsukatani Y, Tamiaki H, Kurisu G, Fujita Y. Chlorophyllide a oxidoreductase Preferentially Catalyzes 8-Vinyl Reduction over B-Ring Reduction of 8-Vinyl Chlorophyllide a in the Late Steps of Bacteriochlorophyll Biosynthesis. Chembiochem 2020; 21:1760-1766. [PMID: 32180325 DOI: 10.1002/cbic.201900785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/25/2020] [Indexed: 11/08/2022]
Abstract
Bacteriochlorophyll a (BChl) is an essential pigment for anoxygenic photosynthesis. In late steps of the BChl biosynthesis of Rhodobacter capsulatus, the C8 vinyl group and C7=C8 double bond of 8-vinyl chlorophyllide a (8 V-Chlide) are reduced by a C8 vinyl reductase (8VR), BciA, and a nitrogenase-like enzyme, chlorophyllide a oxidoreductase (COR), respectively, to produce 3-vinyl-bacteriochlorphyllide a. Recently, we discovered 8VR activity in COR. However, the kinetic parameters of the COR 8VR activity remain unknown, while those of the COR C7=C8 reductase activity and BciA have been reported. Here, we determined the kinetic parameters of COR 8VR activity by using 8 V-Chlide. The Km value for 8 V-Chlide was 1.4 μM, which is much lower than the 6.2 μM determined for the C7=C8 reduction of Chlide. The kinetic parameters of the dual activities of COR suggest that COR catalyzes the reduction of the C8 vinyl group of 8 V-Chlide preferentially over C7=C8 reduction when both substrates are supplied during BChl biosynthesis.
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Affiliation(s)
- Haruki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Tadashi Mizoguchi
- Graduate School of Life Sciences, Ritsumeikan University Kusatsu, Shiga, 525-8577, Japan
| | - Yusuke Tsukatani
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Kanagawa, 237-0061, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University Kusatsu, Shiga, 525-8577, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University Suita, Osaka, 565-0871, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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8
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Abstract
Long-standing radical species have raised noteworthy concerns in organic functional chemistry and materials. However, there remains a substantial challenge to produce long-standing radicals by light, because of the structural dilemmas between photoproduction and stabilization. Herein, we present a pyrrole and chloride assisted photochromic structure to address this issue. In this well-selected system, production and stabilization of a radical species were simultaneously found accompanied by a photochemical process in chloroform. Theoretical study and mechanism construction indicate that the designed π-system provides a superior spin-delocalization effect and a large steric effect, mostly avoiding possible consumptions and making the radical stable for hours even under an oxygen-saturated condition. Moreover, this radical system can be applied for a visualized and quantitative detection towards peroxides, such as 2,2,6,6-tetramethylpiperidine-1-oxyl, hydrogen peroxide, and ozone. As the detection relies on a radical capturing mechanism, a higher sensing rate was achieved compared to traditional redox techniques for peroxide detection. Long-standing radical species have raised noteworthy concerns in organic chemistry and but there remains a substantial challenge to produce long-standing radicals by light. Here, the authors demonstrate a stable dithienylethene derived photochromic radical for detection of peroxides and ozone.
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9
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Sugishima M, Wada K, Unno M, Fukuyama K. Bilin-metabolizing enzymes: site-specific reductions catalyzed by two different type of enzymes. Curr Opin Struct Biol 2019; 59:73-80. [PMID: 30954759 DOI: 10.1016/j.sbi.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/09/2019] [Accepted: 03/04/2019] [Indexed: 02/05/2023]
Abstract
In mammals, the green heme metabolite biliverdin is converted to a yellow anti-oxidant by NAD(P)H-dependent biliverdin reductase (BVR), whereas in O2-dependent photosynthetic organisms it is converted to photosynthetic or light-sensing pigments by ferredoxin-dependent bilin reductases (FDBRs). In NADP+-bound and biliverdin-bound BVR-A, two biliverdins are stacked at the binding cleft; one is positioned to accept hydride from NADPH, and the other appears to donate a proton to the first biliverdin through a neighboring arginine residue. During the FDBR-catalyzed reaction, electrons and protons are supplied to bilins from ferredoxin and from FDBRs and waters bound within FDBRs, respectively. Thus, the protonation sites of bilin and catalytic residues are important for the analysis of site-specific reduction. The neutron structure of FDBR sheds light on this issue.
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Affiliation(s)
- Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan.
