Evolvability of the mode of peptide binding by an RNA

RNA

Volumn 11, Issue 9, 2005, Pages 1364-1373

  Iwazaki, Tetsuya ^a   Li, Xianglan ^a   Harada, Kazuo ^a  

^a TOKYO GAKUGEI UNIVERSITY   (Japan)

Author keywords

Bacterial reporter system; In vivo RNA selection; Molecular evolution; RNA structure; RNA peptide interactions

Indexed keywords

APTAMER; PEPTIDE; POLYPEPTIDE; REV PROTEIN; RNA; RSG 1.2 PEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATION; DNA RESPONSIVE ELEMENT; MOLECULAR RECOGNITION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING;

ELECTROPHORESIS, POLYACRYLAMIDE GEL; ELECTROPHORETIC MOBILITY SHIFT ASSAY; EVOLUTION, MOLECULAR; GENES, ENV; HIV; HUMANS; NUCLEIC ACID CONFORMATION; PEPTIDES; PLASMIDS; PROTEIN BINDING; RNA;

EID: 24044528558     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2560905     Document Type: Article

References (40)

1. Aboul-ela, F., Karn, J., and 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.
2. Austin, R.J., Xia, T., Ren, J., Takahashi, T.T., and Roberts, R.W. 2003. Differential modes of recognition in N peptide-boxB complexes. Biochemistry 42: 14957-14967.
3. Bartel, D.P., Zapp, M.L., Green, M.R., and Szostak, J.W. 1991. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell 67: 529-536.
4. Battiste, J.L., Tan, R., Frankel, A.D., and Williamson, J.R. 1994. Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs. Biochemistry 33: 2741-2747.
5. Battiste, J.L., Mao, H., Rao, N.S., Tan, R., Muhandiram, D.R., Kay, L.E., Frankel, A.D., and Williamson J.R. 1996. α Helix-RNA major groove recognition in an HIV-1 Rev peptide-RRE RNA complex. Science 273: 1547-1551.
6. Cai, Z., Gorin, A., Frederick, R., Ye, X., Hu, W., Majumdar, A., Kettani, A., and Patel, D.J. 1998. Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex. Nat. Struct. Biol. 5: 203-212.
7. Calnan, B.J., Biancalana, S., Hudson, D., and Frankel, A.D. 1991. Analysis of arginine-rich peptides from the HIV Tat protein reveals unusual features of RNA-protein recognition. Genes & Dev. 5: 201-210.
8. Chen, L. and Frankel, A.D. 1994. An RNA-binding peptide from bovine immunodeficiency virus Tat protein recognizes an unusual RNA structure. Biochemistry 33: 2708-2715.
9. _. 1995. A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA. Proc. Natl. Acad. Sci. 92: 5077-5081.
10. Cheng, A.C., Calabro, V., and Frankel, A.D. 2001. Design of RNA binding proteins and ligands. Curr. Opin. Struct. Biol. 11: 478-484.
11. Das, C. and Frankel, A.D. 2003. Sequence and structure space of RNA binding peptides. Biopolymers 70: 80-85.
12. Frankel, A.D. 2000. Fitting peptides into the RNA world. Curr. Opin. Struct. Biol. 10: 332-340.
13. Frankel, A.D. and Smith, C.A. 1998. Induced folding in RNA-protein recognition: More than a simple molecular handshake. Cell 92: 149-151.
14. Franklin, N.C. 1993. Clustered arginine residues of bacteriophage λ N protein are essential to antitermination of transcription, but their locale cannot compensate for boxB loop defects. J. Mol. Biol. 231: 343-360.
15. _. 2004. Morphing molecular specificities between Arm-peptide and NUT-RNA in the antitermination complexes of bacteriophages λ and P22. Mol. Microbiol. 52: 815-822.
16. Friesen, W.J. and Darby, M.K. 1998. Specific RNA binding proteins constructed from zinc fingers. Nat. Struct. Biol. 5: 543-546.
17. Giver, L., Bartel, D., Zapp, M., Pawul, A., Green, M., and Ellington, A.D. 1993. Selective optimization of the Rev-binding element of HIV-1. Nucleic Acids Res. 21: 5509-5516.
18. Gosser, Y., Hermann, T., Majumdar, A., Hu, W., Frederick, R., Jiang, F., Xu, W., and Patel, D.J. 2001. Peptide-triggered conformational switch in HIV-1 RRE RNA complexes. Nat. Struct. Biol. 8: 146-150.
