A docking and modelling strategy for peptide-RNA complexes: Applications to BIV Tat-TAR and HIV Rev-RBE

Folding and Design

Volumn 1, Issue 6, 1996, Pages 463-472

  Srinivasan, Jayashree ^a,b   Leclerc, Fabrice ^a   Xu, Wei ^c   Ellington, Andrew D ^c   Cedergren, Robert ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

Docking; Electrostatics; Hydrogen bonding; RBE RNA; Rev peptide

Indexed keywords

NUCLEAR FACTOR, RRE BINDING; NUCLEAR PROTEIN; REV PROTEIN; TRANSACTIVATOR PROTEIN;

ANIMAL; ARTICLE; BOVINE IMMUNODEFICIENCY LIKE VIRUS; CATTLE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; LONG TERMINAL REPEAT; METABOLISM; PROTEIN BINDING;

ANIMALS; CATTLE; GENE PRODUCTS, REV; GENE PRODUCTS, TAT; HIV; HIV LONG TERMINAL REPEAT; HUMANS; IMMUNODEFICIENCY VIRUS, BOVINE; MODELS, MOLECULAR; NUCLEAR PROTEINS; PROTEIN BINDING;

EID: 0030324870     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(96)00062-4     Document Type: Article

References (36)

1. Strynadka, N.C.J., et al., & James, M.N.G. (1996). Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase. Nat. Struct. Biol. 3, 233-239.
2. Kuntz, I.D., Meng, E.C. & Shoichet, B.K. (1994). Structure-based molecular design. Acc. Chem. Res. 27, 117-123.
3. Grootenhuis, P.D.J., Kollman, P.A., Seibel, G.L., DesJarlais, R.L. & Kuntz, I.D. (1990). Computerized selection of potential DNA-binding compounds. Anti-Cancer Drug Des. 5, 237-242.
4. Grootenhuis, P.D.J., Roe, D.C., Kollman, P.A, & Kuntz, I.D. (1994). Finding potential DNA-binding compounds by using molecular shape. J. Comp. Mol. Des. 8, 731-750).
5. Draper, D.E. (1995). Protein RNA recognition. Annu. Rev. Biochem. 64, 593-620.
6. Puglisi, J.D., Chen, L., Blanchard, S. & Frankel, A.D. (1995). Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science 270, 1200-1203.
7. Ye, X., Kumar, R.A. & Patel, D.J. (1995). Molecular recognition in bovine immunodeficiency virus Tat peptide-TAR RNA complex. Chem. Biol. 2, 827-840.
8. Zapp, M.L., Hope, T.J., Parslow, T.G. & Green M.R. (1991). Oligomerisation and RNA binding domains of the type 1 human immunodeficiency virus Rev protein: a dual function for an arginine-rich binding motif. Proc. Natl. Acad. Sci. USA 88, 7734-7738.
9. Cook, K.S., Fisk, G.J., Hauber, J., Usman, N., Daly, T.J. & Rusche, J.R. (1991). Characterization of HIV-1 Rev protein: binding stoichiometry and minimal RNA substrate. Nucleic Acids Res. 19, 1577-1583.
10. Kjems, J., Calnan, B.J., Frankel, A.D. & Sharp, P.A. (1992). Specific binding of a basic peptide from HIV-1 Rev. EMBO J. 11, 1119-1129.
11. 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.
12. Battiste, J.L., Tan, R., Frankel, A.D. & Williamson, J.R. (1995). Assignment and modelling of the Rev response element (RRE) RNA bound to a Rev peptide using 13C-heteronuclear NMR. J. Biomol. NMR. 6, 375-389.
13. Peterson, R.D., Bartel, D.P., Szostak, J.W., Horvath, S.J. & Feigon, J. (1994). 1H NMR studies of the high affinity Rev binding site of the Rev Responsive Element of HIV-1 mRNA: base pairing and core binding element. Biochemistry 33, 5357-5365.
14. Bartel, D.P., Zapp, M.L., Green, M.R. & Szostak, J.W. (1991). HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell 67, 529-536.
15. Iwai, S., Pritchard, C., Mann, D.A., Karn, J. & Gait, M.J. (1992). Recognition of the high affinity binding site in Rev-responsive element RNA by the human immunodeficiency virus type-1 Rev protein. Nucleic Acids Res. 20, 6465-6472.
