Unraveling the Base Excision Repair Mechanism of Human DNA Glycosylase

Journal of the American Chemical Society

Volumn 137, Issue 31, 2015, Pages 9824-9831

  Sadeghian, Keyarash ^a   Ochsenfeld, Christian ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR MODELING; POSITIVE IONS; QUANTUM THEORY; REACTION INTERMEDIATES; REPAIR;

BASE EXCISION REPAIRS; BLOCK PROCESSING; MOLECULAR MECHANISM; QUANTUM MECHANICS/MOLECULAR MECHANICS; REACTION BARRIERS; REACTION MECHANISM; REPAIR MECHANISM; THEORETICAL INVESTIGATIONS;

DNA;

DNA; DNA GLYCOSYLTRANSFERASE; GUANINE; NUCLEIC ACID BASE; OXYGEN DERIVATIVE; PROTON; RIBOSE;

ARTICLE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; EXCISION REPAIR; HUMAN; ISOMERIZATION; MOLECULAR MECHANICS; OXIDATION; PROTON TRANSPORT; QUANTUM MECHANICS; REACTION ANALYSIS; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; DNA REPAIR; METABOLISM; PROTEIN CONFORMATION;

BIOCATALYSIS; DNA GLYCOSYLASES; DNA REPAIR; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTONS; RIBOSE;

EID: 84939237071     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/jacs.5b01449     Document Type: Article

References (39)

