Peptide design. Helix–helix motifs in synthetic sequences

Abstract

Two centrally positioned α-aminoisobutyryl (Aib) residues have been used to stabilize distinct heptapeptide helical segments in the 15-residue synthetic sequence Boc-Met-Ala-Leu-Aib-Val-Ala-Leu-Acp-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe. The helices are connected by the flexible linker ε-aminocaproic acid (Acp). NMR studies in CDCl₃ establish helical conformations for both independent segments as evidenced by NH–NH nuclear Overhauser effects (NOEs). The peptide strongly aggregates in CDCl₃ with the NH groups of Met(1) and Ala(2) participating in intermolecular hydrogen bonds. In (CD₃)₂SO two solvated helical segments are supported by NMR results. Solvent dependent breakdown of aggregates on addition of (CD₃)₂SO to CDCl₃ solutions is suggested by analysis of chemical shifts and temperature coefficients of NH protons. The observation of several interhelical NOEs in CDCl₃, relatively few NOEs in 10% (CD₃)₂SO–CDCl₃ and their absence in (CD₃)₂SO provides a means of inferring helix orientations. While an antiparallel arrangement resulting in closed aggregate formation is suggested in CDCl₃, a parallel solvated arrangement is favoured in (CD₃)₂SO.

References

1. S. F. Betz, D. P. Raleigh and W. F. DeGrado, Curr. Opin. Struct. Biol., 1993, 3, 601.
2. J. W. Bryson, S. F. Betz, H. S. Lu, D. J. Suich, H. X. Zhou, K. T. O'Neil and W. F. DeGrado, Science, 1995, 270, 935.
3. S. Kamtekar, J. M. Schiffer, H. Xiong, J. M. Babik and M. H. Hecht, Science, 1993, 262, 1680.
4. M. Munson, R. O'Brien, J. M. Sturtevant and L. Regan, Protein Sci., 1994, 3, 2363.
5. K. R. Shoemaker, P. S. Kim, E. J. York, J. M. Stewart and R. L. Baldwin, Nature, 1987, 326, 536.
6. S. Padmanabhan and R. L. Baldwin, Protein Sci., 1994, 3, 1992.
7. A. J. Doig and R. L. Baldwin, Protein Sci., 1995, 4, 1325.
8. F. J. Blanco, G. Ravis and L. Serrano, Nature Struct. Biol., 1994, 1, 584.
9. M. S. Searle, D. H. Williams and L. C. Packman, Nature Struct. Biol., 1995, 2, 999.
10. M. Beauregard, K. Goraj, V. Goffin, K. Haremans, E. Goormaghtigh, J.-M. Ruysschaert and J. A. Martial, Protein Eng., 1991, 4, 745.
11. D. P. Raleigh and W. F. DeGrado, J. Am. Chem. Soc., 1992, 114, 10079.
12. T. Tanaka, H. Kimura, M. Hayashi, Y. Fujiyoshi, K. Fuhuhara and H. Nakamura, Protein Sci., 1994, 3, 419.
13. T. Tanaka, Y. Kuroda, H. Kimura, S. Kidokoro and H. Nakamura, Protein Eng., 1994, 7, 969.
14. M. R. Ghadiri, C. Soares and C. Choi, J. Am. Chem. Soc., 1992, 114, 825.
15. J. M. Berg, Curr. Opin. Struct. Biol., 1993, 3, 585.
16. J. M. Berg, Acc. Chem. Res., 1995, 28, 14.
17. M. Klemba, K. H. Gardner, S. Marino, N. D. Clarke and L. Regan, Nature Struct. Biol., 1995, 2, 368.
18. M. Mutter and S. Vuillemier, Angew. Chem., Int. Ed. Engl., 1989, 28, 535.
19. M. Mutter, G. G. Tuchscherer, C. Miller, K.-H. Altman, R. I. Carey, D. F. Wyss, A. M. Labhardt and J. E. Rivier, J. Am. Chem. Soc., 1992, 114, 1463.
20. G. Tuchsherer and M. Mutter, J. Peptide Science, 1995, 1, 3.
21. P. Balaram, Pure Appl. Chem., 1992, 64, 1061.
22. P. Balaram, Curr. Opin. Struct. Biol., 1992, 2, 845.
23. I. L. Karle, R. B. Rao, S. Prasad, R. Kaul and P. Balaram, J. Am. Chem. Soc., 1994, 116, 10355.
24. I. L. Karle, R. Gurunath, S. Prasad, R. Kaul, R. B. Rao and P. Balaram, J. Am. Chem. Soc., 1995, 117, 9632.
25. I. L. Karle, J. L. Flippen-Anderson, M. Sukumar, K. Uma and P. Balaram, J. Am. Chem. Soc., 1991, 113, 3952.
26. K. Uma, Modular design of synthetic protein mimics. Construction of helices. PhD Thesis, Indian Institute of Science, Bangalore, 1990.
27. T. P. Pitner and D. W. Urry, J. Am. Chem. Soc., 1972, 94, 1399.
28. P. A. Raj and P. Balaram, Biopolymers, 1985, 24, 1131.
29. I. L. Karle, Acta Crystallogr., Sect. B, 1992, 48, 341.
30. I. K. Karle, J. L. Flippen-Anderson, M. Sukumar and P. Balaram, J. Med. Chem., 1992, 35, 3885.
31. I. L. Karle, J. L. Flippen-Anderson, M. Sukumar and P. Balaram, Protein. Struct. Funct. Genet., 1992, 12, 324.
32. E. S. Stevens, N. Sugawara, G. M. Bonora and C. Toniolo, J. Am. Chem. Soc., 1980, 102, 7048.
33. M. Iqbal and P. Balaram, Biopolymers, 1982, 21, 1427.
34. C. Toniolo, G. M. Bonora, V. Bavoso, E. Benedetti, B. DiBlasio, P. Gramaldi, F. Lelj, V. Pavone and C. Pedone, Macromolecules, 1985, 18, 895.
35. I. L. Karle, J. L. Flippen-Anderson, K. Uma and P. Balaram, Biopolymers, 1993, 33, 827.
36. G. M. Whitesides, E. E. Simanek, J. P. Mathias, C. T. Seto, D. N. Chin, M. Mammen and D. M. Gordon, Acc. Chem. Res., 1995, 28, 37.
37. I. L. Karle, J. L. Flippen-Anderson, K. Uma and P. Balaram, Current Science, 1990, 59, 875.
38. A. Banerjee, S. Dutta, A. Pramanik, N. Shamala and P. Balaram, J. Am. Chem. Soc., 1996, 118, 9477.
39. S. M. Miick, G. V. Martinez, W. R. Fiori, A. P. Todd and G. L. Millhauser, Nature, 1992, 359, 653.
40. J. Tirado-Rives, D. L. Maxwell and W. L. Jorgensen, J. Am. Chem. Soc., 1993, 115, 11590.
41. T. S. Sudha, E. K. S. Vijaykumar and P. Balaram, Int. J. Peptide Protein Res., 1983, 22, 464.
42. C. Toniolo, A. Polese, F. Formaggio, M. Crisma and J. Kamphuis, J. Am. Chem. Soc., 1996, 118, 2744.
43. N. H. Andersen, Z. Liu and K. S. Prickett, FEBS Lett., 1996, 399, 47.