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Ibaraki 316-8511, Japan
| | - Keiichi Fukuyama
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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10
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Regnier V, Romero EA, Molton F, Jazzar R, Bertrand G, Martin D. What Are the Radical Intermediates in Oxidative N-Heterocyclic Carbene Organocatalysis? J Am Chem Soc 2018; 141:1109-1117. [PMID: 30561990 DOI: 10.1021/jacs.8b11824] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The oxidation of the Breslow intermediate resulting from the addition of an N-heterocyclic carbene (NHC) to benzaldehyde triggers a fast deprotonation, followed by a second electron transfer, directly affording the corresponding acylium at E > -0.8 V (versus Fc/Fc+). Similarly, the oxidation of the cinnamaldehyde analogue occurs at an even higher potential and is not a reversible electrochemical process. As a whole, and contrary to previous beliefs, it is demonstrated that Breslow intermediates, which are the key intermediates in NHC-catalyzed transformations of aldehydes, cannot undergo a single electron transfer (SET) with mild oxidants ( E < -1.0 V). Moreover, the corresponding enol radical cations are ruled out as relevant intermediates. It is proposed that oxidative NHC-catalyzed radical transformations of enals proceed either through SET from the corresponding electron-rich enolate or through coupled electron-proton transfer from the enol, in any case generating neutral capto-dative radicals. Relevant electrochemical surrogates of these paramagnetic species have been isolated.
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Affiliation(s)
| | - Erik A Romero
- UMI CNRS 3555, Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0343 , United States
| | - Florian Molton
- Univ. Grenoble Alpes , CNRS, DCM , 38000 Grenoble , France
| | - Rodolphe Jazzar
- UMI CNRS 3555, Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0343 , United States
| | - Guy Bertrand
- UMI CNRS 3555, Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0343 , United States
| | - David Martin
- Univ. Grenoble Alpes , CNRS, DCM , 38000 Grenoble , France
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11
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Wilson CB, Aronson S, Clayton JA, Glaser SJ, Han S, Sherwin MS. Multi-step phase-cycling in a free-electron laser-powered pulsed electron paramagnetic resonance spectrometer. Phys Chem Chem Phys 2018; 20:18097-18109. [PMID: 29938285 DOI: 10.1039/c8cp01876f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) is a powerful tool for research in chemistry, biology, physics and materials science, which can benefit significantly from moving to frequencies above 100 GHz. In pulsed EPR spectrometers driven by powerful sub-THz oscillators, such as the free electron laser (FEL)-powered EPR spectrometer at UCSB, control of the duration, power and relative phases of the pulses in a sequence must be performed at the frequency and power level of the oscillator. Here we report on the implementation of an all-quasioptical four-step phase cycling procedure carried out directly at the kW power level of the 240 GHz pulses used in the FEL-powered EPR spectrometer. Phase shifts are introduced by modifying the optical path length of a 240 GHz pulse with precision-machined dielectric plates in a procedure we call phase cycling with optomechanical phase shifters (POPS), while numerical receiver phase cycling is implemented in post-processing. The POPS scheme was successfully used to reduce experimental dead times, enabling pulsed EPR of fast-relaxing spin systems such as gadolinium complexes at temperatures above 190 K. Coherence transfer pathway selection with POPS was used to perform spin echo relaxation experiments to measure the phase memory time of P1 centers in diamond in the presence of a strong unwanted FID signal in the background. The large excitation bandwidth of FEL-EPR, together with phase cycling, enabled the quantitative measurement of instantaneous electron spectral diffusion, from which the P1 center concentration was estimated to within 10%. Finally, phase cycling enabled saturation-recovery measurements of T1 in a trityl-water solution at room temperature - the first FEL-EPR measurement of electron T1.
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Affiliation(s)
- C Blake Wilson
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, USA.
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12
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Herb K, Tschaggelar R, Denninger G, Jeschke G. Double resonance calibration of g factor standards: Carbon fibers as a high precision standard. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 289:100-106. [PMID: 29476927 DOI: 10.1016/j.jmr.2018.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/08/2018] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
The g factor of paramagnetic defects in commercial high performance carbon fibers was determined by a double resonance experiment based on the Overhauser shift due to hyperfine coupled protons. Our carbon fibers exhibit a single, narrow and perfectly Lorentzian shaped ESR line and a g factor slightly higher than gfree with g=2.002644=gfree·(1+162ppm) with a relative uncertainty of 15ppm. This precisely known g factor and their inertness qualify them as a high precision g factor standard for general purposes. The double resonance experiment for calibration is applicable to other potential standards with a hyperfine interaction averaged by a process with very short correlation time.
