Role of ligand binding in structural organization of add a-riboswitch aptamer: A molecular dynamics simulation

Journal of Biomolecular Structure and Dynamics

Volumn 29, Issue 2, 2011, Pages 403-416

  Gong, Zhou ^a   Zhao, Yunjie ^a   Chen, Changjun ^a   Xiao, Yi ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; APTAMER; MAGNESIUM ION; NUCLEOTIDE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; HYDROGEN BOND; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; RIBOSWITCH; STRUCTURE ANALYSIS;

EID: 80052240487     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2011.10507394     Document Type: Article

References (70)

1. Winkler, W. C., Nahvi, A., Sudarsan, N., Barrick, J. E., and Breaker, R. R., 2003. Nat. Struct Biol, 10:701–707.
2. Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S., and Breaker, R. R., 2003. Genes Dev, 17:2688–2697.
3. Sudarsan, N., Barrick, J. E., and Breaker, R. R., 2003. RNA, 9:644–647.
4. Winkler, W. C., Cohen-Chalamish, S., and Breaker, R. R., 2002. Proc Natl Acad Sci U S A, 99:15908–15913.
5. Suess, B., Fink, B., Berens, C., Stentz, R., and Hillen, W., 2004. Nucleic Acids Res, 32:1610–1614.
6. Batey, R. T., Gilbert, S. D., and Montange, R. K., 2004. Nature, 432:411–415.
7. Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C., and Breaker, R. R., 2003. Cell, 113:577–586.
8. Winkler, W., Nahvi, A., and Breaker, R. R., 2002. Nature, 419:952–956.
9. Mandal, M., and Breaker, R. R., 2004. Nat Struct Mol Biol, 11:29–35.
10. Epshtein, V., Mironov, A. S., and Nudler, E., 2003. Proc Natl Acad Sci U S A, 100:5052–5056.
11. Grundy, F. J., Lehman, S. C., and Henkin, T. M., 2003. Proc Natl Acad Sci U S A, 100:12057–12062.
12. Dann, C. E., Wakeman, C. A., Sieling, C. L., Baker, S. C., Irnov, I., and Winkler, W. C., 2007. Cell, 130:878–892.
13. Mironov, A. S., Gusarov, I., Rafikov, R., Lopez, L. E., Shatalin, K., Kreneva, R. A., Perumov, D. A., and Nudler, E., 2002. Cell, 111:747–756.
14. Roth, A., Winkler, W. C., Regulski, E. E., Lee, B. W., Lim, J., Jona, I., Barrick, J. E., Ritwik, A., Kim, J. N., Welz, R., Iwata-Reuyl, D., and Breaker, R. R., 2007. Nat Struct Mol Biol, 14:308–317.
15. Serganov, A., 2009. Curr Opin Struct Biol, 19:251–259.
16. Garst, A. D., and Batey, R. T., 2009. Biochim Biophys Acta, 1789:584–591.
17. Noeske, J., Richter, C., Grund1, M. A., Nasiri, H. R., Schwalbe, H., and Wohnert, J., 2005. Proc Natl Acad Sci U S A, 102:1372–1377.
18. Mandal, M., Lee, M., Barrick, J. E., Weinberg, Z., Emilsson, G. M., Ruzzo, W. L., and Breaker, R. R., 2004. Science, 306:275–279.
19. Nudler, E., and Mironov, A. S., 2004. Trends Biochem Sci, 29:11–17.
20. Brant1, S., 2004. Trends Microbiol, 12:473–475.
21. Mandal, M., and Breaker, R. R., 2004. Nat Rev Mol Cell Biol, 5:451–463.
22. Vitreschak, A. G., Rodionov, D. A., Mironov, A. A., and Gelfand, M. S., 2004. Trends Genet, 20:44–50.
23. Wachter, A., Tunc-Ozdemir, M., Grove, B. C., Green, P. J., Shintani, D. K., and Breaker, R. R., 2007. Plant Cell, 19:3437–3450.
24. Ling, B., Wang, Z., Zhang, R., Meng, X., Liu, Y., Zhang, C., and Liu, C., 2009. J Mol Graph Model, 28:37–45.
25. Serganov, A., Yuan, Y. R., Pikovskaya, O., Polonskaia, A., Malinina, L., Phan, A. T., Hobartner, C., Micura, R., Breaker, R. R., and Patel, D. J., 2004. Chem Biol, 11:1729–1741.
26. Ali, M., Lipfert, J., Seifert, S., Herschlag, D., and Doniach, S., 2009. J Mol Biol
27. Garst, A. D., Heroux, A., Rambo, R. P., and Batey, R. T., 2008. J Biol Chem, 283:22347–22351.
28. Delfosse, V., Bouchard, P., Bonneau, E., Dagenais, P., Lemay, J. F., Lafontaine, D. A., and Legault, P., 2010. Nucleic Acids Res, 38:2057–2068.
29. Stoddard, C. D., Gilbert, S. D., and Batey, R. T., 2008. RNA, 14:675–684.
30. Brenner, M. D., Scanlan, M. S., Nahas, M. K., Ha, T., and Silverman, S. K., 2010. Biochemistry, 49:1596–1605.
