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Qin RC, Ma YY, Wang D, Bao NZ, Liu CG. Preparation of Cellulose Nanofibers from Corn Stalks by Fenton Reaction: A New Insight into the Mechanism by an Experimental and Theoretical Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1907-1920. [PMID: 36652295 DOI: 10.1021/acs.jafc.2c08475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Agricultural biomass wastes are an abundant feedstock for biorefineries. However, most of these wastes are not treated in the right way. Here, corn stalks (CSs) were assigned as the raw material to produce cellulose nanofibers (CNFs) via in situ Fenton oxidation treatment. In order to probe the formation mechanism of an in situ Fenton reactor, the bonding interaction of hydrated Fe2+ ions and fiber has been systemically studied based on adsorption experiments, IR spectroscopy, density functional theory (DFT) calculations, and Raman spectroscopy. The results indicate that the coordination of the hydrated Fe2+ ion to the fiber generates a quasi-octahedral-coordinated sphere around the Fe center. The Jahn-Teller distortion effect of the Fe center promotes the Fe-O2H2 bonding interaction via reduction of the energy gap of the dz2 orbital of the Fe center and π2py/π2pz orbitals of the H2O2 molecule. The oxidation treatment of the pretreated CS by the in situ Fenton process shows the formation of a new carboxyl group on the fiber surface. The scanning electron microscopy image shows that the Fenton-treated fiber was scattered into the nanosized CNFs with a diameter of up to 50 nm. Both experimental and theoretical studies show that the pseudo-first-order kinetic reaction could describe the in situ Fenton kinetics well. Moreover, the proposed catalytic cycle shows that the large thermodynamic barrier is the cleavage of the O-O bond of H2O2 to generate the •OH radical, and the whole catalytic cycle is found to be spontaneous at room temperature.
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Affiliation(s)
- Rui-Cheng Qin
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City132013, P. R. China
| | - Yi-Ying Ma
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City132013, P. R. China
| | - Dan Wang
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City132013, P. R. China
| | - Nan-Zhu Bao
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City132013, P. R. China
| | - Chun-Guang Liu
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City132013, P. R. China
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2
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Liu Y, Wang H, Qian L, Zhao X, Yao L, Wang J, Xing X, Mo G, Chen Z, Wu Z. Bismuth-iron-based precursor: preparation, phase composition, and two methods of thermal treatment. RSC Adv 2020; 10:20713-20723. [PMID: 35517760 PMCID: PMC9054302 DOI: 10.1039/d0ra00177e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/02/2020] [Indexed: 12/04/2022] Open
Abstract
Bismuth ferrite (BiFeO3) is a promising Bi-based perovskite-type material, which is multiferroic due to the coexistence of anti-ferromagnetism and ferroelectricity. During the preparation of pure BiFeO3 nanoparticles, however, the phase structures and species of bismuth–iron-based precursor (BFOH) were still unclear, and so related precursors were prepared. X-ray diffraction, Raman, Fourier transform infrared, and X-ray absorption near-edge structure techniques were used to probe the phase structure and species of the precursors. It was found that the precursor BFOH is composed of Bi6O6(NO3)4(OH)2·2H2O, Bi6O5(NO3)5(OH)3·3H2O, Fe(OH)3, and α-Bi2O3. Calcination treatment and hydrothermal synthesis were used to prepare the pure BiFeO3 phase from the precursor BFOH. The calcination temperature was optimized as 400 °C for preparation of the pure BiFeO3 phase. Meanwhile, hydrothermal conditions for the synthesis of the pure BiFeO3 phase were also optimized as follows: the reaction solution was the mixture solution of Bi(NO3)3·5H2O and Fe(NO3)3·9H2O with cetyltrimethyl ammonium bromide (CTAB) as the surfactant and KOH as the mineralizer; the hydrothermal synthesis was performed at 180 °C for 48 h; the concentration of KOH should be at least 3 M; and the surfactant CTAB can be used to regulate the morphology of the as-prepared BiFeO3 nanoparticles. From the point of view of the microstructure, BiFeO3 nanoparticles prepared by calcination or hydrothermal methods have no notable differences. A formation mechanism from the precursor BFOH to the BiFeO3 product is proposed. By providing an understanding of the precursors, this work is very helpful in the synthesis of bismuth–iron-based nanoparticles. Preparation and phase composition study of bismuth–iron-based precursor, and its thermal treatment by calcination and hydrothermal processes, which can be used to control the synthesis of pure BiFeO3.![]()
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Affiliation(s)
- Yunpeng Liu
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982.,University of Chinese Academy of Sciences, Chinese Academy of Sciences Beijing 100049 China
| | - Hao Wang
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982.,University of Chinese Academy of Sciences, Chinese Academy of Sciences Beijing 100049 China
| | - Lixiong Qian
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982.,University of Chinese Academy of Sciences, Chinese Academy of Sciences Beijing 100049 China
| | - Xiaoyi Zhao
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982.,University of Chinese Academy of Sciences, Chinese Academy of Sciences Beijing 100049 China
| | - Lei Yao
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982
| | - Jiayi Wang
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982
| | - Xueqing Xing
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982
| | - Guang Mo
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982
| | - Zhongjun Chen
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982
| | - Zhonghua Wu
- Institute of High Energy Physics, Chinese Academy of Sciences Beijing 100049 China +86-10-88235982.,University of Chinese Academy of Sciences, Chinese Academy of Sciences Beijing 100049 China
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3
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Singh RK, Blossom BM, Russo DA, Singh R, Weihe H, Andersen NH, Tiwari MK, Jensen PE, Felby C, Bjerrum MJ. Detection and Characterization of a Novel Copper-Dependent Intermediate in a Lytic Polysaccharide Monooxygenase. Chemistry 2019; 26:454-463. [PMID: 31603264 DOI: 10.1002/chem.201903562] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/08/2019] [Indexed: 01/27/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes capable of oxidizing crystalline cellulose which have large practical application in the process of refining biomass. The catalytic mechanism of LPMOs still remains debated despite several proposed reaction mechanisms. Here, we report a long-lived intermediate (t1/2 =6-8 minutes) observed in an LPMO from Thermoascus aurantiacus (TaLPMO9A). The intermediate with a strong absorption around 420 nm is formed when reduced LPMO-CuI reacts with sub-equimolar amounts of H2 O2 . UV/Vis absorption spectroscopy, electron paramagnetic resonance, resonance Raman and stopped-flow spectroscopy suggest that the observed long-lived intermediate involves the copper center and a nearby tyrosine (Tyr175). Additionally, activity assays in the presence of sub-equimolar amounts of H2 O2 showed an increase in the LPMO oxidation of phosphoric acid swollen cellulose. Accordingly, this suggests that the long-lived copper-dependent intermediate could be part of the catalytic mechanism for LPMOs. The observed intermediate offers a new perspective into the oxidative reaction mechanism of TaLPMO9A and hence for the biomass oxidation and the reactivity of copper in biological systems.