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Affiliation(s)
- Konstantin Herb
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland.
| | - Rene Tschaggelar
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland.
| | - Gert Denninger
- 2. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland.
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13
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Tan S, Tan X, Chi Z, Zhang D, Li W. In vitro assessment of the toxicity of lead (Pb 2+) to phycocyanin. CHEMOSPHERE 2018; 192:171-177. [PMID: 29101856 DOI: 10.1016/j.chemosphere.2017.10.159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/22/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
This work reports the influence of lead (Pb2+) on fluorescence characteristics and protein structure of phycocyanin molecules experimentally in vitro. The fluorescence intensity decreases with the increasing concentration of Pb2+ from 0 to 5 × 10-5 mol L-1, showing the fluorescence quenching of phycocyanin by Pb2+. The quenching process is suggested to be static regarding the calculation results and the experimental results of time-resolved fluorescence decay profiles. The synchronous fluorescence spectra show that the effect of Pb2+ on the Tyr residues of phycocyanin is more significant than the Trp residues. The forming of aggregation by the interaction of Pb2+ with phycocyanin molecules is suggested from the results of resonance light scattering spectra. The UV-Vis spectra of the protein skeleton of phycocyanin have a red-shift of about 10 nm with increasing the Pb2+ concentration from 0 to 5 × 10-5 mol L-1, indicating a change in the protein skeleton and its secondary structure. With the increasing Pb2+ concentration, the two negative peaks (209 nm and 218 nm) on circular dichroism spectra become smaller, showing a decrease of the α-helix structure. These results may give people a deeper understanding of that how the heavy metal (Pb2+) can affect the chemo-physical properties of phycocyanin.
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Affiliation(s)
- Songwen Tan
- Department of Environmental Engineering, Harbin Institute of Technology, Weihai, 2# Wenhua West Road, Weihai 264209, PR China
| | - Xu Tan
- Department of Civil and Environmental Engineering, University of Technology Sydney, Sydney 2007, Australia
| | - Zhenxing Chi
- Department of Environmental Engineering, Harbin Institute of Technology, Weihai, 2# Wenhua West Road, Weihai 264209, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73# Huanghe Road, Harbin 150090, PR China; Guangzhou Key Laboratory of Environmental Exposure and Health, School of Environment, Jinan University, Guangzhou 510632, PR China.
| | - Dayin Zhang
- Department of Environmental Engineering, Harbin Institute of Technology, Weihai, 2# Wenhua West Road, Weihai 264209, PR China
| | - Weiguo Li
- Department of Environmental Engineering, Harbin Institute of Technology, Weihai, 2# Wenhua West Road, Weihai 264209, PR China
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14
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Ledermann B, Schwan M, Sommerkamp JA, Hofmann E, Béjà O, Frankenberg-Dinkel N. Evolution and molecular mechanism of four-electron reducing ferredoxin-dependent bilin reductases from oceanic phages. FEBS J 2017; 285:339-356. [PMID: 29156487 DOI: 10.1111/febs.14341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/06/2017] [Accepted: 11/16/2017] [Indexed: 01/17/2023]
Abstract
Ferredoxin-dependent bilin reductases (FDBRs) are a class of enzymes reducing the heme metabolite biliverdin IXα (BV) to form open-chain tetrapyrroles used for light-perception and light-harvesting in photosynthetic organisms. Thus far, seven FDBR families have been identified, each catalysing a distinct reaction and either transferring two or four electrons from ferredoxin onto the substrate. The newest addition to the family is PcyX, originally identified from metagenomics data derived from phage. Phylogenetically, PcyA is the closest relative catalysing the reduction of BV to phycocyanobilin. PcyX, however, converts the same substrate to phycoerythrobilin, resembling the reaction catalysed by cyanophage PebS. Within this study, we aimed at understanding the evolution of catalytic activities within FDBRs using PcyX as an example. Additional members of the PcyX clade and a remote member of the PcyA family were investigated to gain insights into catalysis. Biochemical data in combination with the PcyX crystal structure revealed that a conserved aspartate-histidine pair is critical for activity. Interestingly, the same residues are part of a catalytic Asp-His-Glu triad in PcyA, including an additional Glu. While this Glu residue is replaced by Asp in PcyX, it is not involved in catalysis. Substitution back to a Glu failed to convert PcyX to a PcyA. Therefore, the change in regiospecificity is not only caused by individual catalytic amino acid residues. Rather the combination of the architecture of the active site with the positioning of the substrate triggers specific proton transfer yielding the individual phycobilin products. ENZYMES Suggested EC number for PcyX: 1.3.7.6 DATABASES: The PcyX X-ray structure was deposited in the PDB with the accession code 5OWG.
