Structural and Biophysical Studies of Human PARP-1 in Complex with Damaged DNA

Journal of Molecular Biology

Volumn 395, Issue 5, 2010, Pages 983-994

  Lilyestrom, Wayne ^a   van der Woerd, Mark J ^a   Clark, Nicholas ^a   Luger, Karolin ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

PARP 1 DNA damage; poly(ADP ribose) polymerase 1; small angle X ray scattering

Indexed keywords

DNA; HISTONE; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE 1;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; BIOCHEMISTRY; BIOPHYSICS; CHROMATIN STRUCTURE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA BINDING; DNA DAMAGE; DNA REPAIR; DNA SEQUENCE; ENZYME ACTIVATION; GENETIC STABILITY; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; MOLECULAR MECHANICS; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; RADIATION SCATTERING; STOICHIOMETRY; THERMODYNAMICS;

EID: 73649110221     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.11.062     Document Type: Article

References (33)

1. Ame J.C., Spenlehauer C., and de Murcia G. The PARP superfamily. BioEssays 26 (2004) 882-893
2. Bouchard V.J., Rouleau M., and Poirier G.G. PARP-1, a determinant of cell survival in response to DNA damage. Exp. Hematol. 31 (2003) 446-454
3. D'Amours D., Desnoyers S., D'Silva I., and Poirier G.G. Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem. J. 342 (1999) 249-268
4. Jacobson E.L., Antol K.M., Juarez-Salinas H., and Jacobson M.K. Poly(ADP-ribose) metabolism in ultraviolet irradiated human fibroblasts. J. Biol. Chem. 258 (1983) 103-107
5. Oleinick N.L., and Evans H.H. Poly(ADP-ribose) and the response of cells to ionizing radiation. Radiat. Res. 101 (1985) 29-46
6. Berger N.A. Poly(ADP-ribose) in the cellular response to DNA damage. Radiat. Res. 101 (1985) 4-15
7. McCurry L.S., and Jacobson M.K. Poly(ADP-ribose) synthesis following DNA damage in cells heterozygous or homozygous for the xeroderma pigmentosum genotype. J. Biol. Chem. 256 (1981) 551-553
8. Nolan N.L., Butt T.R., Wong M., Lambrianidou A., and Smulson M.E. Characterization of poly(ADP-ribose)-histone H1 complex formation in purified polynucleosomes and chromatin. Eur. J. Biochem. 113 (1980) 15-25
9. Tulin A., and Spradling A. Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science 299 (2003) 560-562
10. de Murcia G., Schreiber V., Molinete M., Saulier B., Poch O., Masson M., Niedergang C., et al. Structure and function of poly(ADP-ribose) polymerase. Mol. Cell. Biochem. 138 (1994) 15-24
11. Nusinow D., Hernandez-Munoz I., Fazzio T., Shah G., Kraus L., and Panning B. Poly(ADP-ribose) polymerase 1 is inhibited by a histone H2A variant, macroH2A, and contributes to silencing of the inactive X chromosome. J. Biol. Chem. 282 (2007) 12851-12859
12. Petrucco S., and Percudani R. Structural recognition of DNA by poly(ADP-ribose) polymerase-like zinc finger families. FEBS J. 275 (2008) 883-893
13. Tao Z., Gao P., Hoffman D.W., and Liu H.W. Domain C of human poly(ADP-ribose) polymerase-1 is important for enzyme activity and contains a novel zinc-ribbon motif. Biochemistry 47 (2008) 5804-5813
14. Schreiber V., Molinete M., Boeuf H., de Murcia G., and Menissier-de Murcia J. The human poly(ADP-ribose) polymerase nuclear localization signal is a bipartite element functionally separate from DNA binding and catalytic activity. EMBO J. 11 (1992) 3263-3269
15. Gradwohl G., Ménissier de Murcia J.M., Molinete M., Simonin F., Koken M., Hoeijmakers J.H., and de Murcia G. The second zinc-finger domain of poly(ADP-ribose) polymerase determines specificity for single-stranded breaks in DNA. Proc. Natl Acad. Sci. USA 87 (1990) 2990-2994
16. Lonskaya I., Potaman V.N., Shlyakhtenko L.S., Oussatcheva E.A., Lyubchenko Y.L., and Soldatenkov V.A. Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding. J. Biol. Chem. 280 (2005) 17076-17083
17. Pion E., Ullmann G.M., Ame J.C., Gerard D., de Murcia G., and Bombarda E. DNA-induced dimerization of poly(ADP-ribose) polymerase-1 triggers its activation. Biochemistry 44 (2005) 14670-14681
18. Langelier M.F., Servent K.M., Rogers E.E., and Pascal J.M. A third zinc-binding domain of human poly(ADP-ribose) polymerase-1 coordinates DNA-dependent enzyme activation. J. Biol. Chem. 283 (2008) 4105-4114
19. Lipfert J., and Doniach S. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu. Rev. Biophys. Biomol. Struct. 36 (2007) 307-327
20. Koch M.H., Vachette P., and Svergun D.I. Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q. Rev. Biophys. 36 (2003) 147-227
21. Konarev P.V., Petoukhov M.V., Volkov V.V., and Svergun D.I. ATSAS 2.1, a program package for small-angle scattering data analysis. J. Appl. Crystallogr. 39 (2006) 277-286
22. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76 (1999) 2879-2886
23. Petoukhov M.V., and Svergun D.I. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J. 89 (2005) 1237-1250
24. Dantzer F., Ame J.C., Schreiber V., Nakamura J., Menissier-de Murcia J., and de Murcia G. Poly(ADP-ribose) polymerase-1 activation during DNA damage and repair. Methods Enzymol. 409 (2006) 493-510
25. Bai Y., Das R., Millett I.S., Herschlag D., and Doniach S. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc. Natl Acad. Sci. USA 102 (2005) 1035-1040
26. Petrucco S. Sensing DNA damage by PARP-like fingers. Nucleic Acids Res. 31 (2003) 6689-6699
27. Le Cam E., Fack F., Menissier-de Murcia J., Cognet J.A., Barbin A., Sarantoglou V., et al. Conformational analysis of a 139 base-pair DNA fragment containing a single-stranded break and its interaction with human poly(ADP-ribose) polymerase. J. Mol. Biol. 235 (1994) 1062-1071
28. Pion E., Bombarda E., Stiegler P., Ullmann G.M., Mely Y., de Murcia G., and Gerard D. Poly(ADP-ribose) polymerase-1 dimerizes at a 5′ recessed DNA end in vitro: a fluorescence study. Biochemistry 42 (2003) 12409-12417
29. Kamashev D., Balandina A., Mazur A.K., Arimondo P.B., and Rouviere-Yaniv J. HU binds and folds single-stranded DNA. Nucleic Acids Res. 36 (2008) 1026-1036
30. Kamashev D., and Rouviere-Yaniv J. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J. 19 (2000) 6527-6535
31. Konarev P.V., Volkov V.V., Sokolova A.V., Koch M.H.J., and Svergun D.I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36 (2003) 1277-1282
32. Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25 (1992) 495-503
33. Kozin M.B., and Svergun D.I. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 34 (2001) 33-41