Thermodynamics of a β-hairpin structure: Evidence for cooperative formation of folding nucleus

Journal of Molecular Biology

Volumn 295, Issue 2, 2000, Pages 269-278

  Honda, Shinya ^a   Kobayashi, Naohiro ^b   Munekata, Eisuke ^b  

^a NATL INST BIOSCI HUM TECHNOL   (Japan)

^b UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

Calorimetry; Folding; G peptide; Nucleation; Protein G

Indexed keywords

AMINO ACID; PEPTIDE; PROTEIN G;

ARTICLE; CALORIMETRY; CARBOXY TERMINAL SEQUENCE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN QUATERNARY STRUCTURE; STREPTOCOCCUS; THERMODYNAMICS;

POSIBACTERIA; STREPTOCOCCUS;

EID: 0034645735     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3346     Document Type: Article

References (52)

1. Anfinsen C. B. Principles that govern the folding of protein chains. Science. 181:1973;223-230.
2. Baldwin R. L. Seeding protein folding. Trends. Biochem. Sci. 11:1986;6-9.
3. Blanco F. J., Serrano L. Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur. J. Biochem. 230:1995;634-649.
4. Blanco F. J., Rivas G., Serrano L. A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nature Struct. Biol. 1:1994;584-590.
5. Brown J. E., Klee W. A. Helix-coil transition of the isolated amino terminus of ribonuclease. Biochemistry. 10:1971;470-476.
6. Bundi A., Wüthrich K. 1H NMR parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers. 18:1979;285-297.
7. Carrell R. W., Lomas D. A. Conformational disease. Lancet. 350:1997;134-138.
8. Chou P. Y., Scheraga H. A. Calorimetric measurement of enthalpy change in the isothermal helix-coil transition of poly-L-lysine in aqueous solution. Biopolymers. 10:1971;657-680.
9. de Prat-Gay G. Association of complementary fragments and the elucidation of protein folding pathways. Protein Eng. 9:1996;843-847.
10. Dyson H. J., Wright P. E. Peptide conformation and protein folding. Curr. Opin. Struct. Biol. 3:1993;60-65.
11. Dyson H. J., Rance M., Houghten R. A., Wright P. E., Lerner R. A. Folding of immunogenic peptide fragments of proteins in water solution. II. The nascent helix. J. Mol. Biol. 201:1988;201-217.
12. Edelman G. M., Cunningham B. A., Gall W. E., Gottlieb P. D., Rutishauser U., Waxdal M. J. The covalent structure of an entire gammaG immunoglobulin molecule. Proc. Natl Acad. Sci. USA. 63:1969;78-85.
13. Fersht A. R. Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl Acad. Sci. USA. 92:1995;10869-10873.
14. Freire E., Biltonen R. L. Statistical mechanical deconvolution of thermal transitions in macromolecules. I. Theory and applications to homogeneous systems. Biopolymers. 17:1978;463-479.
15. Garel J.-R. Folding of large proteins: multidomain and multisubunit proteins. Creighton T. E. Protein Folding. 1992;405-454 W. H. Freeman and Company, New York.
16. Gellman S. H. Minimal model systems for beta sheet secondary structure in proteins. Curr. Opin. Chem. Biol. 2:1998;717-725.
17. Gill S. C., von Hippel P. H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:1989;319-326.
18. Go N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12:1983;183-210.
19. Gronenborn A. M., Filpula D. R., Essig N. Z., Achari A., Whitlow M., Wingfield P. T., Clore G. M. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science. 253:1991;657-661.
20. Honda S., Kobayashi N., Munekata E., Uedaira H. Fragment reconstitution of a small protein: folding energetics of the reconstituted immunoglobulin binding domain B1 of streptococcal protein G. Biochemistry. 38:1999;1203-1213.
21. Jiménez M. A., Rico M., Herranz J., Santoro J., Nieto J. L. 1H-NMR assignment and folding of the isolated ribonuclease 21-42 fragment. Eur. J. Biochem. 175:1988;101-109.
22. Karplus M., Weaver D. L. Protein-folding dynamics. Nature. 260:1976;404-406.
23. Kidokoro S., Wada A. Determination of thermodynamic functions from scanning calorimetry data. Biopolymers. 26:1987;213-229.
24. Kim P. S., Baldwin R. L. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu. Rev. Biochem. 51:1982;459-489.
25. Kobayashi N., Endo S., Munekata E. Comformational study on the IgG binding domain of protein G. Peptide Chem. 1992:1993;278-280.