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Affiliation(s)
- Benjamin Ledermann
- Department of Biology, Microbiology, Technical University Kaiserslautern, Germany
| | - Meike Schwan
- Department of Biology, Microbiology, Technical University Kaiserslautern, Germany
| | - Johannes A Sommerkamp
- Protein Crystallography, Faculty for Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty for Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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15
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Hagiwara Y, Wada K, Irikawa T, Sato H, Unno M, Yamamoto K, Fukuyama K, Sugishima M. Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin. FEBS Lett 2016; 590:3425-3434. [DOI: 10.1002/1873-3468.12387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Yoshinori Hagiwara
- Department of Biochemistry and Applied Chemistry; National Institute of Technology; Kurume College; Kurume Japan
| | - Kei Wada
- Organization for Promotion of Tenure Track; University of Miyazaki; Kiyotake Japan
| | - Teppei Irikawa
- Department of Biological Sciences; Graduate School of Science; Osaka University; Toyonaka Japan
| | - Hideaki Sato
- Department of Medical Biochemistry; Kurume University School of Medicine; Kurume Japan
| | - Masaki Unno
- Graduate School of Science and Engineering; Ibaraki University; Hitachi Japan
- Frontier Research Center for Applied Atomic Sciences; Ibaraki University; Naka Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry; Kurume University School of Medicine; Kurume Japan
| | - Keiichi Fukuyama
- Department of Biological Sciences; Graduate School of Science; Osaka University; Toyonaka Japan
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry; Kurume University School of Medicine; Kurume Japan
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16
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Oyala PH, Ravichandran KR, Funk MA, Stucky PA, Stich TA, Drennan CL, Britt RD, Stubbe J. Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example. J Am Chem Soc 2016; 138:7951-64. [PMID: 27276098 PMCID: PMC4929525 DOI: 10.1021/jacs.6b03605] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Fluorinated tyrosines
(FnY’s, n = 2
and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the
recently evolved M. jannaschii Y-tRNA synthetase/tRNA
pair. Class Ia RNRs require four redox active Y’s, a stable
Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y’s (356
in β and 731 and 730 in α) to initiate the radical-dependent
nucleotide reduction process. FnY (3,5;
2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-β
and the X-ray structures of each resulting β with a diferric
cluster are reported and compared with wt-β2 crystallized under
the same conditions. The essential diferric-FnY· cofactor is self-assembled from apo FnY-β2, Fe2+, and O2 to produce ∼1
Y·/β2 and ∼3 Fe3+/β2. The FnY· are stable and active in nucleotide
reduction with activities that vary from 5% to 85% that of wt-β2.
Each FnY·-β2 has been characterized
by 9 and 130 GHz electron paramagnetic resonance and high-field electron
nuclear double resonance spectroscopies. The hyperfine interactions
associated with the 19F nucleus provide unique signatures
of each FnY· that are readily distinguishable
from unlabeled Y·’s. The variability of the abiotic FnY pKa’s
(6.4 to 7.8) and reduction potentials (−30 to +130 mV relative
to Y at pH 7.5) provide probes of enzymatic reactions proposed to
involve Y·’s in catalysis and to investigate the importance
and identity of hopping Y·’s within redox active proteins
proposed to protect them from uncoupled radical chemistry.
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Affiliation(s)
- Paul H Oyala
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | | | | | - Paul A Stucky
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Troy A Stich
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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17
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Cerón-Carrasco JP, Jacquemin D, Laurent AD. First computational step towards the understanding of the antioxidant activity of the Phycocyanobilin:Ferredoxin Oxidoreductase in complex with biliverdin IXα. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.10.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Bhayani K, Mitra M, Ghosh T, Mishra S. C-Phycocyanin as a potential biosensor for heavy metals like Hg2+ in aquatic systems. RSC Adv 2016. [DOI: 10.1039/c6ra22753h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fluorescence quenching ability of C-phycocyanin (CPC) as a biosensor for detection of Hg2+ in lower concentrations (μM) in aquatic environment.
