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Stathi P, Fotou E, Moussis V, Tsikaris V, Louloudi M, Deligiannakis Y. Control of Tyrosyl Radical Stabilization by {SiO 2@Oligopeptide} Hybrid Biomimetic Materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9799-9809. [PMID: 35915965 DOI: 10.1021/acs.langmuir.2c00710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Tyrosine radicals are notoriously short-lived/unstable in solution, while they present an impressive degree of stability and versatility in bioenzymes. Herein, we have developed a library of hybrid biomimetic materials (HBMs), which consists of tyrosine-containing oligopeptides covalently grafted on SiO2 nanoparticles, and studied the formation, lifetime, and redox properties of tyrosyl radicals. Using electron paramagnetic resonance spectroscopy, we have studied the radical-spin distribution as a probe of the local microenvironment of the tyrosyl radicals in the HBMs. We find that the lifetime of the tyrosyl radical can be enhanced by up to 6 times, by adjusting three factors, namely, a proximal histidine, the length of the oligopeptide, and the interface with the SiO2 nanomatrix. This is shown to be correlated to a significant lowering of E1/2 from +736 mV, in free tyrosine, to +548 mV in the {12-peptide}@SiO2 material. Moreover, we show that grafting on SiO2 lowers the E1/2 of tyrosine radicals by ∼50 mV in all oligopeptides. Analysis of the spin-distribution by EPR reveals that the positioning of a histidine at a H-bonding distance from the tyrosine further favors tyrosine radical stabilization.
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Affiliation(s)
- Panagiota Stathi
- Department of Chemistry, Laboratory of Biomimetic Catalysis & Hybrid Materials, University of Ioannina, Ioannina 4550, Greece
| | - Evgenia Fotou
- Department of Chemistry, Laboratory of Protein and Peptide Chemistry, University of Ioannina, Ioannina 4550, Greece
| | - Vassilios Moussis
- Department of Chemistry, Laboratory of Protein and Peptide Chemistry, University of Ioannina, Ioannina 4550, Greece
| | - Vassilios Tsikaris
- Department of Chemistry, Laboratory of Protein and Peptide Chemistry, University of Ioannina, Ioannina 4550, Greece
| | - Maria Louloudi
- Department of Chemistry, Laboratory of Biomimetic Catalysis & Hybrid Materials, University of Ioannina, Ioannina 4550, Greece
| | - Yiannis Deligiannakis
- Department of Physics, Laboratory of Physical Chemistry of Materials & Environment, University of Ioannina, Ioannina 4550, Greece
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2
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Ozawa H, Miyazawa T, Burdeos GC, Miyazawa T. Biological Functions of Antioxidant Dipeptides. J Nutr Sci Vitaminol (Tokyo) 2022; 68:162-171. [PMID: 35768247 DOI: 10.3177/jnsv.68.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the history of modern nutritional science, understanding antioxidants is one of the major topics. In many cases, food-derived antioxidants have π conjugate or thiol group in their molecular structures because π conjugate stabilizes radical by its delocalization and two thiol groups form a disulfide bond in its antioxidative process. In recent years, antioxidant peptides have received much attention because for their ability to scavenge free radicals, inhibition of lipid peroxidation, chelation of transition metal ions, as well as their additional nutritional value. Among them, dipeptides are attracting much interest as post-amino acids, which have residues in common with amino acids, but also have different physiological properties and functions from those of amino acids. Especially, dipeptides containing moieties of several amino acid (tryptophan, tyrosine, histidine, cysteine, and methionine) possess potent antioxidant activity. This review summarizes previous details of structural property, radical scavenging activity, and biological activity of antioxidant dipeptide. Hopefully, this review will help provide a new insight into the study of the biological functions of antioxidant dipeptides.
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Affiliation(s)
- Hitoshi Ozawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| | - Taiki Miyazawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| | | | - Teruo Miyazawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
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3
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Bin Mohd Yusof MS, Lim YL, Loh ZH. Ultrafast vibrational wave packet dynamics of the aqueous tyrosyl radical anion induced by photodetachment. Phys Chem Chem Phys 2021; 23:18525-18534. [PMID: 34581329 DOI: 10.1039/d1cp02975d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ultrafast dynamics triggered by the photodetachment of the tyrosinate dianion in aqueous environment shed light on the elementary processes that accompany the interaction of ionizing radiation with biological matter. Photodetachment of the tryosinate dianion yields the tyrosyl radical anion, an important intermediate in biological redox reactions, although the study of its ultrafast dynamics is limited. Here, we utilize femtosecond optical pump-probe spectroscopy to investigate the ultrafast structural reorganization dynamics that follow the photodetachment of the tyrosinate dianion in aqueous solution. Photodetachment of the tyrosinate dianion leads to vibrational wave packet motion along seven vibrational modes that are coupled to the photodetachment process. The vibrational modes are assigned with the aid of density functional theory (DFT) calculations. Our results offer a glimpse of the elementary dynamics of ionized biomolecules and suggest the possibility of extending this approach to investigate the ionization-induced structural rearrangement of other aromatic amino acids and larger biomolecules.
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Affiliation(s)
- Muhammad Shafiq Bin Mohd Yusof
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
| | - Yong Liang Lim
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
| | - Zhi-Heng Loh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
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4
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Dark polymerization of acrylamide induced by tyrosine-containing peptide. Polym Bull (Berl) 2021. [DOI: 10.1007/s00289-020-03343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Watson RA, Offenbacher AR, Barry BA. Detection of Catalytically Linked Conformational Changes in Wild-Type Class Ia Ribonucleotide Reductase Using Reaction-Induced FTIR Spectroscopy. J Phys Chem B 2021; 125:8362-8372. [PMID: 34289692 DOI: 10.1021/acs.jpcb.1c03038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis in all cells. The class Ia Escherichia coli RNR consists of two dimeric subunits, α2 and β2, which form an active but unstable heterodimer of dimers, α2β2. The structure of the wild-type form of the enzyme has been challenging to study due to the instability of the catalytic complex. A long-range proton-coupled electron-transfer (PCET) pathway facilitates radical migration from the Y122 radical-diiron cofactor in the β subunit to an active site cysteine, C439, in the α subunit to initiate the RNR chemistry. The PCET reactions and active site chemistry are spectroscopically masked by a rate-limiting, conformational gate. Here, we present a reaction-induced Fourier transform infrared (RIFTIR) spectroscopic method to monitor the mechanism of the active, wild-type RNR α2β2 complex. This method is employed to obtain new information about conformational changes accompanying RNR catalysis, including the role of carboxylate interactions, deprotonation, and oxidation of active site cysteines, and a detailed description of reversible secondary structural changes. Labeling of tyrosine revealed a conformationally active tyrosine in the β subunit, assigned to Y356β, which is part of the intersubunit PCET pathway. New insights into the roles of the inhibitors, azidoUDP and dATP, and the sensitivity of RIFTIR spectroscopy to detect subtle conformational motions arising from protein allostery are also presented.
