RNA bulges as architectural and recognition motifs

Structure

Volumn 8, Issue 3, 2000, Pages

  Hermann, Thomas ^a   Patel, Dinshaw J ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX FORMATION; CONFORMATIONAL TRANSITION; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MOLECULAR STABILITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; RNA ANALYSIS; RNA STRUCTURE; SHORT SURVEY;

EID: 0034653899     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)00110-6     Document Type: Review

References (64)

1. Ferré-D'Amaré A.R., Doudna J.A. RNA folds: insights from recent crystal structures. Annu. Rev. Biophys. Biomol. Struct. 28:1999;57-73.
2. Hermann T., Patel D.J. Stitching together RNA tertiary architectures. J. Mol. Biol. 294:1999;829-849.
3. Batey R.T., Rambo R.P., Doudna J.A. Tertiary motifs in RNA structure and folding. Angew. Chem. Int. Ed. Engl. 38:1999;2326-2343.
4. Moore P.B. Structural motifs in RNA. Annu. Rev. Biochem. 67:1999;287-300.
5. Weeks K.M., Crothers D.M. Major groove accessibility of RNA. Science. 261:1993;1574-1577.
6. Varani L., Varani G.et al. Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and Parkinsonism linked to chromosome 17. Proc. Natl Acad. Sci. USA. 96:1999;8229-8234.
7. Borer P.N., Pelczer I.et al. Proton NMR and structural features of a 24-nucleotide RNA hairpin. Biochemistry. 34:1995;6488-6503.
8. Portmann S., Grimm S., Workman C., Usman N., Egli M. Crystal structure of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. Chem. Biol. 3:1996;173-184.
9. Greenbaum N.L., Radhakrishnan I., Patel D.J., Hirsh D. Solution structure of the donor site of a trans-splicing RNA. Structure. 4:1996;725-733.
10. Puglisi J.D., Chen L., Blanchard S., Frankel A.D. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science. 270:1995;1200-1203.
11. Ye X., Kumar R.A., Patel D.J. Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex. Chem. Biol. 2:1995;827-840.
12. Ennifar E., Dumas P.et al. The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine-bulges. Structure. 7:1999;1439-1449.
13. Pan T., Uhlenbeck O.C. A small metalloribozyme with a two-step mechanism. Nature. 358:1992;560-563.
14. Wedekind J.E., McKay D.B. Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis. Nat. Struct. Biol. 6:1999;261-268.
15. Hoogstraten C.G., Legault P., Pardi A. NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis. J. Mol. Biol. 284:1998;337-350.
16. Cate J.H., Doudna J.A.et al. Crystal structure of a group I ribozyme domain. principles of RNA packing Science. 273:1996;1678-1685.
17. Cate J.H., Hanna R.L., Doudna J.A. A magnesium ion core at the heart of a ribozyme domain. Nat. Struct. Biol. 4:1997;553-558.
18. Vålegard K., Murray J.B., Stockley P.G., Stonehouse N.J., Liljas L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 371:1994;623-626.
19. Convery M.A., Stockley P.G.et al. Crystal structure of an RNA aptamer-protein complex at 2.8 Å resolution. Nat. Struct. Biol. 5:1998;133-139.
20. Jiang L., Suri A.K., Fiala R., Patel D.J. Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chem. Biol. 4:1997;35-50.
21. Jiang L., Patel D.J. Solution structure of the tobramycin-RNA aptamer complex. Nat. Struct. Biol. 5:1998;769-774.
22. Jiang L., Majumdar A., Hu W., Jaishree T.J., Xu W., Patel D.J. Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer. Structure. 7:1999;817-827.
23. Ye X., Patel D.J.et al. RNA architecture dictates bound peptide conformations. Chem. Biol. 6:1999;657-669.
24. Jiang F., Patel D.J.et al. Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples. Structure. 7:1999;1461-1472.
25. Hermann T., Westhof E. Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations. Structure. 6:1998;1303-1314.
26. Karn J. Tackling Tat. J. Mol. Biol. 293:1999;235-254.
27. Ippolito J.A., Steitz T.A. A 1.3 Å resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation. Proc. Natl Acad. Sci. USA. 95:1998;9819-9824.
28. Zacharias M., Hagerman P.J. The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide. Proc. Natl Acad. Sci. USA. 92:1995;6052-6056.
29. Aboul-ela F., Karn J., Varani G. Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res. 24:1996;3974-3981.
30. Puglisi J.D., Tan R., Calnan B.J., Frankel A.D., Williamson J.R. Conformation of the Tar RNA-arginine complex by NMR spectroscopy. Science. 257:1992;76-80.
31. Aboul-ela F., Karn J., Varani G. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol. 253:1995;313-332.
32. Tao J., Chen L., Frankel A.D. Dissection of the proposed base triple in human immunodeficieny virus TAR RNA indicates the importance of Hoogsten interaction. Biochemistry. 36:1997;3491-3495.
33. Battiste J.L., Williamson J.R.et al. α Helix-RNA major groove recognition in an HIV-1 Rev peptide-RRE RNA complex. Science. 273:1996;1547-1551.
