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Martin R, Lacombat F, Espagne A, Dozova N, Plaza P, Yamamoto J, Müller P, Brettel K, de la Lande A. Ultrafast flavin photoreduction in an oxidized animal (6-4) photolyase through an unconventional tryptophan tetrad. Phys Chem Chem Phys 2017; 19:24493-24504. [DOI: 10.1039/c7cp04555g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast photoreduction of animal (6-4) photolyase: delocalized oxidation hole reaches fourth tryptophan in less than 40 ps.
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Affiliation(s)
- Ryan Martin
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Fabien Lacombat
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Agathe Espagne
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Nadia Dozova
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Pascal Plaza
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Junpei Yamamoto
- Division of Chemistry
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC)
- Joliot
- CEA
- CNRS
- Univ. Paris-Sud
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC)
- Joliot
- CEA
- CNRS
- Univ. Paris-Sud
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
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2
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Morozova OB, Yurkovskaya AV, Kiryutin AS, Yarinich LA, Silnikov VN, Sagdeev RZ. Influence of the charge of amino group on rate and direction of intramolecular electron transfer reaction in shortlived oxidized peptides containing tryptophan and tyrosine. DOKLADY PHYSICAL CHEMISTRY 2013. [DOI: 10.1134/s0012501613100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Morozova OB, Kaptein R, Yurkovskaya AV. Changing the Direction of Intramolecular Electron Transfer in Oxidized Dipeptides Containing Tryptophan and Tyrosine. J Phys Chem B 2012; 116:12221-6. [DOI: 10.1021/jp307956q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Olga B. Morozova
- International Tomography Center, Institutskaya 3a, 630090 Novosibirsk, Russia
- Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia
| | - Robert Kaptein
- Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia
- Bijvoet Center for Biomolecular
Research, Utrecht University, Padualaan
8, NL-3584, The Netherlands
| | - Alexandra V. Yurkovskaya
- International Tomography Center, Institutskaya 3a, 630090 Novosibirsk, Russia
- Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia
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4
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Thorne RE, Chinnapen DJF, Sekhon GS, Sen D. A deoxyribozyme, Sero1C, uses light and serotonin to repair diverse pyrimidine dimers in DNA. J Mol Biol 2009; 388:21-9. [PMID: 19281822 DOI: 10.1016/j.jmb.2009.02.064] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Revised: 02/10/2009] [Accepted: 02/28/2009] [Indexed: 11/19/2022]
Abstract
An in vitro selection search for DNAs capable of catalyzing photochemistry yielded two distinctive deoxyribozymes (DNAzymes) with photolyase activity: UV1C, which repaired thymine dimers within DNA using a UV light of >300 nm wavelength and no extraneous cofactor, and Sero1C, which required the tryptophan metabolite serotonin as cofactor in addition to the UV light. Catalysis by Sero1C conformed to Michaelis-Menten kinetics, and analysis of the action spectrum of Sero1C confirmed that serotonin did indeed serve as a catalytic cofactor rather than as a structural cofactor. Sero1C and UV1C showed strikingly distinct wavelength optima for their respective photoreactivation catalyses. Although the rate enhancements characteristic of the two DNAzymes were similar, the cofactor-requiring Sero1C repaired a substantially broader range of substrates compared to UV1C, including thymine, uracil, and a range of chimeric deoxypyrimidine and ribopyrimidine dimers. Similarities and differences in the properties of these two photolyase DNAzymes suggest, first, that the harnessing of less damaging UV light for the repair of photolesions may have been a primordial catalytic activity of nucleic acids, and, second, the broader substrate range of Sero1C may highlight an evolutionary advantage to coopting amino-acid-like cofactors by functionality-poor nucleic acid enzymes.