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Affiliation(s)
- Ryan Atlee Watson
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Adam R Offenbacher
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States.,Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Bridgette A Barry
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States
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6
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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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Calcium, conformational selection, and redox-active tyrosine YZ in the photosynthetic oxygen-evolving cluster. Proc Natl Acad Sci U S A 2018; 115:5658-5663. [PMID: 29752381 DOI: 10.1073/pnas.1800758115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Photosystem II (PSII), YZ (Tyr161D1) participates in radical transfer between the chlorophyll donor and the Mn4CaO5 cluster. Under flashing illumination, the metal cluster cycles among five Sn states, and oxygen is evolved from water. The essential YZ is transiently oxidized and reduced on each flash in a proton-coupled electron transfer (PCET) reaction. Calcium is required for function. Of reconstituted divalent ions, only strontium restores oxygen evolution. YZ is predicted to hydrogen bond to calcium-bound water and to His190D1 in PSII structures. Here, we report a vibrational spectroscopic study of YZ radical and singlet in the presence of the metal cluster. The S2 state is trapped by illumination at 190 K; flash illumination then generates the S2YZ radical. Using reaction-induced FTIR spectroscopy and divalent ion depletion/substitution, we identify calcium-sensitive tyrosyl radical and tyrosine singlet bands in the S2 state. In calcium-containing PSII, two CO stretching bands are detected at 1,503 and 1,478 cm-1 These bands are assigned to two different radical conformers in calcium-containing PSII. At pH 6.0, the 1,503-cm-1 band shifts to 1,507 cm-1 in strontium-containing PSII, and the band is reduced in intensity in calcium-depleted PSII. These effects are consistent with a hydrogen-bonding interaction between the calcium site and one conformer of radical YZ. Analysis of the amide I region indicates that calcium selects for a PCET reaction in a subset of the YZ conformers, which are trapped in the S2 state. These results support the interpretation that YZ undergoes a redox-coupled conformational change, which is calcium dependent.
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8
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Chemically induced dynamic nuclear polarization study of the reduction of histidine radical in the reactions with aromatic amino acids. Russ Chem Bull 2017. [DOI: 10.1007/s11172-016-1676-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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SATHEESHKUMAR E, YANG J, SRINIVASADESIKAN V, LIN MC. Simultaneous Production and Surface Functionalization of Silver Nanoparticles for Label-free Colorimetric Detection of Copper Ion. ANAL SCI 2017; 33:1115-1121. [DOI: 10.2116/analsci.33.1115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - Jyisy YANG
- Department of Chemistry, National Chung Hsing University
| | - Venkatesan SRINIVASADESIKAN
- Center for Interdisciplinary Molecular Science and Department of Applied Chemistry, National Chiao Tung University
| | - Ming-Chang LIN
- Center for Interdisciplinary Molecular Science and Department of Applied Chemistry, National Chiao Tung University
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10
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Houée-Lévin C, Bobrowski K, Horakova L, Karademir B, Schöneich C, Davies MJ, Spickett CM. Exploring oxidative modifications of tyrosine: An update on mechanisms of formation, advances in analysis and biological consequences. Free Radic Res 2015; 49:347-73. [DOI: 10.3109/10715762.2015.1007968] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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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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12
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Petersen RC. Free-radical polymer science structural cancer model: a review. SCIENTIFICA 2013; 2013:143589. [PMID: 24278767 PMCID: PMC3820302 DOI: 10.1155/2013/143589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 12/20/2012] [Indexed: 06/02/2023]
Abstract
Polymer free-radical lipid alkene chain-growth biological models particularly for hypoxic cellular mitochondrial metabolic waste can be used to better understand abnormal cancer cell morphology and invasive metastasis. Without oxygen as the final electron acceptor for mitochondrial energy synthesis, protons cannot combine to form water and instead mitochondria produce free radicals and acid during hypoxia. Nonuniform bond-length shrinkage of membranes related to erratic free-radical covalent crosslinking can explain cancer-cell pleomorphism with epithelial-mesenchymal transition for irregular membrane borders that "ruffle" and warp over stiff underlying actin fibers. Further, mitochondrial hypoxic conditions produce acid that can cause molecular degradation. Subsequent low pH-activated enzymes then provide paths for invasive cell movement through tissue and eventually blood-born metastasis. Although free-radical crosslinking creates irregularly shaped membranes with structural actin-polymerized fiber extensions as filopodia and lamellipodia, due to rapid cell division the overall cell modulus (approximately stiffness) is lower than normal cells. When combined with low pH-activated enzymes and lower modulus cells, smaller cancer stem cells subsequently have a large advantage to follow molecular destructive pathways and leave the central tumor. In addition, forward structural spike-like lamellipodia protrusions can leverage to force lower-modulus cancer cells through narrow openings. By squeezing and deforming even smaller to allow for easier movement through difficult passageways, cancer cells can travel into adjacent tissues or possibly metastasize through the blood to new tissue.
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Affiliation(s)
- Richard C. Petersen
- Department of Biomaterials and Biomedical Engineering, The University of Alabama at Birmingham, SDB 539, 1919 7th Avenue South, Birmingham, AL 35294, USA
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13
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Keough JM, Zuniga AN, Jenson DL, Barry BA. Redox control and hydrogen bonding networks: proton-coupled electron transfer reactions and tyrosine Z in the photosynthetic oxygen-evolving complex. J Phys Chem B 2013; 117:1296-307. [PMID: 23346921 DOI: 10.1021/jp3118314] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In photosynthetic oxygen evolution, redox active tyrosine Z (YZ) plays an essential role in proton-coupled electron transfer (PCET) reactions. Four sequential photooxidation reactions are necessary to produce oxygen at a Mn(4)CaO(5) cluster. The sequentially oxidized states of this oxygen-evolving cluster (OEC) are called the S(n) states, where n refers to the number of oxidizing equivalents stored. The neutral radical, YZ•, is generated and then acts as an electron transfer intermediate during each S state transition. In the X-ray structure, YZ, Tyr161 of the D1 subunit, is involved in an extensive hydrogen bonding network, which includes calcium-bound water. In electron paramagnetic resonance experiments, we measured the YZ• recombination rate, in the presence of an intact Mn(4)CaO(5) cluster. We compared the S(0) and S(2) states, which differ in Mn oxidation state, and found a significant difference in the YZ• decay rate (t(1/2) = 3.3 ± 0.3 s in S(0); t(1/2) = 2.1 ± 0.3 s in S(2)) and in the solvent isotope effect (SIE) on the reaction (1.3 ± 0.3 in S(0); 2.1 ± 0.3 in S(2)). Although the YZ site is known to be solvent accessible, the recombination rate and SIE were pH independent in both S states. To define the origin of these effects, we measured the YZ• recombination rate in the presence of ammonia, which inhibits oxygen evolution and disrupts the hydrogen bond network. We report that ammonia dramatically slowed the YZ• recombination rate in the S(2) state but had a smaller effect in the S(0) state. In contrast, ammonia had no significant effect on YD•, the stable tyrosyl radical. Therefore, the alterations in YZ• decay, observed with S state advancement, are attributed to alterations in OEC hydrogen bonding and consequent differences in the YZ midpoint potential/pK(a). These changes may be caused by activation of metal-bound water molecules, which hydrogen bond to YZ. These observations document the importance of redox control in proton-coupled electron transfer reactions.
