QM/MM study on the reaction mechanism of O6-alkylguanine-DNA alkyltransferase

Journal of Physical Chemistry B

Volumn 114, Issue 46, 2010, Pages 15296-15300

  Hou, Qianqian ^a   Du, Likai ^a   Gao, Jun ^a   Liu, Yongjun ^a   Liu, Chengbu ^a  

^a BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ENERGY BARRIERS; FUNCTIONAL GROUPS; REPAIR;

ACTIVE SITE; ALKYLTRANSFERASE; B3LYP/6-31G; CARBOCATIONS; CLUSTER MODELS; CYSTEINE RESIDUES; DNA REPAIR PROTEINS; HIGHER-ENERGY BARRIERS; METHYL GROUP; ONE-STEP PROCESS; QM/MM CALCULATIONS; RATE DETERMINING STEP; REACTION MECHANISM; STOICHIOMETRIC REACTION; THEORETICAL STUDY; THIOL GROUPS;

DNA;

EID: 78649598850     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp106714m     Document Type: Article

References (39)

1. Lindahl, T.; Wood, R. D. Science 1999, 286, 1897
2. Shukla, P. K.; Mishra, P. C.; Suhai, S. Int. J. Quantum Chem. 2007, 107, 1270
3. Wyatt, M. D.; Pittman, D. L. Chem. Res. Toxicol. 2006, 19, 1580
4. Mishina, Y.; Duguid, E. M.; He, C. Chem. Rev. 2006, 106, 215
5. Loechler, E. L.; Green, C. L.; Essigmann, J. M. Proc. Natl.Acad. Sci. U.S.A. 1984, 81, 6271
6. Hickman, M. J.; Samson, L. D. Mol. Cell 2004, 14, 105
7. Meikrantz, W.; Bergom, M. A.; Memisoglu, A.; Samson, L. Carcinogenesis 1998, 19, 369
8. Tubbs, J. L.; Pegg, A. E.; Tainer, J. A. DNA Repair 2007, 6, 1100
9. Pegg, A. E.; Fang, Q.; Loktionova, N. A. DNA Repair 2007, 6, 1071
10. Mitra, S. DNA Repair 2007, 6, 1064
11. Kaina, B.; Fritz, G.; Mitra, S.; Coquerelle, T. Carcinogenesis 1991, 12, 1857
12. Daniels, D. S.; Woo, T. T.; Luu, K. X.; Noll, D. M.; Clarke, N. D.; Pegg, A. E.; Tainer, J. A. Nat. Struct. Mol. Biol. 2004, 11, 714
13. Duguid, E. M.; Rice, P. A.; He, C. J. Mol. Biol. 2005, 350, 657
14. Georgieva, P.; Himo, F. Chem. Phys. Lett. 2008, 463, 214
15. Shukla, P. K.; Mishra, P. C. Phys. Chem. Chem. Phys. 2009, 11, 8191
16. Jena, N. R.; Shukla, P. K.; Jena, H. S.; Mishra, P. C.; Suhai, S. J. Phys. Chem. B 2009, 113, 16285
17. Senn, H. M.; Thiel, W. Angew. Chem., Int. Ed. 2009, 48, 1198
18. Gao, J. L.; Ma, S. H.; Major, D. T.; Nam, K.; Pu, J. Z.; Truhlar, D. G. Chem. Rev. 2006, 106, 3188
19. Cui, Q.; Karplus, M. Adv. Protein Chem. 2003, 66, 315
20. Gao, J. L.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467
21. Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700
22. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227
23. Marti-Renom, M. A.; Stuart, A. C.; Fiser, A.; Sanchez, R.; Melo, F.; Sali, A. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 291
24. Daniels, D. S.; Mol, C. D.; Arvai, A. S.; Kanugula, S.; Pegg, A. E.; Tainer, J. A. EMBO J. 2000, 19, 1719
25. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33
26. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187
27. MacKerell, A. J. Phys. Chem. B 1998, 102, 3586
28. Bakowies, D.; Thiel, W. J. Phys. Chem. 1996, 100, 10580
29. Sherwood, P.; de Vries, A. H.; Collins, S. J.; Greatbanks, S. P.; Burton, N. A.; Vincent, M. A.; Hillier, I. H. Faraday Discuss. 1997, 106, 79
30. Bakowies, D.; Thiel, W. J. Phys. Chem. 1996, 100, 10580
31. de Vries, A. H.; Sherwood, P.; Collins, S. J.; Rigby, A. M.; Rigutto, M.; Kramer, G. J. J. Phys. Chem. B 1999, 103, 6133
32. Sherwood, P. J. Mol. Struct. (THEOCHEM) 2003, 632, 1
33. Ahlrichs, R.; Bar, M.; Haser, M.; Horn, H.; Kolmel, C. Chem. Phys. Lett. 1989, 162, 165
34. Smith, W.; Forester, T. R. J. Mol. Graphics Modell. 1996, 14, 136
35. Rasimas, J. J.; Pegg, A. E.; Fried, M. G. J. Biol. Chem. 2003, 278, 7973
36. Noll, D. E.; Clarke, N. D. Nucleic Acids Res. 2001, 29, 4025
37. Edara, S.; Goodtzova, K.; Pegg, A. E. Carcinogenesis 1995, 16, 1637
38. Morgan, S. E.; Kelley, M. R.; Pieper, R. O. J. Biol. Chem. 1993, 268, 19802
39. Guengerich, F. P.; Fang, Q.; Liu, L.; Hachey, D. L.; Pegg, A. E. Biochemistry 2003, 42, 10965