Effects of nucleophile, oxidative damage, and nucleobase orientation on the glycosidic bond cleavage in deoxyguanosine

Journal of Physical Chemistry B

Volumn 114, Issue 6, 2010, Pages 2319-2326

  Shim, Eun Jung ^a   Przybylski, Jennifer L ^a   Wetmore, Stacey D ^a  

^a UNIVERSITY OF LETHBRIDGE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOLOGICAL SYSTEMS; BIOMOLECULES; CHEMICAL BONDS; DENSITY FUNCTIONAL THEORY; ENZYMES; REACTION KINETICS; SUGAR (SUCROSE);

8-OXOGUANINE; ACTIVATED WATER; ACTIVE SITE; BARRIER HEIGHTS; BIOLOGICAL PROCESS; DEGLYCOSYLATION; DNA REPAIR; GASPHASE; GLYCOSIDIC BOND CLEAVAGE; HYDROXYL ANIONS; NON-POLAR; NUCLEOBASES; OVERALL REACTIONS; OXIDATION PRODUCTS; OXIDATIVE DAMAGE; REACTION ENERGETICS; SUGAR MOIETY; THERMODYNAMICS AND KINETICS; WATER COMPLEXES;

NUCLEOPHILES;

EID: 77649096674     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp9113656     Document Type: Article

References (94)