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Affiliation(s)
- Rebecca E Thorne
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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5
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Bender SL, Keough JM, Boesch SE, Wheeler RA, Barry BA. The Vibrational Spectrum of the Secondary Electron Acceptor, A1, in Photosystem I. J Phys Chem B 2008; 112:3844-52. [DOI: 10.1021/jp0775146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shana L. Bender
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - James M. Keough
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Scott E. Boesch
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ralph A. Wheeler
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Bridgette A. Barry
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
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6
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Jenson DL, Evans A, Barry BA. Proton-Coupled Electron Transfer and Tyrosine D of Photosystem II. J Phys Chem B 2007; 111:12599-604. [DOI: 10.1021/jp075726x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David L. Jenson
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Amaris Evans
- 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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7
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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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8
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Yamada Y, Aoki S. Efficient cycloreversion of cis,syn-thymine photodimer by a Zn2+–1,4,7,10-tetraazacyclododecane complex bearing a lumiflavin and tryptophan by chemical reduction and photoreduction of a lumiflavin unit. J Biol Inorg Chem 2006; 11:1007-23. [PMID: 16944231 DOI: 10.1007/s00775-006-0152-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Accepted: 07/21/2006] [Indexed: 11/29/2022]
Abstract
DNA photolyases (EC 4.1.99.3) are enzymes that catalyze photoreversion of cis,syn-thymine photodimer (T[c,s]T), which is one of major photolesion products in DNA, by utilizing UV light. In this work, we have designed and synthesized Zn2+ -1,4,7,10-tetraazacyclododecane complexes bearing a lumiflavin and L: -tryptophan (ZnL3) or L: -phenylalanine (ZnL4) as artificial DNA photolyases. We have found that (ZnL3)red, whose flavin unit was reduced in situ by Na2S2O4, accelerates the photoreversion of T[c,s]T utilizing near-UV light in aqueous solution at pH 7.6 and 11. Interestingly, more efficient photoreversion of T[c,s]T was achieved by UV irradiation of an oxidized form of ZnL3 [(ZnL3)ox] in the presence of an excess amount of Et3N at pH 11. UV-vis and fluorescence measurements and action spectra showed that an oxidized form of flavin of (ZnL3)ox was photoreduced by Et3N into its reduced form (ZnL3)red, which promoted the photoreduction of T[c,s]T. Comparison of the photochemical properties of ZnL3 with those of ZnL4 suggested that a tryptophan unit in ZnL3 contributed to the stabilities of the flavin through intramolecular photoinduced electron transfer.
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Affiliation(s)
- Yasuyuki Yamada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
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9
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Weber S. Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1707:1-23. [PMID: 15721603 DOI: 10.1016/j.bbabio.2004.02.010] [Citation(s) in RCA: 254] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2003] [Accepted: 02/02/2004] [Indexed: 11/19/2022]
Abstract
More than 50 years ago, initial experiments on enzymatic photorepair of ultraviolet (UV)-damaged DNA were reported [Proc. Natl. Acad. Sci. U. S. A. 35 (1949) 73]. Soon after this discovery, it was recognized that one enzyme, photolyase, is able to repair UV-induced DNA lesions by effectively reversing their formation using blue light. The enzymatic process named DNA photoreactivation depends on a non-covalently bound cofactor, flavin adenine dinucleotide (FAD). Flavins are ubiquitous redox-active catalysts in one- and two-electron transfer reactions of numerous biological processes. However, in the case of photolyase, not only the ground-state redox properties of the FAD cofactor are exploited but also, and perhaps more importantly, its excited-state properties. In the catalytically active, fully reduced redox form, the FAD absorbs in the blue and near-UV ranges of visible light. Although there is no direct experimental evidence, it appears generally accepted that starting from the excited singlet state, the chromophore initiates a reductive cleavage of the two major DNA photodamages, cyclobutane pyrimidine dimers and (6-4) photoproducts, by short-distance electron transfer to the DNA lesion. Back electron transfer from the repaired DNA segment is believed to eventually restore the initial redox states of the cofactor and the DNA nucleobases, resulting in an overall reaction with net-zero exchanged electrons. Thus, the entire process represents a true catalytic cycle. Many biochemical and biophysical studies have been carried out to unravel the fundamentals of this unique mode of action. The work has culminated in the elucidation of the three-dimensional structure of the enzyme in 1995 that revealed remarkable details, such as the FAD-cofactor arrangement in an unusual U-shaped configuration. With the crystal structure of the enzyme at hand, research on photolyases did not come to an end but, for good reason, intensified: the geometrical structure of the enzyme alone is not sufficient to fully understand the enzyme's action on UV-damaged DNA. Much effort has therefore been invested to learn more about, for example, the geometry of the enzyme-substrate complex, and the mechanism and pathways of intra-enzyme and enzyme <-->DNA electron transfer. Many of the key results from biochemical and molecular biology characterizations of the enzyme or the enzyme-substrate complex have been summarized in a number of reviews. Complementary to these articles, this review focuses on recent biophysical studies of photoreactivation comprising work performed from the early 1990s until the present.
