MD Studies of the DIS/DIS Kissing Complex Solution and X-Ray Structures

Oligonucleotides

Volumn 13, Issue 6, 2003, Pages 501-514

  Beaurain, François ^a   Laguerre, Michel ^a  

^a INSTITUT EUROPÉEN DE CHIMIE ET BIOLOGIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; GENOMIC RNA; SODIUM ION;

AQUEOUS SOLUTION; ARTICLE; DIMERIZATION; DIMERIZATION INITIATION SITE; DNA PACKAGING; HUMAN IMMUNODEFICIENCY VIRUS; IN VITRO STUDY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; RETROVIRUS; VIRION; VIRUS GENOME; X RAY ANALYSIS; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; HIV-1; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID CONFORMATION; RNA, VIRAL;

HUMAN IMMUNODEFICIENCY VIRUS; RNA VIRUSES; UNIDENTIFIED RETROVIRUS;

EID: 1542303752     PISSN: 15454576     EISSN: None     Source Type: Journal    
DOI: 10.1089/154545703322860816     Document Type: Article

References (37)

1. * and TAR-aptamer. Nucleic Acids Res. 31, 4275-4284.
2. BEGLOV, D., and ROUX, B. (1994). Finite representation of an infinite bulk systems: Solvent boundary potential for computer simulations. J. Chem. Physics 100, 9050-9063.
3. BROOKS, B.R., BRUCCOLERI, R.E., OLAFSON, B.D., STATES, D.J., SWAMINATHAN, S., and KARPLUS, M. (1983). CHARMM: A program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 4, 187-217.
4. CHANG, K.Y., and TINOCO, I. (1994). Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome. Proc. Natl. Acad. Sci. USA 91, 8705-8709.
5. CHANG, K.Y., and TINOCO, I. (1997). The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement. J. Mol. Biol. 269, 52-66.
6. CHEATHAM, T.E., KOLLMAN, P.A., and YOUNG, M.A. (2001). Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise. Biopolymers 56, 232-256.
7. DARDEL, F., MARQUET, R., EHRESMANN, C., EHRESMANN, B., and BLANQUET, S. (1998). Solution studies of dimerization initiation site of HIV-1 genomic RNA. Nucleic Acids Res. 26, 3567-3571.
8. DICKERSON, R.E. (1989). Defenitions and nomenclatures of nucleic acids parameters. J. Biomol. Struct. Dynam. 6, 627-634.
9. ENNIFAR, E., PAILLART, J. C., MARQUET, R., EHRESMANN, B., EHRESMANN, C., DUMAS, P., and WALTER, P. (2003). HIV-1 RNA dimerization initiation site is structurally similar to the ribosomal A site and binds aminoglycoside antibiotics. J. Biol. Chem. 278, 2723-2730.
10. ENNIFAR, E., WALTER, P., EHRESMANN, B., EHRESMANN, C., and DUMAS, P. (2001). Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site. Nat. Struct. Biol. 8, 1064-1068.
11. ESSMAN, U., PERERA, L., BERKOWITZ, M.L., DARDEN, T.D., and PEDERSEN, L.G. (1995). A smooth particle mesh Ewald method. J. Chem. Physics 103, 8577-8593.
12. FENG, Y.X., FU, W., WINTER, A.J., LEVIN, J.G, and REIN, A. (1995). Multiple regions of Harvey sarcoma virus RNA can dimerize in vitro. J. Virol. 69, 2486-2490.
13. FOLOPPE, N., and MACKERELL, A.D. (2000). All-atom empirical force field for nucleic acids: Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem. 21, 105-120.
14. FU, W., GORELICK, R.J., and REIN, A. (1994). Characterization of human immunodeficiency virus type 1 dimeric RNA from wild-type and protease-defective virions. J. Virol. 68, 5013-5018.
15. JORGENSEN, W.L., CHANDRASEKHAR, J., MADURA, J.D., IMPREY, R.W., and KLEIN, M.L. (1983). Comparison of simple potential functions for simulating water. J. Chem. Physics 79, 926-935.
16. JOSSINET, F., PAILLART, J.C., WESTHOF, E., HERMANN, T., SKRIPKIN, E., LODMELL, J. S., EHRESMANN, C., EHRESMANN, B., and MARQUET, R. (1999). Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding. RNA 5, 1222-1234.
