Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase

Journal of the American Chemical Society

Volumn 132, Issue 45, 2010, Pages 16285-16295

  Sadeghian, Keyarash ^a   Bocola, Marco ^a   Merz, Thomas ^a   Schütz, Martin ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACK TRANSFER; ELECTRON TRANSFER; ENZYME BINDING; FLAVIN CHROMOPHORES; FOUR-MEMBERED RINGS; HISTIDINE RESIDUES; HYDROGEN BONDINGS; OXETANES; PHOTO-EXCITATIONS; PHOTO-INDUCED; PHOTOLYASES; PROTON DONATION; PROTONATED; REPAIR MECHANISM; SEMIQUINONES; THEORETICAL STUDY; UV IRRADIATION;

AMINO ACIDS; CHROMOPHORES; DNA; ENZYMES; FREE RADICAL REACTIONS; PHOTOEXCITATION; REPAIR;

CRYSTAL STRUCTURE;

DEOXYRIBODIPYRIMIDINE PHOTOLYASE; OXETANE DERIVATIVE; PYRIMIDINE DERIVATIVE; QUERCETIN; SEMIQUINONE;

ARTICLE; CHROMATOPHORE; CRYSTAL STRUCTURE; DNA REPAIR; ELECTRON; ENZYME BINDING; PROTEIN DNA BINDING; PROTON TRANSPORT; ULTRAVIOLET IRRADIATION;

ANIMALS; CRYSTALLOGRAPHY, X-RAY; DEOXYRIBODIPYRIMIDINE PHOTO-LYASE; DNA; DNA DAMAGE; DNA REPAIR; DROSOPHILA MELANOGASTER; PROTONS; PYRIMIDINE DIMERS; QUANTUM THEORY; RECOMBINATION, GENETIC; ULTRAVIOLET RAYS; WATER;

EID: 78449256909     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja108336t     Document Type: Article

References (66)

