A rationally designed turn-helix peptide

Journal of the American Chemical Society

Volumn 121, Issue 23, 1999, Pages 5575-5576

  Dhanasekaran, M ^a   Fabiola, F ^b   Pattabhi, V ^b   Durani, S ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

^b UNIVERSITY OF MADRAS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PEPTIDE;

ALPHA HELIX; ARTICLE; NUCLEAR OVERHAUSER EFFECT; PEPTIDE ANALYSIS; PROTEIN FOLDING; SEQUENCE ANALYSIS; STEREOCHEMISTRY; STRUCTURE ANALYSIS;

EID: 0033575060     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja984237v     Document Type: Article

References (43)

1. Kim, P. S.; Baldwin, R. L. Annu. Rev. Biochem. 1982, 51, 459-489.
2. (b) Dyson, H. J.; Rance, M.; Houghten, R. A.; Lerner, R. A.; Wright, P. E. J. Mol. Biol. 1988, 201, 161-200.
3. (c) Baldwin, R. L. Trends Biochem. Sci. 1989, 14, 291-294.
4. (d) Scholtz, J. M.; Baldwin, R. L. Annu. Rev. Biophys. Biomol. Struct. 1992, 21, 95-118.
5. (e) Krplus, M.; Weaver, D. L. Protein Sci. 1994, 3, 650-668.
6. (f) Baldwin, R. L. J. Biomol. NMR 1995, 5, 103-109.
7. (g) Alba de, E.; Blanco, F. J.; Jimenez, M. A.; Rico, M.; Nieto, J. L. Eur. J. Biochem. 1995, 233, 283-292.
8. Chou, P. Y.; Fasman, G. D. J. Mol. Biol. 1977, 115, 135-175.
9. (b) Wilmot, C. M.; Thornton, J. M. J. Mol. Biol. 1988, 203, 221-232.
10. (c) Hutchinson, E. G.; Thornton, J. M. Protein Sci. 1994, 3, 2207-2216.
11. Ramirez-Alvarado, M.; Blanco, F. J.; Niemann, H.; Serrano, L. J. Mol. Bio. 1997, 273, 898-912.
12. (b) Maynard, A. J.; Sharman, G. J.; Searle, M. S. J. Am. Chem. Soc. 1998, 120, 1996-2007.
13. (c) Stanger, H. E.; Gellman, S. J. Am. Chem. Soc. 1998, 120, 4236-4237.
14. (d) Das, C.; Raghothama, S.; Balaram, P. J. Am. Chem. Soc. 1998, 120, 5812-5813.
15. Rose, G. D.; Gierasch, L. M.; Smith, J. A. Adv. Protein Chem. 1985, 37, 1-109.
16. (b) Imperiali, B.; Fisher, S. L.; Moats, R. A.; Prins, T. J. J. Am. Chem. Soc. 1992, 114, 3182-3188.
17. (c) Struthers, M. D.; Cheng, R. P.; Imperiali, B. Science 1996, 277, 342-344.
18. Bobde, V.; Beri, S.; Durani, S. Tetrahedron 1993, 49, 5397-5406.
19. (b) Bobde, V.; Sasidhar, Y. U.; Durani, S. Int. J. Pept. Protein Res. 1994, 46, 209-218.
20. (c) Bobde, V.; Beri, S.; Rawale, S.; Satyanarayana, V.; Durani, S. Tetrahedron 1995, 51, 3077-3086.
21. The abbreviations used: Aib, α-aminoisobutyric acid; Boc, tert-butyloxycarbonyl; NOE, nuclear Overhauser effect; ROESY, rotating frame nuclear Overhauser enhancement spectroscopy; DMSO, dimethyl sulfoxide; Asx, the amino acids Asp and Asn.
22. Fabiola, F.; Pattabi, V.; Raju, E. B.; Durani, S. J. Pept. Res. 1997, 50, 352-356.
23. 3CN water. Bodanszky, M.; Bodanszky, A. The Practice of Peptide Synthesis; Springer-Verlag: NewYork, 1984.
24. Wuthrich, K. NMR of Proteins and Nuclic Acids; Wiley: New York, 1986.
25. Val(1)NH, (D)Asp(3)NH, Aib(4)NH, Leu(5)NH, Aib(6)NH, Leu(7)-NH, Ala(S)NH, and NWMe.
26. 6 on a Bruker AM 500 spectrometer with a 10mM peptide solution which showed no chemical shift or line-width variation on a 10-fold dilution and, hence, absence of any noticeable intermolecular aggregation. Resonance assignments were with combined use of TOCSY and ROESY spectra. The ROESY spectra were recorded with a mixing time of 250 ms. The variable-temperature experiments to record the temperature coefficients were at 5° intervals in the range 25-50°C. (a) Jeener, J.; Meier, B. H.; Bachmann, P.; Ernst, R. R. J. Chem. Phys. 1979, 71, 4546-4553. (b) Bax, A.; Davis, D. G. J. Magn. Reson. 1985, 63, 207-213.
