The strength of the 3′-gauche effect dictates the structure of 3′-O-anthraniloyladenosine and its 5′-phosphate, two analogues of the 3′-end of aminoacyl-tRNA

Abstract

Anthranilic acid charged yeast tRNA^Phe or E. coli tRNA^Val are able to form a stable complex with EF-Tu*GTP, hence the 2′- and 3′-O-anthraniloyladenosines and their 5′-phosphate counterparts have been conceived to be the smallest units that are capable of mimicking aminoacyl-tRNA. Since the 3′-O-anthraniloyladenosine also binds more efficiently to the EF-Tu*GTP complex compared to its 2′-isomer, we have herein delineated the stereoelectronic features that dictate the conformation of 3′-O-anthraniloyladenosine and its 5′-phosphate vis-a-vis their 2′-counterparts and we have also addressed how their structures and thermodynamic stabilizations are different from adenosine and 5′-AMP. It has been found that the electron-withdrawing anthraniloyl group exerts gauche effects of variable strengths depending upon whether it is at the 2′- or at 3′-position because of either the presence or absence of O2′–N9 gauche effect, [GE(O2′–C2′–C1′–N9)], thereby steering the pseudorotation of the constituent sugar moiety either to the North (N)-type (C3′-endo) or South (S)-type (C2′-endo) conformation. The 3′-O-anthraniloyladenosine 5′-phosphate has a relatively more stabilized S-type conformation ΔG ° = –4.6 kJ mol^–1) than 3′-O-anthraniloyladenosine itself (ΔG ° = –3.9 kJ mol^–1), whereas the ΔG ° for 2′-O-anthraniloyladenosine and its 5′-monophosphate are respectively –0.9 and –1.8 kJ mol^–1, suggesting that the 3′-gauche effect of the 3′-O-anthraniloyl group is stronger than that of 2′-O-anthraniloyl in the drive of the sugar conformation. Since the EF-Tu can specifically recognize the aminoacylated-tRNA from the non-charged tRNA, we have assessed the free-energy (ΔG °) for this recognition switch to be the least ≈ –2.9 kJ mol^–1 by comparison of ΔG ° of the N⇄pseudorotational equilibrium for 3′-O-anthraniloyladenosine 5′-phosphate and 5′-AMP. The 3′-O-anthraniloyladenosine and its 5′-phosphate are much more flexible than the isomeric 2′-counterparts as is evident from the temperature-dependent coupling constants analysis. The relative rate of the transacylation reaction of 2′(3′)-O-anthraniloyladenosine and its 5′-phosphate is cooperatively dictated by the two-state N⇄S pseudorotational equilibrium of the sugar, which in turn is controlled by a balance of the stereoelectronic 3′- and 2′-gauche effects as well as by the pseudoaxial preference of the 3′-O- or 2′-O-anthraniloyl group. The reason for the larger stabilization of the 2′-endo conformer for 3′-O-anthraniloyladenosine and its 5′-phosphate lies in the fact that the C3′–O3′ bond takes up an optimal gauche orientation with respect to the C4′–O4′ bond dictating the pseudoaxial orientation of the 3′-anthraniloyl residue, which can be achieved only in the S-type sugar conformation with adenin-9-yl and the 2′-OH groups in the pseudoequatorial geometry, compared to the preferred C3′-endo sugar with a pseudoaxial aglycone and 2′-OH found in the 3′-terminal adenosine moiety in the helical 3′-CCA end of uncharged tRNA.

References

1. F. Janiak, V. A. Dell, J. K. Abrahamson, B. S. Watson, D. L. Miller and A. E. Johnson, Biochemistry, 1990, 29, 4268.
2. R. O. Potts, N. C. Ford, Jr. and M. J. Fournier, Biochemistry, 1981, 20, 1653.
3. B. Nawrot, W. Milius, A. Ejchart, S. Limmer and M. Sprinzl, Nucleic Acids Res., 1997, 25, 948.
4. (a) M. Taiji, S. Yokoyama and T. Miyazawa, Nucleic Acids Res., 1982, 11, 161; (b) M. Taiji, S. Yokoyama and T. Miyazawa, Biochemistry, 1985, 98, 1447.
