Sequence requirements for stabilization of a peptide reverse turn in water solution - Proline is not essential for stability

European Journal of Biochemistry

Volumn 255, Issue 2, 1998, Pages 462-471

  Dyson, H Jane ^a   Bolinger, Lizann ^a   Feher, Victoria A ^a   Osterhout Jr , John J ^a   Yao, Jian ^a   Wright, Peter E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Amino acid sequence preference; NMR; Peptide; Proline; Reverse turn

Indexed keywords

AMINO ACID COMPOSITION; ARTICLE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE;

EID: 0032528013     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1998.2550462.x     Document Type: Article

References (39)

1. Brunet, A. P., Huang, E. S., Huffine, M. E., Loeb, J. E., Weltman, R. J. & Hecht, M. H. (1993) The role of turns in the structure of an α-helical protein, Nature 364, 355-358.
2. Predki, P. F., Agrawal, V., Brünger, A. T. & Regan, L. (1996) Amino-acid substitutions in a surface turn modulate protein stability, Nat. Struct. Biol. 3, 54-58.
3. Zhou, H. X., Hoess, R. H. & DeGrado, W. F. (1996) In vitro evolution of thermodynamically stable turns, Nat. Struct. Biol. 3, 446-451.
4. Ybe, J. A. & Hecht, M. H. (1996) Sequence replacements in the central β-turn of plastocyanin, Protein Sci. 5, 814-824.
5. Zimmerman, S. S. & Scheraga, H. A. (1977) Local interactions in bends of proteins, Proc. Natl Acad. Sci. USA 74, 4126-4129.
6. Skolnick, J., Kolinski, A. & Sikorski, A. (1991) Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics, J. Mol. Biol. 221, 499-531.
7. Gu, H. D., Kim, D. & Baker, D. (1997) Contrasting roles for symmetrically disposed β-turns in the folding of a small protein, J. Mol. Biol. 274, 588-596.
8. Montelione, G. T., Arnold, E., Meinwald, Y. C., Stimson, E. R., Demon, J. B., Huang, S.-G., Clardy, J. & Scheraga, H. A. (1984) Chain-folding initiation structures in ribonuclease A: conformational analysis of trans-Ac-Tyr-Pro-Tyr-NHMe and trans-Ac-Tyr-Pro-Asn-NHMe in water and in the solid state, J. Am. Chem. Soc. 106, 7946-7958.
9. Dyson, H. J., Cross, K. J., Houghten, R. A., Wilson, I. A., Wright, P. E. & Lerner, R. A. (1985) The immunodominant site of a synthetic immunogen has a conformational preference in water for a Type-11 reverse turn, Nature 318, 480-483.
10. Chou, P. Y. & Fasman, G. D. (1978) Prediction of the secondary structure of proteins from their amino acid sequence, Adv. Enzymol. 47, 45-148.
11. Dyson, H. J., Rance, M., Houghten, R. A., Lerner, R. A. & Wright, P. E. (1988) Folding of immunogenic peptide fragments of proteins in water solution. 1 Sequence requirements for the formation of a reverse turn, J. Mol. Biol. 201, 161-200.
12. Yao, J., Dyson, H. J. & Wright, P. E. (1994) Three-dimensional structure of a Type VI turn in a linear peptide in water solution: evidence for stacking of aromatic rings as a major stabilizing factor, J. Mol. Biol. 243, 754-766.
13. Yao, J., Feher, V. A., Espejo, B. F., Reymond, M. T., Wright, P. E. & Dyson, H. J. (1994) Stabilization of a Type VI turn in a family of linear peptides in water solution, J. Mol. Biol. 243, 736-753.
14. Yao, J., Brüschweiler, R., Dyson, H. J. & Wright, P. E. (1994) Differential side chain hydration in a linear peptide containing a Type VI turn, J. Am. Chem. Soc. 116, 12051-12052.
15. Houghten, R. A. (1985) General method for the rapid solid-phase synthesis of large numbers of peptides: specificity of antigen-antibody interaction at the level of individual amino acids, Proc. Natl Acad. Sci. USA 82, 5131-5135.
16. 1H NMR spectra of proteins via double quantum filtering, Biochem. Biophys. Res. Commun. 117, 479-485.
17. Drobny, G., Pines, A., Simon, S., Weitekamp, D. & Wemmer, D. (1979) Fourier transform multiple quantum nuclear magnetic resonance, Symp. Faraday Soc. 13, 49-55.
18. 1H spin-spin coupling constants in proteins, Biochem. Biophys. Res. Commun. 113, 967-974.
19. Van Geet, A. L. (1970) Calibration of methanol nuclear magnetic resonance thermometer at low temperature, Anal. Chem. 42, 679-680.
