Characterization of charge change super-repressor mutants of trp repressor: Effects on oligomerization conformation, ligation and stability

Journal of Molecular Biology

Volumn 264, Issue 1, 1996, Pages 32-45

  Reedstrom, Ross J ^a   Martin, Kathleen S ^b   Vangala, Shyam ^a   Mahoney, Steven ^a   Wilker, Erik W ^a   Royer, Catherine A ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b BUTLER UNIVERSITY   (United States)

Author keywords

Fluorescence; Protein folding; Protein protein interactions; trp repressor

Indexed keywords

8 ANILINO 1 NAPHTHALENESULFONIC ACID; REPRESSOR PROTEIN;

ANISOTROPY; ARTICLE; CALORIMETRY; CIRCULAR DICHROISM; CONTROLLED STUDY; ESCHERICHIA COLI; LIGAND BINDING; LIGATION; NONHUMAN; OLIGOMERIZATION; OPERATOR; PHENOTYPE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REPRESSOR GENE; THERMODYNAMICS; TRANSCRIPTION REGULATION;

ESCHERICHIA COLI;

EID: 0030598345     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0621     Document Type: Article

References (57)

1. Arrowsmith, C., Pachter, R., Altman, R. & Jardetzky, O. (1991). The solution structures of Escherichia coli trp repressor and trp aporepressor at an intermediate resolution. Eur. J. Biochem. 202, 53-66.
2. Beechem, J. M. (1992). Global analysis of biochemical and biophysical data. Methods Enzymol. 210, 37-54.
3. Beechem, J. M., Gratton, E., Ameloot, M., Knutson, J. R. & Brand, L. (1989). The global analysis of fluorescence intensity and anisotropy decay data: second-generation theory and programs. In Fluorescence Spectroscopy: Principles and Techniques (Lakowicz, J. R., ed.), vol. 2, pp. 241-306, Plenum Press, New York.
4. Carey, J. (1988). Gel retardation at low pH resolves trp repressor-DNA complexes for quantitative study. Proc. Natl Acad. Sci. USA, 85, 975-979.
5. Carey, J. (1989). Trp repressor arms contribute binding-energy without occupying unique locations on DNA. J. Biol. Chem. 264, 1941-1945.
6. Carey, J., Lewis, D. E. A., Lavoie, T. A. & Yang, J. (1991). How does trp repressor bind to its operator? J. Biol. Chem. 266, 4509-4513.
7. Chou, W. Y., Bieber, C. & Matthews, K. S. (1989). Tryptophan and 8-anilino-1-naphthalenesulfonate compete for binding to trp repressor. J. Biol. Chem. 264, 8309-8313.
8. Czaplicki, J., Arrowsmith, C. & Jardetzky, O. (1991). Segmental differences in the stability of the trp repressor peptide backbone. J. Biomol. NMR, 1, 349-361.
9. Czernik, P. J., Shin, D. S. & Hurlburt, B. K. (1994). Functional selection and characterization of DNA-binding sites for trp repressor of Escherichia coli. J. Biol. Chem. 269, 27869-27875.
10. Fernando, T. & Royer, C. (1992a). Role of protein protein interactions in the regulation of transcription by trp repressor investigated by fluorescence spectroscopy. Biochemistry, 31, 3429-3441.
11. Fernando, T. & Royer, C. A. (1992b). Unfolding of trp repressor studied using fluorescence spectroscopic techniques. Biochemistry, 31, 6683-6691.
12. Freire, E., Mayorga, O. L. & Straume, M. (1990). Isothermal titration calorimetry. Anal. Chem. 62, 950A-959A.
13. Gill, S. C. & von Hippel, P. H. (1989). Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182, 319-326.
14. Gratton, E., Limkeman, M., Lakowicz, J., Maliwal, B. P., Cherek, H. & Laczko, G. (1984). Resolution of mixtures of fluorophores using variable-frequency phase and modulation data. Biophys. J. 46, 479-486.
15. 1 relaxation. J. Mol. Biol. 246, 618-627.