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Affiliation(s)
- Raushan K Singh
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Benedikt M Blossom
- Department of Geosciences and Natural Resource Management, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
| | - David A Russo
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
- Current address: Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Ranjitha Singh
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Høgni Weihe
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | | | - Manish K Tiwari
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Poul E Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
| | - Claus Felby
- Department of Geosciences and Natural Resource Management, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
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Time-Resolved Infrared and Visible Spectroscopy on Cryptochrome aCRY: Basis for Red Light Reception. Biophys J 2019; 117:490-499. [PMID: 31326107 DOI: 10.1016/j.bpj.2019.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
Cryptochromes function as flavin-binding photoreceptors in bacteria, fungi, algae, land plants, and insects. The discovery of an animal-like cryptochrome in the green alga Chlamydomonas reinhardtii has expanded the spectral range of sensitivity of these receptors from ultraviolet A/blue light to almost the complete visible spectrum. The broadened light response has been explained by the presence of the flavin neutral radical as a chromophore in the dark. Concomitant with photoconversion of the flavin, an unusually long-lived tyrosyl radical with a red-shifted ultraviolet-visible spectrum is formed, which is essential for the function of the receptor. In this study, the microenvironment of this key residue, tyrosine 373, was scrutinized using time-resolved Fourier transform infrared spectroscopy on several variants of animal-like cryptochrome and density functional theory for band assignment. The reduced tyrosine takes on distinct hydrogen bond scenarios depending on the presence of the C-terminal extension and of a neighboring cysteine. Upon radical formation, all variants showed a signal at 1400 cm-1, which we assigned to the ν7'a marker band of the CO stretching mode. The exceptionally strong downshift of this band cannot be attributed to a loss of hydrogen bonding only. Time-resolved ultraviolet-visible spectroscopy on W322F, a mutant of the neighboring tryptophan residue, revealed a decrease of the tyrosyl radical lifetime by almost two orders of magnitude, along with a shift of the absorbance maximum from 416 to 398 nm. These findings strongly support the concept of a π-π stacking as an apolar interaction between Y373 and W322 to be responsible for the characteristics of the tyrosyl radical. This concept of radical stabilization has been unknown to cryptochromes so far but might be highly relevant for other homologs with a tetrad of tryptophans and tyrosines as electron donors.
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Pagba CV, McCaslin TG, Veglia G, Porcelli F, Yohannan J, Guo Z, McDaniel M, Barry BA. A tyrosine-tryptophan dyad and radical-based charge transfer in a ribonucleotide reductase-inspired maquette. Nat Commun 2015; 6:10010. [PMID: 26627888 PMCID: PMC4686667 DOI: 10.1038/ncomms10010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/23/2015] [Indexed: 01/29/2023] Open
Abstract
In class 1a ribonucleotide reductase (RNR), a substrate-based radical is generated in the α2 subunit by long-distance electron transfer involving an essential tyrosyl radical (Y122O·) in the β2 subunit. The conserved W48 β2 is ∼10 Å from Y122OH; mutations at W48 inactivate RNR. Here, we design a beta hairpin peptide, which contains such an interacting tyrosine–tryptophan dyad. The NMR structure of the peptide establishes that there is no direct hydrogen bond between the phenol and the indole rings. However, electronic coupling between the tyrosine and tryptophan occurs in the peptide. In addition, downshifted ultraviolet resonance Raman (UVRR) frequencies are observed for the radical state, reproducing spectral downshifts observed for β2. The frequency downshifts of the ring and CO bands are consistent with charge transfer from YO· to W or another residue. Such a charge transfer mechanism implies a role for the β2 Y-W dyad in electron transfer. Tyrosine-tryptophan dyads are known to mediate electron transfer reactions in a range of different proteins. Here, the authors study a beta hairpin peptide, probing the tyrosine-tryptophan interaction and showing no hydrogen bonding but rather charge transfer between the tyrosyl radical and tryptophan'.
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Affiliation(s)
- Cynthia V Pagba
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Tyler G McCaslin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Fernando Porcelli
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo 01100, Italy
| | - Jiby Yohannan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zhanjun Guo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Miranda McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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6
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Barry BA. Reaction dynamics and proton coupled electron transfer: studies of tyrosine-based charge transfer in natural and biomimetic systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:46-54. [PMID: 25260243 DOI: 10.1016/j.bbabio.2014.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/27/2014] [Accepted: 09/10/2014] [Indexed: 11/25/2022]
Abstract
In bioenergetic reactions, electrons are transferred long distances via a hopping mechanism. In photosynthesis and DNA synthesis, the aromatic amino acid residue, tyrosine, functions as an intermediate that is transiently oxidized and reduced during long distance electron transfer. At physiological pH values, oxidation of tyrosine is associated with a deprotonation of the phenolic oxygen, giving rise to a proton coupled electron transfer (PCET) reaction. Tyrosine-based PCET reactions are important in photosystem II, which carries out the light-induced oxidation of water, and in ribonucleotide reductase, which reduces ribonucleotides to form deoxynucleotides. Photosystem II contains two redox-active tyrosines, YD (Y160 in the D2 polypeptide) and YZ (Y161 in the D1 polypeptide). YD forms a light-induced stable radical, while YZ functions as an essential charge relay, oxidizing the catalytic Mn₄CaO₅ cluster on each of four photo-oxidation reactions. In Escherichia coli class 1a RNR, the β2 subunit contains the radical initiator, Y122O•, which is reversibly reduced and oxidized in long range electron transfer with the α2 subunit. In the isolated E. coli β2 subunit, Y122O• is a stable radical, but Y122O• is activated for rapid PCET in an α2β2 substrate/effector complex. Recent results concerning the structure and function of YD, YZ, and Y122 are reviewed here. Comparison is made to recent results derived from bioengineered proteins and biomimetic compounds, in which tyrosine-based charge transfer mechanisms have been investigated. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Offenbacher AR, Watson RA, Pagba CV, Barry BA. Redox-dependent structural coupling between the α2 and β2 subunits in E. coli ribonucleotide reductase. J Phys Chem B 2014; 118:2993-3004. [PMID: 24606240 DOI: 10.1021/jp501121d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the production of deoxyribonucleotides in all cells. In E. coli class Ia RNR, a transient α2β2 complex forms when a ribonucleotide substrate, such as CDP, binds to the α2 subunit. A tyrosyl radical (Y122O•)-diferric cofactor in β2 initiates substrate reduction in α2 via a long-distance, proton-coupled electron transfer (PCET) process. Here, we use reaction-induced FT-IR spectroscopy to describe the α2β2 structural landscapes, which are associated with dATP and hydroxyurea (HU) inhibition. Spectra were acquired after mixing E. coli α2 and β2 with a substrate, CDP, and the allosteric effector, ATP. Isotopic chimeras, (13)Cα2β2 and α2(13)Cβ2, were used to define subunit-specific structural changes. Mixing of α2 and β2 under turnover conditions yielded amide I (C═O) and II (CN/NH) bands, derived from each subunit. The addition of the inhibitor, dATP, resulted in a decreased contribution from amide I bands, attributable to β strands and disordered structures. Significantly, HU-mediated reduction of Y122O• was associated with structural changes in α2, as well as β2. To define the spectral contributions of Y122O•/Y122OH in the quaternary complex, (2)H4 labeling of β2 tyrosines and HU editing were performed. The bands of Y122O•, Y122OH, and D84, a unidentate ligand to the diferric cluster, previously identified in isolated β2, were observed in the α2β2 complex. These spectra also provide evidence for a conformational rearrangement at an additional β2 tyrosine(s), Yx, in the α2β2/CDP/ATP complex. This study illustrates the utility of reaction-induced FT-IR spectroscopy in the study of complex enzymes.
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Affiliation(s)
- Adam R Offenbacher
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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8
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The class Ib ribonucleotide reductase from Mycobacterium tuberculosis has two active R2F subunits. J Biol Inorg Chem 2014; 19:893-902. [PMID: 24585102 DOI: 10.1007/s00775-014-1121-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to their corresponding deoxyribonucleotides, playing a crucial role in DNA repair and replication in all living organisms. Class Ib RNRs require either a diiron-tyrosyl radical (Y·) or a dimanganese-Y· cofactor in their R2F subunit to initiate ribonucleotide reduction in the R1 subunit. Mycobacterium tuberculosis, the causative agent of tuberculosis, contains two genes, nrdF1 and nrdF2, encoding the small subunits R2F-1 and R2F-2, respectively, where the latter has been thought to serve as the only active small subunit in the M. tuberculosis class Ib RNR. Here, we present evidence for the presence of an active Fe 2 (III) -Y· cofactor in the M. tuberculosis RNR R2F-1 small subunit, supported and characterized by UV-vis, X-band electron paramagnetic resonance, and resonance Raman spectroscopy, showing features similar to those for the M. tuberculosis R2F-2-Fe 2 (III) -Y· cofactor. We also report enzymatic activity of Fe 2 (III) -R2F-1 when assayed with R1, and suggest that the active M. tuberculosis class Ib RNR can use two different small subunits, R2F-1 and R2F-2, with similar activity.
