Shape and energetics of a cavity in c-Myb probed by natural and non-natural amino acid mutations

Journal of Molecular Biology

Volumn 292, Issue 4, 1999, Pages 909-920

  Morii, Hisayuki ^a   Uedaira, Hatsuho ^a,b   Ogata, Kazuhiro ^c,d   Ishii, Shunsuke ^b   Sarai, Akinori ^b  

^a NATL INST BIOSCI HUM TECHNOL   (Japan)

^b INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^c KANAGAWA ACADEMY OF SCIENCE AND TECHNOLOGY   (Japan)

^d YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

c Myb DNA binding domain; Cavity; Mutation; Non natural amino acid; Thermodynamics

Indexed keywords

2 AMINOBUTYRIC ACID; ALANINE; ALANINE DERIVATIVE; DNA BINDING PROTEIN; GLYCINE DERIVATIVE; ISOLEUCINE; LEUCINE; MUTANT PROTEIN; NORLEUCINE; NORVALINE; ONCOPROTEIN; VALINE;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING SITE; CIRCULAR DICHROISM; DIFFERENTIAL SCANNING CALORIMETRY; ENTHALPY; PRIORITY JOURNAL; PROTEIN DENATURATION; SPECTROSCOPY; THERMODYNAMICS;

EID: 0033214183     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3099     Document Type: Article

References (32)

1. Alexander P., Fahnestock S., Lee T., Orban J., Bryan P. Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2. Biochemistry. 31:1992;3597-3603.
2. Anton I. A., Frampton J. Tryptophans in myb proteins. Nature. 336:1988;719.
3. D'Aquino J. A., Gómez J., Hilser V. J., Lee K. H., Amzel L. M., Freire E. The magnitude of the backbone conformational entropy change in protein folding. Proteins: Struct. Funct. Genet. 25:1996;143-156.
4. Edward J. T. Molecular volumes and the Stokes-Einstein equation. J. Chem. Education. 47:1970;261-270.
5. Eriksson A. E., Baase W. A., Zhang X.-J., Heinz D. W., Blaber M., Baldwin E. P., Matthews B. W. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science. 255:1992;178-183.
6. Fields G. B., Noble R. L. Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids. Int. J. Pept. Protein Res. 35:1990;161-214.
7. Freskgard P.-O., Martensson L.-G., Jonasson P., Jonsson B.-H., Carlsson U. Assignment of the contribution of the tryptophan residues to the circular dichroism spectrum of human carbonic anhydrase II. Biochemistry. 33:1994;14281-14288.
8. Gabrielsen O. S., Sentenac A., Fromageot P. Specific DNA binding by c-Myb: evidence for a double helix-turn-helix-related motif. Science. 253:1991;1140-1143.
9. Graf T. Myb: a transcriptional activator linking proliferation and differentiation in hematopoietic cells. Curr. Opin. Genet. Dev. 2:1992;249-255.
10. Howe K. M., Reakes C. F. L., Watson R. J. Characterization of the sequence-specific interaction of mouse c-myb protein with DNA. EMBO J. 9:1990;161-169.
11. Kanei-Ishii C., Sarai A., Sawazaki T., Nakagoshi H., He D.-N., Ogata K., Nishimura Y., Ishii S. The tryptophan cluster: a hypothetical structure of the DNA-binding domain of the myb proto-oncogene product. J. Biol. Chem. 265:1990;19990-19995.
12. Katzen A. L., Kornberg T., Bishop J. M. Isolation of the proto-oncogene c-myb from D. melanogaster. Cell. 41:1985;449-456.
13. Kidokoro S., Wada A. Determination of thermodynamic functions from scanning calorimetry data. Biopolymers. 26:1987;213-229.
14. Kidokoro S., Uedaira H., Wada A. Determination of thermodynamic functions from scanning calorimetry data. II. For the system that includes self-dissociation/association process. Biopolymers. 27:1988;271-297.
15. Morii H., Takenawa T., Arisaka F., Shimizu T. Identification of kinesin neck region as a stable α-helical coiled coil and its thermodynamic characterization. Biochemistry. 36:1997a;1933-1942.
16. Morii H., Uedaira H., Ishimura M., Kidokoro S., Kokubu T., Ohashi S. Special folding pathway to tetramer only through the micelle state of the corticotropin-releasing factor. Biochemistry. 36:1997b;15538-15545.
17. Nozaki Y., Tanford C. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. J. Biol. Chem. 246:1971;2211-2217.
18. Oda M., Furukawa K., Ogata K., Sarai A., Ishii S., Nishimura Y., Nakamura H. Identification of indispensable residues for specific DNA-binding in imperfect tandem repeats of c-Myb R2R3. Protein Eng. 10:1997;1407-1414.
19. Oda M., Furukawa K., Ogata K., Sarai A., Nakamura H. Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain. J. Mol. Biol. 276:1998;571-590.
20. Ogata K., Hojo H., Aimoto S., Nakai T., Nakamura H., Sarai A., Ishii S., Nishimura Y. Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core. Proc. Natl Acad. Sci. USA. 89:1992;6428-6432.
21. Ogata K., Morikawa S., Nakamura H., Sekikawa A., Inoue T., Kanai H., Sarai A., Ishii S., Nishimura Y. Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell. 79:1994;639-648.
22. Ogata K., Morikawa S., Nakamura H., Hojo H., Yoshimura S., Zhang R., Aimoto S., Ametani Y., Hirata Z., Sarai A., Ishii S., Nishimura Y. Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb. Nature Struct. Biol. 2:1995;309-320.
23. Ogata K., Kanei-Ishii C., Sasaki M., Hatanaka H., Nagadoi A., Enari M., Nakamura H., Nishimura Y., Ishii S., Sarai A. The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation. Nature Struct. Biol. 3:1996;178-187.
24. Oobatake M., Ooi T. Hydration and heat stability effects on protein unfolding. Prog. Biophys. Mol. Biol. 59:1993;237-284.
25. Ooi T., Oobatake M., Némethy G., Scheraga H. A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl Acad. Sci. USA. 84:1987;3086-3090.
26. Rashin A. A., Rashin B. H., Rashin A., Abagyan R. Evaluating the energetics of empty cavities and internal mutations in proteins. Protein Sci. 6:1997;2143-2158.
27. Saikumar P., Murali R., Reddy E. P. Role of tryptophan repeats and flanking amino acids in Myb-DNA interactions. Proc. Natl Acad. Sci. USA. 87:1990;8452-8456.
28. Sakura H., Kanei-Ishii C., Nagase T., Nakagoshi H., Gonda T. J., Ishii S. Delineation of three functional domains of the transcriptional activator encoded by the c-myb protooncogene. Proc. Natl Acad. Sci. USA. 86:1989;5758-5762.
29. Sarai A., Uedaira H., Morii H., Yasukawa T., Ogata K., Nishimura Y., Ishii S. Thermal stability of the DNA-binding domain of the Myb oncoprotein. Biochemistry. 32:1993;7759-7764.
30. Spolar R. S., Livingstone J. R., Record M. T. Jr. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry. 31:1992;3947-3955.
31. Tanikawa J., Yasukawa T., Enari M., Ogata K., Nishimura Y., Ishii S., Sarai A. Recognition of specific DNA sequences by the c- myb proto-oncogene product: role of three repeat units in the DNA-binding domain. Proc. Natl Acad. Sci. USA. 90:1993;9320-9324.
32. Uedaira H., Morii H., Ogata K., Ishii S., Sarai A. Multi-state thermal transitions of proteins - DNA-binding domain of the c-Myb oncoprotein. Pure Appl. Chem. 70:1998;671-676.