1. Schroeder, G. K.; Wolfenden, R. Biochemistry 2007, 46, 13638-13647.
2. Watson, J. D.; Crick, F. H. C. Cold Spring Harbor Symp. Quant Biol. 1953, 78, 123-131.
3. See, for example: (a) Osman, R.; Miaskiewicz, K.; Weinstein, H. Basic Life Sci. 1991, 58, 423-452.
4. (b) Von Sonntag, C. Basic Life Sci. 1991, 58, 287-321.
5. (c) Ward, J. F. Basic Life Sci. 1991, 58, 403-421
6. (d) Swarts, S. G.; Gilbert, D. C.; Sharma, K. K.; Razskazovskiy, Y.; Purkayastha, S.; Naumenko, K. A.; Bernhard, W. A. Radiat. Res. 2007, 168, 367-381.
7. See, for example: (a) Hamid, S.; Eckert, K. A. Biochemistry 2005, 44, 10378-10387.
8. (b) Kincaid, K.; Beckman, J.; Zivkivic, A.; Halcomb, R. L.; Engels, J. W.; Kuchta, R. D. Nucleic Acids Res. 2005, 33, 2620-2628.
9. Reviewed in: Halliwell, B. J. Neurochem. 2006, 97, 1634-1658.
10. Reviewed in: (a) Hitomi, K.; Iwai, S.; Tainer, J. A. DNA Repair 2007, 6, 410-428.
11. (b) Wilson, D. M.; Bohr, V. A. Mol. Life Sci. 2001, 65, 544-559.
12. (c) Zharkov, D. O. Cell. Mol. Life Sci. 2008, 65, 1544-1565.
13. Reviewed in: (a) Stivers, J. T.; Jiang, Y. L. Chem. Rev. 2003, 103, 2729-2759.
14. (b) Berti, P. J.; McCann, J. A. B. Chem. Rev. 2006, 106, 506-555.
15. (c) Hitomi, K.; Iwai, S.; Tainer, J. A. DNA 2001, 6, 410-428.
16. Loft, S.; Danielsen, P. H. Mikkelen, L.; Risom, L.; Forchhammer, L.; Mølier, P. Biochem. Soc. Trans. 2008, 36, 1071-1076.
17. See, for example: (a) Gannett, P. M.; Lawson, T.; Miller, M.; Thakkar, D. D.; Lord, J. W.; Yau, W. M.; Toth, B. Chem. -Biol. Interact. 1996, 101, 149-164.
18. (b) Wuenschell, G. E.; O'Connor, T. R.; Termini, J. Biochemistry 2003, 42, 3608-3616.
19. (c) Lee, S.; Bowman, B. R.; Ueno, Y.; Wang, S.; Verdine, G. L. J. Am. Chem. 2008, 130, 11570-11571.
20. (d) Hwang, G. T.; Hari, Y.; Romesberg, F. E. Nucleic Acids Res. 2009, 37, 4757-4763.
21. (e) Knutson, C. G.; Rubinson, E. H.; Akingbade, D.; Anderson, C. S.; Stec, D. F.; Petrova, K. V.; Kozekov, I. D.; Guengerich, F. P.; Rizzo, C. J.; Marnett, L. J. Biochemistry 2009, 48, 800-809.
22. (f) Vertessy, B. G.; Toth, J. Acc. Chem. Res. 2009, 42, 97-106.
23. (a) Lindahl, T.; Nyberg, B. Biochemistry 1972, 11, 3610-3618.
24. (b) Lindahl, T.; Karlstro, O. Biochemistry 1973, 12, 5151-5154.
25. (c) Ratsep, P. C.; Pless, R. C. J. Org. Chem. 1988, 53, 3241-3246.
26. (a) Horenstein, B. A.; Schramm, V. L. Biochemistry 1993, 32,7089-7097.
27. (b) Versees, W.; Decanniere, K.; Pelle, R.; Depoorter, J.; Brosens, E.; Parkin, D. W.; Steyaert, J. J. Mol. Biol. 2001, 307, 1363-1379.
28. (c) Versees, W.; Steyaert, J. Curr. Opin. Struct. Biol. 2003, 13, 731-738.
29. (d) Loverix, S.; Geerlings, P.; McNaughton, M.; Augustyns, K.; Vandemeule-broucke, A.; Steyaert, J.; Versees, W. J. Biol. Chem. 2005, 280, 14799-14802.
30. (a) Erion, M. D.; Stoeckler, J. D.; Guida, W. C.; Walter, R. L.; Ealick, S. E. Biochemistry 1997, 36, 11735-11748.
31. (b) Murray, P. E.; McNally, V. A.; Lockyer, S. D.; Williams, K. J.; Stratford, I. J.; Jaffar, M.; Freeman, S. Bioorg. Med. Chem. 2002, 10, 525-530.
32. (c) Birck, M. R.; Schramm, V. L. J. Am. Chem, Soc. 2004, 126, 2447-2453.
33. (d) Hatano, A.; Harano, A.; Kirihara, M. Chem. Lett. 2006, 35, 232-233.
34. (e) Wielgus-Kutrowska, B.; Bzowska, A. Biochim. Biophys. Acta 2006, 1764, 887-902.
35. Milien, A. L.; Archibald, L. A. B.; Hunter, K. C.; Wetmore, S. D. J. Phys. Chem. B 2007, 11, 3800-3812.
36. Milien, A. L.; Wetmore, S. D. Can. J. Chem. 2009, 87, 850-863.
37. Przybylski, J. L.; Wetmore, S. D. J. Phys. Chem. B 2009, 113, 6533-6542.
38. Schutt, K. M.; Sun, K. W. M.; Paugh, R. J.; Milien, A. I.; Navarro-Whyte, L.; Wetmore, S. D.; Manderville, R. A. J. Org. Chem. 2009, 74, 5793-5802.
39. Rios-Font, R.; Bertran, J.; Rodriguez-Santiago, L.; Sodupe, M. J. Phys. Chem. B 2006, 110, 5767-5772.
40. Tehrani, Z. A.; Fattahi, A.; Pourjavadi, A. Carbohyar. Res. 2009, 344, 1-778.
41. (a) Chen, X.-Y.; Berti, P. J.; Schramm, V. L. J. Am. Chem. Soc. 2000, 122, 6527-6534.
42. (b) Birck, M. R.; Schramm, V. L. J. Am. Chem. Soc. 2004, 126, 2447-2453.
43. (c) McCann, J. A. B.; Berti, P. J. J. Am. Chem. 2007, 129, 7055-7064.
44. (d) McCann, J. A. B.; Berti, P. J. J. Am. Chem. Soc. 2008, 130, 5789-5797.
45. Osakabe, T.; Fujii, Y.; Hata, M.; Tsuda, M.; Neya, S.; Hoshino, T. Chem-Bio. Infomatics 2004, 4, 73-92.
46. Schyman, P.; Danielsson, J.; Pinak, M.; Laaksonen, A. J. Phys. Chem. A 2005, 109, 1713-1719.
47. Baik, M.-H.; Friesner, R. A.; Lippard, S. J. J. Am. Chem. Soc. 2002, 124, 4495-4503.
48. Rios-Font, R.; Rodriguez-Santiago, L.; Bertran, J.; Sodupe, M. J. Phys. Chem, B 2007, 111, 6071-6077.