26. Kobayashi N., Honda S., Yoshii H., Uedaira H., Munekata E. Complement assembly of two fragments of the streptococcal protein G B1 domain in aqueous solution. FEBS Letters. 366:1995;99-103.
27. Kobayashi N., Honda S., Munekata E. Fragment reconstitution of a small protein: disulfide mutant of a short C-terminal fragment derived from streptococcal protein G. Biochemistry. 38:1999;3228-3234.
28. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
29. Kuroda Y. Residual helical structure in the C-terminal fragment of cytochrome c. Biochemistry. 32:1993;1219-1224.
30. Levinthal C. Are there pathways for protein folding? J. Chim. Phys. 65:1968;44-45.
31. Linderstrøm-Lang K. U., Schellman J. A. Protein structure and enzyme activity. Boyer P. D., Lardy H., Myrback K. The Enzymes. 1959;443-510 Academic Press, New York.
32. Merutka G., Dyson H. J., Wright P. E. 'Random coil' 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG. J. Biomol. NMR. 5:1995;14-24.
33. Muñoz V., Serrano L., Jiménez M. A., Rico M. Structural analysis of peptides encompassing all alpha-helices of three alpha/beta parallel proteins: Che-Y, flavodoxin and P21-ras: implications for alpha-helix stability and the folding of alpha/beta parallel proteins. J. Mol. Biol. 247:1995;648-669.
34. Muñoz V., Thompson P. A., Hofrichter J., Eaton W. A. Folding dynamics and mechanism of beta-hairpin formation. Nature. 390:1997;196-199.
35. Murphy K. P., Gill S. J. Solid model compounds and the thermodynamics of protein unfolding. J. Mol. Biol. 222:1991;699-709.
36. Oobatake M., Ooi T. Hydration and heat stability effects on protein unfolding. Prog. Biophys. Mol. Biol. 59:1993;237-284.
37. Panchenko A. R., Luthey-Schulten Z., Wolynes P. G. Foldons, protein structural modules, and exons. Proc. Natl Acad. Sci. USA. 93:1996;2008-2013.
38. Privalov P. L. Stability of proteins: small globular proteins. Advan. Protein Chem. 33:1979;167-241.
39. Privalov P. L. Thermodynamic problems of protein structure. Annu. Rev. Biophys. Biophys. Chem. 18:1989;47-69.
40. Privalov P. L., Gill S. J. Stability of protein structure and hydrophobic interaction. Advan. Protein Chem. 39:1988;191-234.
41. Privalov P. L., Makhatadze G. I. Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: protein unfolding effects. J. Mol. Biol. 213:1990;385-391.
42. Ramírez-Alvarado M., Blanco F. J., Serrano L. De novo design and structural analysis of a model beta-hairpin peptide system. Nature Struct. Biol. 3:1996;604-612.
43. Rico M., Santoro J., Bermejo F. J., Herranz J., Nieto J. L., Gallego E., Jiménez M. A. Thermodynamic parameters for the helix-coil thermal transition of ribonuclease-S-peptide and derivatives from 1H-NMR data. Biopolymers. 25:1986;1031-1053.
44. Sancho J., Neira J. L., Fersht A. R. An N-terminal fragment of barnase has residual helical structure similar to that in a refolding intermediate. J. Mol. Biol. 224:1992;749-758.
45. Schaefer M., Bartels C., Karplus M. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J. Mol. Biol. 284:1998;835-848.
46. Scholtz J. M., Marqusee S., Baldwin R. L., York E. J., Stewart J. M., Santoro M., Bolen D. W. Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water. Proc. Natl Acad. Sci. USA. 88:1991;2854-2858.
47. Sheinerman F. B., Brooks C. L. III. Molecular picture of folding of a small alpha/beta protein. Proc. Natl Acad. Sci. USA. 95:1998;1562-1567.
48. Spolar R. S., Ha J. H., Record M. T. Jr. Hydrophobic effect in protein folding and other noncovalent processes involving proteins. Proc. Natl Acad. Sci. USA. 86:1989;8382-8385.
49. Tanford C. Protein denaturation. Advan. Protein Chem. 23:1968;121-282.
50. Taylor J. W., Greenfield N. J., Wu B., Privalov P. L. A calorimetric study of the folding-unfolding of an alpha-helix with covalently closed N and C-terminal loops. J. Mol. Biol. 291:1999;965-976.
51. Waltho J. P., Feher V. A., Merutka G., Dyson H. J., Wright P. E. Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin. Biochemistry. 32:1993;6337-6347.
52. Wright P. E., Dyson H. J., Lerner R. A. Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. Biochemistry. 27:1988;7167-7175.