16. Guenot, J., Fletterick, R. J. & Kollman, P. A. (1994). A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA. Protein Sci. 3, 1276-1285.
17. Gunsalus, R. P. & Yanofsky, C. (1980). Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp repressor. Proc. Natl Acad. Sci. USA, 77, 7117-7121.
18. Gunsalus, R. P., Gunsalus, G. L. & Miguel, A. G. (1986). Intracellular trp repressor levels in Escherichia coli. J. Bacteriol. 167, 272-278.
19. Hurlburt, B. K. & Yanofsky, C. (1990). Enhanced operator binding by trp superrepressors of Escherichia coli. J. Biol. Chem. 265, 7853-7858.
20. Hurlburt, B. K. & Yanofsky, C. (1992). Trp repressor/trp operator interaction: equilibrium and kinetic analysis of complex formation and stability. J. Biol. Chem. 267, 6783-6789.
21. Jin, L. H., Yang, J. & Carey, J. (1993). Thermodynamics of ligand binding to trp repressor. Biochemistry, 32, 7302-7309.
22. Joachimiak, A., Kelley, R. L., Gunsalus, R. P., Yanofsky, C. & Sigler, P. B. (1983). Purification and characterization of trp aporepressor. Proc. Natl Acad. Sci. USA, 80, 668-672.
23. Kelley, R. L. & Yanofsky, C. (1985). Mutational studies with the trp repressor of Escherichia coli support the helix-turn-helix model of repressor recognition of operator DNA. Proc. Natl Acad. Sci. USA, 82, 483-487.
24. Klig, L. S. & Yanofsky, C. (1988). Increased binding of operator DNA by trp super-repressor EK49. J. Biol. Chem. 263, 243-246.
25. Ladbury, J. E., Wright, J. G., Sturtevant, J. M. & Sigler, P. B. (1994). A thermodynamic study of the trp repressor-operator interaction. J. Mol. Biol. 238, 669-681.
26. Lawson, C. L. & Carey, J. (1993). Tandem binding in crystals of a trp repressor-operator half-site complex. Nature, 366, 178-182.
27. Lawson, C. L., Joachimiak, A., Zhang, R. G., Otwinowski, Z., Schevitz, R. W. & Sigler, P. B. (1988). Flexibility of the DNA-binding domains of trp repressor. Proteins: Struct. Funct. Genet. 3, 18-31.
28. LeTilly, V. & Royer, C. A. (1993). Fluorescence anisotropy assays implicate protein-protein interactions in regulating trp repressor DNA binding. Biochemistry, 32, 7753-7758.
29. Liu, Y. C. & Matthews, K. S. (1993). Dependence of trp repressor-operator affinity, stoichiometry, and apparent cooperativity on DNA-sequence and size. J. Biol. Chem. 268, 23239-23249.
30. Liu, Y. C. & Matthews, K. S. (1994). Trp repressor mutations alter DNA complex stoichiometry. J. Biol. Chem. 269, 1692-1698.
31. Livingstone, J. R., Spolar, R. S. & Record, M. T. Jr (1991). Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry, 30, 4237-4244.
32. Mann, C. J., Royer, C. A. & Matthews, C. R. (1993). Tryptophan replacements in the trp aporepressor from Escherichia coli: probing the equilibrium and kinetic folding models. Protein Sci. 2, 1853-1861.
33. Marmorstein, R. Q., Sprizl, M. & Sigler, P. B. (1991). An alkaline phosphatase protection assay to investigate trp repressor/operator interactions. Biochemistry, 30, 1141-1148.
34. Martin, K. S. (1995). Super-repressor mutations modify oligomerization, ligand and DNA binding properties of the trp repressor. PhD thesis, University of Wisconsin-Madison, School of Pharmacy.
35. Martin, K. S., Royer, C. A., Howard, K. P., Carey, J., Liu, Y. C., Matthews, K., Heyduk, E. & Lee, J. C. (1994). Electrostatic forces contribute to interactions between trp repressor dimers. Biophys. J. 66, 1167-1173.
36. Myers, J. K., Pace, C. N. & Scholtz, J. M. (1995). Denaturant m values and heat capacity changes: relation to changes in accessible surface area of protein folding. Protein Sci. 4, 2138-2148.