1. Mitchell, D. L. and Nairn, R. S. Photochem. Photobiol. 1989, 49, 805-809
2. Taylor, J. S. Acc. Chem. Res. 1994, 27, 76-82
3. Vink, A. A. and Roza, L. J. Photochem. Photobiol., B 2001, 65, 101-104
4. Pouget, J. P., Douki, T., Richard, M. J., and Cadet, J. Chem. Res. Toxicol. 2000, 13, 541-549
5. Brash, D. E., Rudolph, J. A., Simon, J. A., Lin, A., McKenna, G. J., Baden, H. P., Halperin, A. J., and Ponten, J. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 10124-8
6. Sinha, R. P. and Hader, D. P. Photochem. Photobiol. Sci. 2002, 1, 225-226
7. Sancar, A. Chem. Rev. 2003, 103, 2203-2207
8. Weber, S. Biochim. Biophys. Acta 2005, 1707, 1-23
9. Essen, L. O. and Klar, T. Cell. Mol. Life Sci. 2006, 63, 1266-1267
10. Boussicault, F. and Robert, M. Chem. Rev. 2008, 108, 2622-2625
11. Sancar, A. and Sancar, G. B. Annu. Rev. Biochem. 1988, 57, 29-67
12. Kao, Y. T., Saxena, C., Wang, L., Sancar, A., and Zhong, D. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 16128-32
13. Kao, Y. T., Saxena, C., Wang, L., Sancar, A., and Zhong, D. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 16128-32
14. Langenbacher, T., Zhao, X., Bieser, G., Heelis, P. F., Sancar, A., and Michel-Beyerle, M. E. J. Am. Chem. Soc. 1997, 119, 10532-10536
15. MacFarlane, A. W. and Stanley, R. J. Biochemistry 2003, 42, 8558-8558
16. Harrison, C. B., O'Neil, L. L., and Wiest, O. J. Phys. Chem. A 2005, 109, 7001-7002
17. Masson, F., Laino, T., Tavernelli, I., Rothlisberger, U., and Hutter, J. J. Am. Chem. Soc. 2008, 130, 3443-3450
18. Masson, F., Laino, T., Rothlisberger, U., and Hutter, J. ChemPhysChem 2009, 10, 400-410
19. Rahn, R. O. and Hosszu, J. L. Photochem. Photobiol. 1969, 10, 131-137
20. Zhao, X., Liu, J., Hsu, D. S., Zhao, S., Taylor, J. S., and Sancar, A. J. Biol. Chem. 1997, 272, 32580-90
21. Heelis, P. F. and Liu, S. J. Am. Chem. Soc. 1997, 119, 2936-2937
22. Hitomi, K., Nakamura, H., Kim, S. T., Mizukoshi, T., Ishikawa, T., Iwai, S., and Todo, T. J. Biol. Chem. 2001, 276, 10103-9
23. Asgatay, S., Petermann, C., Harakat, D., Guillaume, D., Taylor, J.-S., and Clivio, P. J. Am. Chem. Soc. 2008, 130, 12618-9
24. Yamamoto, J., Hitomi, K., Hayashi, R., Getzoff, E. D., and Iwai, S. Biochemistry 2009, 48, 9306-9312
25. Cichon, M. K., Arnold, S., and Carell, T. Angew. Chem., Int. Ed. 2002, 41, 767-770
26. Friedel, M. G., Cichon, M. K., and Carell, T. Org. Biomol. Chem. 2005, 3, 1937-1941
27. Yamamoto, J., Tanaka, Y., and Iwai, S. Org. Biomol. Chem. 2009, 7, 161-166
28. Song, Q.-H., Wang, H.-B., Tang, W.-J., Guo, Q.-X., and Yu, S.-Q. Org. Biomol. Chem. 2006, 4, 291-298
29. Stafforst, T. and Diederichsen, U. Chem. Commun. 2005, 3430-3432
30. Boussicault, F. and Robert, M. J. Phys. Chem. B 2006, 110, 21987-93
31. Joseph, A., Prakash, G., and Falvey, D. E. J. Am. Chem. Soc. 2000, 122, 11219-11225
32. Miranda, M. A., Izquierdo, M. A., and Galindo, F. Org. Lett. 2001, 3, 1965-1967
33. Wang, Y., Gaspar, P. P., and Taylor, J.-S. J. Am. Chem. Soc. 2000, 122, 5510-5519
34. Borg, O. A., Eriksson, L. A., and Durbeej, B. J. Phys. Chem. A 2007, 111, 2351-2351
35. Izquierdo, M. A., Domingo, L. R., and Miranda, M. A. J. Phys. Chem. A 2005, 109, 2602-2607
36. Weber, S., Kay, C. W. M., Mogling, H., Mobius, K., Hitomi, K., and Todo, T. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1319-1322
37. Schleicher, E., Hitomi, K., Kay, C. W., Getzoff, E. D., Todo, T., and Weber, S. J. Biol. Chem. 2007, 282, 4738-4747
38. Li, J., Uchida, T., Ohta, T., Todo, T., and Kitagawa, T. J. Phys. Chem. B 2006, 110, 16724-32
39. Li, J., Uchida, T., Todo, T., and Kitagawa, T. J. Biol. Chem. 2006, 281, 25551-9
40. Usman, A., Brazard, J., Martin, M. M., Plaza, P., Heijde, M., Zabulon, G., and Bowler, C. J. Photochem. Photobiol., B 2009, 96, 38-48
41. Maul, M. J., Barends, T. R. M., Glas, A. F., Cryle, M. J., Domratcheva, T., Schneider, S., Schlichting, I., and Carell, T. Angew. Chem., Int. Ed. 2008, 47, 10076-80
42. Glas, A. F., Schneider, S., Maul, M. J., Hennecke, U., and Carell, T. Chemistry 2009, 15, 10387-96
43. Domratcheva, T. and Schlichting, I. J. Am. Chem. Soc. 2009, 131, 17793-9
44. Li, J., Liu, Z., Tan, C., Guo, X., Wang, L., Sancar, A., and Zhong, D. Nature 2010, 466, 887-890
45. Friesner, R. A. and Guallar, V. Annu. Rev. Phys. Chem. 2005, 56, 389-427
46. Lin, H. and Truhlar, D. G. Theor. Chem. Acc. 2007, 2, 185-199
47. Senn, H. M. and Thiel, W. QM/MM Methods for Biological Systems. In Atomistic Approaches in Modern Biology; Reiher, M., Ed.; Springer: Berlin, 2007.
48. Senn, H. M. and Thiel, W. Angew. Chem., Int. Ed. 2009, 48, 1198-1229
49. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., W. B. A., III, Snoeyink, J., Richardson, J. S., and Richardson, D. C. Nucleic Acids Res. 2007, 35, 375-83
50. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
51. Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., and Kollman, P. J. Comput. Chem. 2003, 24, 1999-2012
52. Case, A. D.; et al. AMBER 10; University of California: San Francisco, 2008.
53. Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T. E., III, Laughton, C. A., and Orozco, M. Biophys. J. 2007, 92, 3817-3819
54. Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280
55. Shao, J., Tanner, S. W., and Cheatham, T. E., III. J. Chem. Theory Comput. 2007, 3, 2312-34
56. Zhang, Y., Kua, J., and McCammon, J. A. J. Phys. Chem. B 2003, 107, 4459-63
57. Sherwood, P. J. Mol. Struct. (THEOCHEM) 2003, 1, 632
58. Smith, W., Yong, C., and Rodger, P. Mol. Simul. 2002, 28, 385
59. Kästner, J., Carr, J. M., Keal, T. W., Thiel, W., Wander, A., and Sherwood, P. J. Phys. Chem. A 2009, 113, 11856-65
60. de Vries, A. H., Sherwood, P., Collins, S. J., Rigby, A. M., Rigutto, M., and Kramer, G. J. J. Phys. Chem. B 1999, 103, 6133-6141
61. Ahlrichs, R., Bär, M., Häser, M., Horn, H., and Kölmel, C. Chem. Phys. Lett. 1989, 162, 165-169
62. Becke, A. D. Phys. Rev. A 1988, 38, 3098
63. Grimme, S. J. Comput. Chem. 2006, 27, 1787-1789
64. Becke, A. D. J. Chem. Phys. 1993, 98, 5648
65. Sadeghian, K. and Schutz, M. J. Am. Chem. Soc. 2007, 129, 4068-4074
66. Sadeghian, K., Bocola, M., and Schutz, M. J. Am. Chem. Soc. 2008, 130, 12501-13