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Ambroz HB, Przybytniak GK. Epr Studies on Radiation-Damaged Dna –the Contribution of Martyn Symons. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967403103165440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This review presents a summary of Professor Martyn Symons’ role in radiation studies on the key biopolymer DNA, a contribution that cannot be overestimated. Some of his achievements are revealed, along with his influence on other research performed all over the world, illustrated by our own work on the effects of transition metal ions (iron and copper) and of thiols on radiation-induced damage to DNA.
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Affiliation(s)
- Hanna B. Ambroz
- Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warszawa, Poland
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Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF. RNA protects a nucleoprotein complex against radiation damage. Acta Crystallogr D Struct Biol 2016; 72:648-57. [PMID: 27139628 PMCID: PMC4854314 DOI: 10.1107/s2059798316003351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/26/2016] [Indexed: 11/10/2022] Open
Abstract
Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.
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Affiliation(s)
- Charles S. Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - John E. McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry I Street, Portsmouth PO1 2DY, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5DD, England
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Markus Gerstel
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Mikhail B. Shevtsov
- Laboratory of Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
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Liu CC, Gebicki JM. Intracellular GSH and ascorbate inhibit radical-induced protein chain peroxidation in HL-60 cells. Free Radic Biol Med 2012; 52:420-6. [PMID: 22080646 DOI: 10.1016/j.freeradbiomed.2011.10.450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Revised: 10/16/2011] [Accepted: 10/19/2011] [Indexed: 10/16/2022]
Abstract
The results of this study suggest that the well-documented loss of GSH and ascorbate in organisms under oxidative stress may be mainly due to their reactions with protein radicals and/or peroxides. Protein hydroperoxides were generated in HL-60 cells exposed to radiation-generated hydroxyl radicals. We found for the first time evidence of chain peroxidation of the proteins in cells, with each hydroxyl radical leading to the formation of about 10 hydroperoxides. Protein peroxidation showed a lag, probably due to the endogenous antioxidant enzymes, with simultaneous loss of the intracellular GSH. Enhancement of the GSH levels by N-acetylcysteine decreased the formation of hydroperoxides, while treatment with l-buthionine sulfoximine had the opposite effect. The effect of variation of GSH levels on the formation of the peroxidized proteins is explained primarily by reduction of the protein hydroperoxides by GSH. Loading of the cells with ascorbate resulted in reduction of the amounts of protein hydroperoxides generated by the radiation, which was proportional to the intracellular ascorbate concentration. In contrast to the GSH, inhibition of protein hydroperoxide formation in the presence of the high (mM) intracellular ascorbate levels achieved was mainly due to the direct scavenging of hydroxyl radicals by the vitamin.
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Affiliation(s)
- Chia-Chi Liu
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
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Peoples AR, Mercer KR, Bernhard WA. What fraction of DNA double-strand breaks produced by the direct effect is accounted for by radical pairs? J Phys Chem B 2010; 114:9283-8. [PMID: 20583765 DOI: 10.1021/jp103362z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The purpose of this investigation was to determine what fraction of double strand breaks (dsb's), generated by the direct effect of ionizing radiation on DNA, can be accounted for by radical pairs. A radical pair is defined as two radicals trapped within a separation distance of <3 nm. Q-band EPR was used to measure the yield of radical pairs in calf thymus DNA films X-irradiated at 4 K. The EPR spectrum of DNA showed no evidence of radical pairs. To determine the relative sensitivity for radical pair detection via Q-band EPR, we measured the yield of radical pairs in single crystals of thymine, G(rp-Thy). Under the same conditions employed for DNA, G(rp-Thy) was approximately 8 nmol/J. The value of G(rp-Thy), in conjunction with the measured signal-to-noise, was used to calculate an upper limit for the yield of radical pairs in DNA, G(max)(rp-DNA) < 0.7-1.4 nmol/J. The upper limit, G(max)(rp-DNA), was compared with the yield of dsb's, G(total)(dsb) = 10 nmol/J, previously measured in pUC18 DNA films by Purkayastha, S.; Milligan, J. R.; Bernhard, W. A. Radiat. Res. 2007, 168, 357. We found that G(total)(dsb) > 2 x G(max)(rp-DNA), implying that a significant fraction of dsb's were not derived from a pair of trappable radicals. At least one of the two precursors needed to form a dsb was a diamagnetic (molecular) product. The hypothesis is that EPR silent lesions are formed through a molecular pathway. For example, a two-electron oxidation of deoxyribose would result in a deoxyribose carbocation intermediate that ultimately leads to a strand break.
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Affiliation(s)
- Anita R Peoples
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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Petrova T, Ginell S, Mitschler A, Kim Y, Lunin VY, Joachimiak G, Cousido-Siah A, Hazemann I, Podjarny A, Lazarski K, Joachimiak A. X-ray-induced deterioration of disulfide bridges at atomic resolution. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1075-91. [PMID: 20944241 DOI: 10.1107/s0907444910033986] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 08/23/2010] [Indexed: 11/10/2022]
Abstract
Overall and site-specific X-ray-induced damage to porcine pancreatic elastase was studied at atomic resolution at temperatures of 100 and 15 K. The experiments confirmed that irradiation causes small movements of protein domains and bound water molecules in protein crystals. These structural changes occur not only at 100 K but also at temperatures as low as 15 K. An investigation of the deterioration of disulfide bridges demonstrated the following. (i) A decrease in the occupancy of S(γ) atoms and the appearance of new cysteine rotamers occur simultaneously. (ii) The occupancy decrease is observed for all S(γ) atoms, while new rotamers arise for some of the cysteine residues; the appearance of new conformations correlates with the accessibility to solvent. (iii) The sum of the occupancies of the initial and new conformations of a cysteine residue is approximately equal to the occupancy of the second cysteine residue in the bridge. (iv) The most pronounced changes occur at doses below 1.4 × 10(7) Gy, with only small changes occurring at higher doses. Comparison of the radiation-induced changes in an elastase crystal at 100 and 15 K suggested that the dose needed to induce a similar level of deterioration of the disulfide bonds and atomic displacements at 15 K to those seen at 100 K is more than two times higher.