5. P. Nissen, M. Kjeldgaard, S. Thirup, G. Polekhina, L. Reshetnikova, B. F. C. Clark and J. Nyborg, Science, 1995, 270, 1464.
6. S. Limmer, M. Vogtherr, B. Nawrot, R. Hillenbrand and M. Spinzl, Angew. Chem., Int. Ed. Engl., 1997, 36, 2485.
7. L. Servillo, C. Balestrieri, L. Quagliuolo, L. Iorio and A. Giovane, Eur. J. Biochem., 1993, 213, 583.
8. B. Nawrot and M. Sprinzl, Nucleosides Nucleotides, 1998, 17, 815.
9. (a) J. Plavec, W. Tong and J. Chattopadhyaya, J. Am. Chem. Soc., 1993, 115, 9734; (b) J. Plavec, N. Garg and J. Chattopadhyaya, J. Chem. Soc., Chem. Commun., 1993, 1011; (c) J. Plavec, L. H. Koole and J. Chattopadhyaya, J. Biochem. Biophys. Methods, 1992, 25, 253; (d) L. H. Koole, H. M. Buck, A. Nyilas and J. Chattopadhyaya, Can. J. Chem., 1987, 65, 2089; (e) L. H. Koole, H. M. Buck, H. Bazin and J. Chattopadhyaya, Tetrahedron, 1987, 43, 2289; (f) L. H. Koole, J. Plavec, H. Liu, B. R. Vincent, M. R. Dyson, P. L. Coe, R. T. Walker, G. W. Hardy, S. G. Rahim and J. Chattopadhyaya, J. Am. Chem. Soc., 1992, 114, 9934; (g) J. Plavec, C. Thibaudeau, G. Viswanadham, C. Sund and J. Chattopadhyaya, J. Chem. Soc., Chem. Commun., 1994, 781; (h) C. Thibaudeau, J. Plavec, K. A. Watanabe and J. Chattopadhyaya, J. Chem. Soc., Chem. Commun., 1994, 537; (i) C. Thibaudeau, J. Plavec, N. Garg, A. Papchikhin and J. Chattopadhyaya, J. Am. Chem. Soc., 1994, 116, 4038; (j) J. Plavec, C. Thibaudeau and J. Chattopadhyaya, J. Am. Chem. Soc., 1994, 116, 6558; (k) C. Thibaudeau, J. Plavec and J. Chattopadhyaya, J. Am. Chem. Soc., 1994, 116, 8033; (l) J. Plavec, PhD Thesis, Department of Bioorganic Chemistry, Uppsala University, Sweden, 1995; (m) J. Plavec, C. Thibaudeau and J. Chattopadhyaya, Tetrahedron, 1995, 51, 11775; (n) C. Thibaudeau, J. Plavec and J. Chattopadhyaya, J. Org. Chem., 1996, 61, 266; (o) J. Chattopadhyaya, Nucleic Acids Symp. Ser., 1996, 35, 111; (p) J. Plavec, C. Thibaudeau and J. Chattopadhyaya, Pure Appl. Chem., 1996, 68, 2137; (q) I. Luyten, C. Thibaudeau and J. Chattopadhyaya, Tetrahedron, 1997, 53, 6433; (r) C. Thibaudeau, A. Földesi and J. Chattopadhyaya, Tetrahedron, 1997, 53, 14043; (s) C. Thibaudeau, A. Földesi and J. Chattopadhyaya, Tetrahedron, 1998, 54, 1857; (t) I. Luyten, C. Thibaudeau and J. Chattopadhyaya, J. Org. Chem., 1997, 62, 8800; (u) C. Thibaudeau and J. Chattopadhyaya, Nucleosides Nucleotides, 1998, 17, 1589; (v) I. Luyten, J. Matulic-Adamic, L. Beigelman and J. Chattopadhyaya, Nucleosides Nucleotides, 1998, 17, 1605; (w) C. Thibaudeau and J. Chattopadhyaya, Nucleosides Nucleotides, 1997, 16, 523; (x) C. Thibaudeau, J. Plavec and J. Chattopadhyaya, J. Org. Chem., 1998, 63, 4967; (y) C. Thibaudeau, A. Kumar, S. Bekiroglu, A. Matsuda, V. E. Marquez and J. Chattopadhyaya, J. Org. Chem., 1998, 63, 5447.