31. Gilbert, S. D., Mediatore, S. J., and Batey, R. T., 2006. J Am Chem Soc, 128:14214–14215.
32. Noeske, J., Buck, J., Furtig, B., Nasiri, H. R., Schwalbe, H., and Wohnert, J., 2007. Nucleic Acids Res, 35:572–583.
33. Noeske, J., Schwalbe, H., and Wohnert, J., 2007. Nucleic Acids Res, 35:5262–5273.
34. Gilbert, S. D., Stoddard, C. D., Wise, S. J., and Batey, R. T., 2006. J Mol Biol, 359:754–768.
35. Ottink, O. M., Rampersad, S. M., Tessari, M., Zaman, G. J., Heus, H. A., and Wijmenga, S. S., 2007. RNA, 13:2202–2212.
36. Sharma, M., Bulusu, G., and Mitra, A., 2009. RNA, 15:1673–1692.
37. Villa, A., Wohnert, J., and Stock, G., 2009. Nucleic Acids Res, 37:4774–4786.
38. Gilbert, S. D., Love, C. E., Edwards, A. L., and Batey, R. T., 2007. Biochemistry, 46:13297–13309.
39. Cai, L., Pei, Z., and Chen, S., 2009. Acta Biophys Sin, 25:65–71.
40. Luo, L., Zhang, S.-W., Chen, W., and Pan, Q., 2009. Acta Biophys Sin, 25:282–286.
41. Cao, Z., and Wang, J., 2010. Acta Biophys Sin, 26:783–789.
42. Priyakumar, U. D., and MacKerell, A. D., Jr. 2010. J Mol Biol, 396:1422–1438.
43. Daldrop, P., Reyes, F. E., Robinson, D. A., Hammond, C. M., Lilley, D. M., Batey, R. T., and Brenk, R., 2011. Chem Biol, 18:324–335.
44. Bastet, L., Dube, A., Masse, E., and Lafontaine, D. A., 2011. Mol Microbiol, 80:1148–1154.
45. Cao, S., and Chen, S. J., 2011. J Phys Chem B, 115:4216–4226.
46. Chen, S. J., 2008. Annual Review of Biophysics, 37:197–214.
47. Rao, G. S., Ramachandran, M. V., and Bajaj, J. S., 2006. J Biomol Struct Dyn, 23:377–384.
48. Zhong, L., 2010. J Biomol Struct Dyn, 28:355–361.
49. Lee, H. M., Jin, B., Han, S. W., and Kim, S. K., 2010. J Biomol Struct Dyn, 28:421–430.
50. Wiesner, J., Kriz, Z., Kuca, K., Jun, D., and Koca, J., 2010. J Biomol Struct Dyn, 28:393–403.
51. Lu, Z. R., Seo, E., Yan, L., Yin, S. J., Si, Y. X., Qian, G. Y., Park, Y. D., and Yang, J. M., 2010. J Biomol Struct Dyn, 28:259–276.
52. He, Y., Chen, C., and Xiao, Y., 2009. J Comput Biol, 16:1719–1730.
53. Xiao, Y., Chen, C., and He, Y., 2009. Int J Mol Sci, 10:2838–2848.
54. He, Y., Zhou, R., Huang, Y., and Xiao, Y., 2009. Comput Biol Chem, 33:325–328.
55. Chen, C., and Xiao, Y., 2008. Bioinformatics, 24:659–665.
56. Chen, C., and Xiao, Y., 2006. Phys Biol, 3:161–171.
57. Chen, C., Xiao, Y., and Zhang, L., 2005. Biophys J, 88:3276–3285.
58. Case, D. A., Darden, T. A., Cheatham, I. T. E., Simmerling, C. L., Wang, R. E.D. J., Luo, R. K.M. M., Pearlman, D. A., Crowley, M., Walker, R. C., Zhang, W., Wang, B., Hayik, S. A. R., Seabra, G., Wong, K. F., Paesani, F., Wu, X., Brozell, S., Tsui, V., Gohlke, H. L. Y., Tan, C., Mongan, J., Hornak, V., Cui, G., Beroza, P., Mathews, D. H., Schafmeister, C., Ross, W. S., and Kollman, P. A., 2006. AMBER 9
59. Cheatham, T. E., Cieplak, P., and Kollman, P. A., 1999. J Biomol Struct Dyn, 16:845–862.
60. Gong, Z., and Xiao, Y., 2010. J Biomol Struct Dyn, 28:431–441.
61. Zhao, Y., Gong, Z., and Xiao, Y., 2011. J Biomol Struct Dyn, 28:815–826.
62. William, J. C., Jorgensen, L., Madura, J. D., Impey, R. W., and Klein, M. L., 1983. J Chem Phys, 79
63. Lemay, J. F., Penedo, J. C., Tremblay, R., Lilley, D. M., and Lafontaine, D. A., 2006. Chem Biol, 13:857–868.
64. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C., 1977. J. Comput Phys, 23:327–341.
65. Loncharich, R. J., Brooks, B. R., and Pastor, R. W., 1992. Biopolymers, 32:523–535.
66. Humphrey, W., Dalke, A., and Schulten, K., 1996. J Mol Graph, 14:33–38. 27–38
67. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E., 2004. J Comput Chem, 25:1605–1612.
68. Jain, N., Zhao, L., Liu, J. D., and Xia, T., 2010. Biochemistry, 49:3703–3714.
69. Greenleaf, W. J., Frieda, K. L., Foster, D. A., Woodside, M. T., and Block, S. M., 2008. Science, 319:630–633.
70. Lin, J. C., and Thirumalai, D., 2008. J Am Chem Soc, 130:14080–14081.