49. Chen, Z.; Zhang, C.; Xue, Y. J. Phys. Chem. B 2009, 113, 10409-10420.
50. (a) Luo, N.; Mehler, E.; Osman, R. Biochemistry 1999, 38, 9209-9220.
51. (b) Osman, R.; Fuxreiter, M.; Luo, N. Comput. Chem. 2000, 24, 331-339.
52. (c) Dinner, A. R.; Blackburn, G. M.; Karplus, M. Nature (London) 2001, 413, 752-755.
53. (d) Ma, A.; Hu, J.; Karplus, M.; Dinner, A. R. Biochemistry 2006, 45, 13687-13696.
54. Rick, S. W.; Abashkin, Y. G.; Hilderbrandt, R. L.; Burt, S. K. Proteins: 1999, 37, 141-151.
55. Calvaresi, M.; Bottoni, A.; Garavelli, M. J. Phys. Chem. B 2007, 111, 6557-6570.
56. Prior, J. J.; Santi, D. V. J. Biol. Chem. 1984, 259, 2429-2434.
57. Cysewski, P.; Bira, D.; Bialkowski, K. J. Mol. Struct. (THEOCHFM) 2004, 678, 77-81.
58. (a) Versees, W.; Loverix, S.; Vandemeulebroucke, A.; Geerlings, P.; Steyaert, J. J. Mol. Biol. 2004, 338, 1-6.
59. (b) Loverix, S.; Versees, W.; Steyaert, J.; Geerlings, P. Int. J. Quantum Chem. 2006, 106, 565-570.
60. (a) Parkin, D. W.; Schramm, V. L. Biochemistry 1995, 34, 13961-13966.
61. (b) Loverix, S.; Geerlings, P.; McNaughton, M.; Augustyns, K.; Vandemeulebroucke, A.; Steyaert, J.; Versees, W. J. Biol. Chem. 2005, 280, 14799-14802.
62. (a) Mazumder, D.; Kahn, K.; Bruice, T. C. J. Am. Chem. Soc. 2002, 124, 8825-8833.
63. (b) Mazumder, D.; Bruice, T. C. J. Am. Chem. Soc. 2002, 124, 14591-14600.
64. (c) Mazumder-Shivakumar, D.; Bruice, T. C. Biochemistry 2005, 44, 7805-7817.
65. (a) Di Laudo, M.; Whittleton, S. R.; Wetmore, S. D. J. Phys. Chem. A 2003, 107, 10406-10413.
66. (b) Whittleton, S. R.; Hunter, K. C.; Wetmore, S. D. J. Phys. Chem. A 2004, 108, 7709-7718.
67. Hunter, K. C.; Millen, A. L.; Wetmore, S. D. J. Phys. Chem. B 2007, 111, 1858-1871.
68. (b) Hunter, K. C.; Wetmore, S. D. J. Phys. Chem. A 2001, 111, 1933-1942.
69. McConnell, T. L.;Wheaton, C. A.; Hunter, K. C.; Wetmore, S. D. J. Phys. Chem, A 2005, 109, 6351-6362.
70. Cadet, J.; Douki, T.; Ravanat, J. L. Acc. Chem Res. 2008, 41, 10751083.
71. Fromme, J. C.; Bruner, S. D.; Yang, W.; Karplus, M.; Verdine, G. L. Nat. Struct. Biol. 2003, 10, 204-211.
72. Fromme, J. C.; Verdine, G. L. Nat. Struct. Biol. 2002, 9, 544-552.
73. (a) Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100.
74. (b) Lee, C. T.; Yang, W. T.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.
75. (c) Becke, A. D. J. Chem. Phys. 1996, 104, 1040-1046.
76. Scott, A. P.; Radom, L. J. Phys. Chem. 1996, 100, 16502-16513.
77. (a) Tomasi, J.; Mennucci, B.; Canees, E. J. Mol. Stuct. (THEOCHEM) 1999, 464, 211-226.
78. (b) Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999-3093.
79. All implicit solvation calculations utilized UAHF radii and the following keywords: rmin = 0.5 and ofac = 0.8.
80. Frisch, M. J. T., G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hartchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Parkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision D.02; Gaussian, Inc.: Wallingford, CT, 2004.
81. (a) Rabow, L, E.; Kow, Y., W. Biochemistry 1997, 36, 5084-5096.
82. (b) Zharkov, D. O.; Rosenquist, T. A.; Gerchman, S. E.; Grollman, A. P. J. Biol. Chem. 2000, 275, 28607-28617.
83. (c) Saparbaev, M.; Sidorkina, O. M.; Jurado, J.; Privezentzev, C. V.; Greenberg, M. M.; Laval, J. Environ. Mol. Mutagen. 2002, 39, 10-17.
84. (a) Harvey, S. C.; Hoekstra, P. J. Phys. Chem. 1972, 76, 2987-2994.
85. (b) King, G.; Lee, F. S.; Warshel, A. J. Chem. Phys. 1991, 95, 4366-4377.
86. (c) García-Moreno E., B.; Dwyer, J. J.; Gittis, A. G.; Lattman, E. E.; Spencer, D. S.; Stites, W. E. Biophys. Chem. 1997, 64, 211-224.
87. (d) Dwyer, J. J.; Gittis, A. G.; Karp, D. A.; Lattman, E. E.; Spencer, D. S.; Stites, W. E.; García-Moreno E., B. BioPhys. J. 2000, 79, 1610-1620.
88. (a) Seela, F.; Debelak, H. Nucleic Acids Res. 2000, 28, 3224-3232.
89. (b) Ryjacek, F.; Engkvist, O.; Vacek, J.; Kratochvil, M.; Hobza, P. J. Phys. Chem. A 2001, 105, 1197-1202.
90. (a) Cheng, X.; Kelso, C.; Hornak, V.; de los Santos, C.; Grollman, A. P.; simmerling.C. J. Am. Chem. Soc. 2005, 127, 13906-13918.
91. (b) Wang, Y.; Reddy, S.; Beard, W. A.; Wilson, S. H.; Schlick, T. Biophys. J. 2007, 92, 3063-3070.
92. (a) Kouchakdjian, M.; Bodepudi, V.; Shibutani, S.; Eisenberg, M.; Johnson, F.; Grollman, A. P.; Patel, D. J. Biochemistry 1991, 30, 1403-1412.
93. (b) McAuleyhecht, K. E.; Leonard, G. A.; Gibson, N. J.; Thomson, J. B.; Watson, W. P.; Hunter, W. N.; Brown, T. Biochemistry 1994, 33, 10266-10270.
94. 1/2 values of greater than 80 years, and therefore these reactions would occur far too slowly for an enzyme-catalyzed process.