Conformational analysis of peptides corresponding to β-hairpins and a β-sheet that represent the entire sequence of the α-spectrin SH3 domain

Journal of Molecular Biology

Volumn 255, Issue 3, 1996, Pages 507-521

  Viguera, Ana Rosa ^a   Jiménez, María Angeles ^b   Rico, Manuel ^b   Serrano, Luis ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b INSTITUTO DE ESTRUCTURA DE LA MATERIA   (Spain)

Author keywords

Circular dichroism; Nuclear magnetic resonance; Peptide conformation and folding; hairpin; sheet

Indexed keywords

FODRIN; PEPTIDE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BETA CHAIN; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE;

EID: 0343059020     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0042     Document Type: Article

References (72)

1. Aue, W. P., Bertholdi, W. & Ernst, R. R. (1976). Two-dimensional spectroscopy. Application to nuclear magnetic resonance. J. Chem. Phys. 64, 2229-2246.
2. Bax, A. & Davis, D. G. (1985). MLEV-17 based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 65, 355-360.
3. Blanco, F. J. & Serrano, L. (1995). Folding of protein G B1 domain studied by the conformational characterization of fragments comprising the secondary structure elements. Eur. J. Biochem. 230, 634-649.
4. Blanco, F. J., Jiménez, M. A., Rico, M., Santoro, J., Herránz, J. & Nieto, J. L. (1991). Tendamistat (12-26) fragment. NMR characterization of isolated β-turn folding intermediates. Eur. J. Biochem. 200, 345-351.
5. Blanco, F. J., Jiménez, M. A., Rico, M., Santoro, J., Herránz, J. & Nieto, J. L. (1992). The homologous angiogenin and ribonuclease N-terminal fragments fold into very similar helices when isolated. Biochem. Biophys. Res. Commun. 182, 1491-1498.
6. Blanco, F. J., Jiménez, M. A., Herranz, J., Rico, M., Santoro, J. & Nieto, J. L. (1993). NMR evidence of a short linear peptide that folds into a β-hairpin in aqueous solution. J. Am. Chem. Soc. 115, 5887-5888.
7. 1 domain. Evidence of trifluoroethanol induced native-like β-hairpin formation. Biochemistry, 33, 6004-6014.
8. Blanco, F. J., Rivas, G. & Serrano, L. (1994b). A short linear peptide that folds into a native β-hairpin in aqueous solution. Nature Struct. Biol. 1, 584-590.
9. Blumenstein, M., Matsueda, G. R., Timmons, S. & Hawiger, J. (1992). A β-turn is present in the 392-411 segment of the human fibrinogen γ-chain. Effects of structural changes in this segment on affinity to antibody 4A5. Biochemistry, 31, 10692-10698.
10. Bothner-By, A., Stephens, R. L. & Lee, J. (1984). Structure determination of a tetrasaccharide: transient nuclear Overhauser effects in the rotating frame. J. Am. Chem. Soc. 106, 811-813.
11. Brahms, S. & Brahms, J. (1980). Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. J. Mol. Biol. 138, 149-178.
12. Brown, J. E. & Klee, W. A. (1971). Helix-coil transition of the isolated amino terminus of ribonuclease. Biochemistry, 10, 470-476.
13. Bruix, M., Perelló, M., Herranz, J., Rico, M. & Nieto, J. L. (1990). Characterization of low populated helical structures in solution by means of NMR proton conformational shifts. Biochem. Biophys. Res. Commun. 167, 1009-1014.
14. Chakrabartty A., Korteme, T., Padmanabhan, S. & Baldwin, R. L. (1993). Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effects on measurements of helix propensities. Biochemistry, 32, 5560-5565.
15. Cox, J. P. L., Evans, P. A., Packman, L. C., Williams, D. H. & Woolfson, D. N. (1993). Dissecting the structure of a partially folded protein. Circular dichroism and nuclear magnetic resonance studies of peptides from ubiquitin. J. Mol. Biol. 234, 483-492.
16. Dasgupta, S. & Bell, J. (1993). Design of helix ends. Int. J. Pept. Res. 41, 499-511.
17. Dill, K. A., Fiebig, K. M. & Chan, H. S. (1993). Cooperativity in protein-folding kinetics. Proc. Natl Acad. Sci. USA, 90, 1942-1946.
18. Dyson, H. J. & Wright, R E. (1991). Defining solution conformations of small linear peptides. Annu. Rev. Biophys. Chem. 20, 519-538.
19. Dyson, H. J. & Wright, P. E. (1993). Peptide conformation and protein folding. Curr. Opin. Struct. Biol. 3, 60-65.
20. Dyson, H. J., Rance, M., Houghten, R. A., Lerner, R. A. & Wright, P. E. (1988a). Folding of inmunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. J. Mol. Biol. 201, 161-200.