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Affiliation(s)
- Khushbu Bhayani
- Department of Salt and Marine Chemicals
- CSIR-Central Salt and Marine Chemical Research Institute
- Bhavnagar
- India
| | - Madhusree Mitra
- Department of Salt and Marine Chemicals
- CSIR-Central Salt and Marine Chemical Research Institute
- Bhavnagar
- India
- AcSIR
| | - Tonmoy Ghosh
- Department of Salt and Marine Chemicals
- CSIR-Central Salt and Marine Chemical Research Institute
- Bhavnagar
- India
- AcSIR
| | - Sandhya Mishra
- Department of Salt and Marine Chemicals
- CSIR-Central Salt and Marine Chemical Research Institute
- Bhavnagar
- India
- AcSIR
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19
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Unno M, Ishikawa-Suto K, Kusaka K, Tamada T, Hagiwara Y, Sugishima M, Wada K, Yamada T, Tomoyori K, Hosoya T, Tanaka I, Niimura N, Kuroki R, Inaka K, Ishihara M, Fukuyama K. Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography. J Am Chem Soc 2015; 137:5452-60. [PMID: 25872660 DOI: 10.1021/jacs.5b00645] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.
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Affiliation(s)
- Masaki Unno
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,‡Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Kumiko Ishikawa-Suto
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,‡Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan.,§Quantum Beam Science Center, Japan Atomic Energy Agency, Naka 319-1195, Japan
| | - Katsuhiro Kusaka
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Taro Tamada
- §Quantum Beam Science Center, Japan Atomic Energy Agency, Naka 319-1195, Japan
| | - Yoshinori Hagiwara
- ∥Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan.,⊥Department of Biochemistry and Applied Chemistry, National Institute of Technology, Kurume College, Kurume 830-8555, Japan
| | - Masakazu Sugishima
- #Department of Medical Biochemistry, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Kei Wada
- ∇Organization for Promotion of Tenure Track, University of Miyazaki, Kiyotake 889-1692, Japan
| | - Taro Yamada
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Katsuaki Tomoyori
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,§Quantum Beam Science Center, Japan Atomic Energy Agency, Naka 319-1195, Japan
| | - Takaaki Hosoya
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,‡Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Ichiro Tanaka
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,‡Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Nobuo Niimura
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Ryota Kuroki
- §Quantum Beam Science Center, Japan Atomic Energy Agency, Naka 319-1195, Japan
| | - Koji Inaka
- ○MARUWA Foods and Biosciences Inc., Yamatokoriyama 639-1123, Japan
| | - Makiko Ishihara
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Keiichi Fukuyama
- ∥Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan.,◆Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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20
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Dark-operative protochlorophyllide oxidoreductase generates substrate radicals by an iron-sulphur cluster in bacteriochlorophyll biosynthesis. Sci Rep 2014; 4:5455. [PMID: 24965831 PMCID: PMC4071322 DOI: 10.1038/srep05455] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 06/09/2014] [Indexed: 11/21/2022] Open
Abstract
Photosynthesis converts solar energy to chemical energy using chlorophylls (Chls). In a late stage of biosynthesis of Chls, dark-operative protochlorophyllide (Pchlide) oxidoreductase (DPOR), a nitrogenase-like enzyme, reduces the C17 = C18 double bond of Pchlide and drastically changes the spectral properties suitable for photosynthesis forming the parental chlorin ring for Chl a. We previously proposed that the spatial arrangement of the proton donors determines the stereospecificity of the Pchlide reduction based on the recently resolved structure of the DPOR catalytic component, NB-protein. However, it was not clear how the two-electron and two-proton transfer events are coordinated in the reaction. In this study, we demonstrate that DPOR initiates a single electron transfer reaction from a [4Fe-4S]-cluster (NB-cluster) to Pchlide, generating Pchlide anion radicals followed by a single proton transfer, and then, further electron/proton transfer steps transform the anion radicals into chlorophyllide (Chlide). Thus, DPOR is a unique iron-sulphur enzyme to form substrate radicals followed by sequential proton- and electron-transfer steps with the protein folding very similar to that of nitrogenase. This novel radical-mediated reaction supports the biosynthesis of Chl in a wide variety of photosynthetic organisms.