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Affiliation(s)
- James M Keough
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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14
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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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15
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Keough JM, Jenson DL, Zuniga AN, Barry BA. Proton coupled electron transfer and redox-active tyrosine Z in the photosynthetic oxygen-evolving complex. J Am Chem Soc 2011; 133:11084-7. [PMID: 21714528 PMCID: PMC3246746 DOI: 10.1021/ja2041139] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton coupled electron transfer (PCET) reactions play an essential role in many enzymatic processes. In PCET, redox-active tyrosines may be involved as intermediates when the oxidized phenolic side chain deprotonates. Photosystem II (PSII) is an excellent framework for studying PCET reactions, because it contains two redox-active tyrosines, YD and YZ, with different roles in catalysis. One of the redox-active tyrosines, YZ, is essential for oxygen evolution and is rapidly reduced by the manganese-catalytic site. In this report, we investigate the mechanism of YZ PCET in oxygen-evolving PSII. To isolate YZ(•) reactions, but retain the manganese-calcium cluster, low temperatures were used to block the oxidation of the metal cluster, high microwave powers were used to saturate the YD(•) EPR signal, and YZ(•) decay kinetics were measured with EPR spectroscopy. Analysis of the pH and solvent isotope dependence was performed. The rate of YZ(•) decay exhibited a significant solvent isotope effect, and the rate of recombination and the solvent isotope effect were pH independent from pH 5.0 to 7.5. These results are consistent with a rate-limiting, coupled proton electron transfer (CPET) reaction and are contrasted to results obtained for YD(•) decay kinetics at low pH. This effect may be mediated by an extensive hydrogen-bond network around YZ. These experiments imply that PCET reactions distinguish the two PSII redox-active tyrosines.
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Affiliation(s)
- James M. Keough
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - David L. Jenson
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Ashley N. Zuniga
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Bridgette A. Barry
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
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16
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Barry BA. Proton coupled electron transfer and redox active tyrosines in Photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2011; 104:60-71. [PMID: 21419640 PMCID: PMC3164834 DOI: 10.1016/j.jphotobiol.2011.01.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 01/25/2011] [Accepted: 01/31/2011] [Indexed: 11/30/2022]
Abstract
In this article, progress in understanding proton coupled electron transfer (PCET) in Photosystem II is reviewed. Changes in acidity/basicity may accompany oxidation/reduction reactions in biological catalysis. Alterations in the proton transfer pathway can then be used to alter the rates of the electron transfer reactions. Studies of the bioenergetic complexes have played a central role in advancing our understanding of PCET. Because oxidation of the tyrosine results in deprotonation of the phenolic oxygen, redox active tyrosines are involved in PCET reactions in several enzymes. This review focuses on PCET involving the redox active tyrosines in Photosystem II. Photosystem II catalyzes the light-driven oxidation of water and reduction of plastoquinone. Photosystem II provides a paradigm for the study of redox active tyrosines, because this photosynthetic reaction center contains two tyrosines with different roles in catalysis. The tyrosines, YZ and YD, exhibit differences in kinetics and midpoint potentials, and these differences may be due to noncovalent interactions with the protein environment. Here, studies of YD and YZ and relevant model compounds are described.
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Affiliation(s)
- Bridgette A Barry
- School of Chemistry and Biochemistry and The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, 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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18
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Sibert RS, Josowicz M, Barry BA. Control of proton and electron transfer in de novo designed, biomimetic β hairpins. ACS Chem Biol 2010; 5:1157-68. [PMID: 20919724 DOI: 10.1021/cb100138m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosine side chains are involved in proton coupled electron transfer reactions (PCET) in many complex proteins, including photosystem II (PSII) and ribonucleotide reductase. For example, PSII contains two redox-active tyrosines, TyrD (Y160D2) and TyrZ (Y161D1), which have different protein environments, midpoint potentials, and roles in catalysis. TyrD has a midpoint potential lower than that of TyrZ, and its protein environment is distinguished by potential π-cation interactions with arginine residues. Designed biomimetic peptides provide a system that can be used to investigate how the protein matrix controls PCET reactions. As a model for the redox-active tyrosines in PSII, we are employing a designed, 18 amino acid β hairpin peptide in which PCET reactions occur between a tyrosine (Tyr5) and a cross-strand histidine (His14). In this peptide, the single tyrosine is hydrogen-bonded to an arginine residue, Arg16, and a second arginine, Arg12, has a π-cation interaction with Tyr5. In this report, the effect of these hydrogen bonding and electrostatic interactions on the PCET reactions is investigated. Electrochemical titrations show that histidine substitutions change the nature of PCET reactions, and optical titrations show that Arg16 substitution changes the pK of Tyr5. Removal of Arg16 or Arg12 increases the midpoint potential for tyrosine oxidation. The effects of Arg12 substitution are consistent with the midpoint potential difference, which is observed for the PSII redox-active tyrosine residues. Our results demonstrate that a π-cation interaction, hydrogen bonding, and PCET reactions alter redox-active tyrosine function. These interactions can contribute equally to the control of midpoint potential and reaction rate.