10. (a) H. P. M. de Leeuw, C. A. G. Haasnoot and C. Altona, Isr. J. Chem., 1980, 20, 108; (b) C. Altona and M. Sundaralingam, J. Am. Chem. Soc., 1972, 94, 8205; (c) C. Altona and M. Sundaralingham, J. Am. Chem. Soc., 1973, 95, 2333.
11. (a) J. Feigon, A. H. J. Wang, G. A. van der Marel, J. H. van Boom and A. Rich, Nucleic Acids Res., 1984, 12, 1243; (b) S. Tran-Dinh, J. Taboury, J.-M. Neumann, T. Huynh-Dinh, B. Genissel, B. Langlois d'Estaintot and J. Igolen, Biochemistry, 1984, 23, 1362; (c) P. W. Davis, K. Hall, P. Cruz, I. Tinoco and T. Neilson, Nucleic Acids Res., 1986, 14, 1279; (d) P. W. Davis, R. W. Adamiak and I. Tinoco, Biopolymers, 1990, 29, 109; (e) P. Agback, A. Sandstrom, S.-I. Yamakage, C. Sund, C. Glemarec and J. Chattopadhyaya, J. Biochem. Biophys. Methods, 1993, 27, 229; (f) P. Agback, C. Glemarec, L. Yin, A. Sandstrom, J. Plavec, C. Sund, S.-I. Yamakage, G. Wiswanadham, B. Rousse, N. Puri and J. Chattopadhyaya, Tetrahedron Lett., 1993, 34, 3929.
12. (a) N. S. Zefirov, Zh. Org. Khim., 1970, 6, 1761; (b) N. S. Zefirov, L. G. Gurvich, A. S. Shashkov, M. Z. Krimer and E. A. Vorob'eva, Tetrahedron, 1976, 32, 1211; (c) R. Hoffmann, Acc. Chem. Res., 1971, 4, 1; (d) N. D. Epiotis, S. Sarkanen, D. Bjorkquist, L. Bjorkquist and R. Yates, J. Am. Chem. Soc., 1974, 96, 4075; (e) K. B. Wiberg, Acc. Chem. Res., 1996, 29, 229; (f) W. K. Olson and J. L. Sussman, J. Am. Chem. Soc., 1982, 104, 270; (g) W. K. Olson, J. Am. Chem. Soc., 1982, 104, 278.
13. (a) F. A. A. M. De Leeuw and C. Altona, J. Comput. Chem., 1983, 4, 428 and PSEUROT, QCPE program No 463; (b) C. A. G. Haasnoot, F. A. A. M. de Leeuw and C. Altona, Tetrahedron, 1980, 36, 2783.
14. J. E. Kilpatrick, K. S. Pitzer and R. Spitzer, J. Am. Chem. Soc., 1947, 69, 2483.
15. (a) E. Diez, J. S. Fabian, J. Guilleme, C. Altona and L. A. Donders, Mol. Phys., 1989, 68, 49; (b) L. A. Donders, F. A. A. M. de Leeuw and C. Altona, Magn. Reson. Chem., 1989, 27, 556; (c) C. Altona, J. H. Ippel, A. J. A. W. Hoekzema, C. Erkelens, G. Groesbeek and L. A. Donders, Magn. Reson. Chem., 1989, 27, 564; (d) J. van Wijk, unpublished results.