Folding of an Ala-Ala-Ala tripeptide into a β-turn via hydrophobic encapsulation

Journal of the American Chemical Society

Volumn 128, Issue 29, 2006, Pages 9280-9281

  Tashiro, Shohei ^a   Kobayashi, Masahide ^a   Fujita, Makoto ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

TRIALANINE; TRIPEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; ENCAPSULATION; HYDROPHOBICITY; MOLECULAR DYNAMICS; NUCLEAR OVERHAUSER EFFECT; PEPTIDE ANALYSIS; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ANALYSIS;

ALANINE; HYDROPHOBICITY; MODELS, MOLECULAR; OLIGOPEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 33746344038     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja061722e     Document Type: Article

References (26)

1. Zimm, B. H.; Bragg, J. K. J. Chem. Phys. 1959, 31, 526-535.
2. Design of β-hairpin structures: (a) Blanco, F. J.; Jiménez, M. A.; Herranz, J.; Rico, M.; Santoro, J.; Nieto, J. L. J. Am. Chem. Soc. 1993, 115, 5887-5888.
3. (b) Searle, M. S.; Williams, D. H.; Packman, L. C. Nat. Struct. Biol. 1995, 2, 999-1006.
4. (c) Ramírez-Alvarado, M.; Blanco, F. J.; Serrano, L. Nat. Struct. Biol. 1996, 3, 604-612.
5. (d) Haque, T. S.; Gellman, S. H. J. Am. Chem. Soc. 1997, 119, 2303-2304.
6. (e) de Alba, E.; Jiménez, M. A.; Rico, M. J. Am. Chem. Soc. 1997, 119, 175-183.
7. (f) Ottesen, J. J.; Imperiali, B. Nat. Struct. Biol. 2001, 8, 535-539.
8. (g) Venkatraman, J.; Gowda, G. A. N.; Balaram, P. J. Am. Chem. Soc. 2002, 124, 4987-4994.
9. (h) Tatko, C. D.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 9372-9373
10. (i) Ciani, B.; Jourdan, M.; Searle, M. S. J. Am. Chem. Soc. 2003, 125, 9038-9047.
11. (j) Pochan, D. J.; Schneider, J. P.; Kretsinger, J.; Ozbas, B.; Rajagopal, K.; Haines, L. J. Am. Chem. Soc. 2003, 125, 11802-11803.
12. For reviews on β-turn mimetic, see: (a) Giannis, A.; Kolter, T. Angew. Chem., Int. Ed. Engl. 1993, 32, 1244-1267.
13. (b) Schneider, J. P.; Kelly, J. W. Chem. Rev. 1995, 95, 2169-2187.
14. (c) Hanessian, S.; McNaughton-Smith, G.; Lombart, H.-G.; Lubell, W. D. Tetrahedron 1997, 53, 12789-12854.
15. (d) Stigers, K. D.; Soth, M. J.; Nowick, J. S. Curr. Opin. Chem. Biol. 1999, 3, 714-723.
16. (e) Burgess, K. Acc. Chem. Res. 2001, 34. 826-835.
17. Fujita, N.; Biradha, K.; Fujita, M.; Sakamoto, S.; Yamaguchi, K. Angew. Chem., Int. Ed. 2001, 40, 1718-1721.
18. The association constant for the 1-2 complex could not be directly determined by titration because of little change in absorbance and fluorescence on complexation. Thus, the association constant of an aromatic tripeptide was measured by UV titration. Then, the association constant for 1·2 was estimated by an NMR competition experiment with the aromatic peptide. The association constants of other peptides were also estimated by NMR competition experiments with 2: see the Supporting Information.
19. Dyson, H. J.; Wright, P. E. Annu. Rev. Biophys. Biophys. Chem. 1991. 20, 519-538.
20. Brünger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-kunstleve, R. W.; Jiang, J.-S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Crystallogr. Sect. A 1998, 54, 905-921.
21. Calculated structure by CNS was exactly categorized as β-turn type I.
22. Structure refinements were carried out using MacroModel 8.0 and the OPLS-AA force field.
23. Unfortunately, we could not assign NOEs between the terminal Gly residues due to fatal overlapping of their proton signals. Nevertheless, we considered that 9 must be folded into a hairpin-like structure because 9 cannot take other conformations in the cavity of 1 when optimized under restraints of NOE distances at the turn Ala3-Ala4-Ala5 region. Of course, the conformation of terminal Gly residues can be dynamic.
24. Selective recognition of tripeptides in self-assembled cage: Tashiro, S.; Tominaga, M.; Kawano, M.; Therrien, B.; Ozeki, T.; Fujita, M. J. Am. Chem. Soc. 2005, 127, 4546-4547.
25. Stabilization of α-helix in self-assembled bowl: (a) Tashiro, S.; Tominaga, M.; Yamaguchi, Y.; Kato, K.; Fujita, M. Angew. Chem., Int. Ed. 2006, 45, 241-244.
26. (b) Tashiro, S.; Tominaga, M.; Yamaguchi, Y.; Kato, K.; Fujita, M. Chem.-Eur. J. 2006, 12, 3211-3217.