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21
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Edwards DT, Zhang Y, Glaser SJ, Han S, Sherwin MS. Phase cycling with a 240 GHz, free electron laser-powered electron paramagnetic resonance spectrometer. Phys Chem Chem Phys 2013; 15:5707-19. [PMID: 23474874 DOI: 10.1039/c3cp44492a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) powered by a free electron laser (FEL) has been shown to dramatically expand the capabilities of EPR at frequencies above ~100 GHz, where other high-power sources are unavailable. High-power pulses are necessary to achieve fast (<10 ns) spin rotations in order to alleviate the limited excitation bandwidth and time resolution that typically hamper pulsed EPR at these high frequencies. While at these frequencies, an FEL is the only source that provides ~1 kW of power and can be tuned continuously up to frequencies above 1 THz, it has only recently been implemented for one- and two-pulse EPR, and the capabilities of the FEL as an EPR source are still being expanded. This manuscript presents phase cycling of two pulses in an FEL-EPR spectrometer operating at 240 GHz. Given that the FEL, unlike amplifiers, cannot be easily phase-locked to a reference source, we instead apply retrospective data processing to measure the relative phase of each FEL pulse in order to correct the signal phase accordingly. This allows the measured signal to be averaged coherently, and the randomly changing phase of the FEL pulse results in a stochastic phase cycle, which, in the limit of many pulses, efficiently cancels artifacts and improves sensitivity. Further, the relative phase between the first and second pulse, which originates from the difference in path length traversed by each pulse, can be experimentally measured without phase-sensitive detection. We show that the relative phase of the two pulses can be precisely tuned, as well as distinctly switched by a fixed amount, with the insertion of a dielectric material into the quasi-optical path of one of the pulses. Taken together, these techniques offer many of the advantages of arbitrary phase control, and allow application of phase cycling to dramatically enhance signal quality in pulsed EPR experiments utilizing high-power sources that cannot be phase-locked.
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Affiliation(s)
- Devin T Edwards
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA.
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22
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Sahu ID, McCarrick RM, Lorigan GA. Use of electron paramagnetic resonance to solve biochemical problems. Biochemistry 2013; 52:5967-84. [PMID: 23961941 PMCID: PMC3839053 DOI: 10.1021/bi400834a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information about a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers of the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin-labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems that are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
| | | | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
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23
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Kabasakal BV, Gae DD, Li J, Lagarias JC, Koehl P, Fisher AJ. His74 conservation in the bilin reductase PcyA family reflects an important role in protein-substrate structure and dynamics. Arch Biochem Biophys 2013; 537:233-42. [DOI: 10.1016/j.abb.2013.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
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24
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Matsuoka H, Shen JR, Kawamori A, Nishiyama K, Ohba Y, Yamauchi S. Proton-Coupled Electron-Transfer Processes in Photosystem II Probed by Highly Resolved g-Anisotropy of Redox-Active Tyrosine YZ. J Am Chem Soc 2011; 133:4655-60. [DOI: 10.1021/ja2000566] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hideto Matsuoka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira-2-1-1, Aobaku, Sendai 980-8577, Japan
| | - Jian-Ren Shen
- Graduate School of Natural Science and Technology, Department of Biology, Faculty of Science, Okayama University, Naka-Tsushima, Okayama 700-8530, Japan
| | - Asako Kawamori
- Agape-Kabutoyama Institute of Medicine, Kabutoyama-cho 54-3, Nishinomiya 662-0001, Japan
| | - Kei Nishiyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira-2-1-1, Aobaku, Sendai 980-8577, Japan
| | - Yasunori Ohba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira-2-1-1, Aobaku, Sendai 980-8577, Japan
| | - Seigo Yamauchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira-2-1-1, Aobaku, Sendai 980-8577, Japan
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25
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Abstract
PEB (phycoerythrobilin) is a pink-coloured open-chain tetrapyrrole molecule found in the cyanobacterial light-harvesting phycobilisome. Within the phycobilisome, PEB is covalently bound via thioether bonds to conserved cysteine residues of the phycobiliprotein subunits. In cyanobacteria, biosynthesis of PEB proceeds via two subsequent two-electron reductions catalysed by the FDBRs (ferredoxin-dependent bilin reductases) PebA and PebB starting from the open-chain tetrapyrrole biliverdin IXα. A new member of the FDBR family has been identified in the genome of a marine cyanophage. In contrast with the cyanobacterial enzymes, PebS (PEB synthase) from cyanophages combines both two-electron reductions for PEB synthesis. In the present study we show that PebS acts via a substrate radical mechanism and that two conserved aspartate residues at position 105 and 206 are critical for stereospecific substrate protonation and conversion. On the basis of the crystal structures of both PebS mutants and presented biochemical and biophysical data, a mechanism for biliverdin IXα conversion to PEB is postulated and discussed with respect to other FDBR family members.