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Jiang G, Wang M, Gu X, Chen T, Shang Y, Tang Y, Jiang G, Shi Y. Synthesis, structure and characterization of Fe6molecular clusters with peripheral sulfur atom-capped silver nanoparticles. CrystEngComm 2014. [DOI: 10.1039/c3ce41444b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Offenbacher AR, Burns LA, Sherrill CD, Barry BA. Redox-linked conformational control of proton-coupled electron transfer: Y122 in the ribonucleotide reductase β2 subunit. J Phys Chem B 2013; 117:8457-68. [PMID: 23822111 DOI: 10.1021/jp404757r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosyl radicals play essential roles in biological proton-coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of α2 and β2 homodimeric subunits. In class Ia RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O(•))-diferric cofactor is located in β2. Although Y122O(•) is extremely stable in free β2, Y122O(•) is highly reactive in the quaternary substrate-α2β2 complex and serves as a radical initiator in catalytic PCET between β2 and α2. In this report, we investigate the structural interactions that control the reactivity of Y122O(•) in a model system, isolated E. coli β2. Y122O(•) was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific (13)C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE = 16.7 ± 1.0 at 25 °C) on this reaction. These data suggest that the one-electron, HU-mediated reduction of Y122O(•) is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE = 11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O(•)-diferric cofactor (SIE = 1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O(•) and the iron cluster.
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Affiliation(s)
- Adam R Offenbacher
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Tomter AB, Zoppellaro G, Andersen NH, Hersleth HP, Hammerstad M, Røhr ÅK, Sandvik GK, Strand KR, Nilsson GE, Bell CB, Barra AL, Blasco E, Le Pape L, Solomon EI, Andersson KK. Ribonucleotide reductase class I with different radical generating clusters. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Cranswick MA, Meier KK, Shan X, Stubna A, Kaizer J, Mehn MP, Münck E, Que L. Protonation of a peroxodiiron(III) complex and conversion to a diiron(III/IV) intermediate: implications for proton-assisted O-O bond cleavage in nonheme diiron enzymes. Inorg Chem 2012; 51:10417-26. [PMID: 22971084 PMCID: PMC3462276 DOI: 10.1021/ic301642w] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Oxygenation of a diiron(II) complex, [Fe(II)(2)(μ-OH)(2)(BnBQA)(2)(NCMe)(2)](2+) [2, where BnBQA is N-benzyl-N,N-bis(2-quinolinylmethyl)amine], results in the formation of a metastable peroxodiferric intermediate, 3. The treatment of 3 with strong acid affords its conjugate acid, 4, in which the (μ-oxo)(μ-1,2-peroxo)diiron(III) core of 3 is protonated at the oxo bridge. The core structures of 3 and 4 are characterized in detail by UV-vis, Mössbauer, resonance Raman, and X-ray absorption spectroscopies. Complex 4 is shorter-lived than 3 and decays to generate in ~20% yield of a diiron(III/IV) species 5, which can be identified by electron paramagnetic resonance and Mössbauer spectroscopies. This reaction sequence demonstrates for the first time that protonation of the oxo bridge of a (μ-oxo)(μ-1,2-peroxo)diiron(III) complex leads to cleavage of the peroxo O-O bond and formation of a high-valent diiron complex, thereby mimicking the steps involved in the formation of intermediate X in the activation cycle of ribonucleotide reductase.
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Affiliation(s)
- Matthew A. Cranswick
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Katlyn K. Meier
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Xiaopeng Shan
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Audria Stubna
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Jószef Kaizer
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Mark P. Mehn
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
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Spectroscopic studies of the iron and manganese reconstituted tyrosyl radical in Bacillus cereus ribonucleotide reductase R2 protein. PLoS One 2012; 7:e33436. [PMID: 22432022 PMCID: PMC3303829 DOI: 10.1371/journal.pone.0033436] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/08/2012] [Indexed: 11/24/2022] Open
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate limiting step in DNA synthesis where ribonucleotides are reduced to the corresponding deoxyribonucleotides. Class Ib RNRs consist of two homodimeric subunits: R1E, which houses the active site; and R2F, which contains a metallo cofactor and a tyrosyl radical that initiates the ribonucleotide reduction reaction. We studied the R2F subunit of B. cereus reconstituted with iron or alternatively with manganese ions, then subsequently reacted with molecular oxygen to generate two tyrosyl-radicals. The two similar X-band EPR spectra did not change significantly over 4 to 50 K. From the 285 GHz EPR spectrum of the iron form, a g1-value of 2.0090 for the tyrosyl radical was extracted. This g1-value is similar to that observed in class Ia E. coli R2 and class Ib R2Fs with iron-oxygen cluster, suggesting the absence of hydrogen bond to the phenoxyl group. This was confirmed by resonance Raman spectroscopy, where the stretching vibration associated to the radical (C-O, ν7a = 1500 cm−1) was found to be insensitive to deuterium-oxide exchange. Additionally, the 18O-sensitive Fe-O-Fe symmetric stretching (483 cm−1) of the metallo-cofactor was also insensitive to deuterium-oxide exchange indicating no hydrogen bonding to the di-iron-oxygen cluster, and thus, different from mouse R2 with a hydrogen bonded cluster. The HF-EPR spectrum of the manganese reconstituted RNR R2F gave a g1-value of ∼2.0094. The tyrosyl radical microwave power saturation behavior of the iron-oxygen cluster form was as observed in class Ia R2, with diamagnetic di-ferric cluster ground state, while the properties of the manganese reconstituted form indicated a magnetic ground state of the manganese-cluster. The recent activity measurements (Crona et al., (2011) J Biol Chem 286: 33053–33060) indicates that both the manganese and iron reconstituted RNR R2F could be functional. The manganese form might be very important, as it has 8 times higher activity.
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Barry BA, Chen J, Keough J, Jenson D, Offenbacher A, Pagba C. Proton Coupled Electron Transfer and Redox Active Tyrosines: Structure and Function of the Tyrosyl Radicals in Ribonucleotide Reductase and Photosystem II. J Phys Chem Lett 2012; 3:543-554. [PMID: 22662289 PMCID: PMC3362996 DOI: 10.1021/jz2014117] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Proton coupled electron transfer (PCET) reactions are important in many biological processes. Tyrosine oxidation/reduction can play a critical role in facilitating these reactions. Two examples are photosystem II (PSII) and ribonucleotide reductase (RNR). RNR is essential in DNA synthesis in all organisms. In E. coli RNR, a tyrosyl radical, Y122(•), is required as a radical initiator. Photosystem II (PSII) generates molecular oxygen from water. In PSII, an essential tyrosyl radical, YZ(•), oxidizes the oxygen evolving center. However, the mechanisms, by which the extraordinary oxidizing power of the tyrosyl radical is controlled, are not well understood. This is due to the difficulty in acquiring high-resolution structural information about the radical state. Spectroscopic approaches, such as EPR and UV resonance Raman (UVRR), can give new information. Here, we discuss EPR studies of PCET and the PSII YZ radical. We also present UVRR results, which support the conclusion that Y122 undergoes an alteration in ring and backbone dihedral angle when it is oxidized. This conformational change results in a loss of hydrogen bonding to the phenolic oxygen. Our analysis suggests that access of water is an important factor in determining tyrosyl radical lifetime and function. TOC graphic.