37. Otwinowski, Z., Sigler, P. B., Schevitz, R. W., Zhang, R. G., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F. & Lawson, C. L. (1988). Crystal structure of trp repressor/operator complex at atomic resolution. Nature, 335, 321-329.
38. Pace, C. N. (1986). Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131, 266-280.
39. Paluh, J. L. & Yanofsky, C. (1986). High-level production and rapid purification of the Escherichia coli trp repressor. Nucl. Acids Res. 14, 7851-7860.
40. Perrin, F. (1926). Polarisation de la lumière de fluorescence. Vie moyenne des molécules dans l'etat excité. J. Phys. Radium. 6, 390-401.
41. 15N-labelled protein. Eur. J. Biochem. 225, 601-608.
42. Reedstrom, R. J. & Royer, C. A. (1995). Evidence for coupling of folding and function in trp repressor: physical characterization of the superrepressor mutant AV77. J. Mol. Biol. 253, 266-276.
43. Royer, C. A. (1992). Investigation of the structural determinants of the intrinsic fluorescence emission of the trp repressor using single tryptophan mutants. Biophys. J. 63, 741-750.
44. Royer, C. A. (1993). Improvements in the numerical analysis of thermodynamic data from biomolecular complexes. Anal. Biochem. 210, 91-97.
45. Royer, C. A., Mann, C. J. & Matthews, C. R. (1993). Resolution of the fluorescence equilibrium unfolding profile of trp aporepressor using single tryptophan mutants. Protein Sci. 2, 1844-1852.
46. Schevitz, R. W., Otwinowski, Z., Joachimiak, A., Lawson, C. L. & Sigler, P. B. (1985). The three-dimensional structure of trp repressor. Nature, 317, 782-786.
47. Semisotnov, G. V., Rodionova, N. A., Razgulyaev, O. I., Uversky, V. N., Gripas, A. F. & Gilmanshin, R. I. (1991). Study of the "molten globule" intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers, 31, 119-128.
48. Shapiro, M., Arvidson, D. N., Pfau, J. & Youderian, P. (1993). The challenge-phage assay reveals differences in the binding equilibria of mutant Escherichia coli trp super-repressors in vivo. Nucl. Acids Res. 21, 5661-5666.
49. Shortle, D. (1995). Staphylococcal nuclease: a showcase of m-value effects. Advan. Protein Chem. 46, 217-247.
50. Spolar, R. S. & Record, M. T. (1994). Coupling of local folding to site-specific binding of proteins to DNA. Science, 263, 777-784.
51. Spolar, R. S., Livingstone, J. R. & Record, M. T. Jr (1992). 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, 3947-3955.
52. Tasayco, M. L. & Carey, J. (1992). Ordered self-assembly of polypeptide fragments to form native-like dimeric trp repressor. Science, 255, 594-597.
53. Weber, G. (1966). Polarization of fluorescence of solutions. In Fluorescence and Phosphorescence Analysis (Hercules, D. M., ed.), pp. 217-240, Interscience, New York.
54. Yang, J. T., Wu, C.-S. C. & Martinez, H. M. (1986). Calculation of protein conformation from circular dichroism. Methods Enzymol. 130, 208-269.
55. Zhang, H., Zhao, D. Q., Revington, M., Lee, W. T., Jia, X., Arrowsmith, C. & Jardetzky, O. (1994). The solution structures of the trp repressor-operator DNA complex. J. Mol. Biol. 238, 592-614.
56. Zhang, R.-g., Joachimiak, A., Lawson, C. L., Schevitz, R. W., Otwinowski, Z. & Sigler, P. B. (1987). The crystal structure of trp aporepressor at 1.8 Å shows how binding tryptophan enhances DNA affinity. Nature, 327, 591-597.
57. Zhao, D., Arrowsmith, C. H., Jia, X. & Jardetzky, O. (1993). Refined solution structures of the Escherichia coli trp holorepressor and aporepressor. J. Mol. Biol. 229, 735-746.