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

Journal of Molecular Biology

Volumn 278, Issue 2, 1998, Pages 293-299

  Marsden, Ian ^a,b   Jin, Changwen ^a   Liao, Xiubei ^a  

^a UNIVERSITY OF ILLINOIS   (United States)

^b ABBOTT LABORATORIES   (United States)

Author keywords

3D structure; Genesis; HNF forkhead; NMR; NOE

Indexed keywords

HEPATOCYTE NUCLEAR FACTOR 3; NUCLEAR FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; BINDING SITE; CONTROLLED STUDY; DNA HELIX; NUCLEAR MAGNETIC RESONANCE IMAGING; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW; X RAY CRYSTALLOGRAPHY;

EID: 0032079679     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1703     Document Type: Editorial

References (20)

1. Bravieri, R., Shiyanova, T., Chen, T. H., Overdier, D. & Liao, X. (1997). Different DNA contact schemes are used by two winged helix proteins to recognize a DNA binding sequence. Nucl. Acids Res. 25, 2888-2896.
2. Clark, K. L., Halay, E. D., Lai, E. & Burley, S. K. (1993). Cocrystal structure of the HNF-3/forkhead DNA recognition motif resembles histone H5. Nature, 364, 412-420.
3. Clevidence, D. E., Overdier, D. G., Tao, W., Qian, X., Pani, L., Lai, E. & Costa, R. H. (1993). Identification of nine tissue-specific transcription factors of the hepatocyte nuclear factors 3 and forkhead DNA binding domain family. Proc. Natl Acad. Sci. USA, 90, 3948-3952.
4. Fesik, S. W. & Zuiderweg, E. R. (1990). Heteronuclear three-dimensional NMR spectroscopy of isotopically labelled biological macromolecules. Quart. Rev. Biophys. 23, 97-131.
5. Güntert, P., Braun, W. & Wüthrich, K. (1991). Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517-530.
6. Kaufmann, E. & Knöchel, W. (1996). Five years on the wings of forkhead. Mech. Dev. 57, 3-20.
7. Koradi, R., Billeter, M. & Wuthrich, K. (1996). MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55.
8. Lai, E., Prezioso, V. R., Smith, E., Litvin, O., Costa, R. H. & Darnell, J. E., Jr (1990). Hepatocyte nuclear factor 3 alpha belongs to a gene family in mammals that is homologous to the Drosophila homeotic gene forkhead. Genes Dev. 4, 1427-1436.
9. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl Crystallog. 26, 283-291.
10. Marsden, I., Chen, Y., Jin, C. & Liao, X. (1997). Evidence that the DNA binding specificity of winged helix proteins is mediated by a structural change in the amino sequence adjacent to the principal DNA binding helix. Biochemistry, 36, 13248-13255.
11. Muhandiram, D. R. & Kay, L. E. (1994). Gradient-enhanced triple-resonance 3-dimensional NMR experiments with improved sensitivity. J. Magn. Reson. ser. B, 103, 203-216.
12. Overdier, D. G., Porcella, A. & Costa, R. H. (1994). HNF-3/fkh domain protein chimeras suggest that sequences outside of the recognition helix are involved in DNA binding specificity. Mol. Cell. Biol. 14, 2755-2766.
13. Palmer, A. G., Cavanagh, J., Wright, P. E. & Rance, M. (1991). Sensitivity improvement in proton detected two-dimensional heteronuclear correlation NMR spectroscopy. J. Magn. Reson. 93, 203-216.
14. Pierrou, S., Hellqvist, M., Samuelsson, L., Enerbäck, S. & Carlsson, P. (1994). Cloning and characterization of seven human forkhead proteins: binding site specificity and DNA bending. EMBO J. 13, 5002-5012.
15. Rosen, M. K., Gardner, K. H., Willis, R. C., Parris, W. E., Pawson, T. & Kay, L. E. (1996). Selective methyl group protonation of perdeuterated proteins. J. Mol. Biol. 263, 627-636.
16. Sutton, J., Costa, R., Klug, M., Field, L., Xu, D., Largaespada, D. A., Fletcher, C. F., Jenkins, N. A., Copeland, N. G., Klemsz, M. & Hromas, R. (1996). Genesis, a winged helix transcriptional repressor with expression restricted to embryonic stem cells. J. Biol. Chem. 271, 23126-23133.
17. Weigel, D. & Jäckle, H. (1990). The forkhead domain: a novel DNA binding motif of eukaryotic transcription factors? Cell, 63, 455-456.
18. Wishart, D. S. & Sykes, B. D. (1994a). Chemical shifts as a tool for structure determination. Methods Enzymol. 239, 363-392.
19. 13C NMR chemical-shift data. J. Biomol. NMR, 4, 171-180.
20. Wuthrich, K. (1986). NMR of Proteins and Nucleic Acids, Wiley Interscience Publication, New York, NY.