17. KALÉ, L., SKEEL, R., BHANDARKAR, M., BRUNNER, R., GURSOY, A., KRAWETZ, N., PHILLIPS, J., SHINOZAKI, A., VARADARAJAN, K., and SCHULTEN, K. (1999). NAMD2: Greater scalability for parallel molecular dynamics. J. Computational Physics 151, 283-312.
18. LEE, A.J., and CROTHERS, D.M. (1998). The solution structure of an RNA loop-loop complex: The ColE1 inverted loop sequence. Structure 6, 993-1005.
19. LEONTIS, N.B., STOMBAUGH, J., and WESTHOF, E. (2002). The non Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 30, 3497-3531.
20. LEVITT, M., and WARSHELL, A. (1978). Extreme conformational flexibility of the furanose ring in DNA and RNA. J. Am. Chem. Soc. 100, 2607-2613.
21. LODMELL, J.S., EHRESMANN, C., EHRESMANN, B., and MARQUET, R. (2000). Convergence of natural and artificial evolution on an RNA loop-loop interaction: The HIV-1 dimerization initiation site. Nucleic Acids Res. 6, 1267-1276.
22. LODMELL, J.S., EHRESMANN, C., EHRESMANN, B., and MARQUET, R. (2001). Structure and dimerization of HIV-1 kissing loop aptamers. J. Mol. Biol. 311, 475-490.
23. LU, X. J., SHAKKED, Z., and OLSON, W.K. (2000). A-DNA conformational motifs in ligand bound double helices. J. Mol. Biol. 300, 819-840.
24. MARINO, J.P., GREGORIAN, R.S., CSANKOVSZKI, G., and CROTHERS, D.M. (1995). Bent helix formation between RNA hairpins with complementary loops. Science 268, 1448-1454.
25. MASQUIDA, B., and WESTHOF, E. (2000). On the wobble GoU and related pairs. RNA 6, 9-15,
26. MUJEEB, A., CLEVER, J.L., BILLECI, T.M., JAMES, T.L., and PARSLOW, T.G. (1998). Structure of the dimer initiation complex of HIV-1 genomic RNA. Nat. Struct. Biol. 5, 432-436.
27. MURIAUX, D., DE ROCQUIGNY, H., ROQUES, B.P., and PAOLETTI, J. (1996). NCp7 activates HIV-1Lai RNA dimerization by converting a transient loop-loop complex into a stable dimer. J. Biol. Chem. 371, 33686-33692.
28. MURIAUX, D., GIRARD, P.M., BONNET-MATHONIERE, B., and PAOLETTI, J. (1995). Dimerization of HIV-1 Lai RNA at low ionic strengh. J. Biol. Chem. 270, 8209-8216.
29. PAILLART, J.C., WESTHOF, E., EHRESMANN, C., EHRESMANN, B., and MARQUET, R. (1997). Noncanonical interactions in a kissing loop complex: The dimerization initiation site of HIV-1 genomic RNA. J. Mol. Biol. 270, 36-49.
30. PATTABIRAMAN, N., MARTINEZ, H.M., and SHAPIRO, B.A. (2002). Molecular modeling dynamics studies of HIV-1 kissing loop studies. J. Biomol. Struct. Dynam. 20, 397-411.
31. POLGE, E., DARLIX, J.L., PAOLETTI, J., and FOSSE, P. (2000). Characterization of loose and tight dimer forms of avian leukosis virus RNA. J. Mol. Biol. 300, 41-56.
32. REIN, A., HARVIN, D.P., MIRRO, J., ERNST, S.M., and GORELICK, R.J. (1994). Evidence that a central domain of nucleocapsid protein is required for RNA packaging in murine leukemia virus. J. Virol. 68, 6124-6129.
33. RYCKAERT, J.P., CICCOTTI, G., and BERENDSEN, H.J.C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Physics 23, 327-341.
34. SKRIPKIN, E., PAILLART, J.C., MARQUET, R., EHRESMANN, B., and EHRESMANN, C. (1994). Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro, Proc. Natl. Acad. Sci. USA 91, 4945-4949.
35. THEILLEUX-DELALANDE, V., GIRARD, F., HUYNHDINH, T., LANCELOT, G., and PAOLETTI, J. (2000). The HIV-1(Lai) RNA dimerization. Thermodynamic parameters associated with the transition from the kissing complex to the extended dimer. Eur. J. Biochem. 267, 2711-2719.
36. TOMIZAWA, J. (1984). Control of ColE1 plasmid replication: The process of binding of RNA I to the primer transcript. Cell 38, 861-870.
37. TOMIZAWA, J. (1985). Control of ColE1 plasmid replication: Initial interaction of RNA I and the primer transcript is reversible. Cell 40, 527-535.