Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy

Science

Volumn 272, Issue 5266, 1996, Pages 1343-1347

  Yang, Yinshan ^a   Kochoyan, Michel ^b,c   Burgstaller, Petra ^d   Westhof, Eric ^e   Famulok, Michael ^d  

^a INSERM   (France)

^b CENTRE DE BIOCHIMIE STRUCTURALE   (France)

^c ECOLE POLYTECHNIQUE   (France)

^d UNIVERSITY OF MUNICH   (Germany)

^e INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CITRULLINE; NUCLEOTIDE; PURINE;

ARTICLE; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RNA CAPPING; RNA STRUCTURE;

EID: 0029972909     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.272.5266.1343     Document Type: Article

References (52)

1. D. L. Robertson and G. F. Joyce, Nature 344, 467 (1990); C. Tuerk and L. Gold, Science 249, 505 (1990); A. D. Ellington and J. W. Szostak, Nature 346, 818 (1990).
2. D. L. Robertson and G. F. Joyce, Nature 344, 467 (1990); C. Tuerk and L. Gold, Science 249, 505 (1990); A. D. Ellington and J. W. Szostak, Nature 346, 818 (1990).
3. D. L. Robertson and G. F. Joyce, Nature 344, 467 (1990); C. Tuerk and L. Gold, Science 249, 505 (1990); A. D. Ellington and J. W. Szostak, Nature 346, 818 (1990).
4. J. W. Szostak, Trends Biochem. Sci. 17, 89 (1992); G.F. Joyce, Curr. Opin. Struct. Biol. 4, 331 (1994); S. J. Klug and M. Famulok, Mol. Biol. Rep. 20, 97 (1994); L. Gold, J. Biol. Chem. 270, 13581 (1995); _, B. Polisky, O. Uhlenbeck, M. Yarus, Annu. Rev. Biochem. 64, 763 (1995); A. D. Ellington, Curr. Biol. 4, 427 (1994); I. Hirao and A. D. Ellington, ibid. 5, 1017 (1995).
5. J. W. Szostak, Trends Biochem. Sci. 17, 89 (1992); G.F. Joyce, Curr. Opin. Struct. Biol. 4, 331 (1994); S. J. Klug and M. Famulok, Mol. Biol. Rep. 20, 97 (1994); L. Gold, J. Biol. Chem. 270, 13581 (1995); _, B. Polisky, O. Uhlenbeck, M. Yarus, Annu. Rev. Biochem. 64, 763 (1995); A. D. Ellington, Curr. Biol. 4, 427 (1994); I. Hirao and A. D. Ellington, ibid. 5, 1017 (1995).
6. J. W. Szostak, Trends Biochem. Sci. 17, 89 (1992); G.F. Joyce, Curr. Opin. Struct. Biol. 4, 331 (1994); S. J. Klug and M. Famulok, Mol. Biol. Rep. 20, 97 (1994); L. Gold, J. Biol. Chem. 270, 13581 (1995); _, B. Polisky, O. Uhlenbeck, M. Yarus, Annu. Rev. Biochem. 64, 763 (1995); A. D. Ellington, Curr. Biol. 4, 427 (1994); I. Hirao and A. D. Ellington, ibid. 5, 1017 (1995).
7. J. W. Szostak, Trends Biochem. Sci. 17, 89 (1992); G.F. Joyce, Curr. Opin. Struct. Biol. 4, 331 (1994); S. J. Klug and M. Famulok, Mol. Biol. Rep. 20, 97 (1994); L. Gold, J. Biol. Chem. 270, 13581 (1995); _, B. Polisky, O. Uhlenbeck, M. Yarus, Annu. Rev. Biochem. 64, 763 (1995); A. D. Ellington, Curr. Biol. 4, 427 (1994); I. Hirao and A. D. Ellington, ibid. 5, 1017 (1995).
8. J. W. Szostak, Trends Biochem. Sci. 17, 89 (1992); G.F. Joyce, Curr. Opin. Struct. Biol. 4, 331 (1994); S. J. Klug and M. Famulok, Mol. Biol. Rep. 20, 97 (1994); L. Gold, J. Biol. Chem. 270, 13581 (1995); _, B. Polisky, O. Uhlenbeck, M. Yarus, Annu. Rev. Biochem. 64, 763 (1995); A. D. Ellington, Curr. Biol. 4, 427 (1994); I. Hirao and A. D. Ellington, ibid. 5, 1017 (1995).