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Affiliation(s)
- Stefan Weber
- Institute of Experimental Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany.
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10
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Anderson LB, Ouellette AJA, Eaton-Rye J, Maderia M, MacCoss MJ, Yates JR, Barry BA. Evidence for a Post-Translational Modification, Aspartyl Aldehyde, in a Photosynthetic Membrane Protein. J Am Chem Soc 2004; 126:8399-405. [PMID: 15237995 DOI: 10.1021/ja0478781] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In oxygenic photosynthesis, photosystem II (PSII) carries out the oxidation of water and reduction of plastoquinone. Three PSII subunits contain reactive groups that covalently bind amines and phenylhydrazine. It has been proposed that these reactive groups are carbonyl-containing, co- or post-translationally modified amino acids. To identify modified amino acid residues in one of the PSII subunits (CP47), tandem mass spectrometry was performed. Modified residues were affinity-tagged with either biotin-LC-hydrazide or biocytin hydrazide, which are known to label carbonyl groups. The affinity-tagged subunit was isolated by denaturing gel electrophoresis, and tryptic peptides were then subjected to affinity purification and tandem mass spectrometry. This procedure identified a hydrazide-labeled peptide, which has the sequence XKEGR. This result is supported by quantitative results acquired from peptide mapping and methylamine labeling. The gene sequence and these tandem data predict that the first amino acid, X, which is labeled with the hydrazide reagent, is a modified form of aspartic acid. On the basis of these data, we propose that D348 of the CP47 subunit is post- or co-translationally modified to give a novel amino acid side chain, aspartyl aldehyde.
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Affiliation(s)
- Lorraine B Anderson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, USA
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11
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Sancar A. Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem Rev 2003; 103:2203-37. [PMID: 12797829 DOI: 10.1021/cr0204348] [Citation(s) in RCA: 931] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics, Mary Ellen Jones Building, CB 7260, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA.
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12
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Ayala I, Range K, York D, Barry BA. Spectroscopic properties of tyrosyl radicals in dipeptides. J Am Chem Soc 2002; 124:5496-505. [PMID: 11996592 DOI: 10.1021/ja0164327] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [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, including prostaglandin H synthase, galactose oxidase, ribonucleotide reductase, and photosystem II. Magnetic resonance and vibrational spectroscopy provide methods with which to study the structures of redox-active amino acids in proteins. In this report, ultraviolet photolysis was used to generate tyrosyl radicals from polycrystalline tyrosinate or dipeptides, and the structure of the radical was investigated with EPR and reaction-induced FT-IR spectroscopy at 77 K. Photolysis at 77 K is expected to generate a neutral tyrosyl radical through oxidation of the aromatic ring. EPR and FT-IR results obtained from (13)C-labeled tyrosine were consistent with that expectation. Surprisingly, labeling of the tyrosyl amino group with (15)N also resulted in isotope-shifted bands in the photolysis spectrum. The force constant of a NH deformation mode increased when the tyrosyl radical was generated. These data suggest an interaction between the pi system of the tyrosyl radical and the amino group. In spectra acquired from the dipeptides, evidence for a sequence-dependent interaction between the tyrosyl radical and the amide bond of the dipeptide was also obtained. We postulate that perturbation of the amino or the amide/imide groups may occur through a spin polarization mechanism, which is indirectly detected as a change in NH force constant. This conclusion is supported by density functional calculations, which suggest a conformationally sensitive delocalization of spin density onto the amino and carboxylate groups of the tyrosyl radical. These experiments provide a step toward a detailed spectral interpretation for protein-based tyrosyl radicals.
