Gas-phase studies of substrates for the DNA mismatch repair enzyme MutY

Journal of the American Chemical Society

Volumn 134, Issue 48, 2012, Pages 19839-19850

  Michelson, Anna Zhachkina ^a   Rozenberg, Aleksandr ^a   Tian, Yuan ^a   Sun, Xuejun ^a   Davis, Julianne ^a   Francis, Anthony W ^b   O'Shea, Valerie L ^b   Halasyam, Mohan ^b   Manlove, Amelia H ^c   David, Sheila S ^b,c   Lee, Jeehiun K ^a  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY OF UTAH   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC MECHANISMS; DATA SUPPORT; DEPURINATION; DIFFERENT MECHANISMS; GAIN INSIGHT; GASPHASE; GLYCOSYLASE; INTRINSIC PROPERTY; MISMATCH REPAIR; NON-ENZYMATIC; PROTON AFFINITY; TAUTOMERIC ENERGY; THERMOCHEMICAL PROPERTIES;

CHEMISTRY; SYNTHESIS (CHEMICAL);

HYDROGEN BONDS;

ADENINE; DNA GLYCOSYLASE MUTY;

ARTICLE; DNA STRUCTURE; ENZYME MECHANISM; GAS; HYDROGEN BOND; MISMATCH REPAIR; PROTON TRANSPORT;

ADENINE; CATALYSIS; DNA GLYCOSYLASES; DNA MISMATCH REPAIR; GASES; HYDROGEN-ION CONCENTRATION; MOLECULAR STRUCTURE; PHASE TRANSITION; SUBSTRATE SPECIFICITY; TEMPERATURE;

EID: 84870655088     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja309082k     Document Type: Article

References (69)

