Backbone dynamics of a winged helix protein and its DNA complex at different temperatures: Changes of internal motions in Genesis upon binding to DNA

Journal of Molecular Biology

Volumn 292, Issue 3, 1999, Pages 641-651

  Jin, Changwen ^a   Liao, Xiubei ^a  

^a UNIVERSITY OF ILLINOIS   (United States)

Author keywords

DNA binding; Genesis; NMR; Relaxation; Winged helix motif

Indexed keywords

DNA BINDING PROTEIN; GENESIS; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; DNA PROTEIN COMPLEX; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN SECONDARY STRUCTURE; TEMPERATURE SENSITIVITY;

EID: 0033600846     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3106     Document Type: Article

References (30)

1. Abragam A. Principles of Nuclear Magnetism. 1961;Oxford University Press, London.
2. 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. Biochemistry. 31:1992;5269-5278.
3. Bloom M., Reevers L. W., Wells E. J. Spin echos and chemical exchange. J. Chem. Phys. 42:1965;1615-1642.
4. Bravieri R., Shyyanova T., Chen T. H., Overdier D., Liao X. Different DNA contact schemes are used by two winged helix proteins to recognize a DNA binding sequence. Nucl. Acids Res. 25:1997;2888-2896.
5. Brüschweiler R., Liao X., Wright P. E. Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling. Science. 268:1995;886-889.
6. Clark K. L., Halay E. D., Lai E., Burley S. K. Cocrystal structure of the HNF-3/fork head DNA recognition motif resembles histone H5. Nature. 364:1993;412-420.
7. Clevidence D. E., Overdier D. G., Tao W., Qian X., Pani L., Lai E., Costa R. H. Identification of nine tissue-specific transcription factors of the hepatocyte nuclear factor 3/forkhead DNA-binding-domain family. Proc. Natl Acad. Sci. USA. 90:1993;3948-3952.
8. Fairbrother W. J., Liu J., Pisacane P. I., Silwkowski M. X., Palmer A. G. III. Backbone dynamics of the EGF-like domain of heregulin-α J. Mol. Biol. 279:1998;1149-1161.
9. 15N relaxation data exclusively. J. Biomol. NMR. 6:1995;153-162.
10. 15N]glycine benzyl ester. J. Am. Chem. Soc. 110:1988;2378-2383.
11. Ishima R., Nagayama K. Quasi-spectral- density function analysis for nitrogen-15 nuclei in proteins. J. Magn. Reson. ser. B. 108:1995;73-76.
12. 15N relaxation NMR. Biochemistry. 37:1998;6179-6187.
13. Jin C., Marsden I., Chen X., Liao X. Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex. J. Mol. Biol. 289:1999;683-690.
14. Kaufmann E., Knöchel W. Five years on the wings of fork head. Mech. Dev. 57:1996;3-20.
15. Lai E., Prezioso V. R., Smith E., Litvin O., Costa R. H., Darnell J. E. Jr. HNF-3γ, a hepatocyte-enriched transcription factor of novel structure is regulated transcriptionally. Genes Dev. 4:1990;1427-1436.
16. αnuclear spin relaxation. J. Biomol. NMR. 9:1997;287-298.
17. Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1, Theory and range of validity. J. Am. Chem. Soc. 104:1982a;4546-4558.
18. Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104:1982b;4559-4570.
19. Mandel A. M., Akke M., Palmer A. G. III. Dynamics of ribonuclease H: temperature dependence of motions on multiple time scales. Biochemistry. 35:1996;16009-16023.
20. Markley J. L., Horsley W. J., Klein M. P. Spin-lattice relaxation measurements in slowly relaxing complex spectra. J. Chem. Phys. 55:1971;3604-3605.
21. Marsden I., Jin C., Liao X. Structural changes in the region directly adjacent to the DNA-binding helix highlight a possible mechanism to explain the observed changes in the sequence-specific binding of winged helix proteins. J. Mol. Biol. 278:1998;293-299.
22. Overdier D. G., Porcella A., Costa R. H. HNF-3/fkh domain protein chimeras suggest that sequences outside of the recognition helix are involved in DNA binding specificity. Mol. Cell. Biol. 14:1994;2755-2766.
23. Palmer A. G. III, Williams J., McDermott A. Nuclear magnetic resonance studies of biopolymer dynamics. J. Phys. Chem. 100:1996;13293-13310.
24. Peng J. W., Gagner G. Mapping of the spectral densities of N-H bond motions in eglin c using heteronuclear relaxation experiments. Biochemistry. 31:1992;8571-8586.
25. Peng J. W., Gagner G. Frequency spectrum of NH bonds in eglin c from spectral density mapping at multiple fields. Biochemistry. 34:1995;16733-16752.
26. Press W. H., Flannery B. P., Teukolsky S. A., Vetterling W. T. Numerical Recipes. 1989;Cambridge University Press, Cambridge.
27. Shiyanova T., Liao X. The dissociation rate of a winged helix protein-DNA complex is influenced by non-DNA contact residues. Arch. Biochem. Biophys. 15:1999;356-362.
28. Sutton J., Costa R., Klug M., Field L., Xu D., Largraespada D. A., Fletcher C. F., Jenkins N. A., Copeland N. G., Klemsz M., Hromas R. Genesis, a winged helix transcriptional repressor with expression restricted to embryonic stem cells. J. Biol. Chem. 271:1996;23126-23133.
29. Vogt P. K., Li J., Freyaldenhoven B. S. Revelations of a captive: retroviral Qin and the oncogenicity of winged helix proteins. Virology. 238:1997;1-7.
30. Weigel D., Jackle H. The fork head domain: a novel DNA binding motif of eukaryotic transcription factors. Cell. 63:1990;455-456.