27. 6 on a Bruker AM 500 spectrometer with a 10mM peptide solution which showed no chemical shift or line-width variation on a 10-fold dilution and, hence, absence of any noticeable intermolecular aggregation. Resonance assignments were with combined use of TOCSY and ROESY spectra. The ROESY spectra were recorded with a mixing time of 250 ms. The variable-temperature experiments to record the temperature coefficients were at 5° intervals in the range 25- 50°C. (a) Jeener, J.; Meier, B. H.; Bachmann, P.; Ernst, R. R. J. Chem. Phys. 1979, 71, 4546-4553. (b) Bax, A.; Davis, D. G. J. Magn. Reson. 1985, 63, 207-213.
28. (c) Davis, D. G.; Bax A. J. Am. Chem. Soc 1985, 107, 2821-2823.
29. (d) Rance, M. J. Magn. Reson. 1987, 65, 2821-2823.
30. Molecular dynamics simulation was with INSIGHT/DISCOVER package (Biosym Technologies, San Diego, CA). A distance-dependent dielectric constant (2.5r where r is distance in Å) was used, and Asp was assumed to be always in charged form. All hydrogens were treated explicitly, and all ω dihedrals were constrained as trans by a 100 kcal/rad energetic penalty. Distance constraint with a force constant of 25 kcal/mol was applied in the form of a flat-bottom potential well with a common lower bound of 2.0 Å and an upper bound of 2.5, 3.0, 3.5,4.0, or 4.5 Å, in accordance with the NOE intensity. The starting structures minimized with all restraints in place, first with steepest descent and then with conjugate gradient algorithm, were subjected to simulated annealing. A two hundred picosecond MD run at 1000 K was followed by cooling to 300 K in 7 steps for a total of 35 ps, and then steepest descent and conjugate gradient minimization. One hundred final energy minimized structures were sampled at 2 ps intervals.
31. Interproton distance restraints were generated from the integrals of ROESY cross-peak volumes, using a reference distance of 1.85 Å for Pro δ protons. No stereospecific assignments were made and, hence, pseudo atom corrections were applied for all diastereotopic protons when imposing the NOE restraints. Wuthrich, K.; Billeter, M.; Braun, W. J. Mol. Biol. 1983, 169, 949-961.
32. dδ/dT values of <-3 ppb/K are typical for solvent-shielded NHs and >-4ppb/K are typical for solvent-exposed NHs. Kessler, H. Angew. Chem., Int. Ed. Engl. 1982, 21, 512-523.
33. o). (a) Sheldrick, G. M. Crystallographic Computing 3; Oxford University Press: Oxford, U.K., 1985; p 175. (b) Sheldrick, G. M. SHELXS 93; Program for Crystal Structure Determination; University of Gottingen: Gottingen, Germany, 1993.
34. o). (a) Sheldrick, G. M. Crystallographic Computing 3; Oxford University Press: Oxford, U.K., 1985; p 175. (b) Sheldrick, G. M. SHELXS 93; Program for Crystal Structure Determination; University of Gottingen: Gottingen, Germany, 1993.
35. (a) Venkatachalam, C. M. Biopolymers 1968, 6, 1425-1436.
36. (b) Toniolo, C.; Benedetti, E. Trends Biochem. Sci. 1991, 16, 350-353.
37. (c) Benedetti, E.; Di Blasio, B.; Pavone, V.; Pedone, C.; Toniolo, C.; Crisma, M. Biopolymers 1992, 32, 453-456.
38. (a) Richardson, J. S.; Richardson, D. C. Science 1988, 240, 1648-1652.
39. (b) Dasgupta, S.; Bell, J. A. Int. J. Pept. Protein Res. 1993, 41, 499-511.
40. (c) Forood, B.; Feliciano, E. J.; Nambiar, K. P. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 838-842.
41. (d) Zhou, H. X.; Lyu, P.; Wemmer, D. E.; Kallenbach, N. R. Proteins: Struct., Funct., Genet. 1994, 18, 1-7.
42. (e) Doig, A. J.; Baldwin, R. L. Protein Sci. 1995, 4, 1325-1336.
43. (f) Aurora, R.; Rose, G. D. Protein Sci. 1998, 7, 21-38.