1. David, S. S.; Williams, S. D. Chem. Rev. 1998, 98, 1221-1261
2. Lindahl, T. Nature 1993, 362, 709-715
3. Klaunig, J. E.; Kamendulis, L. M. Annu. Rev. Pharmacol. Toxicol. 2004, 44, 239-267
4. Neeley, W. L.; Essigmann, J. M. Chem. Res. Toxicol. 2006, 19, 491-505
5. Shigenaga, M. K.; Park, J.-W.; Cundy, K. C.; Gimeno, C. J.; Ames, B. N. Methods Enzymol. 1990, 186, 521-530
6. Dizdaroglu, M. Biochemistry 1985, 24, 4476-4481
7. Burrows, C. J.; Muller, J. G. Chem. Rev. 1998, 98, 1109-1152
8. McAuley-Hecht, K. E.; Leonard, G. A.; Gibson, N. J.; Thomson, J. B.; Watson, W. P.; Hunter, W. N.; Brown, T. Biochemistry 1994, 33, 10266-10270
9. Cunningham, R. P. Mutat. Res. 1997, 383, 189-196
10. Michaels, M. L.; Tchou, J.; Grollman, A. P.; Miller, J. H. Biochemistry 1992, 31, 10964-10968
11. David, S. S.; O'Shea, V. L.; Kundu, S. Nature 2007, 447, 941-950
12. Michaels, M. L.; Miller, J. H. J. Bacteriol. 1992, 174, 6321-6325
13. Michaels, M. L.; Cruz, C.; Grollman, A. P.; Miller, J. H. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 7022-7025
14. Lee, S.; Verdine, G. L. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 18497-18502
15. McCann, J. A. B.; Berti, P. J. J. Am. Chem. Soc. 2008, 130, 5789-5797
16. Fromme, J. C.; Banerjee, A.; Huang, S. J.; Verdine, G. L. Nature 2004, 427, 652-656
17. Brunk, E.; Arey, J. S.; Rothlisberger, U. J. Am. Chem. Soc. 2012, 134, 8608-8616
18. Kurinovich, M. A.; Lee, J. K. J. Am. Chem. Soc. 2000, 122, 6258-6262
19. Liu, M.; Xu, M.; Lee, J. K. J. Org. Chem. 2008, 73, 5907-5914
20. Sun, X.; Lee, J. K. J. Org. Chem. 2010, 75, 1848-1854
21. Sharma, S.; Lee, J. K. J. Org. Chem. 2002, 67, 8360-8365
22. Zhachkina, A.; Liu, M.; Sun, X.; Amegayibor, S.; Lee, J. K. J. Org. Chem. 2009, 74, 7429-7440
23. Sun, X.; Lee, J. K. J. Org. Chem. 2007, 72, 6548-6555
24. Lee, J. K. Int. J. Mass Spectrom. 2005, 240, 261-272
25. DeCarlo, L.; Prakasha Gowda, A. S.; Suo, Z.; Spratt, T. E. Biochemistry 2008, 47, 8157-8164
26. Francis, A. W.; Helquist, S. A.; Kool, E. T.; David, S. S. J. Am. Chem. Soc. 2003, 125, 16235-16242
27. Kurinovich, M. A.; Lee, J. K. Chem. Commun. 2002, 2354-2355
28. Sharma, S.; Lee, J. K. J. Org. Chem. 2004, 69, 7018-7025
29. Liu, M.; Li, T.; Amegayibor, S.; Cardoso, D. S.; Fu, Y.; Lee, J. K. J. Org. Chem. 2008, 73, 9283-9291
30. Kurinovich, M. A.; Lee, J. K. J. Am. Soc. Mass Spectrom. 2002, 13, 985-995
31. Chesnavich, W. J.; Su, T.; Bowers, M. T. J. Chem. Phys. 1980, 72, 2641-2655
32. Su, T.; Chesnavich, W. J. J. Chem. Phys. 1982, 76, 5183-5185
33. Cooks, R. G.; Kruger, T. L. J. Am. Chem. Soc. 1977, 99, 1279-1281
34. McLuckey, S. A.; Cameron, D.; Cooks, R. G. J. Am. Chem. Soc. 1981, 103, 1313-1317
35. McLuckey, S. A.; Cooks, R. G.; Fulford, J. E. Int. J. Mass Spectrom. Ion Phys. 1983, 52, 165-174
36. Green-Church, K. B.; Limbach, P. A. J. Am. Soc. Mass Spectrom. 2000, 11, 24-32
37. Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Science 1989, 246, 64-71
38. Drahos, L.; Vékey, K. J. Mass Spectrom. 1999, 34, 79-84
39. Ervin, K. M. Chem. Rev. 2001, 101, 391-444
40. Gronert, S.; Feng, W. Y.; Chew, F.; Wu, W. Int. J. Mass Spectrom. 2000, 195/196, 251-258
41. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
42. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789
43. Kohn, W.; Becke, A. D.; Parr, R. G. J. Chem. Phys. 1996, 100, 12974-12980
44. Frisch, M. J.; Gaussian 03; Gaussian, Inc.: Wallingford, CT, 2004.
45. Frisch, M. J.; Gaussian 09; Gaussian, Inc.: Wallingford, CT, 2009.
46. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995-2001
47. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V. J. Comput. Chem. 2003, 24, 669-681
48. Takano, Y.; Houk, K. N. J. Chem. Theory Comput. 2005, 1, 70-77
49. Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Coe, J. V.; Tuttle, T. R. J. Phys. Chem. A 1998, 102, 7787-7794
50. Chipman, D. M. J. Phys. Chem. A 2002, 106, 7413-7422
51. Livingston, A. L.; O'Shea, V. L.; Kim, T.; Kool, E. T.; David, S. S. Nat. Chem. Biol. 2008, 4, 51-58
52. Chepanoske, C. L.; Langelier, C. R.; Chmiel, N. H.; David, S. S. Org. Lett. 2000, 2, 1341-1344
53. Porello, S. L.; Williams, S. D.; Kuhn, H.; Michaels, M. L.; David, S. S. J. Am. Chem. Soc. 1996, 118, 10684-10692
54. Hunter, E. P.; Lias, S. G. Proton Affinity Evaluation. In NIST Chemistry WebBook; Linstrom, P. G.; Mallard, W. G., Eds.; NIST Standard Reference Database Number 69; National Institute of Standards and Technology: Gaithersburg, MD; http://webbook.nist.gov (retrieved Aug 28, 2012).
55. Eyet, N.; Villano, S. M.; Bierbaum, V. M. Int. J. Mass Spectrom. 2009, 283, 26-29
56. Porello, S. L.; Leyes, A. E.; David, S. S. Biochemistry 1998, 37, 14756-14764
57. Wolken, J. K.; Yao, C.; Turecek, F.; Polce, M. J.; Wesdemiotis, C. Int. J. Mass Spectrom. 2007, 267, 30-42
58. Shukla, M. K.; Leszczynski, J. Chem. Phys. Lett. 2006, 429, 261-265
59. Plekan, O.; Feyer, V.; Richter, R.; Coreno, M.; Vallosera, G.; Prince, K. C.; Trofimov, A. B.; Zaytseva, I. L.; Moskovskaya, T. E.; Gromov, E. V.; Schirmer, J. J. Phys. Chem. A 2009, 113, 9376-9385
60. Trygubenko, S. A.; Bogdan, T. V.; Rueda, M.; Orozco, M.; Luque, F. J.; Sponer, J.; Slavicek, P.; Hobza, P. Phys. Chem. Chem. Phys. 2002, 4, 4192-4203
61. Colominas, C.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 1996, 118, 6811-6821 and references therein
62. Bennett, M. T.; Rodgers, M. T.; Hebert, A. S.; Ruslander, L. E.; Eisele, L.; Drohat, A. C. J. Am. Chem. Soc. 2006, 128, 12510-12519
63. Guan, Y.; Manuel, R. C.; Arvai, A. S.; Parikh, S. S.; Mol, C. D.; Miller, J. H.; Lloyd, R. S.; Tainer, J. A. Nat. Struct. Biol. 1998, 5, 1058-1064
64. Podolyan, Y.; Gorb, L.; Leszczynski, J. J. Phys. Chem. A 2000, 104, 7346-7352 and references therein
65. Hanus, M.; Kabelac, M.; Rejnek, J.; Ryjacek, F.; Hobza, P. J. Phys. Chem. B 2004, 208, 2087-2097
66. Russo, N.; Toscano, M.; Grand, A.; Jolibois, F. J. Comput. Chem. 1998, 19, 989-1000
67. Huang, Y.; Kenttämaa, H. J. Phys. Chem. A 2004, 108, 4485-4490
68. Chandra, A. K.; Nguyen, M. T.; Uchimaru, T.; Zeegers-Huyskens, T. J. Phys. Chem. A 1999, 103, 8853-8860
69. Del Bene, J. E. J. Phys. Chem. 1983, 87, 367-371