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Affiliation(s)
- Robin S. Sibert
- Department of Chemistry and Biochemistry
- Petit Institute for Bioengineering and Bioscience
| | | | - Bridgette A. Barry
- Department of Chemistry and Biochemistry
- Petit Institute for Bioengineering and Bioscience
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19
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Berthomieu C, Hienerwadel R. Fourier transform infrared (FTIR) spectroscopy. PHOTOSYNTHESIS RESEARCH 2009; 101:157-170. [PMID: 19513810 DOI: 10.1007/s11120-009-9439-x] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 05/15/2009] [Indexed: 05/26/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy probes the vibrational properties of amino acids and cofactors, which are sensitive to minute structural changes. The lack of specificity of this technique, on the one hand, permits us to probe directly the vibrational properties of almost all the cofactors, amino acid side chains, and of water molecules. On the other hand, we can use reaction-induced FTIR difference spectroscopy to select vibrations corresponding to single chemical groups involved in a specific reaction. Various strategies are used to identify the IR signatures of each residue of interest in the resulting reaction-induced FTIR difference spectra. (Specific) Isotope labeling, site-directed mutagenesis, hydrogen/deuterium exchange are often used to identify the chemical groups. Studies on model compounds and the increasing use of theoretical chemistry for normal modes calculations allow us to interpret the IR frequencies in terms of specific structural characteristics of the chemical group or molecule of interest. This review presents basics of FTIR spectroscopy technique and provides specific important structural and functional information obtained from the analysis of the data from the photosystems, using this method.
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Affiliation(s)
- Catherine Berthomieu
- Commissariat à l' Energie Atomique, Laboratoire des Interactions Protéine Métal, DSV/Institut de Biologie Environnementale et Biotechnologie, CNRS-CEA-Université Aix-Marseille II, Saint Paul-lez-Durance Cedex, France.
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20
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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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21
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Offenbacher A, White KN, Sen I, Oliver AG, Konopelski JP, Barry BA, Einarsdóttir O. A spectroscopic investigation of a tridentate Cu-complex mimicking the tyrosine-histidine cross-link of cytochrome C oxidase. J Phys Chem B 2009; 113:7407-17. [PMID: 19438285 DOI: 10.1021/jp9010795] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme-copper oxidases have a crucial role in the energy transduction mechanism, catalyzing the reduction of dioxygen to water. The reduction of dioxygen takes place at the binuclear center, which contains heme a3 and CuB. The X-ray crystal structures have revealed that the C6' of tyrosine 244 (bovine heart numbering) is cross-linked to a nitrogen of histidine 240, a ligand to CuB. The role of the cross-linked tyrosine at the active site still remains unclear. In order to provide insight into the function of the cross-linked tyrosine, we have investigated the spectroscopic and electrochemical properties of chemical analogues of the CuB-His-Tyr site. The analogues, a tridentate histidine-phenol cross-linked ether ligand and the corresponding Cu-containing complex, were previously synthesized in our laboratory (White, K.; et al. Chem. Commun. 2007, 3252-3254). Spectrophotometric titrations of the ligand and the Cu-complex indicate a pKa of the phenolic proton of 8.8 and 7.7, respectively. These results are consistent with the cross-linked tyrosine playing a proton delivery role at the cytochrome c oxidase active site. The presence of the phenoxyl radical was investigated at low temperature using electron paramagnetic resonance (EPR) and Fourier transform infrared (FT-IR) difference spectroscopy. UV photolysis of the ligand, without bound copper, generated a narrow g=2.0047 signal, attributed to the phenoxyl radial. EPR spectra recorded before and after UV photolysis of the Cu-complex showed a g=2 signal characteristic of oxidized copper, suggesting that the copper is not spin-coupled to the phenoxyl radical. An EPR signal from the phenoxyl radical was not observed in the Cu-complex, either due to spin relaxation of the two unpaired electrons or to masking of the narrow phenoxyl radical signal by the strong copper contribution. Stable isotope (13C) labeling of the phenol ring (C1') Cu-complex, combined with photoinduced difference FT-IR spectroscopy, revealed bands at 1485 and 1483 cm(-1) in the 12C-minus-13C-isotope-edited spectra of the ligand and Cu-complex, respectively. These bands are attributed to the radical v7a stretching frequency and are shifted to 1468 and 1472 cm(-1), respectively, with 13C1' labeling. These results show that a radical is generated in both the ligand and the Cu-complex and support the unambiguous assignment of a vibrational band to the phenoxyl radical v7a stretching mode. These data are discussed with respect to a possible role of the cross-linked tyrosine radical in cytochrome c oxidase.
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Affiliation(s)
- Adam 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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22
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Kumar M, Kozlowski PM. Role of Tyrosine Residue in the Activation of Co−C Bond in Coenzyme B12-Dependent Enzymes: Another Case of Proton-Coupled Electron Transfer? J Phys Chem B 2009; 113:9050-4. [DOI: 10.1021/jp903878y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manoj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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23
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Svistunenko DA, Jones GA. Tyrosyl radicals in proteins: a comparison of empirical and density functional calculated EPR parameters. Phys Chem Chem Phys 2009; 11:6600-13. [DOI: 10.1039/b905522c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Shafaat HS, Leigh BS, Tauber MJ, Kim JE. Resonance Raman Characterization of a Stable Tryptophan Radical in an Azurin Mutant. J Phys Chem B 2008; 113:382-8. [PMID: 19072535 DOI: 10.1021/jp809329a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hannah S. Shafaat
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Brian S. Leigh
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Michael J. Tauber
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Judy E. Kim
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
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25
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Brynda M, David Britt R. Density Functional Theory calculations on the magnetic properties of the model tyrosine radical-histidine complex mimicking tyrosyl radical YD · in photosystem II. RESEARCH ON CHEMICAL INTERMEDIATES 2007. [DOI: 10.1163/156856707782169426] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Range K, Ayala I, York D, Barry BA. Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment. J Phys Chem B 2007; 110:10970-81. [PMID: 16771350 DOI: 10.1021/jp061503f] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes such as prostaglandin H synthase, ribonucleotide reductase, and photosystem II (PSII). Spectroscopic characterization of tyrosyl radicals in these systems provides a powerful experimental probe into the role of the enzyme in mediation of long-range electron transfer processes. Interpretation of such data, however, relies critically on first establishing a spectroscopic fingerprint of isotopically labeled tyrosinate and tyrosyl radicals in nonenzymatic environments. In this report, FT-IR results obtained from tyrosinate, tyrosyl radical (produced by ultraviolet photolysis of polycrystalline tyrosinate), and their isotopologues at 77 K are presented. Assignment of peaks and isotope shifts is aided by density-functional B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) calculations of tyrosine and tyrosyl radical in several different charge and protonation states. In addition, characterization of the potential energy surfaces of tyrosinate and tyrosyl radical as a function of the backbone and ring torsion angles provides detailed insight into the sensitivity of the vibrational frequencies to conformational changes. These results provide a detailed spectroscopic interpretation, which will elucidate the structures of redox-active tyrosine residues in complex protein environments. Specific application of these data is made to enzymatic systems.