9. J. W. Szostak, Trends Biochem. Sci. 17, 89 (1992); G.F. Joyce, Curr. Opin. Struct. Biol. 4, 331 (1994); S. J. Klug and M. Famulok, Mol. Biol. Rep. 20, 97 (1994); L. Gold, J. Biol. Chem. 270, 13581 (1995); _, B. Polisky, O. Uhlenbeck, M. Yarus, Annu. Rev. Biochem. 64, 763 (1995); A. D. Ellington, Curr. Biol. 4, 427 (1994); I. Hirao and A. D. Ellington, ibid. 5, 1017 (1995).
10. J. W. Szostak, Trends Biochem. Sci. 17, 89 (1992); G.F. Joyce, Curr. Opin. Struct. Biol. 4, 331 (1994); S. J. Klug and M. Famulok, Mol. Biol. Rep. 20, 97 (1994); L. Gold, J. Biol. Chem. 270, 13581 (1995); _, B. Polisky, O. Uhlenbeck, M. Yarus, Annu. Rev. Biochem. 64, 763 (1995); A. D. Ellington, Curr. Biol. 4, 427 (1994); I. Hirao and A. D. Ellington, ibid. 5, 1017 (1995).
11. F. H. Allain and G. Varani, J. Mol. Biol. 250, 333 (1995); C. Cheong, G. Varani G, I. Tinoco Jr., Nature 346, 680 (1990); G. Varani, C. Cheong, I. Tinoco Jr., Biochemistry 30, 3280 (1991); J. Santa Lucia Jr. and D. H. Turner, Biochemistry 32, 12612 (1993); H. A. Heus and A. Pardi, Science 253, 191 (1991); E. V. Puglisi, J. D. Puglisi, J. R. Williamson, U. L. RajBhandary, Proc. Natl. Acad. Sci. U.S.A. 91, 11467 (1994).
12. F. H. Allain and G. Varani, J. Mol. Biol. 250, 333 (1995); C. Cheong, G. Varani G, I. Tinoco Jr., Nature 346, 680 (1990); G. Varani, C. Cheong, I. Tinoco Jr., Biochemistry 30, 3280 (1991); J. Santa Lucia Jr. and D. H. Turner, Biochemistry 32, 12612 (1993); H. A. Heus and A. Pardi, Science 253, 191 (1991); E. V. Puglisi, J. D. Puglisi, J. R. Williamson, U. L. RajBhandary, Proc. Natl. Acad. Sci. U.S.A. 91, 11467 (1994).
13. F. H. Allain and G. Varani, J. Mol. Biol. 250, 333 (1995); C. Cheong, G. Varani G, I. Tinoco Jr., Nature 346, 680 (1990); G. Varani, C. Cheong, I. Tinoco Jr., Biochemistry 30, 3280 (1991); J. Santa Lucia Jr. and D. H. Turner, Biochemistry 32, 12612 (1993); H. A. Heus and A. Pardi, Science 253, 191 (1991); E. V. Puglisi, J. D. Puglisi, J. R. Williamson, U. L. RajBhandary, Proc. Natl. Acad. Sci. U.S.A. 91, 11467 (1994).
14. F. H. Allain and G. Varani, J. Mol. Biol. 250, 333 (1995); C. Cheong, G. Varani G, I. Tinoco Jr., Nature 346, 680 (1990); G. Varani, C. Cheong, I. Tinoco Jr., Biochemistry 30, 3280 (1991); J. Santa Lucia Jr. and D. H. Turner, Biochemistry 32, 12612 (1993); H. A. Heus and A. Pardi, Science 253, 191 (1991); E. V. Puglisi, J. D. Puglisi, J. R. Williamson, U. L. RajBhandary, Proc. Natl. Acad. Sci. U.S.A. 91, 11467 (1994).
15. F. H. Allain and G. Varani, J. Mol. Biol. 250, 333 (1995); C. Cheong, G. Varani G, I. Tinoco Jr., Nature 346, 680 (1990); G. Varani, C. Cheong, I. Tinoco Jr., Biochemistry 30, 3280 (1991); J. Santa Lucia Jr. and D. H. Turner, Biochemistry 32, 12612 (1993); H. A. Heus and A. Pardi, Science 253, 191 (1991); E. V. Puglisi, J. D. Puglisi, J. R. Williamson, U. L. RajBhandary, Proc. Natl. Acad. Sci. U.S.A. 91, 11467 (1994).
