Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction

Proceedings of the National Academy of Sciences of the United States of America

Volumn 95, Issue 19, 1998, Pages 11077-11082

  Torres, Rhonda A ^a   Bruice, Thomas C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROXYL GROUP; MAGNESIUM ION; METAL ION; NUCLEIC ACID BASE; PHOSPHATE; RIBOZYME;

CATALYSIS; CHEMICAL REACTION; CONFERENCE PAPER; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME DEGRADATION; ENZYME MECHANISM; MOLECULAR DYNAMICS; PRIORITY JOURNAL;

EID: 0032530132     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.95.19.11077     Document Type: Article

References (38)

1. Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R. & Bruening, G. (1986) Science 231, 1577-1580.
2. Buzayan, J. M., Gerlach, W. L. & Brucning, G. (1986) Proc. Natl. Acad. Sci. USA 83, 8859-8862.
3. Buzayan, J. M., Gerlach, W. L. & Bruening, G. (1986) Nature (London) 323, 349-353.
4. Uhlenbeck, O. C. (1987) Nature (London) 328, 596-600.
5. Ruffner, D. E., Stormo, G. D. & Uhlenbeck, O. C. (1990) Biochemistry 29, 10695-10702.
6. Hertel, K. J., Pardi, A., Uhlenbeck, O. C., Koizumi, M., Ohtsuka, E., Uesugi, S., Cedergren, R., Eckstein, F., Gerlach, W. L., Hodgson, R. & Symons, R. H. (1992) Nucleic Acids Res. 20, 3252.
7. Hasseloff, J. & Gerlach, W. L. (1988) Nature (London) 334, 585-591.
8. Westheimer, F. H. (1968) Acc. Chem. Res. 1, 70-78.
9. van Tol, H., Buzayan, J. M., Feldstein, P. A., Eckstein, F. & Bruening, G. (1990) Nucleic Acids Res. 18, 1971-1975.
10. Slim, G. & Gait, M. J. (1991) Nucleic Acids Res. 19, 1183-1188.
11. Koizumi, M. & Ohtsuka, E. (1991) Biochemistry 30, 5145-5150.
12. Dahm, S. A. & Uhlenbeck, O. C. (1991) Biochemistry 30, 9464-9469.
13. Dahm, S. C., Derrick, W. B. & Uhlenbeck, O. C. (1993) Biochemistry 32, 13040-13045.
14. Dempcy, R. O. & Bruice, T. C. (1994) J. Am. Chem. Soc. 116, 4511-4512.
15. Bruice, T. C., Tsubouchi, A., Dempcy, R. O. & Olson, L. P. (1996) J. Am. Chem. Soc. 116, 9867-9875.
16. Mei, H. Y., Kaaret, T. W. & Bruice, T. C. (1989) Proc. Natl. Acad. Sci. 86, 9727-9731.
17. Pley, H. W., Flaherty, K. M. & McKay, D. B. (1994) Nature (London) 372, 68-74.
18. Scott, W. G., Finch, J. T. & Klug, A. (1995) Cell 81, 991-1002.
19. Scott, W. G., Murray, J. B., Arnold, J. R. P., Stoddard, B. L. & Klug, A. (1996) Science 274, 2065-2069.
20. Murray, J. B., Terwey, D. P., Maloney, L., Kerpelsky, A., Usman, N., Beigclman, L. & Scott, W. G. (1998) Cell 92, 665-673.
21. Lightstone, F. C. & Bruice, T. C. (1994) J. Am. Chem. Soc. 116, 10789-10790.
22. Lightstone, F. C. & Bruice, T. C. (1996) J. Am. Chem. Soc. 118, 2595-2605.
23. Lightstone, F. C. & Bruice, T. C. (1997) J. Am. Chem, Soc. 119, 9103-9113.
24. Åqvist, J. (1990) J. Phys. Chem. 94, 8021-8024.
25. Jorgensen, W. L., Chandrasekhar, J. & Madura, J. D. (1983) J. Chem. Phys. 79, 926-935.
26. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E. I., Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K. & Kollman, P. A. (1995) in AMBER (Univ. of California Press, San Francisco).
27. Cheatham, T. E. I., Miller, J. L., Fox, T., Darden, T. A. & Kollman, P. A. (1995) J. Am. Chem. Soc. 117, 4193-4194.
28. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T. A., Lee, H. & Pedersen, L. G. (1995) J. Chem. Phys. 103, 8577-8593.
29. Darden, T. A., York, D. & Pedersen, L. G. (1993) J. Chem. Phys. 98, 10089-10092.
30. Chen, Z. M., Çagin, T. & Goddard, W. A., III (1997) J. Comp. Chem. 18, 1365-1370.
31. van Gunsteren, W. F. & Berendsen, H. J. C. (1977) Mol. Phys. 34, 1311-1327.
32. Huang, C. C., Pettersen, E. F., Klein, T. E., Ferrin, T. E. & Landridge, R. (1991) J. Mol. Graph. 9, 230-236.
33. Ferrin, T. E., Huang, C. C., Jarvis, L. E. & Landridge, R. (1988) J. Mol. Graph. 6, 13-27.
34. McKay, D. B. (1996) Catalytic RNA: Nucleic Acids and Molecular Biology (Springer, New York), 161-172.
35. McKay, D. B. (1996) RNA 2, 395-403.
36. Thomson, J. B., Tuschl, T. & Eckstein, F. (1996) Catalyic RNA: Nucleic Acids and Molecular Biology (Springer, New York), 173-196.
37. Zhou, D. M., Usman, N., Wincott, F. E., Matulic-Adamic, J., Orita, M., Zhang, L. H., Komiyama, M., Kumar, P. K. R. & Taira, K. (1996) J. Am. Chem. Soc. 118, 5862-5866.
38. Uchimaru, T., Uebayasi, M., Hirose, T., Tsuzuki, S., Yliniemelä, A., Tanabe, K. & Taira, K. (1996) J. Org. Chem. 61, 1599-1608.