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26
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Fradelos G, Wesolowski TA. The Importance of Going beyond Coulombic Potential in Embedding Calculations for Molecular Properties: The Case of Iso-G for Biliverdin in Protein-Like Environment. J Chem Theory Comput 2010; 7:213-22. [DOI: 10.1021/ct100415h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgios Fradelos
- Université de Genève, Département de Chimie Physique 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Tomasz A. Wesolowski
- Université de Genève, Département de Chimie Physique 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
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27
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Stoll S, Ozarowski A, Britt RD, Angerhofer A. Atomic hydrogen as high-precision field standard for high-field EPR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 207:158-63. [PMID: 20813570 PMCID: PMC2956851 DOI: 10.1016/j.jmr.2010.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 06/08/2010] [Accepted: 08/06/2010] [Indexed: 05/05/2023]
Abstract
We introduce atomic hydrogen trapped in an octaisobutylsilsesquioxane nanocage (H@iBuT₈) as a new molecular high-precision magnetic field standard for high-field EPR spectroscopy of organic radicals and other systems with signals around g=2. Its solid-state EPR spectrum consists of two 0.2 mT wide lines separated by about 51 mT and centered at g≈2. The isotropic g factor is 2.00294(3) and essentially temperature independent. The isotropic ¹H hyperfine coupling constant is 1416.8(2) MHz below 70 K and decreases slightly with increasing temperature to 1413.7(1) MHz at room temperature. The spectrum of the standard does not overlap with those of most organic radicals, and it can be easily prepared and is stable at room temperature.
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Affiliation(s)
- Stefan Stoll
- Department of Chemistry, University of California, One Shields Ave, Davis, California 95616, USA
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - R. David Britt
- Department of Chemistry, University of California, One Shields Ave, Davis, California 95616, USA
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28
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Crystal Structures of the Substrate-Bound Forms of Red Chlorophyll Catabolite Reductase: Implications for Site-Specific and Stereospecific Reaction. J Mol Biol 2010; 402:879-91. [DOI: 10.1016/j.jmb.2010.08.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 08/07/2010] [Accepted: 08/11/2010] [Indexed: 01/05/2023]
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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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Kohler AC, Gae DD, Richley MA, Stoll S, Gunn A, Lim S, Martin SS, Doukov TI, Britt RD, Ames JB, Lagarias JC, Fisher AJ. Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants. Biochemistry 2010; 49:6206-18. [PMID: 20557110 DOI: 10.1021/bi100728q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heme-derived linear tetrapyrroles (phytobilins) in phycobiliproteins and phytochromes perform critical light-harvesting and light-sensing roles in oxygenic photosynthetic organisms. A key enzyme in their biogenesis, phycocyanobilin:ferredoxin oxidoreductase (PcyA), catalyzes the overall four-electron reduction of biliverdin IXalpha to phycocyanobilin--the common chromophore precursor for both classes of biliproteins. This interconversion occurs via semireduced bilin radical intermediates that are profoundly stabilized by selected mutations of two critical catalytic residues, Asp105 and His88. To understand the structural basis for this stabilization and to gain insight into the overall catalytic mechanism, we report the high-resolution crystal structures of substrate-loaded Asp105Asn and His88Gln mutants of Synechocystis sp. PCC 6803 PcyA in the initial oxidized and one-electron reduced radical states. Unlike wild-type PcyA, both mutants possess a bilin-interacting axial water molecule that is ejected from the active site upon formation of the enzyme-bound neutral radical complex. Structural studies of both mutants also show that the side chain of Glu76 is unfavorably located for D-ring vinyl reduction. On the basis of these structures and companion (15)N-(1)H long-range HMQC NMR analyses to assess the protonation state of histidine residues, we propose a new mechanistic scheme for PcyA-mediated reduction of both vinyl groups of biliverdin wherein an axial water molecule, which prematurely binds and ejects from both mutants upon one electron reduction, is required for catalytic turnover of the semireduced state.