34. Ye X., Gorin A., Ellington A.D., Patel D.J. Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 Rev peptide-RNA aptamer complex. Nat. Struct. Biol. 3:1996;1026-1033.
35. Hermann T., Westhof E. Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA. J. Mol. Biol. 276:1998;903-912.
36. Hermann T., Westhof E. Docking of cationic antibiotics to negatively charged pockets in RNA folds. J. Med. Chem. 42:1999;1250-1261.
37. Grate D., Wilson C. Role REVersal. understanding how RRE RNA binds its peptide ligand Structure. 5:1997;7-11.
38. Naryshkin N.A., Gait M.J., Ivanovskaya M.G. RNA recognition and regulation of HIV-1 gene expression by viral factor Tat. Biochemistry (Moscow). 63:1998;489-503.
39. Patel D.J. Adaptive recognition in RNA complexes with peptides and protein modules. Curr. Opin. Struct. Biol. 9:1999;74-87.
40. Hermann T., Westhof E. Saccharide-RNA recognition. Biopolymers. 48:1998;155-165.
41. Mei H.-Y., Czarnik A.W.et al. Inhibition of an HIV-1 Tat-derived peptide binding to TAR RNA by aminoglycoside antibiotics. Bioorg. Med. Chem. Lett. 5:1995;2755-2760.
42. Zapp M.L., Stern S., Green M.R. Small molecules that selectively block RNA binding of HIV-1 Rev protein inhibit Rev function and viral production. Cell. 74:1993;969-978.
43. Leclerc F., Cedergren R. Modeling RNA-ligand interactions: the Rev-binding element RNA-aminoglycoside complex. J. Med. Chem. 41:1998;175-182.
44. Ratmeyer L., Wilson W.D.et al. Inhibition of HIV-1 Rev-RRE interaction by diphenylfuran derivatives. Biochemistry. 35:1996;13689-13696.
45. Hamy F., Klimkait T.et al. An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication. Proc. Natl Acad. Sci. USA. 94:1997;3548-3553.
46. Dassonneville L., Hamy F., Colson P., Houssier C., Bailly C. Binding of Hoechst 33258 to the TAR RNA of HIV-1. Recognition of a pyrimidine bulge-dependent structure. Nucleic Acids Res. 25:1997;4487-4492.
47. Mei H.-Y., Czarnik A.W.et al. Inhibitors of protein-RNA complexation that target the RNA. specific recognition of human immunodeficieny virus type 1 TAR RNA by small organic molecules Biochemistry. 37:1998;14204-14212.
48. Gelus N., Bailly C., Hamy F., Klimkait T., Wilson W.D., Boykin D.W. Inhibition of HIV-1 Tat-TAR interaction by diphenylfuran derivatives: effects of the terminal basic side chains. Bioorg. Med. Chem. 7:1999;1089-1096.
49. Kappen L.S., Goldberg I.H. Bulge-specific cleavage in transactivation response region RNA and its DNA analogue by neocarzinostatin chromophore. Biochemistry. 34:1995;5997-6002.
50. Kappen L.S., Goldberg I.H. Effect of ribonucleotide substitution on nucleic acid bulge recognition by neocarzinostatin. Bioorg. Med. Chem. 5:1997;1221-1227.
51. Hermann T., Westhof E. Non-Watson-Crick base pairs in RNA-protein recognition. Chem. Biol. 1999;R335-R343.
52. Bartel D.P., Zapp M.L., Green M.R., Szostak J.W. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell. 67:1991;529-536.
53. Giver L., Bartel D., Zapp M., Pawul A, Green M., Ellington A.D. Selective optimization of the Rev-binding element of HIV-1. Nucleic Acids Res. 21:1993;5509-5516.
54. Fan P., Suri A.K., Fiala R., Live D., Patel D.J. Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol. 58:1996;480-500.
55. Diener J.L., Moore P.B. Solution structure of a substrate for the archaeal pre-tRNA splicing endonucleases: the bulge-helix-bulge motif. Mol. Cell. 1:1998;883-894.
56. Conn G.L., Draper D.E., Lattmann E.E., Gittis A.G. Crystal structure of a conserved ribosomal protein-RNA complex. Science. 284:1999;1171-1174.
57. Wimberly B.T., Guymon R., McCutcheon J.P., White S.W., Ramakrishnan V. A detailed view of a ribosomal active site. the structure of the L11-RNA complex Cell. 97:1999;491-502.
58. Thompson L., Daniels C. Recognition of exon-intron boundaries by the Halobacterium volcanii tRNA intron endonuclease. J. Biol. Chem. 265:1990;18104-18111.
59. Lykke-Andersen J., Garrett R. Structural characteristics of the stable RNA introns of archaeal hyperthermophiles and their splicing junctions. J. Mol. Biol. 243:1994;846-855.
60. Kleman-Leyer K., Armbruster D., Daniels C. Properties of the H. volcanii tRNA intron endonuclease reveal a relationship between the archeal and eukaryal tRNA intron processing systems. Cell. 89:1997;839-847.
61. Li H., Trotta C.R., Abelson J. Crystal structure and evolution of a transfer RNA splicing enzyme. Science. 280:1998;279-284.
62. Clemons W.M., May J.L.C., Wimberly B.T., McCutcheon J.P., Capel M.S., Ramakrishnan V. Structure of a bacterial 30S ribosomal subunit at 5. 5 Å resolution. Nature. 400:1999;833-840.
63. Ban N., Nissen P., Hansen J., Capel M., Moore P.B., Steitz T.A. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature. 400:1999;841-847.
64. Cate J.H., Yusupov M.M., Yusupova G.Z., Earnest T.N., Noller H.F. X-ray crystal structures of 70S ribosome functional complexes. Science. 285:1999;2095-2104.