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Affiliation(s)
- Tatiana Petrova
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
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Zhou Y, Nelson WH. Free Radicals in l-Arginine·HCl·H2O Single Crystals X-irradiated at 66K- EPR, ENDOR, EIE and DFT Studies. J Phys Chem B 2010; 114:5567-82. [DOI: 10.1021/jp911943n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yiying Zhou
- Department of Physics and Astronomy, Georgia State University, P.O. Box 4106, Atlanta, Georgia 30302-4106
| | - William H. Nelson
- Department of Physics and Astronomy, Georgia State University, P.O. Box 4106, Atlanta, Georgia 30302-4106
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Black PJ, Swarts SG. Ex vivo analysis of irradiated fingernails: chemical yields and properties of radiation-induced and mechanically-induced radicals. HEALTH PHYSICS 2010; 98:301-8. [PMID: 20065698 PMCID: PMC3684967 DOI: 10.1097/hp.0b013e3181b0c045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A qualitative and quantitative analysis of the radicals underlying the radiation-induced signal (RIS) in fingernails was conducted in an attempt to identify properties of these radicals that could be used for biodosimetry purposes. A qualitative analysis of RIS showed the presence of at least three components, two of which were observed at low doses (<50 Gy) and the third required higher doses (>500 Gy). The low dose signal, obtained by reconstruction, consists of a 10 gauss singlet at g = 2.0053 and an 18 gauss doublet centered at g = 2.0044. Based on the initial slope of the dose-response curve, the chemical (radical) yields of the radicals giving rise to the singlet and doublet were 327 (+/-113) and 122 (+/-9) nmol J-1 (standard error, SE), respectively. At doses below 50 Gy, the singlet signal is the dominant component. Above this dose range, the signal intensity of the singlet rapidly dose-saturates. At doses <50 Gy, there is a small contribution of the doublet signal that increases in its proportion of the RIS as dose increases. A third component was revealed at high dose with a spectral extent of approximately 100 gauss and displayed peaks due to g anisotropy at g = 2.056, 2.026, and 1.996. The total radical yield calculated from the initial slope of the dose-response curve averaged 458 +/- (116) nmol J-1 (SE) in irradiated nail clippings obtained from six volunteers. Such high yields indicate that nails are a strong candidate for biodosimetry at low doses. In a comparison of relative stabilities of the radicals underlying the singlet and doublet signals, the stability of the doublet signal is more sensitive to the moisture content of the nail than the singlet. This differential in radical stabilities could provide a method for removing the doublet signal under controlled exposures to high humidities (>70% relative humidity). The decay of the singlet signal in RIS varies with exposure of a nail clipping to differing ambient humidities. However, long exposures (>6 h) to relative humidities of 72-94% results in singlet intensities that approach 7.0 +/- (3.2)% (standard deviation) of the original intensities in an irradiated nail. This result suggests the existence of a subpopulation of radicals underlying the singlet signal that is relatively insensitive to decay under exposure of nails even to high humidities. Therefore, exposures of an irradiated nail clipping under controlled humidities may provide a method for estimating the exposure dose of the nail that is based on the intensity of the signal of the humidity insensitive radical population underlying the singlet signal.
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Affiliation(s)
- Paul J. Black
- Department of Biochemistry/Biophysics University of Rochester, Rochester, New York 14642
| | - Steven G. Swarts
- Department of Radiation Oncology, University of Rochester, Rochester, New York 14642
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X-ray photochemistry in iron complexes from Fe(0) to Fe(IV) – Can a bug become a feature? Inorganica Chim Acta 2008. [DOI: 10.1016/j.ica.2007.10.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cho DW, Choi JH, Oh SW, Quan C, Yoon UC, Wang R, Yang S, Mariano PS. Single Electron Transfer-Promoted Photocyclization Reactions of Linked Acceptor−Polydonor Systems: Effects of Chain Length and Type on the Efficiencies of Macrocyclic Ring-Forming Photoreactions of Tethered α-Silyl Ether Phthalimide Substrates. J Am Chem Soc 2008; 130:2276-84. [DOI: 10.1021/ja076846l] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dae Won Cho
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea, and Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Jung Hei Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea, and Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Sun Wha Oh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea, and Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Chunsheng Quan
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea, and Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Ung Chan Yoon
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea, and Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Runtang Wang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea, and Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Shaorong Yang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea, and Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Patrick S. Mariano
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea, and Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
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The Synthetic Potential of SET Photochemistry of Silicon-Substituted Polydonor-Linked Phthalimides. B KOREAN CHEM SOC 2006. [DOI: 10.5012/bkcs.2006.27.8.1099] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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The influence of dithiothreitol on DNA radiolysis in frozen aqueous solution:. Radiat Phys Chem Oxf Engl 1993 2002. [DOI: 10.1016/s0969-806x(01)00455-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Chapter 2 Triggering of photomovement - molecular basis. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1568-461x(01)80006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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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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Nguyen KL, Steryo M, Kurbanyan K, Nowitzki KM, Butterfield SM, Ward SR, Stemp EDA. DNA−Protein Cross-Linking from Oxidation of Guanine via the Flash−Quench Technique. J Am Chem Soc 2000. [DOI: 10.1021/ja993502p] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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