Molecular dynamics simulation for probing the flexibility of the 35 nucleotide sl1 sequence kissing complex from hiv-1lai genomic rna

Journal of Biomolecular Structure and Dynamics

Volumn 24, Issue 5, 2007, Pages 471-479

  Mazier, Sonia ^a   Genest, Daniel ^a  

^a UNIVERSITÉ D'ORLÉANS   (France)

Author keywords

HIV; Kissing Complex; Molecular dynamics; RNA

Indexed keywords

GENOMIC RNA; MONOMER;

ARTICLE; BASE PAIRING; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA CONFORMATION; RNA STABILITY; RNA STRUCTURE; VIRUS CAPSID;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33947491695     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2007.10507135     Document Type: Article

References (48)

1. Murti, K. G., Bondurant, M., and Tereba, A., 1981. J Virol, 37:411–419.
2. Bender, W., Chien, Y. H., Chattopadhyay, S., Vogt, P. K., Gardner, M. B., and Davidson, N., 1978. J Virol, 25:888–896.
3. Bender, W., and Davidson, N., 1976. Cell, 7:595–607.
4. Kung, H. J., Bailey, J. M., Davidson, N., Nicolson, M. O., and McAllister, R. M., 1975. J Virol, 16:397–411.
5. Kung, H. J., Hu, S., Bender, W., Bailey, J. M., Davidson, N., Nicolson, M. O., and McAllister, R. M., 1976. Cell, 7:609–620.
6. Aldovini, A., and Young, R. A., 1990. J Virol, 64:1920–1926.
7. Clavel, F., and Orenstein, J. M., 1990. J Virol, 64:5230–5234.
8. Hayashi, T., Shioda, T., Iwakura, Y., and Shibuta, H., 1992. Virology, 188:590–599.
9. Lever, A., Gottlinger, H., Haseltine, W., and Sodroski, J., 1989. J Virol, 63:4085–4087.
10. Fu, W., Gorelick, R. J., and Rein, A., 1994. J Virol, 68:5013–5018.
11. Shen, N., Jette, L., Liang, C., Wainberg, M. A., and Laughrea, M., 2000. J Virol, 74:5729–5735.
12. Laughrea, M., and Jette, L., 1994. Biochemistry, 33:13464–13474.
13. Marquet, R., Paillart, J. C., Skripkin, E., Ehresmann, C., and Ehresmann, B., 1994. Nucleic Acids Res, 22:145–151.
14. Muriaux, D., Girard, P. M., Bonnet-Mathoniere, B., and Paoletti, J., 2098. J Biol Chem, 270:8 216 (1995)
15. Skripkin, E., Paillart, J. C., Marquet, R., Ehresmann, B., and Ehresmann, C., 1994. Proc Natl Acad Sci USA, 91:4945–4949.
16. Dardel, F., Marquet, R., Ehresmann, C., Ehresmann, B., and Blanquet, S., 1998. Nucleic Acids Res, 26:3567–3571.
17. Ennifar, E., and Dumas, P., 2006. J Mol Biol, 356:771–782.
18. Muriaux, D., De Rocquigny, H., Roques, B. P., and Paoletti, J., 1996. J Biol Chem, 271:33686–33692. (a)
19. Muriaux, P. Fosse, and Paoletti, J., 1996. Biochemistry, 35:5075–5082. (b)
20. Clever, J., Sassetti, C., and Parslow, T. G., 1995. J Virol, 69:2101–2109.
21. Greatorex, J., Gallego, J., Varani, G., and Lever, A., 2002. J Mol Biol, 322:543–557.
22. Baba, S., Takahashi, K., Noguchi, S., Takaku, H., Koyanagi, Y., Yamamoto, N., and Kawai, G., 2005. J Biochem (Tokyo), 138:583–592.
23. Ennifar, P. Walter, Ehresmann, B., Ehresmann, C., and Dumas, P., 2001. Nat Struct Biol, 8:1064–1068.
24. Ennifar, E., Yusupov, M., Walter, P., Marquet, R., Ehresmann, B., Ehresmann, C., and Dumas, P., 1999. Structure, 7:1439–1449.
25. Girard, F., Barbault, F., Gouyette, C., Huynh-Dinh, T., Paoletti, J., and Lancelot, G., 1999. J Biomol Struct Dyn, 16:1145–1157.
26. Kieken, F., Arnoult, E., Barbault, F., Paquet, F., Huynh-Dinh, T., Paoletti, J., Genest, D., and Lancelot, G., 2002. Eur Biophys J, 31:521–531.
27. Kieken, F., Paquet, F., Brule, F., Paoletti, J., and Lancelot, G., 2006. Nucleic Acids Res, 34:343–352.
28. Mujeeb, A., Clever, J. L., Billeci, T. M., James, T. L., and Parslow, T. G., 1998. Nat Struct Biol, 5:432–436.
29. Mujeeb, A., Parslow, T. G., Zarrinpar, A., Das, C., and James, T. L., 1999. FEBS Lett, 458:387–392.
30. Ulyanov, N. B., Mujeeb, A., Du, Z., Tonelli, M., Parslow, T. G., and James, T. L., 2006. J Biol Chem
31. Takahashi, K. I., Baba, S., Chattopadhyay, P., Koyanagi, Y., Yamamoto, N., Takaku, H., and Kawai, G., 2000. Rna, 6:96–102.
32. Shen, N., Jette, L., Wainberg, M. A., and Laughrea, M., 2001. J Virol, 75:10543–10549.
33. Paillart, J. C., Dettenhofer, M., Yu, X. F., Ehresmann, C., Ehresmann, B., and Marquet, R., 2004. J Biol Chem, 279:48397–48403.
34. Lawrence, D. C., Stover, C. C., Noznitsky, J., Wu, Z., and Summers, M. F., 2003. J Mol Biol, 326:529–542.
35. Yuan, Y., Kerwood, D. J., Paoletti, A. C., Shubsda, M. F., and Borer, P. N., 2003. Biochemistry, 42:5259–5269.
36. Cheatham, T. E., Cieplak, P., and Kollman, P. A., 1999. J Biomol Struct Dyn, 16:845–862.
37. Humphrey, W., Dalke, A., and Schulten, K., 1996. J Molec Graphics, 14
38. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C., 1977. J Comput Phys, 23:327–341.
39. Darden, T., Toukmaji, A., and Pedersen, L. G., 1997. J Chim Phys, 94:1346–1364.
40. Darden, T., York, D., and Pedersen, L., 1993. J Chem Phys, 98:10089–10092.
41. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L., 1995. J Chem Phys, 103:8577–8593.
42. Ewald, P. P., 1921. Ann Phys, 64:253–287.
43. Toukmaji, A., Paul, D., and Board, J. A., 1996. PDPTA,:33–43.
44. Aci, S., Gangneux, L., Paoletti, J., and Genest, D., 2004. Biopolymers, 74:177–188.
45. Beaurain, F., and Laguerre, M., 2003. Oligonucleotides, 13:501–514.
46. Reblova, K., Spackova, N., Sponer, J. E., Koca, J., and Sponer, J., 2003. Nucleic Acids Res, 31:6942–6952.
47. Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H., 1999. J Mol Biol, 288:911–940.
48. Zucker, M., 2003. Nucleic Acids Res, 31:3406–3415.