Radiation damage to a DNA-binding protein. Combined circular dichroism and molecular dynamics simulation analysis

Radiation Research

Volumn 170, Issue 5, 2008, Pages 604-612

  Mazier, S ^a   Villette, S ^a   Goffinont, S ^a   Renouard, S ^a   Maurizot, J C ^a   Genest, D ^a   Spotheim Maurizot, M ^a  

^a CENTRE DE BIOPHYSIQUE MOLÉCULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; DOPA; TYROSINE;

ARTICLE; BINDING KINETICS; BINDING SITE; CIRCULAR DICHROISM; DNA SEQUENCE; IRRADIATION; MOLECULAR DYNAMICS; OPERATOR GENE; OXIDATION KINETICS; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN STABILITY; PROTEIN STRUCTURE; RADIATION INJURY; RADIOSENSITIVITY; SIMULATION;

BACTERIAL PROTEINS; BINDING SITES; CIRCULAR DICHROISM; COMPUTER SIMULATION; DIHYDROXYPHENYLALANINE; DNA-BINDING PROTEINS; PROTEIN FOLDING; RADIATION DOSAGE; REPRESSOR PROTEINS;

EID: 55549129950     PISSN: 00337587     EISSN: None     Source Type: Journal    
DOI: 10.1667/RR1411.1     Document Type: Article

References (36)