1. Lindahl, T. Nature 1993, 362, 709 10.1038/362709a0
2. Friedberg, E. C. Nature 2003, 421, 436-440 10.1038/nature01408
3. Hollstein, M.; Shomer, B.; Greenblatt, M.; Soussi, T.; Hovig, E.; Montesano, R.; Harris, C. C. Nucleic Acids Res. 1996, 24, 141-6 10.1093/nar/24.1.141
4. Roldan-Arjona, T. Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 8016-8020
5. Bjoras, M. EMBO J. 1997, 16, 6314-6322 10.1093/emboj/16.20.6314
6. Rosenquist, T. A.; Zharkov, D. O.; Grollman, A. P. Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 7429-7434 10.1073/pnas.94.14.7429
7. David, S. S.; O'Shea, V. L.; Kundu, S. Nature 2007, 447, 941-50 10.1038/nature05978
8. Norman, D. P. G.; Bruner, S. D.; Verdine, G. L. J. Am. Chem. Soc. 2001, 123, 359-360 10.1021/ja003144m
9. Norman, D. P. G.; Chung, S. J.; Verdine, G. L. Biochemistry 2003, 42, 1564-72 10.1021/bi026823d
10. Chung, S. J.; Verdine, G. L. Chem. Biol. 2004, 11, 1643-9 10.1016/j.chembiol.2004.09.014
11. Morland, I.; Luna, L.; Gustad, E.; Seeberg, E.; Bjørås, M. DNA Repair 2005, 4, 381-7 10.1016/j.dnarep.2004.11.002
12. Vidal, A. E. Nucleic Acids Res. 2001, 29, 1285-1292 10.1093/nar/29.6.1285
13. Fromme, J. C.; Bruner, S. D.; Yang, W.; Karplus, M.; Verdine, G. L. Nat. Struct. Biol. 2003, 10, 204-11 10.1038/nsb902
14. Bruner, S. D.; Norman, D. P.; Verdine, G. L. Nature 2000, 403, 859-866 10.1038/35002510
15. Crenshaw, C. M.; Nam, K.; Oo, K.; Kutchukian, P. S.; Bowman, B. R.; Karplus, M.; Verdine, G. L. J. Biol. Chem. 2012, 287, 24916-28 10.1074/jbc.M111.316497
16. McKibbin, P. L.; Kobori, A.; Taniguchi, Y.; Kool, E. T.; David, S. S. J. Am. Chem. Soc. 2012, 134, 1653-61 10.1021/ja208510m
17. Calvaresi, M.; Bottoni, A.; Garavelli, M. J. Phys. Chem. B 2007, 111, 6557-70 10.1021/jp071581i
18. Šebera, J.; Trantírek, L.; Tanaka, Y.; Sychrovský, V. J. Phys. Chem. B 2012, 116, 12535-44 10.1021/jp309098d
19. Sadeghian, K.; Flaig, D.; Blank, I. D.; Schneider, S.; Strasser, R.; Stathis, D.; Winnacker, M.; Carell, T.; Ochsenfeld, C. Angew. Chem., Int. Ed. 2014, 53, 10044-8 10.1002/anie.201403334
20. Davis, I. W.; Leaver-Fay, A.; Chen, V. B.; Block, J. N.; Kapral, G. J.; Wang, X.; Murray, L. W.; Arendall, W. B., III; Snoeyink, J.; Richardson, J. S.; Richardson, D. C. Nucleic Acids Res. 2007, 35, 375-83 10.1093/nar/gkm216
21. Gordon, J. C.; Myers, J. B.; Folta, T.; Shoja, V.; Heath, L. S.; Onufriev, A. Nucleic Acids Res. 2005, 33, W368 10.1093/nar/gki464
22. Case, D.; Darden, T.; Cheatham, T. E., III; Simmerling, C.; Wang, J.; Duke, R.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D.; Seetin, M.; Sagui, C.; Babin, V.; Kollman, P. AMBER 10; University of California: San Francisco, 2008.
23. Miller, J. H.; Fan-Chiang, C.-C. P.; Straatsma, T. P.; Kennedy, M. a. J. Am. Chem. Soc. 2003, 125, 6331-6 10.1021/ja029312n
24. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926 10.1063/1.445869
25. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802 10.1002/jcc.20289
26. Sherwood, P.; de Vries, A. H.; Guest, M. F.; Schreckenbach, G.; Catlow, C. R. A.; French, S. A.; Sokol, A. A.; Bromley, S. T.; Thiel, W.; Turner, A. J.; Billeter, S.; Terstegen, F.; Thiel, S.; Kendrick, J.; Rogers, S. C.; Casci, J.; Watson, M.; King, F.; Karlsen, E.; Sjøvoll, M.; Fahmi, A.; Schäfer, A.; Lennartz, C. J. Mol. Struct.: THEOCHEM 2003, 1, 632 10.1016/S0166-1280(03)00285-9
27. Kussmann, J.; Ochsenfeld, C. J. Chem. Phys. 2013, 138, 134114 10.1063/1.4796441
28. TURBOMOLE, version 6.5; TURBOMOLE GmbH: Karlsruhe, Germany, 2013; http://www.turbomole.com.
29. Smith, W.; Yong, C. W.; Rodger, P. M. Mol. Simul. 2002, 28, 385-471 10.1080/08927020290018769
30. de Vries, A. H.; Sherwood, P.; Collins, S. J.; Rigby, A. M.; Rigutto, M.; Kramer, G. J. J. Phys. Chem. B 1999, 103, 6133-6141 10.1021/jp9913012
31. Kästner, J.; Carr, J. M.; Keal, T. W.; Thiel, W.; Wander, A.; Sherwood, P. J. Phys. Chem. A 2009, 113, 11856-65 10.1021/jp9028968
32. Becke, A. D. Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100 10.1103/PhysRevA.38.3098
33. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785-789 10.1103/PhysRevB.37.785
34. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. J. Chem. Phys. 2010, 132, 154104 10.1063/1.3382344
35. Schäfer, A.; Horn, H.; Ahlrichs, R. J. Chem. Phys. 1992, 97, 2571-2577 10.1063/1.463096
36. Kussmann, J.; Beer, M.; Ochsenfeld, C. WIREs Comp. Mol. Sci. 2013, 3, 614-636 10.1002/wcms.1138
37. Blank, I. D.; Sadeghian, K.; Ochsenfeld, C. Sci. Rep. 2015, 5, 10369 10.1038/srep10369
38. Fromme, J. C.; Verdine, G. L. J. Biol. Chem. 2003, 278, 51543-51548 10.1074/jbc.M307768200
39. We found it much more likely that the glycosidic is broken first, thus forming the oxacarbenium ion, before N9 can be protonated.