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Affiliation(s)
- Idelisa Ayala
- Department of Biochemistry, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108-1022, USA
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13
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Kim S, Barry BA. Reaction-Induced FT-IR Spectroscopic Studies of Biological Energy Conversion in Oxygenic Photosynthesis and Transport§. J Phys Chem B 2001. [DOI: 10.1021/jp0042516] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Ikeda H, Yoshida K, Ozeki M, Saito I. Synthesis and characterization of flavin-tethered peptide nucleic acid. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)00228-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Kim S, Patzlaff JS, Krick T, Ayala I, Sachs RK, Barry BA. Isotope-Based Discrimination between the Infrared Modes of Plastosemiquinone Anion Radicals and Neutral Tyrosyl Radicals in Photosystem II‡,§. J Phys Chem B 2000. [DOI: 10.1021/jp000410+] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Stemp ED, Barton JK. The flash-quench technique in protein-DNA electron transfer: reduction of the guanine radical by ferrocytochrome c. Inorg Chem 2000; 39:3868-74. [PMID: 11196782 DOI: 10.1021/ic0000698] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electron transfer from a protein to oxidatively damaged DNA, specifically from ferrocytochrome c to the guanine radical, was examined using the flash-quench technique. Ru(phen)2dppz2+ (dppz = dipyridophenazine) was employed as the photosensitive intercalator, and ferricytochrome c (Fe3+ cyt c), as the oxidative quencher. Using transient absorption and time-resolved luminescence spectroscopies, we examined the electron-transfer reactions following photoexcitation of the ruthenium complex in the presence of poly(dA-dT) or poly(dG-dC). The luminescence-quenching titrations of excited Ru(phen)2dppz2+ by Fe3+ cyt c are nearly identical for the two DNA polymers. However, the spectral characteristics of the long-lived transient produced by the quenching depend strongly upon the DNA. For poly(dA-dT), the transient has a spectrum consistent with formation of a [Ru(phen)2dppz3+, Fe2+ cyt c] intermediate, indicating that the system regenerates itself via electron transfer from the protein to the Ru(III) metallointercalator for this polymer. For poly(dG-dC), however, the transient has the characteristics expected for an intermediate of Fe2+ cyt c and the neutral guanine radical. The characteristics of the transient formed with the GC polymer are consistent with rapid oxidation of guanine by the Ru(III) complex, followed by slow electron transfer from Fe2+ cyt c to the guanine radical. These experiments show that electron holes on DNA can be repaired by protein and demonstrate how the flash-quench technique can be used generally in studying electron transfer from proteins to guanine radicals in duplex DNA.
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Affiliation(s)
- E D Stemp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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17
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Lee E, Medvedev ES, Stuchebrukhov AA. Calculation of Quantum Parameters for Nonadiabatic Redox Reactions. Application to Photoreduction of Flavin in DNA Photolyase. J Phys Chem B 2000. [DOI: 10.1021/jp000167e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- EunJoo Lee
- Department of Chemistry, University of California, Davis, California 95616, and Institute of Chemical Physics Problems, Russian Academy of Sciences, 142432 Chernogolovka, Moscow, Russia
| | - Emile S. Medvedev
- Department of Chemistry, University of California, Davis, California 95616, and Institute of Chemical Physics Problems, Russian Academy of Sciences, 142432 Chernogolovka, Moscow, Russia
| | - Alexei A. Stuchebrukhov
- Department of Chemistry, University of California, Davis, California 95616, and Institute of Chemical Physics Problems, Russian Academy of Sciences, 142432 Chernogolovka, Moscow, Russia
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18
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Aubert C, Vos MH, Mathis P, Eker AP, Brettel K. Intraprotein radical transfer during photoactivation of DNA photolyase. Nature 2000; 405:586-90. [PMID: 10850720 DOI: 10.1038/35014644] [Citation(s) in RCA: 324] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Amino-acid radicals play key roles in many enzymatic reactions. Catalysis often involves transfer of a radical character within the protein, as in class I ribonucleotide reductase where radical transfer occurs over 35 A, from a tyrosyl radical to a cysteine. It is currently debated whether this kind of long-range transfer occurs by electron transfer, followed by proton release to create a neutral radical, or by H-atom transfer, that is, simultaneous transfer of electrons and protons. The latter mechanism avoids the energetic cost of charge formation in the low dielectric protein, but it is less robust to structural changes than is electron transfer. Available experimental data do not clearly discriminate between these proposals. We have studied the mechanism of photoactivation (light-induced reduction of the flavin adenine dinucleotide cofactor) of Escherichia coli DNA photolyase using time-resolved absorption spectroscopy. Here we show that the excited flavin adenine dinucleotide radical abstracts an electron from a nearby tryptophan in 30 ps. After subsequent electron transfer along a chain of three tryptophans, the most remote tryptophan (as a cation radical) releases a proton to the solvent in about 300 ns, showing that electron transfer occurs before proton dissociation. A similar process may take place in photolyase-like blue-light receptors.