1. C. Ménard, D. Johann, M. Lowenthal, T. Muanza, M. Sproull, S. Ross, J. Gulley, E. Petricoin, C. N. Coleman and K. Camphausen, Discovering clinical biomarkers of ionizing radiation exposure with serum proteomic analysis. Cancer Res. 66, 1844-1850 (2006).
2. P. H. von Hippel, From "simple" DNA-protein interactions to the macromolecular machine of gene expression. Annu. Rev. Biophys. Biomol. Struct. 36, 79-106 (2007).
3. C. J. Wilson, H. Zhan, L. Swint-Kruse and K. S. Matthews, The lactose repressor system: Paradigms for transcription regulation, allosteric behavior, and protein folding. Cell. Mol. Life Sci. 64, 3-16 (2007).
4. C. G. Kalodimos, G. E. Folkers, R. Boelens and R. Kaptein, Strong DNA binding by covalently linked dimeric Lac headpiece: evidence for the crucial role of the hinge helices. Proc. Natl. Acad. Sci. USA 98, 6039-6044 (2001).
5. C. G. Kalodimos, A. M. Bonvin, R. K. Salinas, R. Wechselberger, R. Boelens and R. Kaptein, Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J. 21, 2866-2876 (2002).
6. C. G. Kalodimos, R. Boelens and R. Kaptein, A residue-specific view of the association and dissociation pathway in protein-DNA recognition. Nat. Struct. Biol. 9, 193-197 (2002).
7. C. K. Kalodimos, R. Boelens and R. Kaptein, Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the Lac repressor system. Chem. Rev. 104, 3567-3586 (2004).
8. C. A. Spronk, M. Slijper, J. H. van Boom, R. Kaptein and R. Boelens, Formation of the hinge helix in the lac repressor is induced upon binding to the lac operator. Nat. Struct. Biol. 3, 916-919 (1996).
9. V. P. Chuprina, J. A. Rullmann, R. M. Lamerichs, J. H. van Boom, R. Boelens and R. Kaptein, Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. J. Mol. Biol. 234, 446-462 (1993).
10. M. Slijper, A. M. Bonvin, R. Boelens and R. Kaptein, Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator. J. Mol. Biol. 259, 761-773 (1996).
11. S. Eon, F. Culard, D. Sy, M. Charlier and M. Spotheim-Maurizot, Radiation disrupts protein-DNA complexes through damage to the protein. The lac repressor-operator system. Radiat. Res. 156, 110-117 (2001).
12. M. Charlier, S. Eon, E. Sèche, S. Bouffard, F. Culard and M. Spotheim-Maurizot, Radiolysis of lac repressor by γ rays and heavy ions. A two hits model for protein inactivation. Biophys. J. 82, 2373-2382 (2002).
13. E. R. Stadtman, Oxidation of free amino acids and amino acid residues in protein by radiolysis and by metal-catalysed reactions. Annu. Rev. Biochem. 62, 797-821 (1993).
14. J. Du and J. M. Gebicki, Proteins are major initial cell targets of hydroxyl free radicals. Int. J. Biochem. Cell. Biol. 36, 2334-2343 (2004).
15. •-) in aqueous solution. J. Phys. Chem. Ref. Data 17, 513-886 (1988).
16. G. Xu and M. Chance, Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem. Rev. 107, 3514-3543 (2007).
17. E. L. Finley, J. Dillon, R. K. Crouch and K. L. Schey, Radiolysis-induced oxidation of bovine γ-crystalline. Photochem. Photobiol. 68, 9-15 (1998).
18. M. Begusova, M. Spotheim-Maurizot, D. Sy, V. Michalik and M. Charlier, RADACK, a stochastic simulation of hydroxyl radical attack to DNA. J. Biomol. Struct. Dyn. 19, 141-158 (2001).
19. N. Gillard, M. Begusova, B. Castaing and M. Spotheim-Maurizot, Radiation affects binding of Fpg repair protein to an abasic site containing DNA. Radiat. Res. 162, 566-571 (2004).
20. M. Begusova, N. Gillard, D. Sy, B. Castaing, M. Charlier and M. Spotheim-Maurizot, Radiolysis of DNA-protein complexes. Radiat. Phys. Chem. 72, 265-270 (2005).
21. N. Gillard, S. Goffinont, C. Bure, M. Davidkova, J. C. Maurizot, M. Cadene and M. Spotheim-Maurizot, Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor. Biochem. J. 403, 463-472 (2007).
22. R. Jain, H. G. Freund, E. Budzinsky and M. Sharma, Radiation-induced formation of 3,4-dihydroxyphenylalanine in tyrosine-containing peptides and proteins as a function of X-irradiation dose. Bioconjug. Chem. 8, 173-178 (1997).
23. L. R. Karam, M. Dizdaroglu and M. G. Simic, OH radical induced products of tyrosine peptides. Int. J. Radiat. Biol. 46, 715-724 (1984).
24. T. G. Huggins, M. C. Wells-Knecht, N. A. Detorie, J. W. Baynes and S. Thorpe, Formation of o-tyrosine and dityrosine in proteins during radiolytic and metal-catalysed oxidation. J. Biol. Chem. 268, 12341-12347 (1993).
25. T. M. Jovin, N. Geisler and K. Weber, Amino-terminal fragments of Escherichia coli lac repressor bind to DNA. Nature 269, 668-672 (1977).
26. N. Sreerama and R. W. Woody, Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON and CDSSTR methods with an expanded reference set. Anal. Biochem. 287, 252-260 (2000).
27. D. A. Case, D. A. Pearlman, J. W. Caldwell, T. E. Cheatham, 3rd, J. Wang, W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Merz and P. A. Kollman, AMBER 7. University of California, San Francisco, 2002. [http://amber.scripps.edu/]
28. T. E. Cheatham, 3rd, P. Cieplak and P. A. Kollman, A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16, 845-862 (1999).
29. R. E. Duke and L. G. Pedersen, PMEMD 3. University of North Carolina, Chapel Hill, 2003. [http://www.psc.edu/general/software/packages/pmemd/pmemd. html]
30. J. P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, Numerical integration of the Cartesian equation of motion of a system with constraints: molecular dynamics of N-alkanes. J. Comput. Phys. 23, 327-341 (1977).
31. R. Koradi, M. Billeter and K. Wüthrich, MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graphics 14, 51-55 (1996).
32. W. Humphrey, A. Dalke and K. Schulten, VMD - Visual Molecular Dynamics. J. Mol. Graph. 14, 33-38 (1996).
33. A. Synytsya, P. Alexa, J. de Boer, M. Loewe, M. Moosburger, M. Wurkner and K. Volka, Raman spectroscopic study of serum albumins: an effect of proton and g irradiation. J. Raman Spectrosc. 38, 1646-1655 (2007).
34. M. Schnarr and J. C. Maurizot, Stability of the lac repressor headpiece against thermal denaturation and tryptic hydrolysis. Biochim. Biophys. Acta 702, 155-162 (1982).
35. F. Culard, A. Gervais, G. de Vuyst, M. Spotheim-Maurizot and M. Charlier, Response of a DNA-binding protein to radiation-induced oxidative stress. J. Mol. Biol. 328, 1185-1195 (2003).
36. V. Stisova, S. Goffinont, M. Spotheim-Maurizot and M. Davidkova, Radiation damage to DNA-protein specific complexes: The estrogen response element-estrogen receptor complex. Radiat. Prot. Dosimetry 122, 106-109 (2006).