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Mozziconacci O, Haywood J, Gorman EM, Munson E, Schöneich C. Photolysis of recombinant human insulin in the solid state: formation of a dithiohemiacetal product at the C-terminal disulfide bond. Pharm Res 2011; 29:121-33. [PMID: 21748537 DOI: 10.1007/s11095-011-0519-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 06/17/2011] [Indexed: 10/18/2022]
Abstract
PURPOSE Exposure of protein pharmaceuticals to light can result in chemical and physical modifications, potentially leading to loss of potency, aggregation, and/or immunogenicity. To correlate these potential consequences with molecular changes, the nature of photoproducts and their mechanisms of formation must be characterized. The present study focuses on the photochemical degradation of insulin in the solid state. METHODS Solid insulin was characterized by solid-state NMR, polarized optical microscopy and scanning electron microscopy; various insulin preparations were exposed to UV light prior to product analysis by mass spectrometry. RESULTS UV-exposure of solid human insulin results in photodissociation of the C-terminal intrachain disulfide bond, leading to formation of a CysS(•) thiyl radical pair which ultimately disproportionates into thiol and thioaldehyde species. The high reactivity of the thioaldehyde and proximity to the thiol allow the formation of a dithiohemiacetal structure. Dithiohemiacetal is formed during the UV-exposure of both crystalline and amorphous insulin. CONCLUSIONS Dithiohemiacetals represent novel structures generated through the photochemical modification of disulfide bonds. This is the first time that such structure is identified during the photolysis of a protein in the solid state.
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Affiliation(s)
- Olivier Mozziconacci
- Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, Kansas 66047, USA
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17
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Offenbacher AR, Chen J, Barry BA. Perturbations of aromatic amino acids are associated with iron cluster assembly in ribonucleotide reductase. J Am Chem Soc 2011; 133:6978-88. [PMID: 21486062 DOI: 10.1021/ja107918g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The β2 subunit of class Ia ribonucleotide reductases (RNR) contains an antiferromagnetically coupled μ-oxo bridged diiron cluster and a tyrosyl radical (Y122•). In this study, an ultraviolet resonance Raman (UVRR) difference technique describes the structural changes induced by the assembly of the iron cluster and by the reduction of the tyrosyl radical. Spectral contributions from aromatic amino acids are observed through UV resonance enhancement at 229 nm. Vibrational bands are assigned by comparison to histidine, phenylalanine, tyrosine, tryptophan, and 3-methylindole model compound data and by isotopic labeling of histidine in the β2 subunit. Reduction of the tyrosyl radical reveals Y122• Raman bands at 1499 and 1556 cm(-1) and Y122 Raman bands at 1170, 1199, and 1608 cm(-1). There is little perturbation of other aromatic amino acids when Y122• is reduced. Assembly of the iron cluster is shown to be accompanied by deprotonation of histidine. A p(2)H titration study supports the assignment of an elevated pK for the histidine. In addition, structural perturbations of tyrosine and tryptophan are detected. For tryptophan, comparison to model compound data suggests an increase in hydrogen bonding and a change in conformation when the iron cluster is removed. pH and (2)H(2)O studies imply that the perturbed tryptophan is in a low dielectric environment that is close to the metal center and protected from solvent exchange. Tyrosine contributions are attributed to a conformational or hydrogen-bonding change. In summary, our work shows that electrostatic and conformational perturbations of aromatic amino acids are associated with metal cluster assembly in RNR. These conformational changes may contribute to the allosteric effects, which regulate metal binding.
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Affiliation(s)
- Adam R Offenbacher
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Chalón MC, Wilke N, Pedersen J, Rufini S, Morero RD, Cortez L, Chehín RN, Farias RN, Vincent PA. Redox-active tyrosine residue in the microcin J25 molecule. Biochem Biophys Res Commun 2011; 406:366-70. [PMID: 21329661 DOI: 10.1016/j.bbrc.2011.02.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 02/11/2011] [Indexed: 11/24/2022]
Abstract
Microcin J25 (MccJ25) is a 21 amino acid lasso-peptide antibiotic produced by Escherichia coli and composed of an 8-residues ring and a terminal 'tail' passing through the ring. We have previously reported two cellular targets for this antibiotic, bacterial RNA polymerase and the membrane respiratory chain, and shown that Tyr9 is essential for the effect on the membrane respiratory chain which leads to superoxide overproduction. In the present paper we investigated the redox behavior of MccJ25 and the mutant MccJ25 (Y9F). Cyclic voltammetry measurements showed irreversible oxidation of both Tyr9 and Tyr20 in MccJ25, but infrared spectroscopy studies demonstrated that only Tyr9 could be deprotonated upon chemical oxidation in solution. Formation of a long-lived tyrosyl radical in the native MccJ25 oxidized by H₂O₂ was demonstrated by Electron Paramagnetic Resonance Spectroscopy; this radical was not detected when the reaction was carried out with the MccJ25 (Y9F) mutant. These results show that the essential Tyr9, but not Tyr20, can be easily oxidized and form a tyrosyl radical.
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Affiliation(s)
- Miriam C Chalón
- Departamento de Bioquímica de la Nutrición, Instituto Superior de Investigaciones Biológicas (Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de Tucumán) and Instituto de Química Biológica Dr Bernabé Bloj, Chacabuco 461, 4000 San Miguel de Tucumán, Tucumán, Argentina
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Offenbacher AR, Vassiliev IR, Seyedsayamdost MR, Stubbe J, Barry BA. Redox-linked structural changes in ribonucleotide reductase. J Am Chem Soc 2009; 131:7496-7. [PMID: 19489635 DOI: 10.1021/ja901908j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides. Class I RNRs are composed of two homodimeric proteins, alpha2 and beta2. The class Ia E. coli beta2 contains dinuclear, antiferromagnetically coupled iron centers and one tyrosyl free radical, Y122*/beta2. Y122* acts as a radical initiator in catalysis. Redox-linked conformational changes may accompany Y122 oxidation and provide local control of proton-coupled electron transfer reactions. To test for such redox-linked structural changes, FT-IR spectroscopy was employed in this work. Reaction-induced difference spectra, associated with the reduction of Y122* by hydroxyurea, were acquired from natural abundance, (2)H(4) tyrosine, and (15)N tyrosine labeled beta2 samples. Isotopic labeling led to the assignment of a 1514 cm(-1) band to the upsilon19a ring stretching vibration of Y122 and of a 1498 cm(-1) band to the upsilon7a CO stretching vibration of Y122*. The reaction-induced spectra also exhibited amide I bands, at 1661 and 1652 cm(-1). A similar set of amide I bands, with frequencies of 1675 and 1651 cm(-1), was observed when Y* was generated by photolysis in a pentapeptide, which matched the primary sequence surrounding Y122. This result suggests that reduction of Y122* is linked with structural changes at nearby amide bonds and that this perturbation is mediated by the primary sequence. To explain these data, we propose that a structural perturbation of the amide bond is driven by redox-linked electrostatic changes in the tyrosyl radical aromatic ring.