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Affiliation(s)
- Kevin Range
- Department of Chemistry, Lock Haven University of Pennsylvania, Lock Haven, Pennsylvania 17745, USA
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27
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Kovacic P. Protein electron transfer (mechanism and reproductive toxicity): iminium, hydrogen bonding, homoconjugation, amino acid side chains (redox and charged), and cell signaling. ACTA ACUST UNITED AC 2007; 81:51-64. [PMID: 17539014 DOI: 10.1002/bdrc.20086] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This contribution presents novel biochemical perspectives of protein electron transfer (ET) with focus on the iminium nature of the peptide link, along with relationships to reproductive toxicity. The favorable influence of hydrogen bonding on protein ET has been widely documented. Hydrogen bonding of the zwitterionic peptide enhances iminium character. A wide array of such bonding agents is available in vivo, with many reports on the peptide link itself. ET proceeds along the backbone, due in part, to homoconjugation. Redox amino acids (AAs), mainly tyrosine (Tyr), tryptophan (Typ), histidine (His), cysteine (Cys), disulfide, and methionine (Met), are involved in the competing processes for radical formation: direct hydrogen atom abstraction versus electron and proton loss. It appears that the radical or radical cation generated during the redox process is capable of interacting with n-electrons of the backbone. Beneficial effects of cationic AAs impact the conduction process. A relationship apparently exists involving cell signaling, protein conduction, and radicals or electrons. In addition, the link between protein ET and reproductive toxicity is examined. A key element is the role of reactive oxygen species (ROS) generated by protein ET. There is extensive evidence for involvement of ROS in generation of birth defects. The radical species arise in protein mainly by ET transformations by enzymes, as illustrated in the case of alcoholism.
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Affiliation(s)
- Peter Kovacic
- Department of Chemistry, San Diego State University, San Diego, California 92065-1030, USA.
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28
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McCracken J, Vassiliev IR, Yang EC, Range K, Barry BA. ESEEM studies of peptide nitrogen hyperfine coupling in tyrosyl radicals and model peptides. J Phys Chem B 2007; 111:6586-92. [PMID: 17518496 PMCID: PMC2518650 DOI: 10.1021/jp071402x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosyl radicals are important in long-range electron transfer in several enzymes, but the protein environmental factors that control midpoint potential and electron transfer rate are not well understood. To develop a more detailed understanding of the effect of protein sequence, we have performed 14N and 15N electron spin echo envelope modulation (ESEEM) measurements on tyrosyl radical, generated either in polycrystalline tyrosinate or in its 15N-labeled isotopomer, by UV photolysis. 14N-ESEEM was also performed on tyrosyl radical generated in tyrosine-containing pentapeptide samples. Simulation of the 14N- and 15N-tyrosyl radical ESEEM measurements yielded no significant isotropic hyperfine splitting to the amine or amide nitrogen; the amplitude of the anisotropic, nitrogen hyperfine coupling (0.21 MHz) was consistent with a dipole-dipole distance of 3.0 A. Density functional theory was used to calculate the isotropic and anisotropic hyperfine couplings to the amino nitrogen in four different tyrosyl radical conformers. Comparison with the simulated data suggested that the lowest energy radical conformer, generated in tyrosine at pH 11, has a 76 degrees Calpha-Cbeta-C1'-C2' ring and a -73 degrees C-Calpha-Cbeta-C1' backbone dihedral angle. In addition, the magnitude, orientation, and asymmetry of the nuclear quadrupole coupling tensor were derived from analysis of the tyrosyl radical 14N-ESEEM. The simulations showed differences in the coupling and orientation of the nuclear quadrupole tensor, when the tyrosinate and pentapeptide samples were compared. These results suggest sequence- or conformation-induced changes in the ionic character of the NH bond in different tyrosine-containing peptides.
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Affiliation(s)
- John McCracken
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA.
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29
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Iwaki M, Puustinen A, Wikström M, Rich PR. Structural and Chemical Changes of the PMIntermediate ofParacoccus denitrificansCytochromecOxidase Revealed by IR Spectroscopy with Labeled Tyrosines and Histidine†. Biochemistry 2006; 45:10873-85. [PMID: 16953573 DOI: 10.1021/bi061114b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural and chemical changes in the P(M) intermediate of Paracoccus denitrificans cytochrome c oxidase have been investigated by attenuated total reflection-Fourier transform infrared spectroscopy. Prior studies of P(M) minus oxidized (O) IR difference spectra of unlabeled, universally (15)N-labeled and ring-d(4)-tyrosine-labeled proteins (Iwaki, M., Puustinen, A., Wikström, M., and Rich, P. R. (2004) Biochemistry 43, 14370-14378). provided a basis for band assignments to changes in metal centers and the covalently linked His-Tyr ligand of Cu(B) and highlighted a structural alteration of the protonated Glu278 in the P(M) intermediate. This work has been extended to equivalent measurements on enzymes with (13)C(9)(15)N-labeled and ring-(13)C(6)-labeled tyrosine and with (13)C(6)(15)N(3)-labeled histidine. Histidine labeling allows the assignment of troughs at 1104 and 973 cm(-1) in reduced minus O spectra to histidine changes, whereas tyrosine labeling moves otherwise obscured tyrosine bandshifts to 1454-1437 and 1287-1284 cm(-1). P(M) minus O spectra reveal bands at 1506, 1311, and 1094 cm(-1) in the oxidized state that are replaced by a band at 1519 cm(-1) in P(M). These bands shift with both tyrosine- and histidine-labeling, providing evidence for their assignment to the covalent His-Tyr and for its chemical change in P(M). Comparisons of isotope effects on the amide I regions in P(M) minus O spectra demonstrate that amide carbonyl bonds of tyrosine and histidine are major contributors. This suggests a structural alteration in P(M) that is centered on the His276-Pro277-Glu278-Val279-Tyr280 pentapeptide formed by the His-Tyr covalent linkage. This structural change is proposed to mediate the perturbation of the IR band of the protonated Glu278 headgroup.