16. F. H. Allain and G. Varani, J. Mol. Biol. 250, 333 (1995); C. Cheong, G. Varani G, I. Tinoco Jr., Nature 346, 680 (1990); G. Varani, C. Cheong, I. Tinoco Jr., Biochemistry 30, 3280 (1991); J. Santa Lucia Jr. and D. H. Turner, Biochemistry 32, 12612 (1993); H. A. Heus and A. Pardi, Science 253, 191 (1991); E. V. Puglisi, J. D. Puglisi, J. R. Williamson, U. L. RajBhandary, Proc. Natl. Acad. Sci. U.S.A. 91, 11467 (1994).
17. B. Wimberly, G. Varani, I. Tinoco Jr., Biochemistry 32, 1078 (1993); G. Varani, B. Wimberly, I. Tinoco Jr., ibid. 28, 7760 (1989); J. D. Puglisi, J. R. Wyatt, I. Tinoco Jr., J. Mol. Biol. 214, 437 (1990); Biochemistry 29, 4215 (1990).
18. B. Wimberly, G. Varani, I. Tinoco Jr., Biochemistry 32, 1078 (1993); G. Varani, B. Wimberly, I. Tinoco Jr., ibid. 28, 7760 (1989); J. D. Puglisi, J. R. Wyatt, I. Tinoco Jr., J. Mol. Biol. 214, 437 (1990); Biochemistry 29, 4215 (1990).
19. B. Wimberly, G. Varani, I. Tinoco Jr., Biochemistry 32, 1078 (1993); G. Varani, B. Wimberly, I. Tinoco Jr., ibid. 28, 7760 (1989); J. D. Puglisi, J. R. Wyatt, I. Tinoco Jr., J. Mol. Biol. 214, 437 (1990); Biochemistry 29, 4215 (1990).
20. B. Wimberly, G. Varani, I. Tinoco Jr., Biochemistry 32, 1078 (1993); G. Varani, B. Wimberly, I. Tinoco Jr., ibid. 28, 7760 (1989); J. D. Puglisi, J. R. Wyatt, I. Tinoco Jr., J. Mol. Biol. 214, 437 (1990); Biochemistry 29, 4215 (1990).
21. J. D. Puglisi, R. Tan, B. J. Calnan, A. D. Frankel, J. R. Williamson, Science 257, 76 (1992).
22. J. D. Puglisi, L. Chen, S. Blanchard, A. D. Frankel, ibid. 270, 1200 (1995).
23. R. D. Peterson, D. P. Bartel, J. W. Szostak, S. J. Horvath, J. Feigon, Biochemistry 33, 5357 (1994).
24. M. Famulok, J. Am. Chem. Soc. 116, 1698 (1994).
25. P. Burgstaller, M. Kochoyan, M. Famulok, Nucleic Acids Res. 23, 4769 (1995).
26. 2O were performed with a jump and return (27) reading pulse at 5° and 13°C Assignments were obtained up to the 3′ sugar protons for most residues. Resonance assignments of the bound amino acid were obtained from the exchange crosspeaks with the free amino acid in the NOESY spectra and confirmed by TOCSY experiments (12).
27. 2O were performed with a jump and return (27) reading pulse at 5° and 13°C Assignments were obtained up to the 3′ sugar protons for most residues. Resonance assignments of the bound amino acid were obtained from the exchange crosspeaks with the free amino acid in the NOESY spectra and confirmed by TOCSY experiments (12).
28. K. Wüthrich, NMR of Proteins and Nucleic Acids (Wiley. New York, 1986).
29. Y. Yang and M. Kochoyan, unpublished results.
30. The two unassigned G imino resonances show a NOE to the independently assigned G29-imino or A29-H2 proton. In the the preliminary structures generated without these assignments, the G34 imino proton was always located at >8 Å from the H2 or imino proton of nucleotide 29. Therefore, the two unassigned resonances belong to G9 and G30. One of them shows a NOE to the H8 proton of G9 and was consequently assigned to G30, because such a NOE cannot be observed within a nucleotide. The other resonance was assigned by default to G9.
31. For U32 this observation is further supported by the chemical probing data because it can be modified by CMCT in the presence of the bound amino acid, indicating that the imino proton is solvent accessible (Rg. 1A). For G34, see Fig. 4 legend.