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Affiliation(s)
- C Aubert
- Section de Bioénergétique (CNRS URA 2096), CEA Saclay, Gif-sur-Yvette, France
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19
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Razeghifard MR, Kim S, Patzlaff JS, Hutchison RS, Krick T, Ayala I, Steenhuis JJ, Boesch SE, Wheeler RA, Barry BA. In Vivo, in Vitro, and Calculated Vibrational Spectra of Plastoquinone and the Plastosemiquinone Anion Radical. J Phys Chem B 1999. [DOI: 10.1021/jp991942x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Reza Razeghifard
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Sunyoung Kim
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Jason S. Patzlaff
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ronald S. Hutchison
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Thomas Krick
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Idelisa Ayala
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Jacqueline J. Steenhuis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Scott E. Boesch
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ralph A. Wheeler
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Bridgette A. Barry
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
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20
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Aubert C, Mathis P, Eker AP, Brettel K. Intraprotein electron transfer between tyrosine and tryptophan in DNA photolyase from Anacystis nidulans. Proc Natl Acad Sci U S A 1999; 96:5423-7. [PMID: 10318899 PMCID: PMC21875 DOI: 10.1073/pnas.96.10.5423] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light-induced electron transfer reactions leading to the fully reduced, catalytically competent state of the flavin adenine dinucleotide (FAD) cofactor have been studied by flash absorption spectroscopy in DNA photolyase from Anacystis nidulans. The protein, overproduced in Escherichia coli, was devoid of the antenna cofactor, and the FAD chromophore was present in the semireduced form, FADH., which is inactive for DNA repair. We show that after selective excitation of FADH. by a 7-ns laser flash, fully reduced FAD (FADH-) is formed in less than 500 ns by electron abstraction from a tryptophan residue. Subsequently, a tyrosine residue is oxidized by the tryptophanyl radical with t(1)/(2) = 50 microseconds. The amino acid radicals were identified by their characteristic absorption spectra, with maxima at 520 nm for Trp. and 410 nm for TyrO. The newly discovered electron transfer between tyrosine and tryptophan occurred for approximately 40% of the tryptophanyl radicals, whereas 60% decayed by charge recombination with FADH- (t(1)/(2) = 1 ms). The tyrosyl radical can also recombine with FADH- but at a much slower rate (t(1)/(2) = 76 ms) than Trp. In the presence of an external electron donor, however, TyrO. is rereduced efficiently in a bimolecular reaction that leaves FAD in the fully reduced state FADH-. These results show that electron transfer from tyrosine to Trp. is an essential step in the process leading to the active form of photolyase. They provide direct evidence that electron transfer between tyrosine and tryptophan occurs in a native biological reaction.
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Affiliation(s)
- C Aubert
- Section de Bioénergétique, Commissariat à l'Energie Atomique Saclay (Centre National de la Recherche Scientifique, Unité de Recherche Associée 2096) 91191 Gif-sur-Yvette Cedex, France
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Hahn J, Michel-Beyerle ME, Rösch N. Binding of Pyrimidine Model Dimers to the Photolyase Enzyme: A Molecular Dynamics Study. J Phys Chem B 1999. [DOI: 10.1021/jp984197h] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jutta Hahn
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, D-85747 Garching, Germany
| | | | - Notker Rösch
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, D-85747 Garching, Germany
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