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Affiliation(s)
- Masayo Iwaki
- Glynn Laboratory of Bioenergetics, Department of Biology, University College London, UK
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30
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Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
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31
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Si S, Bhattacharjee RR, Banerjee A, Mandal TK. A Mechanistic and Kinetic Study of the Formation of Metal Nanoparticles by Using Synthetic Tyrosine-Based Oligopeptides. Chemistry 2006; 12:1256-65. [PMID: 16278916 DOI: 10.1002/chem.200500834] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Synthetic oligopeptides containing redox-active tyrosine residues have been employed to prepare gold and silver nanoparticles. In this reduction process an electron from the tyrosinate ion of the peptide is transferred to the metal ion at basic pH through the formation of a tyrosyl radical, which is eventually converted to its dityrosine form during the reaction. This reaction mechanism was confirmed from UV-visible, fluorescence, and EPR spectroscopy and was found to be pH-dependent. Transmission electron microscopy measurement shows that the average size and the monodispersity of gold nanoparticles increase as the number of tyrosine residues in the peptide increases. The kinetic study, based on spectrophotometric measurements of the surface plasmon resonance optical property, shows that the rate of formation of gold nanoparticles was much faster at higher pH than at lower pH and was also dependent on the number of tyrosine residues present in the peptide. The dityrosine form of the peptide was found to retain reducing properties like those of tyrosine in basic medium.
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Affiliation(s)
- Satyabrata Si
- Polymer Science Unit, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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32
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Ayala I, Perry JJP, Szczepanski J, Tainer JA, Vala MT, Nick HS, Silverman DN. Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine. Biophys J 2005; 89:4171-9. [PMID: 16150974 PMCID: PMC1366982 DOI: 10.1529/biophysj.105.060616] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Accepted: 08/11/2005] [Indexed: 01/07/2023] Open
Abstract
Incorporation of 3-fluorotyrosine and site-specific mutagenesis has been utilized with Fourier transform infrared (FTIR) spectroscopy and x-ray crystallography to elucidate active-site structure and the role of an active-site residue Tyr34 in human manganese superoxide dismutase (MnSOD). Calculated harmonic frequencies at the B3LYP/6-31G** level of theory for L-tyrosine and its 3-fluorine substituted analog are compared to experimental frequencies for vibrational mode assignments. Each of the nine tyrosine residues in each of the four subunits of the homotetramer of human MnSOD was replaced with 3-fluorotyrosine. The crystal structures of the unfluorinated and fluorinated wild-type MnSOD are nearly superimposable with the root mean-square deviation for 198 alpha-carbon atoms at 0.3 A. The FTIR data show distinct vibrational modes arising from 3-fluorotyrosine in MnSOD. Comparison of spectra for wild-type and Y34F MnSOD showed that the phenolic hydroxyl of Tyr34 is hydrogen bonded, acting as a proton donor in the active site. Comparison with crystal structures demonstrates that the hydroxyl of Tyr34 is a hydrogen bond donor to an adjacent water molecule; this confirms the participation of Tyr34 in a network of residues and water molecules that extends from the active site to the adjacent subunit.
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Affiliation(s)
- Idelisa Ayala
- Department of Pharmacology, University of Florida, Gainesville, Florida 32610, USA
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33
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Abstract
Tyrosyl radicals are important in long-range electron transfer in several enzymes, but the protein environmental factors that control midpoint potential and electron-transfer rate are not well understood. To develop a more detailed understanding of the effect of protein sequence on their photophysical properties, we have studied the spectroscopic properties of tyrosyl radicals at 85 K. Tyrosyl radical was generated by UV-photolysis of pentapeptides in polycrystalline samples. The sequence of the pentapeptides was chosen to mimic peptide sequences found in redox-active tyrosine containing enzymes, ribonucleotide reductase and photosystem II. From EPR studies, we report that the EPR line shape of the tyrosyl radical depends on peptide sequence. We also present the first evidence for a component of the tyrosyl radical EPR signal, which decays on the seconds time scale at 85 K. We suggest that this transient results from a spontaneous, small conformational rearrangement in the radical. From FT-IR studies, we show that amide I vibrational bands (1680-1620 cm(-1)) and peptide bond skeletal vibrations (1230-1090 cm(-1)) are observed in the photolysis spectra of tyrosine-containing pentapeptides. From these data, we conclude that oxidation of the tyrosine aromatic ring perturbs the electronic structure of the peptide bond in tyrosine-containing oligopeptides. We also report sequence-dependent alterations in these bands. These results support the previous suggestion (J. Am. Chem. Soc. 2002, 124, 5496) that spin delocalization can occur from the tyrosine aromatic ring into the peptide bond. We hypothesize that these sequence-dependent effects are mediated either by electrostatics or by changes in conformer preference in the peptides. Our findings suggest that primary structure influences the functional properties of redox-active tyrosines in enzymes.
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Affiliation(s)
- Ilya R Vassiliev
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0363, USA
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34
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Sacksteder CA, Bender SL, Barry BA. Role for bound water and CH-pi aromatic interactions in photosynthetic electron transfer. J Am Chem Soc 2005; 127:7879-90. [PMID: 15913378 DOI: 10.1021/ja050659a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosystem I (PSI) is one of two photosynthetic reaction centers present in plants, algae, and cyanobacteria and catalyzes the reduction of ferredoxin and the oxidation of cytochrome c or plastocyanin. The PSI primary chlorophyll donor, which is oxidized in the primary electron-transfer events, is a heterodimer of chl a and a' called P700. It has been suggested that protein relaxation accompanies light-induced electron transfer in this reaction center (Dashdorj, N.; Xu, W.; Martinsson, P.; Chitnis, P. R.; Savikhin, S. Biophys. J. 2004, 86, 3121. Kim, S.; Sacksteder, C. A.; Bixby, K. A.; Barry, B. A. Biochemistry 2001, 40, 15384). To investigate the details of electron transfer and relaxation events in PSI, we have employed several experimental approaches. First, we report a pH-dependent viscosity effect on P700+ reduction; this result suggests a role for proton transfer in the PSI electron-transfer reactions. Second, we find that changes in hydration alter the rate of P700+ reduction and the interactions of P700 with the protein environment. This result suggests a role for bound water in electron transfer to P700+. Third, we present evidence that deuteration of the tyrosine aromatic side chain perturbs the vibrational spectrum, associated with P700+ reduction. We attribute this result to a linkage between CH-pi interactions and electron transfer to P700+.
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Affiliation(s)
- Colette A Sacksteder
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, USA
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35
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Barry BA, Einarsdóttir O. Insights into the Structure and Function of Redox-Active Tyrosines from Model Compounds. J Phys Chem B 2005; 109:6972-81. [PMID: 16851792 DOI: 10.1021/jp044749y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Redox-active tyrosine residues play important roles in long distance electron-transfer reactions in enzymes, including prostaglandin H synthase, ribonucleotide reductase, and photosystem II. In cytochrome c oxidase, a cross-linked tyrosine-histidine cofactor has been proposed to play a role in proton and electron transfer reactions. Studies of tyrosyl radicals in model compounds, generated by UV photolysis, have recently provided new information about the structure and function of these redox-active species. The results of these studies, which combine magnetic resonance and optical spectroscopies, are described in this review.