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Affiliation(s)
- A R Offenbacher
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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20
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Hienerwadel R, Diner BA, Berthomieu C. Molecular origin of the pH dependence of tyrosine D oxidation kinetics and radical stability in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:525-31. [DOI: 10.1016/j.bbabio.2008.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 04/01/2008] [Accepted: 04/02/2008] [Indexed: 11/27/2022]
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21
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Mamantov A. Possible New Reaction Mechanisms of Dideoxynucleosides as Anti-Aids Drugs. PROGRESS IN REACTION KINETICS AND MECHANISM 2008. [DOI: 10.3184/146867807x310783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Evidence is presented that a major class of drugs, the dideoxynucleosides (ddNs) and nucleoside/nucleotide analogues, may inhibit the symptoms of acquired immunodeficiency syndrome (AIDS) by initiation of inactivation at the ribonucleotide reductase (RNR) enzyme stage and/or inactivation of reverse transcriptase enzyme or at a stage more initial than that of the currently accepted DNA chain termination hypothesis. For example, it has been previously shown that ribonucleotide diphosphate reductase (RDPR) and ribonucleotide triphosphate reductase (RTPR) are inactivated with 2′-chloro-2 ‘-deoxyuridine 5′-diphosphate-([3′-3H]ClUDP) and triphosphate ([3′-3H]ClUTP) by reaction with an intermediate furanone, Scheme 2. RDPR has also been inactivated by 2‘-azido-2‘-deoxyuridine 5‘-diphosphate (N3UDP). Furthermore, addition of hydroxyurea to RNR can inhibit DNA synthesis which results in a rapid depletion of limiting deoxynucleotide triphosphate (dNTP) pools. There are similar perturbations of dNTP pools upon interaction of human RNR with 3‘-azido-2‘,3 ‘-dideoxythymidine (AZT), in human cell studies involving AZT/HIV and in adenosine/coformycin experiments in relation to inherited immunodeficiency, Table 1. Also, the herein proposed reduction mechanisms of nucleotides by RNR ( e.g., a single electron transfer from the nucleotide base to the phenol moiety of the tyrosyl radical of RNR via a pathway involving the thiyl radical of a cysteine residue) can also account for the chemistry of some antiretroviral drugs, the ddNs. Analyses are presented that the RNR reductions of regular unsubstituted nucleotides may occur predominantly via initial 2’ C-H abstraction instead of the originally proposed 3’ C-H abstraction mechanism. Also, it is noted that the fate of the phenol moiety of the tyrosyl unit in some RNR reactions with 2‘-halo-2‘-deoxynucleotides is not clear. The proposed reaction mechanisms may provide guidance for the development of potentially effective anti-AIDS drugs.
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Affiliation(s)
- Andrew Mamantov
- Office of Pollution Prevention and Toxics, U.S. Environmental Protection Agency, 1200 Pennsylvania Avenue, Washington, DC 20460, USA
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22
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Que L, True AE. Dinuclear Iron- and Manganese-Oxo Sites in Biology. PROGRESS IN INORGANIC CHEMISTRY 2007. [DOI: 10.1002/9780470166390.ch3] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Stubbe J. Ribonucleotide reductases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 63:349-419. [PMID: 2407066 DOI: 10.1002/9780470123096.ch6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- J Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
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Fontecave M, Nordlund P, Eklund H, Reichard P. The redox centers of ribonucleotide reductase of Escherichia coli. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 65:147-83. [PMID: 1570768 DOI: 10.1002/9780470123119.ch4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M Fontecave
- Laboratoire d'Etudes Dynamiques et Structurales de la Sélectivité, Université Joseph Fourier, Grenoble, France
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25
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Berthomieu C, Hienerwadel R. Vibrational spectroscopy to study the properties of redox-active tyrosines in photosystem II and other proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1707:51-66. [PMID: 15721606 DOI: 10.1016/j.bbabio.2004.03.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 03/31/2004] [Indexed: 11/27/2022]
Abstract
Tyrosine radicals play catalytic roles in essential metalloenzymes. Their properties--midpoint potential, stability...--or environment varies considerably from one enzyme to the other. To understand the origin of these properties, the redox tyrosines are studied by a number of spectroscopic techniques, including Fourier transform infrared (FTIR) and resonance Raman (RR) spectroscopy. An increasing number of vibrational data are reported for the (modified-) redox active tyrosines in ribonucleotide reductases, photosystem II, heme catalase and peroxidases, galactose and glyoxal oxidases, and cytochrome oxidase. The spectral markers for the tyrosinyl radicals have been recorded on models of (substituted) phenoxyl radicals, free or coordinated to metals. We review these vibrational data and present the correlations existing between the vibrational modes of the radicals and their properties and interactions formed with their environment: we present that the nu7a(C-O) mode of the radical, observed both by RR and FTIR spectroscopy at 1480-1515 cm(-1), is a sensitive marker of the hydrogen bonding status of (substituted)-phenoxyl and Tyr*, while the nu8a(C-C) mode may probe coordination of the Tyr* to a metal. For photosystem II, the information obtained by light-induced FTIR difference spectroscopy for the two redox tyrosines TyrD and TyrZ and their hydrogen bonding partners is discussed in comparison with those obtained by other spectroscopic methods.
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Affiliation(s)
- Catherine Berthomieu
- CEA-Cadarache, Laboratoire de Bioénergétique Cellulaire, UMR 6191 CNRS-CEA-Aix-Marseille II, Univ.-Méditerranée CEA 1000, Bât. 156, F-13108 Saint-Paul-lez-Durance, Cedex, France.
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26
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Lu S, Libby E, Saleh L, Xing G, Bollinger JM, Moënne-Loccoz P. Characterization of NO adducts of the diiron center in protein R2 of Escherichia coli ribonucleotide reductase and site-directed variants; implications for the O2 activation mechanism. J Biol Inorg Chem 2004; 9:818-27. [PMID: 15311337 DOI: 10.1007/s00775-004-0582-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Accepted: 07/06/2004] [Indexed: 11/30/2022]
Abstract
The R2 subunit of Escherichia coli ribonucleotide reductase contains a diiron site that reacts with O(2) to produce a tyrosine radical (Y122.). In wild-type R2 (R2-wt), the first observable reaction intermediate is a high-valent [Fe(III)-Fe(IV)] state called compound X, but in related diiron proteins such as methane monooxygenase, Delta(9)-desaturase, and ferritin, peroxodiiron(III) complexes have been characterized. Substitution of iron ligand D84 by E within the active site of R2 allows an intermediate (mu-1,2-peroxo)diiron species to accumulate. To investigate the possible involvement of a bridging peroxo species within the O(2) activation sequence of R2-wt, we have characterized the iron-nitrosyl species that form at the diiron sites in R2-wt, R2-D84E, and R2-W48F/D84E by using vibrational spectroscopy. Previous work has shown that the diiron center in R2-wt binds one NO per iron to form an antiferromagnetically coupled [(FeNO)(7)](2) center. In the wt and variant proteins, we also observe that both irons bind one NO to form a (FeNO)(7) dimer where both Fe-N-O units share a common vibrational signature. In the wt protein, nu(Fe-NO), delta(Fe-N-O), and nu(N-O) bands are observed at 445, 434 and 1742 cm(-1), respectively, while in the variant proteins the nu(Fe-NO) and delta(Fe-N-O) bands are observed approximately 10 cm(-1) higher and the nu(N-O) approximately 10 cm(-1) lower at 1735 cm(-1). These results demonstrate that all three proteins accommodate fully symmetric [(FeNO)(7)](2) species with two identical Fe-N-O units. The formation of equivalent NO adducts in the wt and variant proteins strongly favors the formation of a symmetric bridging peroxo intermediate during the O(2) activation process in R2-wt.