32. A. T. Brunger, X-PLOR User Manual, Version 3.1 (Yale University, New Haven, CT, 1992).
33. η of citrulline.
34. η protons of the amino acid. The H5 proton of U32 is in axial contact with the six-membered ring of A33 in a position where ring current effects are expected to be at a maximum (28). The involvement of G9 in the overall stability of the structure is supported by the observation that a mutant RNA with a G9-C42 base pair is unable to bind its cognate amino acid (12). Furthermore, the localization of G9 in the 3D structure of the complexes implies partial unstacking and solvent exposure of the functional groups of adenine 8, and indeed that residue is more sensitive to chemical modifcation in the presence of the amino acid (9).
35. A hydrogen bond is assumed when the distance between the acceptor and donor heavy atoms is <3.5 Å in all X-PLOR conformers. The term probable hydrogenbond is used when only 8 out of 10 conformers satisfy this condition.
36. Z. Otwinowski et al., Nature 335, 321 (1988).
37. L. Chen and A. D. Frankel, Proc. Natl. Acad. Sci. U.S.A 92, 5077 (1995).
38. H. Siomi, M. Choi, M. C. Siomi, R. L Nussbaum, G. Dreyfuss, Cell 77, 33 (1994).
39. X. Ye, R. A. Kumar, D. J. Patel, Chem. Biol. 2, 827 (1995).
40. In the aptamer of citrulline, whose urea group is uncharged, the oxygen array might be stabilized by a sodium ion [as observed for G quartet in tetraplex structures (32)]. In the aptamer of arginine, the positively charged guanido group might provide some stabilization to the array, while hindering cation binding.
41. C. G. Burd and G. Dreyfuss, Science 265, 615 (1994); K. Nagai and I. W. Mattaj, Eds., RNA-Protein Interactions (Oxford Univ. Press, Oxford, 1994).
42. C. G. Burd and G. Dreyfuss, Science 265, 615 (1994); K. Nagai and I. W. Mattaj, Eds., RNA-Protein Interactions (Oxford Univ. Press, Oxford, 1994).
43. C. Pabo and R. Sauer, Annu. Rev. Biochem. 61, 1053 (1992).
44. J. Tao and A. D. Frankel, Proc. Natl. Acad. Sci. U.S.A. 89, 2723 (1992).
45. P. Plateau and M. Guéron, J. Am. Chem. Soc. 104, 7310 (1982).
46. C. Giessner Prettre, B. Pullman, P. Borer, L.-S. Kan, P. Ts'o, Biopolymers 15, 2277 (1976).
47. V. Sklenar and A. Bax, J. Magn. Reson. 74, 469 (1987); G. Kellogg and P. Moore, FEBS Lett. 327, 261 (1993).
48. V. Sklenar and A. Bax, J. Magn. Reson. 74, 469 (1987); G. Kellogg and P. Moore, FEBS Lett. 327, 261 (1993).
49. E. Westhof, P. Dumas, D. Moras, J. Mol. Biol. 184, 119 (1985).
50. C. Massire, C. Gaspin, E. Westhof, J. Mol. Graphics 12, 201 (1994).
51. G. Laughlan et al., Science 265, 520 (1994).
52. Supported by grants from the Deutsche Forschungsgemeinschaft to M.F. and the European Union (grant Biot-CT93-0345) to M.K., E.W., and M.F. M.K. thanks M. Guéron and J. L. Leroy for critical reading of the manuscript. Coordinates have been deposited at the Protein Data Bank (accession number 1KOC and 1 KOD) and will be directly accessible on the Web server of the Centre de Biochimie Structurale at http:\\tome.cbs.univ-montp1.fr.