Density functional theory study of the reaction mechanism of the DNA repairing enzyme alkylguanine alkyltransferase

Chemical Physics Letters

Volumn 463, Issue 1-3, 2008, Pages 214-218

  Georgieva, Polina ^a   Himo, Fahmi ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; DNA; POSITIVE IONS; POTENTIAL ENERGY; QUANTUM CHEMISTRY;

ALKYL GROUPS; ALKYLTRANSFERASE; DENSITY FUNCTIONAL THEORY STUDIES; NUCLEOPHILIC ATTACK; POTENTIAL ENERGY CURVES; QUANTUM CHEMICAL MODELING; REACTION MECHANISM; STATIONARY POINTS;

DENSITY FUNCTIONAL THEORY;

EID: 51349146401     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2008.08.043     Document Type: Article

References (50)

1. Mishina Y., Duguid E.M., and He C. Chem. Rev. 106 (2006) 215
2. O'Brien P. Chem. Rev. 106 (2006) 720
3. Lindahl T., and Wood R.D. Science 286 (1999) 1897
4. Shärer O.D. Angew. Chem. Int. Ed. 42 (2003) 2946
5. Huffman J.L., Sundheim O., and Tainer J.A. Mut. Res. 577 (2005) 55
6. For recent reviews on AGT, see the thematic issue of DNA Repair, 6 (8), 2007.
7. Mitra S. DNA Repair 6 (2007) 1064
8. Pegg A.E., Fang Q., and Loktionova N.A. DNA Repair 6 (2007) 1071
9. Tubbs J.L., Pegg A.E., and Tainer J.A. DNA Repair 6 (2007) 1100
10. Xu-Welliver M., and Pegg A.E. Carcinogenesis 23 (2002) 823
11. Gerson S.L. J. Clin. Oncol. 20 (2002) 2388
12. Fang Q., and Gerson S.L. Clin. Cancer Res. 12 (2006) 328
13. Moore M.H., Gulbis J.M., Dodson E.J., Demple B., and Moody P.C. EMBO J. 13 (1994) 1495
14. Hashimoto H., Inoue T., Nishioka M., Fujiwara S., Takagi M., Imanaka T., and Kai Y. J. Mol. Biol. 292 (1999) 707
15. Daniels D.S., Mol C.D., Arvai A.S., Kanugula S., Pegg A.E., and Tainer J.A. EMBO J. 19 (2000) 1719
16. Daniels D.S., and Tainer J.A. Mut. Res. 460 (2000) 151
17. Wibley J.E.A., Pegg A.E., and Moody P.C.E. Nucl. Acids Res. 28 (2000) 393
18. Daniels D.S., Woo T.T., Luu K.X., Noll D.M., Clarke N.D., Pegg A.E., and Tainer J.A. Nat. Struct. Mol. Biol. 11 (2004) 714
19. Duguid E.M., Rice P.A., and He C. J. Mol. Biol. 350 (2005) 657
20. Roberts A., Pelton J.G., and Wemmer D.E. Magn. Reson. Chem. 44 (2006) 71
21. Morgan S.E., Kelley M.R., and Pieper R.O. J. Biol. Chem. 268 (1993) 19802
22. Chan C.-L., Wu Z., Ciardelli T., Eastman A., and Bresnick E. Arch. Biochem. Biophys. 300 (1993) 193
23. Edara S., Goodtzova K., and Pegg A.E. Carcinogenesis 16 (1995) 1637
24. Goodtzova K., Kanugula S., Edara S., and Pegg A.E. Biochem. 37 (1998) 12489
25. Noll D.E., and Clarke N.D. Nucl. Acids Res. 29 (2001) 4025
26. Rasimas J.J., Pegg A.E., and Fried M.G. J. Biol. Chem. 278 (2003) 7973
27. Guengerich F.P., Fang Q., Liu L., Hachey D.L., and Pegg A.E. Biochem. 42 (2003) 10965
28. Lee C., Yang W., and Parr R.G. Phys. Rev. B 37 (1988) 85
29. Becke A.D. Phys. Rev. A 38 (1988) 3098
30. Becke A.D. J. Chem. Phys. 96 (1992) 2155
31. Becke A.D. J. Chem. Phys. 97 (1992) 9173
32. Becke A.D. J. Chem. Phys. 98 (1993) 5648
33. Himo F. Biophys. Biochim. Acta 1707 (2005) 24
34. Hopmann K.H., Hallberg B.M., and Himo F. J. Am. Chem. Soc. 127 (2005) 14339
35. Himo F., Guo J.-D., Rinaldo-Matthis A., and Nordlund P. J. Phys. Chem. B 109 (2005) 20004
36. Hopmann K.H., and Himo F. Chem. Eur. J. 12 (2006) 6898
37. Himo F. Theor. Chem. Acc. 116 (2006) 232
38. Chen S.-L., Fang W.-H., and Himo F. J. Phys. Chem. B 111 (2007) 1253
39. Sevastik R., and Himo F. Bioorg. Chem. 35 (2007) 444
40. Hopmann K.H., Guo J.-D., and Himo F. Inorg. Chem. 46 (2007) 4850
41. Velichkova P., and Himo F. J. Phys. Chem. B 109 (2005) 8216
42. Velichkova P., and Himo F. J. Phys. Chem. B 110 (2006) 16
43. M.J. Frisch et al., Gaussian 03 (Revision C.02), Gaussian Inc., Wallingford, CT, 2004.
44. Barone V., and Cossi M. J. Phys. Chem. A 102 (1998) 1995
45. Cammi R., Mennucci B., and Tomasi J. J. Phys. Chem. A 103 (1999) 9100
46. Klamt A., and Schüürmann G. J. Chem. Soc. Perkin. Trans. 2 (1993) 799
47. Tomasi J., Mennucci B., and Cammi R. Chem. Rev. 105 (2005) 2999
48. Hu C.-H., Brinck T., and Hult K. Int. J. Quantum Chem. 69 (1998) 89
49. According to classical transition state theory, a barrier of ca 18 kcal/mol corresponds to a reaction rate of 1/s at room temperature.
50. Lynch B.J., Fast P.L., Harris M., and Truhlar D.G. J. Phys. Chem. A 104 (2000) 4811