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Affiliation(s)
- Shen Lu
- Department of Environmental & Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Science University, Beaverton, OR 97006-8921, USA
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Pujols-Ayala I, Barry BA. Tyrosyl radicals in Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:205-16. [PMID: 15100033 DOI: 10.1016/j.bbabio.2003.07.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2003] [Revised: 07/31/2003] [Accepted: 07/31/2003] [Indexed: 11/23/2022]
Abstract
In PSII, there are two redox-active tyrosines, D and Z, with different midpoint potentials and different reduction kinetics. The factors responsible for these functional differences have not yet been elucidated. Recent model compound studies of tyrosinate and of tyrosine-containing dipeptides have demonstrated that perturbations of the amino and amide/imide group occur when the tyrosyl aromatic ring is oxidized [J. Am. Chem. Soc. 124 (2002) 5496]. Accompanying density functional calculations suggested that this perturbation is due to spin density delocalization from the aromatic ring onto the amino nitrogen. The implication of this finding is that spin density delocalization may occur in redox-active, tyrosine-containing enzymes, like Photosystem II. In this paper, we review the supporting evidence for the hypothesis that tyrosyl radical spin density delocalizes into the peptide bond in a conformationally sensitive, sequence-dependent manner. Our experimental measurements on tyrosyl radicals in dipeptides have suggested that the magnitude of the putative spin migration may be sequence-dependent. Vibrational spectroscopic studies on the tyrosyl radicals in Photosystem II, which are consistent with spin migration, are reviewed. Migration of the unpaired spin may provide a mechanism for control of the direction and possibly the rate of electron transfer.
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Affiliation(s)
- Idelisa Pujols-Ayala
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1479 Gortner Ave., St. Paul, MN 55108, USA
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Affiliation(s)
- R P Pesavento
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Eklund H, Uhlin U, Färnegårdh M, Logan DT, Nordlund P. Structure and function of the radical enzyme ribonucleotide reductase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 77:177-268. [PMID: 11796141 DOI: 10.1016/s0079-6107(01)00014-1] [Citation(s) in RCA: 256] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze all new production in nature of deoxyribonucleotides for DNA synthesis by reducing the corresponding ribonucleotides. The reaction involves the action of a radical that is produced differently for different classes of the enzyme. Class I enzymes, which are present in eukaryotes and microorganisms, use an iron center to produce a stable tyrosyl radical that is stored in one of the subunits of the enzyme. The other classes are only present in microorganisms. Class II enzymes use cobalamin for radical generation and class III enzymes, which are found only in anaerobic organisms, use a glycyl radical. The reductase activity is in all three classes contained in enzyme subunits that have similar structures containing active site cysteines. The initiation of the reaction by removal of the 3'-hydrogen of the ribose by a transient cysteinyl radical is a common feature of the different classes of RNR. This cysteine is in all RNRs located on the tip of a finger loop inserted into the center of a special barrel structure. A wealth of structural and functional information on the class I and class III enzymes can now give detailed views on how these enzymes perform their task. The class I enzymes demonstrate a sophisticated pattern as to how the free radical is used in the reaction, in that it is only delivered to the active site at exactly the right moment. RNRs are also allosterically regulated, for which the structural molecular background is now starting to be revealed.
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Affiliation(s)
- H Eklund
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center, Box 590, S-751 24, Uppsala, Sweden.
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Baldwin J, Voegtli WC, Khidekel N, Moënne-Loccoz P, Krebs C, Pereira AS, Ley BA, Huynh BH, Loehr TM, Riggs-Gelasco PJ, Rosenzweig AC, Bollinger JM. Rational reprogramming of the R2 subunit of Escherichia coli ribonucleotide reductase into a self-hydroxylating monooxygenase. J Am Chem Soc 2001; 123:7017-30. [PMID: 11459480 DOI: 10.1021/ja002114g] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The outcome of O2 activation at the diiron(II) cluster in the R2 subunit of Escherichia coli (class I) ribonucleotide reductase has been rationally altered from the normal tyrosyl radical (Y122*) production to self-hydroxylation of a phenylalanine side-chain by two amino acid substitutions that leave intact the (histidine)2-(carboxylate)4 ligand set characteristic of the diiron-carboxylate family. Iron ligand Asp (D) 84 was replaced with Glu (E), the amino acid found in the cognate position of the structurally similar diiron-carboxylate protein, methane monooxygenase hydroxylase (MMOH). We previously showed that this substitution allows accumulation of a mu-1,2-peroxodiiron(III) intermediate, which does not accumulate in the wild-type (wt) protein and is probably a structural homologue of intermediate P (H(peroxo)) in O2 activation by MMOH. In addition, the near-surface residue Trp (W) 48 was replaced with Phe (F), blocking transfer of the "extra" electron that occurs in wt R2 during formation of the formally Fe(III)Fe(IV) cluster X. Decay of the mu-1,2-peroxodiiron(III) complex in R2-W48F/D84E gives an initial brown product, which contains very little Y122* and which converts very slowly (t1/2 approximately 7 h) upon incubation at 0 degrees C to an intensely purple final product. X-ray crystallographic analysis of the purple product indicates that F208 has undergone epsilon-hydroxylation and the resulting phenol has shifted significantly to become a ligand to Fe2 of the diiron cluster. Resonance Raman (RR) spectra of the purple product generated with 16O2 or 18O2 show appropriate isotopic sensitivity in bands assigned to O-phenyl and Fe-O-phenyl vibrational modes, confirming that the oxygen of the Fe(III)-phenolate species is derived from O2. Chemical analysis, experiments involving interception of the hydroxylating intermediate with exogenous reductant, and Mössbauer and EXAFS characterization of the brown and purple species establish that F208 hydroxylation occurs during decay of the peroxo complex and formation of the initial brown product. The slow transition to the purple Fe(III)-phenolate species is ascribed to a ligand rearrangement in which mu-O2- is lost and the F208-derived phenolate coordinates. The reprogramming to F208 monooxygenase requires both amino acid substitutions, as very little epsilon-hydroxyphenylalanine is formed and pathways leading to Y122* formation predominate in both R2-D84E and R2-W48F.
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Affiliation(s)
- J Baldwin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Diner BA. Amino acid residues involved in the coordination and assembly of the manganese cluster of photosystem II. Proton-coupled electron transport of the redox-active tyrosines and its relationship to water oxidation. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1503:147-63. [PMID: 11115631 DOI: 10.1016/s0005-2728(00)00220-6] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The combination of site-directed mutagenesis, isotopic labeling, new magnetic resonance techniques and optical spectroscopic methods have provided new insights into cofactor coordination and into the mechanism of electron transport and proton-coupled electron transport in photosystem II. Site-directed mutations in the D1 polypeptide of this photosystem have implicated a number of histidine and carboxylate residues in the coordination and assembly of the manganese cluster, responsible for photosynthetic water oxidation. Many of these are located in the carboxy-terminal region of this polypeptide close to the processing site involved in its maturation. This maturation is a required precondition for cluster assembly. Recent proposals for the mechanism of water oxidation have directly implicated redox-active tyrosine Y(Z) in this mechanism and have emphasized the importance of the coupling of proton and electron transfer in the reduction of Y(Z)(radical) by the Mn cluster. The interaction of both homologous redox-active tyrosines Y(Z) and Y(D) with their respective homologous proton acceptors is discussed in an effort to better understand the significance of such coupling.
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Affiliation(s)
- B A Diner
- CR&D, Experimental Station, E.I. du Pont de Nemours and Co., Wilmington DE 19880-0173, USA.