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Affiliation(s)
- Bridgette A Barry
- School of Chemistry and Biochemistry, and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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36
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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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Iwaki M, Puustinen A, Wikström M, Rich PR. ATR-FTIR Spectroscopy and Isotope Labeling of the PM Intermediate of Paracoccus denitrificans Cytochrome c Oxidase. Biochemistry 2004; 43:14370-8. [PMID: 15533041 DOI: 10.1021/bi048545j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of the P(M) intermediate of Paracoccus denitrificans cytochrome c oxidase was investigated by perfusion-induced attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy. Transitions from the oxidized to P(M) state were initiated by perfusion with CO/oxygen buffer, and the extent of conversion was quantitated by simultaneously monitoring visible absorption changes. In prior work, tentative assignments of bands were proposed for heme a(3), a change in the environment of the protonated state of a carboxylic acid, and a covalently linked histidine-tyrosine ligand to Cu(B) that has been found in the catalytic site. In this work, reduced minus oxidized difference spectra at pH 6.5 and 9.0 and P(M) minus oxidized difference spectra at pH 9.0 were compared in unlabeled, universally (15)N-labeled, and tyrosine-ring-d(4)-labeled proteins to improve these assignments. In the reduced minus oxidized difference spectrum, (15)N labeling resulted in large changes in the amide II region and a 9 cm(-1) downshift in a 1105 cm(-1) trough that is attributed to histidine. In contrast, changes induced by tyrosine-ring-d(4) labeling were barely detectable where the isotope-sensitive bands are expected. Both isotope substitutions had large effects on P(M) minus oxidized difference spectra. A prominent trough at 1542 cm(-1) was shifted to 1527 cm(-1) with (15)N labeling, and its magnitude was diminished with the appearance of a 1438 cm(-1) trough with tyrosine-ring-d(4) labeling. Both isotope substitutions also had large effects on a 1314 cm(-1) trough in the same spectra. These shifts indicate that the bands are linked to both a nitrogenous compound and a tyrosine, the most obvious candidate being the covalent histidine-tyrosine ligand of Cu(B). Comparison with model material data suggests that the tyrosine hydroxyl group is protonated when the binuclear center is oxidized but deprotonated in the P(M) intermediate. Positive bands at 1519 and 1570 cm(-1) were replaced with bands at 1504 and 1556 cm(-1), respectively, with tyrosine-ring-d(4) labeling, are characteristic of upsilon(7a)(C-O) and upsilon(C-C) bands of neutral phenolic radicals, and most likely reflect the formation of the neutral radical state of the histidine-tyrosine ligand in P(M).
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Affiliation(s)
- Masayo Iwaki
- Glynn Laboratory of Bioenergetics, Department of Biology, University College London, UK
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Affiliation(s)
- Eunsuk Kim
- Department of Chemistry, Johns Hopkins University, Charles and 34th Streets, Baltimore, Maryland 21218, USA
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Karunakaran C, Zhang H, Crow JP, Antholine WE, Kalyanaraman B. Direct Probing of Copper Active Site and Free Radical Formed during Bicarbonate-dependent Peroxidase Activity of Bovine and Human Copper,Zinc-superoxide Dismutases. J Biol Chem 2004; 279:32534-40. [PMID: 15123612 DOI: 10.1074/jbc.m314272200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using X-band electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopy at liquid helium temperatures, the Cu(II) coordination geometry at the active site of bovine and human copper,zinc-superoxide dismutases (bSOD1 and hSOD1) treated with H(2)O(2) and bicarbonate (HCO(3)(-)) was examined. The time course EPR of wild type human SOD1 (WT hSOD1), W32F hSOD1 mutant (tryptophan 32 substituted with phenylalanine), and bSOD1 treated with H(2)O(2) and HCO(3)(-) shows an initial reduction of active site Cu(II) to Cu(I) followed by its oxidation back to Cu(II) in the presence of H(2)O(2). However, HCO(3)(-) induced a Trp-32-derived radical from WT hSOD1 but not from bSOD1. The mutation of Trp-32 by phenylalanine totally eliminated the Trp-32 radical signal generated from W32F hSOD1 treated with HCO(3)(-) and H(2)O(2). Further characterization of the free radical was performed by UV irradiation of WT hSOD1 and bSOD1 that generated tryptophanyl and tyrosyl radicals. Both proton ((1)H) and nitrogen ((14)N) ENDOR studies of bSOD1 and hSOD1 in the presence of H(2)O(2) revealed a change in the geometry of His-46 (or His-44) and His-48 (or His-46) coordinated to Cu(II) at the active site of WT hSOD1 and bSOD1, respectively. However, in the presence of HCO(3)(-) and H(2)O(2), both (1)H and (14)N ENDOR spectra were almost identical to those derived from native bSOD1. We conclude that HCO(3)(-)-derived oxidant does not alter significantly the Cu(II) active site geometry and histidine coordination to Cu(II) in SOD1 as does H(2)O(2) alone; however, the oxidant derived from HCO(3)(-) (i.e. carbonate anion radical) reacts with surface-associated Trp-32 in hSOD1 to form the corresponding radical.
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Affiliation(s)
- Chandran Karunakaran
- Department of Biophysics and Free Radical Research Center, Medical College of Wisconsin, Milwaukee, 53226, 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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Iwaki M, Puustinen A, Wikström M, Rich PR. ATR-FTIR spectroscopy of the P(M) and F intermediates of bovine and Paracoccus denitrificans cytochrome c oxidase. Biochemistry 2003; 42:8809-17. [PMID: 12873142 DOI: 10.1021/bi034522d] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structures of P(M) and F intermediates of bovine and Paracoccus denitrificans cytochrome c oxidase were investigated by perfusion-induced attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy. Transitions from the "fast" oxidized state to the P(M) or F states were initiated by perfusion with buffer containing either CO/oxygen or H(2)O(2). Intermediates were quantitated by simultaneous monitoring of visible absorption changes in the protein film. For both bovine and P. denitrificans oxidase, the major features of the IR difference spectrum of P(M) were similar when produced by CO/oxygen or by H(2)O(2) treatments. These IR difference spectra were distinctly different from the IR difference spectrum of F that formed with extended treatment with H(2)O(2). Some IR bands could be assigned tentatively to perturbations of heme a(3) ring modes and substituents, and these perturbations were greater in P(M) than in F. Other bands could be assigned to surrounding protein changes. Strong perturbation of the environment of a carboxylic acid, most likely E-242 (bovine numbering), occurred in P(M) and relaxed back in F. A second redox-sensitive carboxylic acid was also perturbed in the bovine P(M) intermediate. Further consistent signatures of P(M) in both oxidases that were absent in F were strong negative bands at 1547 and 1313 cm(-1) in bovine oxidase (1542 and 1314 cm(-1) in P. denitrificans) and a positive band at approximately 1519 cm(-1). From comparison with available IR data on model compounds, it is suggested that these reflect changes in the covalent tyrosine-histidine ligand to Cu(B). These findings are discussed in relation to the oxidase catalytic cycle.
