Predicting RNA structures: The model of the RNA element binding Rev meets the NMR structure

Folding and Design

Volumn 2, Issue 2, 1997, Pages 141-147

  Leclerc, Fabrice ^a   Srinivasan, Jayashree ^a   Cedergren, Robert ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

REV PROTEIN; VIRUS RNA;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; CONFORMATION; FORECASTING; HUMAN IMMUNODEFICIENCY VIRUS 1; METABOLISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN BINDING; REPRODUCIBILITY;

BINDING SITES; COMPUTER SIMULATION; FORECASTING; GENE PRODUCTS, REV; HIV-1; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; REPRODUCIBILITY OF RESULTS; RNA, VIRAL;

EID: 0030623530     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(97)00019-9     Document Type: Article

References (21)

1. Leclerc, F., Cedergren, R. & Ellington, A.E. (1994). A three-dimensional model of the Rev-binding element of HIV-1 derived from analyses of aptamers. Nat. Struct. Biol. 1, 293-300.
2. Tuerk, C. & Gold, L (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 405-510.
3. Ellington, A.E. & Szostak, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
4. Giver, L, Bartel, D., Zapp, M., Pawul, A., Green, M. & Ellington, A.D. (1993). Selection and design of high-affinity RNA ligands for HIV-1 Rev. Nucleic Acids Res. 21, 5509-5516.
5. Major, F., Turcotte, M., Gautheret, D., Lapalme, G., pillion, E. & Cedergren, R. (1991). The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science 253, 1255-1260.
6. Gautheret, D., Major, F. & Cedergren, R. (1993). Modeling the threedimensional structure of RNA using discrete nucleotide conformational sets./ Mol. Biol. 229, 1049-1064.
7. Battiste, J.L., Tan, R., Frankel, A.D. & Williamson, J.R. (1995). Assignment and modeling of the Rev response element RNA bound to a Rev peptide using 13C-heteronuclear NMR. J. Biomol. NMR 6, 375-389.
8. Peterson, R.D., Bartel, O.P., Szostak, J.W., Horvath, S.S. & Feigon, J. (1994). 1H NMR studies of the high-affinity Rev binding site of the Rev responsive element of HIV-1 mRNA: base pairing in the core binding element. Biochemistry 33, 5357-5365.
9. Rick, S.W. & Berne B.J. (1994). The aqueous solvation of water: a comparison of continuum methods with molecular dynamics. J. Am. Chem. Soc. 116, 3949-3954.
10. Le, S.-Y., Pattabiraman, N. & Maizel, J.V., Jr. (1994). RNA tertiary structure of the HIV RRE domain II containing non-Watson-Crick base pairs GG and GA: molecular modeling studies. Nucleic Acids Res. 22, 3966-3976.
11. Saenger, W. (1988). Principles of Nucleic Acid Structure. (2nd edn), Springer Verlag, New York.
12. Arnott, S., Hukins, D.W.L. & Dover, S.D. (1972). Optimised parameters for RNA double helices. Biochem. Biophys. Res. Commun. 48, 1392-1399.
13. Pearlman, D.A. & Kim, S. (1986). Conformational studies of nucleic acids: III. Empirical multiple correlation functions for nucleic acid torsion angles. J. Biomol. Struct. Dyn. 4, 49-67.
14. McConnell, K.J., Nirmala, R., Young, M.A., Ravishanker, G. & Beveridge, D.L. (1994). A nanosecond molecular dynamics trajectory for a B DNA double helix: evidence for substates. J. Am. Chem. Soc. 116, 4461-4462.
15. Swaminathan, S., Ravishanker, G. & Beveridge, D.L. (1991). Molecular dynamics of B-DNA including water and counterions: a 140-ps trajectory for d(CGCGAATTCGCG) based on the GROMOS force field. J. Am. Chem. Soc. 113, 5027-5040.
16. Puglisi, J.D., Tan, R, Canlan, B.J., Frankel, A.D. & Williamson, J.R. (1992). Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science 257, 76-80.
17. Aboul-ela, F., Kam, J. & Varani, G. (1995). The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol. 253, 313-332.
18. Weiner, SJ. & Weiner, P., et al., (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.
19. Wiener, S.J., Kollman, P.A., Nguyen, D.T. & Case, D.A. (1986). An allatom forcefield for simulations of proteins and nucleic acid. J. Comp. Chem. 7, 230- 252.
20. Gilson, M.K. & Honig, B.H. (1988). Energetics of charge-charge interactions in proteins. Proteins 3, 32-53.
21. Klapper, I., Hagstrom, R., Fine, R., Sharp, K. & Honig, B. (1986). Focusing of electric fields in the active site of Cu-Zn Superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins 1, 47-59.