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32
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Voegtli WC, Khidekel N, Baldwin J, Ley BA, Bollinger, JM, Rosenzweig AC. Crystal Structure of the Ribonucleotide Reductase R2 Mutant that Accumulates a μ-1,2-Peroxodiiron(III) Intermediate during Oxygen Activation. J Am Chem Soc 2000. [DOI: 10.1021/ja991839l] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Walter C. Voegtli
- Contribution from the Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, and the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Nelly Khidekel
- Contribution from the Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, and the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jeffrey Baldwin
- Contribution from the Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, and the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Brenda A. Ley
- Contribution from the Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, and the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - J. Martin Bollinger,
- Contribution from the Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, and the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Amy C. Rosenzweig
- Contribution from the Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, and the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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33
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Solomon EI, Brunold TC, Davis MI, Kemsley JN, Lee SK, Lehnert N, Neese F, Skulan AJ, Yang YS, Zhou J. Geometric and electronic structure/function correlations in non-heme iron enzymes. Chem Rev 2000; 100:235-350. [PMID: 11749238 DOI: 10.1021/cr9900275] [Citation(s) in RCA: 1351] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
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Müller J, Kikuchi A, Bill E, Weyhermüller T, Hildebrandt P, Ould-Moussa L, Wieghardt K. Phenoxyl radical complexes of chromium(III), manganese(III), cobalt(III), and nickel(II). Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(99)00314-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Hanson MA, Schmidt PP, Strand KR, Gräslund A, Solomon EI, Andersson KK. Resonance Raman Evidence for a Hydrogen-Bonded Oxo Bridge in the R2 Protein of Ribonucleotide Reductase from Mouse. J Am Chem Soc 1999. [DOI: 10.1021/ja990995p] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Melissa A. Hanson
- Department of Chemistry, Stanford University Stanford, California 94305-5080 Department of Biochemistry, University of Oslo N-0316 Oslo, Norway Department of Biophysics, Stockholm University S-106 91 Stockholm, Sweden
| | - Peter P. Schmidt
- Department of Chemistry, Stanford University Stanford, California 94305-5080 Department of Biochemistry, University of Oslo N-0316 Oslo, Norway Department of Biophysics, Stockholm University S-106 91 Stockholm, Sweden
| | - Kari R. Strand
- Department of Chemistry, Stanford University Stanford, California 94305-5080 Department of Biochemistry, University of Oslo N-0316 Oslo, Norway Department of Biophysics, Stockholm University S-106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Department of Chemistry, Stanford University Stanford, California 94305-5080 Department of Biochemistry, University of Oslo N-0316 Oslo, Norway Department of Biophysics, Stockholm University S-106 91 Stockholm, Sweden
| | - Edward I. Solomon
- Department of Chemistry, Stanford University Stanford, California 94305-5080 Department of Biochemistry, University of Oslo N-0316 Oslo, Norway Department of Biophysics, Stockholm University S-106 91 Stockholm, Sweden
| | - K. Kristoffer Andersson
- Department of Chemistry, Stanford University Stanford, California 94305-5080 Department of Biochemistry, University of Oslo N-0316 Oslo, Norway Department of Biophysics, Stockholm University S-106 91 Stockholm, Sweden
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36
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Ivancich A, Mattioli TA, Un S. Effect of Protein Microenvironment on Tyrosyl Radicals. A High-Field (285 GHz) EPR, Resonance Raman, and Hybrid Density Functional Study. J Am Chem Soc 1999. [DOI: 10.1021/ja990562m] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anabella Ivancich
- Contribution from the Section de Bioénergétique and Section de Biophysique des Protéines et des Membranes, URA 2096 CNRS, Département de Biologie Cellulaire et Moléculaire, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Tony A. Mattioli
- Contribution from the Section de Bioénergétique and Section de Biophysique des Protéines et des Membranes, URA 2096 CNRS, Département de Biologie Cellulaire et Moléculaire, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Sun Un
- Contribution from the Section de Bioénergétique and Section de Biophysique des Protéines et des Membranes, URA 2096 CNRS, Département de Biologie Cellulaire et Moléculaire, CEA Saclay, 91191 Gif-sur-Yvette, France
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37
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Berthomieu C, Boullais C, Neumann JM, Boussac A. Effect of 13C-, 18O- and 2H-labeling on the infrared modes of UV-induced phenoxyl radicals. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1998; 1365:112-6. [PMID: 15339636 DOI: 10.1016/s0005-2728(98)00056-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/1998] [Revised: 02/26/1998] [Accepted: 03/02/1998] [Indexed: 11/19/2022]
Abstract
The structure and environment of redox active tyrosines present in several metalloenzymes can be studied by resonance Raman spectroscopy or Fourier transform infrared difference spectroscopy. Assignments of the vibrational modes in vivo often requires in vitro studies on model compounds. This approach is briefly reviewed. New results are shown on the influence of isotope-labeling on the infrared spectra of tyrosine, [Formula: see text] and phenol radicals obtained in vitro by UV-irradiation. The infrared spectra of the radicals are dominated by the [Formula: see text] mode at 1515-1504 cm(-1). The frequency shifts induced on this mode by (13)C- (2)H-, and (18)O-labeling are reported.
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Affiliation(s)
- C Berthomieu
- Section de Bioénergétique, Département de Biologie Cellulaire et Moléculaire, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
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Kim S, Barry BA. The protein environment surrounding tyrosyl radicals D. and Z. in photosystem II: a difference Fourier-transform infrared spectroscopic study. Biophys J 1998; 74:2588-600. [PMID: 9591683 PMCID: PMC1299599 DOI: 10.1016/s0006-3495(98)77965-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Photosystem II contains two redox-active tyrosine residues, termed D and Z, which have different midpoint potentials and oxidation/reduction kinetics. To understand the functional properties of redox-active tyrosines, we report a difference Fourier-transform infrared (FT-IR) spectroscopic study of these species. Vibrational spectra associated with the oxidation of each tyrosine residue are acquired; electron paramagnetic resonance (EPR) and fluorescence experiments demonstrate that there is no detectable contribution of Q(A)- to these spectra. Vibrational lines are assigned to the radicals by isotopic labeling of tyrosine. Global 15N labeling, 2H exchange, and changes in pH identify differences in the reversible interactions of the two redox-active tyrosines with N-containing, titratable amino acid side chains in their environments. To identify the amino acid residue that contributes to the spectrum of D, mutations at His189 in the D2 polypeptide were examined. Mutations at this site result in substantial changes in the spectrum of tyrosine D. Previously, mutations at the analogous histidine, His190 in the D1 polypeptide, were shown to have no significant effect on the FT-IR spectrum of tyrosine Z (Bernard, M. T., et al. 1995. J. Biol. Chem. 270:1589-1594). A disparity in the number of accessible, proton-accepting groups could influence electron transfer rates and energetics and account for functional differences between the two redox-active tyrosines.