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Affiliation(s)
- Masayo Iwaki
- Glynn Laboratory of Bioenergetics, Department of Biology, University College London, Gower Street, UK
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Pujols-Ayala I, Sacksteder CA, Barry BA. Redox-active tyrosine residues: role for the peptide bond in electron transfer. J Am Chem Soc 2003; 125:7536-8. [PMID: 12812492 DOI: 10.1021/ja035005l] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photosystem II (PSII) catalyzes the light-driven oxidation of water and reduction of plastoquinone. In PSII, redox-active tyrosine Z conducts electrons between the primary chlorophyll donor and the manganese cluster, which is the catalytic site. In this report, difference FT-IR spectroscopy is used to show that oxidation of redox-active tyrosine Z causes perturbations of the peptide bond. PSII data were acquired on control samples, as well as samples in which tyrosine was 2H4 (ring)-labeled. Comparison to model compound data, acquired both from tyrosinate and its 2H4 isotopomer, was performed. The PSII FT-IR spectrum exhibited vibrational bands that are assignable to imide and amide vibrational modes. In previous work, we have shown that oxidation of tyrosinate perturbs the terminal amino group of tyrosinate (Ayala, I.; Range, K.; York, D.; Barry, B. A. J. Am. Chem. Soc. 2002, 124, 5496-5505). Density functional calculations on tyrosinate supported the interpretation that the perturbation is due to spin delocalization onto the amino group. In tyrosine-containing dipeptides, perturbations of the peptide bond were observed. Therefore, the imide and amide perturbations observed here are attributed to spin delocalization into the peptide bond in PSII. Migration of the electron hole in PSII may be consistent with peptide bond involvement in tyrosyl radical-based electron-transfer reactions.
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Affiliation(s)
- Idelisa Pujols-Ayala
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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Narváez AJ, Kálmán L, LoBrutto R, Allen JP, Williams JC. Influence of the protein environment on the properties of a tyrosyl radical in reaction centers from Rhodobacter sphaeroides. Biochemistry 2002; 41:15253-8. [PMID: 12484763 DOI: 10.1021/bi0264566] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of the local environment on the formation of a tyrosyl radical was investigated in modified photosynthetic reaction centers from Rhodobacter sphaeroides. The reaction centers contain a tyrosine residue placed approximately 10 A from a highly oxidizing bacteriochlorophyll dimer. Measurements by both optical and electron paramagnetic resonance spectroscopy revealed spectral features that are assigned as arising primarily from an oxidized bacteriochlorophyll dimer at low pH values and from a tyrosyl radical at high pH values, with a well-defined transition that occurred with a pK(a) of 6.9. A model based on the wild-type structure indicated that the Tyr at M164 is likely to form a hydrogen bond with His M193 and to interact weakly with Glu M173. Substitution of Tyr or Glu for His at M193 increased the pK(a) for the transition from 6.9 to 8.9, while substitution of Gln for His M193 resulted in a higher pK(a) value. Substitution of Glu M173 with Gln resulted in loss of the partial formation of the tyrosyl that occurs in the other mutants at low pH values. The results are interpreted in terms of the ability of the residues to act as proton acceptors for the oxidized tyrosine, with the pK(a) values reflecting those of either the putative proton acceptor or the tyrosine, in accord with general models of amino acid radicals.
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Affiliation(s)
- A J Narváez
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
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Pujols-Ayala I, Barry BA. Histidine 190-D1 and glutamate 189-D1 provide structural stabilization in photosystem II. Biochemistry 2002; 41:11456-65. [PMID: 12234188 DOI: 10.1021/bi026172l] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In photosynthesis, photosystem II (PSII) conducts the light-driven oxidation of water to oxygen. Tyrosine Z is Tyr 161 of the D1 polypeptide; Z acts as an intermediary electron carrier in water oxidation. In this report, EPR spectroscopy was used to study the effect of His 190 and Glu 189 on Z* yield and reduction kinetics. Neither mutation has a significant impact on the EPR line shape of Z*. At room temperature and pH 7.5, the E189Q-D1 mutation has a single turnover Z* yield that is 84% compared to wild-type. The H190Q-D1 mutation decreases the Z* yield at room temperature by a factor of 2.6 but has a more modest effect (factor of 1.6) at -10 degrees C. The temperature dependence is shown to be primarily reversible. Neither mutation has a dramatic effect on Z* decay kinetics. The Z* minus Z FT-IR spectrum, recorded at pH 7.5 on H190Q, reveals perturbations, including an increased spectral contribution from a PSII chlorophyll. The Z* minus Z FT-IR spectrum, recorded at pH 7.5 on E189Q, shows perturbations, including a decreased contribution from the carboxylate side chain of a glutamate or aspartate. Temperature-dependent changes in H190Q-D1 and E189Q-D1 Z. yield are attributed to a reversible conformational change, which alters the electron-transfer rate from Z to P(680)(+). On the basis of these results, we conclude that H190 and E189 play a role in the structural stabilization of PSII. We postulate that some or all of the phenotypic changes observed in H190Q and E189Q mutants may be caused by structural alterations in PSII.
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Affiliation(s)
- Idelisa Pujols-Ayala
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108-1022, USA
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Iwaki M, Breton J, Rich PR. ATR-FTIR difference spectroscopy of the P(M) intermediate of bovine cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1555:116-21. [PMID: 12206902 DOI: 10.1016/s0005-2728(02)00265-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Perfusion-induced attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was used to investigate changes induced in protein and cofactors of bovine cytochrome c oxidase when it was converted from the oxidised state to the catalytic P(M) intermediate. The transition was induced in a film of detergent-depleted 'fast' oxidase with a buffer containing CO and O(2). The extent of formation of the P(M) state was quantitated simultaneously by monitoring formation of its characteristic 607-nm band with a scanned visible beam reflected off the top surface of the prism. The P(M) minus O FTIR difference spectrum is distinctly different from the redox spectra reported to date and includes features that can be assigned to changes of haem a(3) and surrounding protein. Tentative assignments are made based on vibrational data of related proteins and model compounds.
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Affiliation(s)
- Masayo Iwaki
- The Glynn Laboratory of Bioenergetics, Department of Biology, University College London, UK
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