16. Giver, L., Bartel, D., Zapp, M., Pawul, A., Green, M. & Ellington, A.D. (1993). Selective optimization of the Rev-binding element of HIV-1. Nucleic Acids Res. 21, 5509-5516.
17. Tan, R., Chen, L., Buettner, J.A., Hudson, D. & Frankel, A.D. (1993). RNA recognition by an isolated α-helix. Cell 73, 1031-1040.
18. Daly, T.J., Doten, R.C., Rusche, J.R. & Auer, M. (1995). The amino terminal domain of HIV-1 Rev is required for discrimination of the RRE from nonspecific RNA. J. Mol. Biol. 253, 243-258.
19. Scanlon, M.J., Fairlie, D.P., Craik, D.J., Englebretsen, D.R. & West, M.L. (1995). NMR solution structure of the RNA-binding peptide from human immunodeficiency virus (type 1) Rev. Biochemistry 34, 8242-8249.
20. Jensen, T.H., Leffers, H. & Kjems, J. (1995). Intermolecular binding sites of human immunodeficiency virus type 1 Rev protein determined by protein footprinting. J. Biol. Chem. 270, 13777-13784.
21. Tan, R. & Frankel, A.D. (1994). Costabilization of peptide and RNA structure in an HIV Rev peptide-RRE complex. Biochemistry 33, 14579-14585.
22. Pritchard, C.E., et al., & Gait, M.J. (1994). Methylphosphonate mapping of phosphate contacts critical for RNA recognition by the human immunodeficiency virus tat and rev proteins. Nucleic Acids Res. 22, 2592-2600.
23. Shu-Yun, L., Pattabiraman, N. & Maizel, J.V., Jr.(1994). RNA tertiary structure of the HIV RRE domain II containing non-Watson-Crick base pairs G:G and G:A: molecular modelling studies. Nucleic Acids Res. 22, 3966-3976.
24. Hammerschmid, M., et al., & Hauber, J. (1994). Scanning mutagenesis of the arginine-rich regions of the human immunodeficiency virus type 1 rev trans activator. J. Virol. 68, 7329-7335.
25. Doig, A.J. & Baldwin, R.L. (1995). N- and C-capping preferences for all 20 amino acids in alpha-helical peptides. Proteins Sci. 4, 1325-1336.
26. Battiste, J.L., et al., & Williamson, J.R. (1996). α-Helix-RNA major groove recognition in an HIV-1 Rev peptide-RRE RNA complex. Science 273, 1547-1551.
27. Xu, W. & Ellington, A.E. (1996). Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope. Proc. Natl. Acad. Sci. USA 93, 7475-7480.
28. Weiner, S. J., et al., & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.
29. Weiner, S.J., Kollman, P.A., Nguyen, D.T. & Case, D.A. (1986). An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7, 230-252.
30. Cheong, C., Varani, G. & Tinoco, I. (1990). Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature 346, 680-682.
31. Klapper, I., Hägstrom, R., Fine, R., Sharp, K. & Honig, B. (1986). Focussing of electric field in the active site of Cu-Zn superoxide dismutase: effect of the ionic strength and amino acid modification. Proteins 1, 47-59.
32. Gilson, M.K. & Honig, B.H. (1988). Energetics of charge-charge interactions in proteins. Proteins 3, 32-53.
33. Zacharias, M., Luty, B.A., Davis, M.E. & McCammon, A.J. (1992). Poisson-Boltzmann analysis of the λ repressor-operator interaction. Biophys. J. 63, 1280-1285.
34. Jain, A. & Murcko, M.A. (1995). Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 38, 4953-4967.
35. Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, E. & Cedergren, R. (1991). The combination of symbolic and numerical computation for three dimensional modelling of RNA. Science 253, 1255-1260.
36. Gautheret, D., Major, F. & Cedergren, R. (1993). Modelling the three dimensional structure of RNA using discrete nucleotide conformational sets. J. Mol. Biol. 229, 1049-1064.