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Affiliation(s)
- S Kim
- Department of Biochemistry, University of Minnesota, St. Paul 55108-1022, USA
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40
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Schnepf R, Sokolowski A, Müller J, Bachler V, Wieghardt K, Hildebrandt P. Resonance Raman Spectroscopic Study of Phenoxyl Radical Complexes. J Am Chem Soc 1998. [DOI: 10.1021/ja972269x] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert Schnepf
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim, Germany
| | - Achim Sokolowski
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim, Germany
| | - Jochen Müller
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim, Germany
| | - Vinzenz Bachler
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim, Germany
| | - Karl Wieghardt
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim, Germany
| | - Peter Hildebrandt
- Contribution from the Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34−36, D-45470 Mülheim, Germany
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41
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Sokolowski A, Müller J, Weyhermüller T, Schnepf R, Hildebrandt P, Hildenbrand K, Bothe E, Wieghardt K. Phenoxyl Radical Complexes of Zinc(II). J Am Chem Soc 1997. [DOI: 10.1021/ja970417d] [Citation(s) in RCA: 151] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Achim Sokolowski
- Contribution from the Max-Planck-Institut für Strahlenchemie, P.O. Box 10 13 65, D-45413 Mülheim an der Ruhr, Germany
| | - Jochen Müller
- Contribution from the Max-Planck-Institut für Strahlenchemie, P.O. Box 10 13 65, D-45413 Mülheim an der Ruhr, Germany
| | - Thomas Weyhermüller
- Contribution from the Max-Planck-Institut für Strahlenchemie, P.O. Box 10 13 65, D-45413 Mülheim an der Ruhr, Germany
| | - Robert Schnepf
- Contribution from the Max-Planck-Institut für Strahlenchemie, P.O. Box 10 13 65, D-45413 Mülheim an der Ruhr, Germany
| | - Peter Hildebrandt
- Contribution from the Max-Planck-Institut für Strahlenchemie, P.O. Box 10 13 65, D-45413 Mülheim an der Ruhr, Germany
| | - Knut Hildenbrand
- Contribution from the Max-Planck-Institut für Strahlenchemie, P.O. Box 10 13 65, D-45413 Mülheim an der Ruhr, Germany
| | - Eberhard Bothe
- Contribution from the Max-Planck-Institut für Strahlenchemie, P.O. Box 10 13 65, D-45413 Mülheim an der Ruhr, Germany
| | - Karl Wieghardt
- Contribution from the Max-Planck-Institut für Strahlenchemie, P.O. Box 10 13 65, D-45413 Mülheim an der Ruhr, Germany
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42
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Ribonucleotide reductases — a group of enzymes with different metallosites and a similar reaction mechanism. METAL SITES IN PROTEINS AND MODELS 1997. [DOI: 10.1007/3-540-62870-3_5] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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43
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Wallar BJ, Lipscomb JD. Dioxygen Activation by Enzymes Containing Binuclear Non-Heme Iron Clusters. Chem Rev 1996; 96:2625-2658. [PMID: 11848839 DOI: 10.1021/cr9500489] [Citation(s) in RCA: 977] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bradley J. Wallar
- Department of Biochemistry, Medical School, 4-225 Millard Hall, University of Minnesota, Minneapolis, Minnesota 55455
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44
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Swarts JC, Sykes A. Kinetic studies on the reduction of the R2 protein of E. coli ribonucleotide reductase by [Co(sep)]2+ and [Co(9-aneN3)2]2+. Inorganica Chim Acta 1996. [DOI: 10.1016/0020-1693(95)04862-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Hoganson CW, Sahlin M, Sjöberg BM, Babcock GT. Electron Magnetic Resonance of the Tyrosyl Radical in Ribonucleotide Reductase fromEscherichia coli. J Am Chem Soc 1996. [DOI: 10.1021/ja953979a] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Sahlin M, Lassmann G, Pötsch S, Sjöberg BM, Gräslund A. Transient free radicals in iron/oxygen reconstitution of mutant protein R2 Y122F. Possible participants in electron transfer chains in ribonucleotide reductase. J Biol Chem 1995; 270:12361-72. [PMID: 7759477 DOI: 10.1074/jbc.270.21.12361] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Ferrous iron/oxygen reconstitution of the mutant R2 apoprotein Y122F leads to formation of a diferric center similar to that of the wild-type R2 protein of Escherichia coli ribonucleotide reductase. This reconstitution reaction requires two extra electrons, supplied or transferred by the protein matrix of R2. We observed several transient free radical species using stopped flow and freeze quench EPR and stopped flow UV-visible spectroscopy. Three of the radicals occur in the time window 0.1-2 s, i.e. concomitant with formation of the diferric site. They include a strongly iron-coupled radical (singlet EPR signal) observed only at < or = 77 K, a singlet EPR signal observed only at room temperature, and a radical at Tyr-356 (light absorption at 410 nm), an invariant residue proposed to be part of an electron transfer chain in catalysis. Three additional transient radicals species are observed in the time window 6 s to 20 min. Two of these are conclusively identified, by specific deuteration, as tryptophan radicals. Comparing side chain geometry and distance to the iron center with EPR characteristics of the radicals, we propose certain Trp residues in R2 as likely to harbor these transient radicals.
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Affiliation(s)
- M Sahlin
- Department of Molecular Biology, Stockholm University, Arrhenius Laboratories, Sweden
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47
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Swarts JC, Aquino MA, Han JY, Lam KY, Sykes AG. Kinetic studies on the reduction of the tyrosyl radical of the R2 subunit of E. coli ribonucleotide reductase. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1247:215-24. [PMID: 7696311 DOI: 10.1016/0167-4838(94)00233-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Kinetic studies at 25 degrees C, I = 0.100 M (NaCl), on the reduction of the tyrosyl radical of the R2 protein of E. coli ribonucleotide reductase with hydroxyurea (HU), N-methylhydroxylamine, catechol, and seven hydroxamic acid derivatives are reported. There are no pH-dependences in the range 6.2-8.6 investigated except that introduced with N-methylhydroxylamine which itself protonates in this range. At pH 7.6 the rate constant (0.46 M-1 s-1) for the HU reaction is in agreement with earlier values. Slower reactions are observed with the bulkier acetohydroxamic (0.020 M-1 s-1) and benzohydroxamic acids (0.040 M-1 s-1). In the case of N-methylhydroxylamine the rate constant (0.41 M-1 s-1 at pH 7.6) decreases with pH, and it is concluded that the protonated form CH3NH2+OH(pKa = 6.2) has little or no reactivity with Tyr. For this reaction under air-free conditions a second-stage (0.027 M-1 s-1) corresponding to reduction of Fe(III)2 is observed. Mid-point redox potentials for the reductants and estimates of reduction potentials applying in the case of the protein are considered. The reactions with 1,2-dihydroxybenzene (catechol) and 3,4-dihydroxybenzohydroxamic acid (Didox) also have two stages, when the initial Tyr reduction, rate constants/M-1 s-1 for catechol (3.2) and Didox (0.010), is followed by removal of the Fe(III) to give catechol and catechol like Fe(III)-complexed products. The single stage reactions of the hydroxamic acid derivatives which incorporate charged amino-acid groups L-glutamic acid, L-histidine, L-glycine and L-lysine, are slow, and saturation kinetics are observed consistent with association (small K values) prior to redox. The mechanism of reduction of R2-Tyr by all of the reagents studied is discussed.
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Affiliation(s)
- J C Swarts
- Department of Chemistry, University of Newcastle, Newcastle upon Tyne, UK
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48
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Bernard MT, MacDonald GM, Nguyen AP, Debus RJ, Barry BA. A difference infrared study of hydrogen bonding to the Z. tyrosyl radical of photosystem II. J Biol Chem 1995; 270:1589-94. [PMID: 7829489 DOI: 10.1074/jbc.270.4.1589] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Photosystem II, the photosynthetic water oxidizing complex, contains two well characterized redox active tyrosines, D and Z. D forms a stable radical of unknown function. Z is an electron carrier between the primary chlorophyll donor and the manganese catalytic site. The vibrational difference spectra associated with the oxidation of tyrosines Z and D have been obtained through the use of infrared spectroscopy (MacDonald, G. M., Bixby, K.A., and Barry, B.A. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 11024-11028). Here, we examine the effect of deuterium exchange on these vibrational difference spectra. While the putative C-O vibration of stable tyrosine radical D. downshifts in 2H2O, the putative C-O vibration of tyrosine radical Z. does not. This result is consistent with the existence of a hydrogen bond to the phenol oxygen of the D. radical; we conclude that a hydrogen bond is not formed to the Z. radical. In an effort to identify the amino acid residue that is the proton acceptor for Z, we have performed global 15N labeling. While significant 15N shifts are observed in the vibrational difference spectrum, substitution of a glutamine for a histidine that is predicted to lie in the environment of tyrosine Z has little or no effect on the difference infrared spectrum. There is also no significant change in the yield or lineshape of the Z. EPR signal under continuous illumination in this mutant. Our results are inconsistent with the possibility that this residue, histidine 190 of the D1 polypeptide, acts as the sole proton acceptor for tyrosine Z.
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Affiliation(s)
- M T Bernard
- Department of Biochemistry, University of Minnesota, St. Paul 55108
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49
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Affiliation(s)
- B A Barry
- Department of Biochemistry, University of Minnesota, St. Paul 55108, USA
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50
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Berthomieu C, Boussac A. FTIR and EPR study of radicals of aromatic amino acids 4-methylimidazole and phenol generated by UV irradiation. ACTA ACUST UNITED AC 1995. [DOI: 10.1002/bspy.350010304] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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