19. Harada, K. and Frankel, A.D. 1998. In vivo selection of specific RNAbinding polypeptides using a transcriptional antitermination reporter assay. In RNA-protein interactions: A practical approach (ed. C.W.J. Smith), pp. 217-236. Oxford University Press, Oxford, UK.
20. Harada, K., Martin, S.S., and Frankel, A.D. 1996. Selection of RNAbinding peptides in vivo. Nature 380: 175-179.
21. Harada, K., Martin, S.S., Tan, R., and Frankel, A.D. 1997. Molding a peptide into an RNA site by in vivo peptide evolution. Proc. Natl. Acad. Sci. 94: 11887-11892.
22. Heaphy, S., Finch, J.T., Gait, M.J., Karn, J., and Singh, M. 1991. Human immunodeficiency virus type 1 regulator of virion expression, rev, forms nucleoprotein filaments after binding to a purinerich "bubble" located within the rev-responsive region of viral mRNAs. Proc. Natl. Acad. Sci. 88: 7366-7370.
23. Jain, C. and Belasco, J.G. 1996. A structural model for the HIV-1 Rev-RRE complex deduced from altered-specificity Rev variants isolated by a rapid genetic strategy. Cell 87: 115-125.
24. Kjems, J., Brown, M., Chang, D.D., and Sharp, P.A. 1991. Structural analysis of the interaction between the human immunodeficiency virus Rev protein and the Rev response element. Proc. Natl. Acad. Sci. 88: 683-687.
25. Kjems, J., Calnan, B.J., Frankel, A.D., and Sharp, P.A. 1992. Specific binding of a basic peptide from HIV-1 Rev. EMBO J. 11: 1119-1129.
26. Legault, P., Li, J., Mogridge, J., Kay, L.E., and Greenblatt, J. 1998. NMR structure of the bacteriophage λ N peptide/boxB RNA complex: Recognition of a GNRA fold by an arginine-rich motif. Cell 93: 289-299.
27. Leulliot, N. and Varani, G. 2001. Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture. Biochemistry 40: 7947-7956.
28. Patel, D.J. 1999. Adaptive recognition in RNA complexes with peptides and protein modules. Curr. Opin. Struct. Biol. 9: 74-87.
29. Peled-Zehavi, H., Horiya, S., Das, C., Harada, K., and Frankel, A.D. 2003. Selection of RRE RNA binding peptides using a kanamycin antitermination assay. RNA 9: 252-261.
30. Peterson, R.D. and Feigon, J. 1996. Structural change in Rev responsive element RNA of HIV-1 on binding Rev peptide. J. Mol. Biol. 264: 863-877.
31. Puglisi, J.D., Tan, R., Calnan, B.J., Frankel, A.D., and Williamson, J.R. 1992. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science 257: 76-80.
32. Puglisi, J.D., Chen, L., Blanchard, S., and Frankel, A.D. 1995. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science 270: 1200-1203.
33. Smith, C.A., Crotty, S., Harada, Y., and Frankel, A.D. 1998. Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins. Biochemistry 37: 10808-10814.
34. Smith, C.A., Calabro, V., and Frankel, A.D. 2000. An RNA-binding chameleon. Mol. Cell 6: 1067-1076.
35. Tan, R. and Frankel, A.D. 1994. Costabilization of peptide and RNA structure in an HIV Rev peptide-RRE complex. Biochemistry 33: 14579-14585.
36. _. 1998. A novel glutamine-RNA interaction identified by screening libraries in mammalian cells. Proc. Natl. Acad. Sci. 95: 4247-4252.
37. Tan, R., Chen, L. Buettner, J.A., Hudson, D., and Frankel, A.D. 1993. RNA recognition by an isolated α-helix. Cell 73: 1031-1040.
38. Tiley, L.S., Malim, M.H., Tewary, H.K., Stockley, P.G., and Cullen, B.R. 1992. Identification of a high-affinity RNA-binding site for the human immunodeficiency virus type 1 Rev protein. Proc. Natl. Acad. Sci. 89: 758-762.
39. Weeks, K.M. and Crothers, D.M. 1993. Major groove accessibility of RNA. Science 261: 1574-1577.
40. Zhang, Q., Harada, K., Cho, H.S., Frankel, A.D., and Wemmer, D.E. 2001. Structural characterization of the complex of the Rev response element RNA with a selected peptide. Chem. Biol. 8: 511-520.