Characterisation of the isolated Che Y C-terminal fragment (79-129). Exploring the structure/stability/folding relationships of the α/β parallel protein Che Y

European Journal of Biochemistry

Volumn 243, Issue 1-2, 1997, Pages 384-392

  Bruix, Marta ^a   Muñoz, Victor ^b   Campos Olivas, Ramón ^a   Del Bosque, José Ramón ^a   Serrano, Luis ^b   Rico, Manuel ^a  

^a INSTITUTO DE ESTRUCTURA DE LA MATERIA   (Spain)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Che Y; Fragment stability; Non native secondary structure; Protein fragment; Structure stability folding relationship

Indexed keywords

LIGANDIN;

AMINO ACID SEQUENCE; ARTICLE; CIRCULAR DICHROISM; ESCHERICHIA COLI; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE;

EID: 0031030716     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.1997.0384a.x     Document Type: Article

References (60)

1. Aue, W. P., Bartholdi, E. & Ernst, R. R. (1976) Two dimensional spectroscopy. Application to nuclear magnetic resonance, J. Chem. Phys. 64, 2229-2246.
2. Baldwin, R. L. (1993) Pulsed H/D-exchange studies on folding intermediates, Curr. Opin. Struct. Biol. 3, 84-91.
3. Bax, A. & Davis, D. G. (1985) MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy, J. Magn. Reson. 65, 355-360.
4. Belsollel, L., Prieto, J., Serrano, L. & Coll, M. (1994) Magnesium binding to the bacterial chemotaxis protein Che Y results in large conformational changes involving its functional surface, J. Mol. Biol. 238, 489-495.
5. Bellsolell, L., Cronet, P., Majolero, M., Serrano, L. & Coll, M. (1996) The three-dimensional structure of two mutants of the signal transduction protein Che Y suggest its molecular activation mechanism, J. Mol. Biol. 257, 116-128.
6. Blanco, F. J., Rivas, G. & Serrano, L. (1994) A short linear peptide that folds into a native β-hairpin in aqueous solution, Nat. Struct. Biol. 1, 584-590.
7. Blanco, F. J. & Serrano, L. (1995) Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements, Eur. J. Biochem. 230, 634-649.
8. Brown, J. E. & Klee, W. A. (1971) Helix-coil transition of the isolated amino terminus of ribonuclease, Biochemistry 10, 4710-476.
9. Buck, M., Radford, S. E. & Dobson, C. M. (1993) A partially folded state of hen egg white lysozyme in trifluoroethanol: structural characterization and implications for protein folding, Biochemistry 32, 669-678.
10. Buck, M., Schwalbe, H. & Dobson, C. M. (1995) Characterization of conformational preferences in a partly folded protein by heteronuclear NMR spectroscopy: Assigment and secondary structure analysis of hen egg-white lysozyme in trifluoroethanol, Biochemistry 34, 13219-13232.
11. Cammers-Goodwin, A., Allen, T. J., Oslick, S. L., McClure, K. F., Lee, J. H. & Kemp, D. S. (1996) Mechanism of stabilization of helical conformations of polypeptides by water containing trifluoroethanol, J. Am. Chem. Soc. 118, 3082-3090.
12. Chen, Y. H., Yang, J. T. & Chau, K. H. (1974) Determination of the helix and β-form of proteins in aqueous solution by circular dichroism, Biochemistry 13, 3350-3359.
13. 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 dicroism and nuclear magnetic resonance studies of peptides from ubiquitin, J. Mol. Biol. 234, 483-492.
14. 2+ binding site, J. Mol. Biol. 249, 654-664.
15. Dyson, H. J. & Wright, P. E. (1991) Defining solution conformations of small linear peptides, Annu. Rev. Biophys. Chem. 20, 519-538.
16. 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 I. Myohemerythrin, J. Mol. Biol. 226, 795-817.
17. 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.
18. Dyson, H. J. & Wright, P. E. (1993) Peptide conformation and protein folding, Curr. Opin. Struct. Biol. 3, 60-65.
19. Fan, P., Bracken, C. & Baum, J. (1993) Structural characterization of Monellin in the alcohol-denaturated state by NMR: evidence for β-sheet to α-helix conversion, Biochemistry 32, 1573-1582.
20. Ferhst, A. R. (1995) Characterizating transition states in protein folding: an essential step in the puzzle, Curr. Opin. Struct. Biol. 5, 79-84.
21. Filimonov, V. V., Prieto, J., Martinez, J. C., Bruix, M., Mateo, P. L. & Serrano, L. (1993) Thermodynamic analysis of the chemotatic protein from Escherichia coli, Che Y, Biochemistry 32, 12 906-12 921.
22. Gill, S. C. & von Hippel, P. H. (1989) Calculation of protein extintion coefficients from aminoacid sequences data, Anal. Biochem. 182, 319-326.
23. Higuchi, R., Krummel, B. & Saiki, R. K. (1988) A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions, Nucleic Acids Res. 16, 7351-7367.
24. Itzhaki, L. S., Neira, J. L., Ruiz-Sanz, J., Prat-Gay, G. de & Fersht, A. R. (1995a) Search for nucleation sites in smaller fragments of chymotripsin inhibitor 2, J. Mol. Biol. 254, 289-304.
25. Itzhaki, L. S., Otzen, D. E. & Fersht, A. R. (1995b) The structure of the transition state for folding of chymotripsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding, J. Mol. Biol. 254, 260-288.
26. 1H-NMR studies on the conformational properties of peptide fragments from the C-terminal domain of thermolysin, Eur. J. Biochem. 211, 569-581.
27. 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.
28. Kim, K.-S., Fuchs, J. A. & Woodward, C. K. (1993) Hydrogen exchange identifies native-state motional domains important in protein folding, Biochemistry 32, 9600-9608.
