Double-metal-ion/single-metal-ion mechanisms of the cleavage reaction of ribozymes: First-principles molecular dynamics simulations of a fully hydrated model system

Journal of Chemical Theory and Computation

Volumn 1, Issue 5, 2005, Pages 925-934

  Boero, Mauro ^a   Tateno, Masaru ^b,d   Terakura, Kiyoyuki ^c,d   Oshiyama, Atsushi ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33644970162     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct050066q     Document Type: Article

References (70)

1. Zhou, D.; Taira, K. Chem. Rev. 1998, 98, 991-1026.
2. Perreault, D. M.; Anslyn, E. V. Angew. Chem., Int. Ed. Engl. 1997, 36, 432-450.
3. Hutchins, C. J.; Rathjen, P. D.; Forster, A. C.; Symons, R. H. Nucleic Acids Res. 1986, 14, 3627-3640.
4. Uhlenbeck, O. C. Nature 1987, 328, 596-600.
5. Haseloff, J.; Gerlach, W. L. Nature 1988, 334, 585-591.
6. Koizumi, M.; Iwai, S.; Otsuka, E. Nucleic Acids Res. 1989, 17, 7059-7071.
7. Pley, H. W.; Flaherty, K. M.; McKay, D. B. Nature 1994, 372, 68-74.
8. Murray, J. B.; Terwey, D. P.; Maloney, L.; Karpeisky, A.; Usman, N.; Biegelman, L.; Scott, W. G. Cell 1998, 92, 665-673.
9. Buzayan, J. M.; Gerlach, W. L.; Bruening, G. Nature 1986, 323, 349-353.
10. Santoro, S. W.; Joyce, G. F. Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 4262-4266.
11. Carola, C.; Eckstein, F. Curr. Opin. Chem. Biol. 1999, 3, 274-283.
12. Bramlage, B.; Luzi, E.; Eckstein, F. Trends Biotechnol. 1998, 16, 434-438.
13. Hermann, T.; Auffinger, P.; Westhof, E. Eur. Biophys. J. 1998, 27, 153-165.
14. Fedor, M. J. J. Mol. Biol. 2000, 297, 269-291.
15. Joyce, G. F. Science 2000, 289, 401-402.
16. Schlutes, E. A.; Bartel, D. P. Science 2000, 289, 448-452.
17. Yoshinari, K.; Taira, K. Nucleic Acids Res. 2000, 28, 1730-1742.
18. Taira, K.; Nishikawa, S. In Gene regulation: biology of antisense RNA and DNA. Erickson, R. P., Izant, J. G., Eds.; Raven Press: New York, 1992; pp 35-54.
19. Takagi, Y.; Warashina, M.; Stec, W. J.; Yoshinari, K.; Taira, K. Nucleic Acids Res. 2001, 29, 1815-1834.
20. Oshima, K.; Kawasaki, H.; Soda, Y.; Tani, K.; Asano, S.; Taira, K. Cancer Res. 2003, 63, 6809-6814.
21. Pyle, A. M. Science 1993, 261, 709-714.
22. Steitz, T. A.; Steitz, J. A. Proc. Natl Acad. Sci. U. S. A. 1993, 90, 6498-6502.
23. Uchimaru, T.; Uebayashi, M.; Tanabe, K.; Taira, K. FASEB J. 1993, 7, 137-142.
24. Scott, W. G.; Murray, J. B.; Arnold, J. R. P.; Stoddard, B. L.; Klug, A. Science 1996, 274, 2065-2069.
25. Kuimelis, R. G.; McLaughlin, L. W. Chem. Rev. 1998, 98, 1027-1044.
26. Zhou, D. M.; Taira, K. Proc. Natl. Acad. Sci. USA 1997, 94, 14343-14348.
27. Zhou, J.; Zhou, D.; Takagi, Y.; Kasai, Y.; Inoue, A.; Baba, T.; Taira, K. Nucleic Acids Res. 2002, 30, 2374-2382.
28. Li, Y.; Breaker, R. R. J. Am. Chem. Soc. 1999, 121, 5364-5372.
29. Noodleman, L.; Lovell, T.; Han, W. G.; Li, J.; Himo, F. Chem. Rev. 2004, 104, 459-508.
30. Torres, R. A.; Himo, F.; Bruice, T. C.; Noodleman, L.; Lovell, T. J. Am. Chem. Soc. 2003, 125, 9861-9867.
31. Boero, M.; Terakura, K.; Tateno, M. J. Am. Chem. Soc. 2002, 124, 8949-8957.
32. Zhang, B.; Cech, T. R. Chem. Biol. 1998, 5, 539-553.
33. Kuwabara, T.; Warashima, M.; Taira, K. Trends Biotechnol. 2000, 18, 462-468.
34. Uchimaru, T.; Tanabe, K.; Nishikawa, S.; Taira, K. J. Am. Chem. Soc. 1991, 113, 4351-4353.