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Affiliation(s)
- Amanda C Kohler
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA
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Shang L, Rockwell NC, Martin SS, Lagarias JC. Biliverdin amides reveal roles for propionate side chains in bilin reductase recognition and in holophytochrome assembly and photoconversion. Biochemistry 2010; 49:6070-82. [PMID: 20565135 DOI: 10.1021/bi100756x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Linear tetrapyrroles (bilins) perform important antioxidant and light-harvesting functions in cells from bacteria to humans. To explore the role of the propionate moieties in bilin metabolism, we report the semisynthesis of mono- and diamides of biliverdin IXalpha and those of its non-natural XIIIalpha isomer. Initially, these were examined as substrates of two types of NADPH-dependent biliverdin reductase, BVR and BvdR, and of the representative ferredoxin-dependent bilin reductase, phycocyanobilin:ferredoxin oxidoreductase (PcyA). Our studies indicate that the NADPH-dependent biliverdin reductases are less accommodating to amidation of the propionic acid side chains of biliverdin IXalpha than PcyA, which does not require free carboxylic acid side chains to yield its phytobilin product, phycocyanobilin. Bilin amides were also assembled with BV-type and phytobilin-type apophytochromes, demonstrating a role for the 8-propionate in the formation of the spectroscopically native P(r) dark states of these biliprotein photosensors. Neither ionizable propionate side chain proved to be essential to primary photoisomerization for both classes of phytochromes, but an unsubstituted 12-propionate was required for full photointerconversion of phytobilin-type phytochrome Cph1. Taken together, these studies provide insight into the roles of the ionizable propionate side chains in substrate discrimination by two bilin reductase families while further underscoring the mechanistic differences between the photoconversions of BV-type and phytobilin-type phytochromes.
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Affiliation(s)
- Lixia Shang
- Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, California 95616, USA
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32
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Shafaat HS, Leigh BS, Tauber MJ, Kim JE. Spectroscopic Comparison of Photogenerated Tryptophan Radicals in Azurin: Effects of Local Environment and Structure. J Am Chem Soc 2010; 132:9030-9. [DOI: 10.1021/ja101322g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hannah S. Shafaat
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
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33
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Hagiwara Y, Sugishima M, Khawn H, Kinoshita H, Inomata K, Shang L, Lagarias JC, Takahashi Y, Fukuyama K. Structural insights into vinyl reduction regiospecificity of phycocyanobilin:ferredoxin oxidoreductase (PcyA). J Biol Chem 2010; 285:1000-7. [PMID: 19887371 PMCID: PMC2801226 DOI: 10.1074/jbc.m109.055632] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 09/26/2009] [Indexed: 11/06/2022] Open
Abstract
Phycocyanobilin:ferredoxin oxidoreductase (PcyA) is the best characterized member of the ferredoxin-dependent bilin reductase family. Unlike other ferredoxin-dependent bilin reductases that catalyze a two-electron reduction, PcyA sequentially reduces D-ring (exo) and A-ring (endo) vinyl groups of biliverdin IXalpha (BV) to yield phycocyanobilin, a key pigment precursor of the light-harvesting antennae complexes of red algae, cyanobacteria, and cryptophytes. To address the structural basis for the reduction regiospecificity of PcyA, we report new high resolution crystal structures of bilin substrate complexes of PcyA from Synechocystis sp. PCC6803, all of which lack exo-vinyl reduction activity. These include the BV complex of the E76Q mutant as well as substrate-bound complexes of wild-type PcyA with the reaction intermediate 18(1),18(2)-dihydrobiliverdin IXalpha (18EtBV) and with biliverdin XIIIalpha (BV13), a synthetic substrate that lacks an exo-vinyl group. Although the overall folds and the binding sites of the U-shaped substrates of all three complexes were similar with wild-type PcyA-BV, the orientation of the Glu-76 side chain, which was in close contact with the exo-vinyl group in PcyA-BV, was rotated away from the bilin D-ring. The local structures around the A-rings in the three complexes, which all retain the ability to reduce the A-ring of their bound pigments, were nearly identical with that of wild-type PcyA-BV. Consistent with the proposed proton-donating role of the carboxylic acid side chain of Glu-76 for exo-vinyl reduction, these structures reveal new insight into the reduction regiospecificity of PcyA.
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Affiliation(s)
- Yoshinori Hagiwara
- From the Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Masakazu Sugishima
- the Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Htoi Khawn
- the Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Hideki Kinoshita
- the Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Katsuhiko Inomata
- the Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Lixia Shang
- the Section of Molecular and Cellular Biology, University of California, Davis, California 95616, and
| | - J. Clark Lagarias
- the Section of Molecular and Cellular Biology, University of California, Davis, California 95616, and
| | - Yasuhiro Takahashi
- the Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Keiichi Fukuyama
- From the Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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