29. Kraulis, P. J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24, 946-950.
30. Kumar, A., Ernst, R. R. & Wülhrich, 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.
31. Liu, Z.-P., Rizo, J. & Gierasch, L. M. (1994) Equilibrium folding studies of cellular retinoic acid binding protein, a predominantly β-sheet protein, Biochemistry 33, 134-142.
32. López-Hernández, E. & Serrano, L. (1996) Structure of the transition state for folding of the 129 aa protein Che Y resembles that of a smaller protein, C1-2, Folding & Design 1, 43-55.
33. Lowry, D. F., Roth, A. F., Bupert, P. B., Dahlquist, F. W., Moy, F. J., Domaille, P. J & Matsumura, P. (1994) Signal transduction in Chemotaxis. A propagating conformational change upon phosphorylation of Che Y, J. Biol. Chem. 269, 26 358-26 362.
34. Marion, D. & Wüthrich, K. (1983) Application of phase-sensitive two-dimensional correlated spectroscopy (COSY) for measurements of proton-proton spin-spin coupling constants, Biochem. Biophys. Res. Commun. 113, 967-974.
35. Matthews, B. W. (1993) Structural and genetic analysis of protein folding and stability, Curr. Opin. Struct. Biol. 3, 589-593.
36. 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration of the peptide series GGXGG, J. Biomol. NMR 5, 14-24.
37. 15N) NMR spectroscopy, Biochemistry 33, 10 731-10 742.
38. Muñoz, V., López, E. M., Jager, M. & Serrano, L. (1994) Kinetic characterization of the chemotactic protein from Excherichia coli, Che Y. Kinetic analysis of the inverse hydrophobic effect, Biochemistry 33, 5858-5866.
39. Muñoz, V. & Serrano, L. (1994) Elucidating the folding problem of helical peptides using empirical parameters, Nat. Struct. Biol. 1, 399-409.
40. Muñoz, V. & Serrano, L. (1995a) Elucidating the folding problem of α-helical peptides using empirical parameters, II. Helix macrodipole effects and rational modification of the helical content of natural peptides, J. Mol. Biol. 245, 275-296.
41. Muñoz, V. & Serrano, L. (1995b) Analysis of i,i + 5 and i,i + 8 hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif, Biochemistry 34, 15 301-15 306.
42. Muñoz, V., Serrano, L., Jiménez, M. A. & Rico, M. (1995a) Structural analysis of peptides encompassing all the α-helices of three α/β parallel proteins: Che Y, flavodoxin and P21-Ras: Implications for α-helix stability and the folding of α/β parallel proteins, J. Mol. Biol. 247, 648-669.
43. Muñoz, V., Blanco, F. & Serrano, L. (1995b) The 'hydrophobic-staple' motif. A role for loop-residues in α-helix stability and protein folding, Nat. Struct. Biol. 2, 380-385.
44. Muñoz, V. & Serrano, L. (1997) Development of the multiple sequence approximation within the Agadir model of α-helix formation. Comparison with Zimm-Bragg and Lifson-Roig formalisms, Biopolymers, in the press.
45. Nelson, J. W. & Kallenbach, N. R. (1989) Persistence of the α-helix stop signal in the S-peptide in trifluoroethanol solutions, Biochemistry 28, 5256-5261.
46. Radford, S. E., Buck, M., Topping, K. D., Dobson, C. M. & Evans, P. A. (1992) Hydrogen exchange in native and denaturated states of hen egg-white lysozyme, Proteins Struct. Funct. Genet. 14, 237-248.
47. Sancho, J. & Ferst, A. R. (1992) Dissection of an enzyme by protein engineering. The N and C-terminal fragments of Barnase form a native-like complex with restored enzymic activity, J. Mol. Biol. 224, 741-747.
48. Santoro, J., Bruix, M., Pascual, J., López, E., Serrano, L. & Rico, M. (1995) Three-dimensional structure of chemotactic Che Y protein in aqueous solution by nuclear magnetic resonance methods, J. Mol. Biol. 247, 717-725.
49. 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.
50. Serrano, L. (1995) Comparison between the φ distribution of the amino acids in the protein database and NMR data indicates that the amino acids have various φ propensities in the random coil conformation, J. Mol. Biol. 254, 322-333.
51. Shiraki, K., Nishikawa, K. & Goto, Y. (1995) Trifluoroethanol-induced stabilization of the α-helical structure of β-lactoglobulin: implication for non-hierarchical protein folding, J. Mol. Biol. 245, 180-194.
52. Stock, J. B., Stock, A. M. & Mottonen, J. M. (1990) Signal transduction in bacteria, Nature 344, 395-400.
53. Viguera, A. R., Jiménez, M. A., Rico, M. & Serrano, L. (1995) Conformational analysis of peptides corresponding to β-hairpins and a β-sheet, that represent the entire sequence of α-spectrin SH3-domain, J. Mol. Biol. 255, 507-521.
54. Viguera, A. R. & Serrano, L. (1995) Experimental analysis of the Shellman motif, J. Mol. Biol. 251, 150-160.
55. Volz, K. & Matsumura, P. (1991) Crystal structure of Escherichia coli Che Y refined at 1.7 Å resolution, J. Biol. Chem. 266, 15 511-15 519.
56. Volz, K. (1993) Structural conservation in the Che Y superfamily, Biochemistry 32, 11 741-11 753.
57. 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.
58. 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects, J. Biomol. NMR 5, 67-81.
59. Woodward, C. (1993) Is the slow-exchange core the protein folding core?, Trends Biochem. Sci. 18, 359-360.
60. Wüthrich, K. (1986) NMR of proteins and nucleic acids, John Wiley & Sons, New York.