35. Dejaegere, A.; Lim, C.; Karplus, M. J. Am. Chem. Soc. 1991, 113, 4353-4355.
36. Lim, C.; Karplus, M. J. Am. Chem. Soc. 1990, 112, 5872-5873.
37. Storer, J. W.; Uchimaru, T.; Tanabe, K.; Uebayashi, M.; Nishikawa, S.; Taira, K. J. Am. Chem. Soc. 1991, 113, 5216-5219.
38. Yliniemela, A.; Uchimaru, T.; Tanabe, K.; Taira, K. J. Am. Chem. Soc. 1993, 115, 3032-3033.
39. Uchimaru, T.; Stec, W. J.; Tsuzuki, S.; Hirose, T.; Tanabe, K.; Taira, K. Chem. Phys. Lett. 1996, 263, 691-696.
40. Doltsinis, N. L.; Sprik, M. Phys. Chem. Chem. Phys. 2003, 5, 2612-2618.
41. Akola, J.; Jones, R. O. J. Phys. Chem B 2003, 107, 11774-11783.
42. Alber, F.; Folkers, G.; Carloni, P. THEOCHEM 1999, 489, 237-245.
43. Takagi, Y.; Taira, K. J. Am. Chem. Soc. 2002, 124, 3850-3852.
44. Sawata, S.; Komiyama, M.; Taira, K. J. Am. Chem. Soc. 1995, 117, 2357-2358.
45. Weinstein, L. B.; Jones, B. C.; Cosstick, R.; Cech, T. R. Nature 1997, 388, 805-808.
46. Oivanen, M.; Kuusela, S.; Lönnberg, H. Chem. Rev. 1998, 98, 961-990.
47. Lyne, P. D.; Karplus, M. J. Am. Chem. Soc. 2000, 122, 166-167.
48. Dahm, S. C.; Derrick, W. B.; Uhlenbeck, O. C. Biochemistry 1993, 32, 13040-13045.
49. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
50. CPMD code by J. Hutter et al. at MPI für Festkörperforschung and IBM Zurich Research Laboratory (1990-2004).
51. Kohn, W.; Sham, L. J. Phys. Rev. A: At. Mol. Opt. Phys. 1965, 140, A1133-A1138.
52. Hamprecht, F. A.; Cohen, A. J.; Tozer, D. J.; Handy, N. C. J. Chem. Phys. 1998, 109, 6264-6271.
53. Boese, A. D.; Doltsinis, N. L.; Handy, N. C.; Sprik M. J. Chem. Phys. 2000, 112, 1670-1678.
54. Troullier, N.; Martins, J. L. Phys. Rev. B: Condens. Matter Mater. Phys. 1991, 43, 1993-2006.
55. Louie, S. G.; Froyen, F.; Cohen, M. L. Phys. Rev. B: Condens. Matter Mater. Phys. 1982, 26, 1738-1742.
56. Nose, S. Mol. Phys. 1984, 52, 255-268.
57. Nose, S. J. Chem. Phys. 1984, 81, 511-519.
58. Hoover, W. G. Phys. Rev. A: At. Mol. Opt. Phys. 1985, 31, 1695-1697.
59. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 12562-12566.
60. Iannuzzi, M.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2003, 90, 238302.
61. Sprik, M.; Ciccotti, G. J. Chem. Phys. 1998, 109, 7737-7744.
62. Segall, M. D.; Shah, R.; Pickard, C. J.; Payne, M. C. Phys. Rev. B: Condens. Matter Mater. Phys. 1996, 54, 16317-16320.
63. Boero, M.; Ikeshoji, T.; Teralura, K.; Liew, C. C.; Parrinello, M. J. Am. Chem. Soc. 2004, 126, 6280-6286.
64. Here and in every metadynamics simulation, the time has to be intended as the progress in the FES exploration and not as a "real" time, as explained in refs 59 and 60. Hence, it gives the energetically ordered sequence of the various steps of the reaction path along with the energy difference with respect to the initial potential well of the reactants.
65. +.
66. In each case, the LUMO is a diffuse orbital, precursor state of a solvated electron. See, e.g., Boero, M.; Parrinello, M.; Terakura, K.; Ikeshoji, T.; Liew, C. C. Phys. Rev. Lett. 2003, 90, 226403.
67. Hermann, T.; Auffinger, P.; Scott, W. G.; Westhof, E. Nucleic Acids Res. 1997, 25, 3421-3427.
68. Gregersen, B. A.; Lopez, X.; York, D. M. J. Am. Chem. Soc. 2004, 126, 7504-7513.
69. Warashima, M.; Takagi, Y.; Stec, W. J.; Taira, K. Curr. Opin. Biotechnol. 2000, 11, 354-362.
70. Murray, J. B.; Scott, W. G. J. Mol. Biol. 2000, 296, 33-41.