20. Bothner-By, A. A., Stephens, R. L., Lee, J.-M., Warren, C. D. & Jeanloz, R. W. (1984) Structure determination of a tetrasaccharide: Transient nuclear Overhauser effects in the rotating frame, J. Am. Chem. Soc. 106, 811-813.
21. Kessler, H., Griesinger, C., Kerssebaum, R., Wagner, K. & Ernst, R. R. (1987) Separation of cross-relaxation and J cross-peaks in 2D rotating-frame NMR spectroscopy, J. Am. Chem. Soc. 109, 607-609.
22. Wright, P. E., Dyson, H. J., Feher, V. A., Tennant, L. L., Waltho, J. P., Lerner, R. A. & Case, D. A. (1990) Folding of peptide fragments of proteins in aqueous solution, in UCLA Symp. Mol. Cell. Biol. New Ser. 109, 1-13.
23. 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG, J. Biomol. NMR 5, 14-24.
24. Dyson, H. J., Merutka, G., Waltho, J. P., Lerner, R. A. & Wright, P. E. (1992) Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding I. Myohemerythrin, J. Mol. Biol. 226, 795-817.
25. Dyson, H. J., Sayre, J. R., Merutka, G., Shin, H.-C., Lerner, R. A. & Wright, P. E. (1992) Folding of peptide fragments comprising the complete sequence of proteins: models for the initiation of protein folding II Plastocyanin, J. Mol. Biol. 226, 819-835.
26. 'H-nuclear magnetic resonance spectroscopy in peptides related to the N terminus of bovine pancreatic trypsin inhibitor, J. Mol. Biol. 230, 312-322.
27. Lumb, K. J. & Kim, P. S. (1994) Formation of a hydrophobic cluster in denatured bovine pancreatic trypsin inhibitor, J. Mol. Biol. 236, 412-420.
28. Dyson, H. J. & Wright, P. E. (1991) Defining solution conformations of small linear peptides, Annu. Rev. Biophys. Biophys. Chem. 20, 519-538.
29. Serrano, L. (1995) Comparison between the φ distribution of the amino acids in the protein database and NMR data indicates that amino acids have various φ propensities in the random coil conformation, J. Mol. Biol. 254, 322-333.
30. Smith, L. J., Bolin, K. A., Schwalbe, H., MacArthur, M. W., Thornton, J. M. & Dobson, C. M. (1996) Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations, J. Mol. Biol. 255, 494-506.
31. 1H nuclear magnetic resonance spectra. Computation of sterically allowed proton-proton distances and statistical analysis of proton-proton distances in single crystal protein conformations, J. Mol. Biol. 155, 321-346.
32. Dyson, H. J., Rance, M., Houghten, R. A., Wright, P. E. & Lerner, R. A. (1988) Folding of immunogenic peptide fragments of proteins in water solution. II The nascent helix, J. Mol. Biol. 201, 201-217.
33. Hutchinson, E. G. & Thornton, J. M. (1994) A revised set of potentials for beta-turn formation in proteins, Protein Sci. 3, 2207-2216.
34. Wilmot, C. M. & Thornton, J. M. (1988) Analysis and prediction of the different types β-turn in proteins, J. Mol. Biol. 203, 221-232.
35. Milburn, P. J., Konishi, Y., Meinwald, Y. C. & Scheraga, H. A. (1987) Chain reversals in model peptides: Studies of cystine-containing cyclic peptides. 1. Conformational free energies of cyclization of hexapeptides of sequence Ac-Cys-X-Pro-Gly-Y-Cys-NHMe, J. Am. Chem. Soc. 109, 4486-4496.
36. Milburn, P. J., Meinwald, Y. C., Takahashi, S., Ooi, T. & Scheraga, H. A. (1988) Chain reversals in model peptides: studies of cystine-containing cyclic peptides. II. Effects of valyl residues and possible i-to-(i + 3) attractive ionic interactions on cyclization of [Cys1], [Cys6] hexapeptides, Int. J. Pept. Protein Res. 31, 311-321.
37. Johnson, W. C. Jr, Pagano, T. G., Basson, C. T., Madri, J. A., Gooley, P. & Armitage, I. M. (1993) Biologically active Arg-Gly-Asp oligopeptides assume a type II β-turn in solution, Biochemistry 32, 268-273.
38. Reed, J., Hull, W. E., von der Lieth, C.-W., Kübler, D., Suhai, S. & Kinzel, V. (1988) Secondary structure of the Arg-Gly-Asp recognition site in proteins involved in cell-surface adhesion. Eur. J. Biochem. 178, 141-154.
39. Krezel, A. M., Wagner, G., Seymour-Ulmer, J. & Lazarus, R. A. (1994) Structure of the RGD protein Decorsin: conserved motif and distinct function in leech proteins that affect blood clotting, Science 264, 1944-1947.