21. Dyson, H. J., Rance, M., Houghten, R. A., Wright, P. E. & Lerner, R. A. (1988b). Folding of inmunogenic peptide fragments of proteins in water solution. II. The nascent helix. J. Mol. Biol. 201, 201-217.
22. 1H-NMR. Biochemistry, 29, 7828-7837.
23. Dyson, H. J., Merutka, G., Waltho, J. P., Lerner, R. A. & Wright, P. E. (1992a). Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding II. Myohemerythrin. J. Mol. Biol. 226, 795-817.
24. Dyson, H. J., Sayre, J. R., Merutka, G., Shin, H.-C., Lerner, R. A. & Wright, P. E. (1992b). Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding II. Plastocyanin. J. Mol. Biol. 226, 819-835.
25. Fan, P., Bracken, C. & Baum, J. (1993). Structural characterization of monellin in the alcohol denatured state by NMR: evidence for β-sheet to α-helix conversion. Biochemistry, 32, 1573-1582.
26. Finkelstein, A. V. & Ptitsyn, O. B. (1976). A theory of protein molecule self organization. 4. Helical and irregular local structures of unfolded protein chains. J. Mol. Biol. 103, 15-24.
27. Forood, B., Feliciano, E. J. & Nambiar, K. P. (1993). Stabilization of α-helical structures in short peptides via end capping. Proc. Natl Acad. Sci. USA, 90, 838-842.
28. Freire, E., Haynie, D. & Xie, D. (1993). Molecular basis of cooperativity in protein folding IV. CORE: A general cooperative folding model. Proteins: Struct. Funct. Genet. 17, 111-123.
29. Gill, S. C. & von Hippel, P. H. (1989). Extinction coefficients from amino acids sequence data. Anal. Biochem. 182, 319-326.
30. Goodman, E. M. & Kim, P. S. (1989). Folding of a peptide corresponding to the α-helix in bovine pancreatic trypsin inhibitor. Biochemistry, 28, 4343-4347.
31. Harper, E. T. & Rose, G. D. (1993). Helix stop signals in proteins and peptides: the capping box. Biochemistry, 32, 7605-7609.
32. Hartman, R., Schwaner, R. C. & Hermans, J. (1974). Beta poly (l-lysine). A model system for biological self-assembly. J. Mol. Biol. 90, 415-429.
33. Hilbich, C., Kisters-Woike, B., Reed, J., Masters, C. L. & Beyreuther, K. (1991). Aggregation and secondary structure of synthetic amyloid βA4 peptides of Alzheimer's disease. J. Mol. Biol. 218, 149-163.
34. Ilyina, E. & Mayo, K. H. (1995). Multiple native like conformations trapped via self-association-induced hydrophobic collapse of the 33-residue β-sheet from platelet factor 4. Biochem. J. 306, 407-419.
35. Jiménez, M. A., Blanco, F. J., Rico, M., Santoro, J., Herránz, J. & Nieto, J. L. (1992). Periodic properties of proton conformational shifts in isolated protein helices. An experimental study. Eur. J. Biochem. 207, 39-49.
36. 1H-NMR studies on the conformational properties of peptide fragments from the C-terminal domain of thermolysin. Eur. J. Biochem. 211, 569-581.
37. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 20, 1080-1085.
38. Karplus, M. (1959). Contact electron-spin coupling of nuclear magnetic moments. J. Chem. Phys. 30, 11-15.
39. Kemmink, J. & Creighton, T. E. (1993). Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding. J. Mol. Biol. 234, 861-878.
40. Kemmink, J. & Creighton, T. E. (1995). The physical properties of local interactions of tyrosine residues in peptides and unfolded proteins. J. Mol. Biol. 245, 251-260.
41. Kumar, A., Ernst, R. R. & Wuthrich, K. (1980). A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun. 95, 1-6.
42. Lyu, P. C., Wemmer, D. E., Zhou, H., Pinker, R. J. & Kallenbach, N. R. (1993). Capping interactions in isolated α-helices: position-dependence substitution effects and structure of a serine-capped peptide helix. Biochemistry, 32, 421-425.
43. 1H spin-spin coupling constants in proteins. Biochem. Biophys. Res. Commun. 113, 967-974.
44. 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG. J. Biomol. NMR, 5, 14-24.
45. Muga, A., Surewicz, W. K., Wong, P. T. T. & Mantsch, H. H. (1990). Structural studies with the uropathogenic peptide derived from retinal S antigen. Biochemistry, 29, 2925-2930.
46. Muñoz, V. & Serrano, L. (1995). Elucidating the folding problem of helical peptides using empirical parameters, 3: temperature and pH dependence. J. Mol. Biol. 245, 297-308.
47. Muñoz, V., Jiménez, M. A., Rico, M. & Serrano, L. (1995). Structural analysis of peptides encompassing all α-helices of three α/β parallel proteins. Chey-Y, flavodoxin and p21-ras: Implications for α-helix stability and the folding of α/β parallel protein. J. Mol. Biol. 247, 648-669.
48. Musacchio, A., Noble, M. E. M., Pautit, R., Wierenga, R. & Saraste, M. (1992). Crystal structure of a Src-homology 3 (SH3) domain. Nature, 359, 851-855.
49. Musacchio, A., Wilmanns, M. & Saraste, M. (1994). Structure and function of the SH3 domain. Prog. Phiophys. Mol. Biol. 61, 283-297.
50. Oas, T. G. & Kim, P. S. (1988). A peptide model of a protein folding intermediate. Nature, 336, 42-48.
51. Osterman, M. G. & Kaiser, E. T. (1985). Design and characterization of peptides with amphiphilic β-strand structures. J. Cell. Biochem. 29, 57-72.
52. Piantini, U., So rensen, O. W. & Ernst, R. R. (1982). Multiple quantum filters for elucidating NMR coupling networks. J. Am. Chem. Soc. 104, 6800-6801.
53. Reily M. D., Thanabal, V. & Omecinsky D. O. (1992). Structure-induced carbon-13 chemical shifts: a sensitive measure of transient localized secondary structure in peptides. J. Am. Chem. Soc. 114, 6251-6252.
54. Sautilis, J. & Liepins, E. (1990). Quantitative evaluation of interproton distances in peptides by two-dimensional Overhauser effect spectroscopy. J. Magn. Reson. 87, 80-91.
55. Segawa, S. I., Fukuno, T., Fujiwara, K. & Noda, Y (1991). Local structures in unfolded lysozyme and correlation with secondary structures in the native conformation: helix forming or breaking propensities of peptide segments. Biopolymers, 31, 497-509.
56. Shin, H.-C., Merutka, G., Waltho, J. P., Tennant, L. L., Dyson, H. J. & Wright, P. E. (1993). Peptide models of protein folding initiation sites. 3. The G-H helical hairpin of myoglobin. Biochemistry, 32, 6356-6364.
57. Shoemaker, K. P., Kim, P. S., York, E. J., Stewart, J. M. & Baldwin, R. L. (1987). Tests of helix dipole model for stabilization of α-helices. Nature, 326, 563-567.
58. Viguera, A. R., Martínez, J. C., Filimonov, V. V., Mateo, P. L. & Serrano, L. (1994a). The thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two state folding transition. Biochemistry, 33, 2142-2150.
59. Viguera, A. R., Arrondo, J. L. R., Musacchio, A., Saraste, M. & Serrano, L. (1994b). Characterization of the interaction of different SH3 domains with natural polyproline peptides. Biochemistry, 33, 10925-10933.
60. Viguera, A. R., Blanco, F. J. & Serrano, L. (1995). The order of secondary structure elements does not determine the final fold of a protein but does affect its folding kinetics. J. Mol. Biol. 247, 670-681.
61. Wilmot, C. M. & Thornton, J. M. (1988). Analysis and prediction of the different types of β-turn in proteins. J. Mol. Biol. 203, 221-232.
62. Wishart, D. S., Sykes, B. D. & Richards, F. M. (1991). Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol. 222, 311-333.
63. 15N random coil NMR chemical shifts of the common amino acids. 1. Investigations of the nearest-neighbor effects. J. Biomol. NMR, 5, 67-81.
64. Wright, P. E., Dyson, H. J. & Lerner, R. A. (1988). Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. Biochemistry, 27, 7167-7175.
65. Wu, L. C., Laub, P. B., Elöve, G. A., Carey, J. & Roder, H. (1993). A noncovalent peptide complex as model for an early folding intermediate of cytochrome. Biochemistry, 32, 10271-10276.
66. Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. John Wiley & Sons, New York.
67. Wüthrich, K., Wieder, G., Wagner, G. & Braun, W. (1982). Sequential resonance assignments as a basis for determination of spatial protein structures by high resolution magnetic resonance. J. Mol. Biol. 155, 311-319.
68. Wüthrich, K., Billeter, K. & Braun, W. (1984). Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances. J. Mol. Biol. 180, 715-740.
69. Yang, J. J., Pitkeathly, M. & Radford S. E. (1994). Far-UV circular dichroism reveals a conformational switch in a peptide fragment from the β-sheet of hen lysozyme. Biochemistry, 3, 7345-7353.
70. Yao, J., Feher, V. A., Espejo, B. F., Reymond, M. T., Wright, P. E. & Dyson, H. J. (1994a). Stabiliztion of a type VI turn in a family of linear peptides in water solution. J. Mol. Biol. 243, 736-753.
71. Yao, J., Dyson, H. J. & Wright, P. E. (1994b). Three-dimensional structure of a type VI turn in a linear peptide in water solution. J. Mol. Biol. 243, 754-766.
72. Zhou, H. X., Lyu, P., Wemmer, D. E. & Kallenbach, N. R. (1994). Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: evidence for an N-terminal capping box. Proteins: Struct. Funct. Genet. 18, 1-7.