Conformational dynamics and molecular recognition: Backbone dynamics of the estrogen receptor DNA-binding domain

Journal of Molecular Biology

Volumn 289, Issue 4, 1999, Pages 963-979

  Wikström, Anja ^a   Berglund, Helena ^b   Hambraeus, Charlotta ^a   Van Den Berg, Susanne ^b   Härd, Torleif ^b  

^a SÖDERTÖRN UNIVERSITY   (Sweden)

^b NONE

Author keywords

DNA binding proteins; Molecular recognition; NMR spectroscopy; Protein dynamics; Steroid hormone receptors

Indexed keywords

DNA BINDING PROTEIN; ESTROGEN RECEPTOR; GLUCOCORTICOID RECEPTOR; NITROGEN 15; ZINC;

ARTICLE; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN CONFORMATION;

EID: 0033019594     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2806     Document Type: Article

References (56)

1. Abragam A. Principles of Nuclear Magnetism. 1961;Clarendon Press, Oxford.
2. Akke M., Palmer A. G. Monitoring macromolecular motions on microsecond to millisecond time scales by R1ρ-R1 constant relaxation time NMR spectroscopy. J. Am. Chem. Soc. 118:1996;911-912.
3. 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. Biochemistry. 31:1992;5269-5278.
4. Baumann H., Paulsen K., Lovács H., Berglund H., Wright A. P. H., Gustafsson J.-Å., Härd T. Refined solution structure of the glucocorticoid receptor DNA-binding domain. Biochemistry. 32:1993;13463-13471.
5. Berglund H., Lovács H., Dahlman-Wright K., Gustafsson J.-Å., Härd T. Backbone dynamics of the glucocorticoid receptor DNA-binding domain. Biochemistry. 31:1992;12001-12011.
6. Berglund H., Wolf-Watz M., Lundbäck T., van den Berg S., Härd T. Structure and dynamics of the glucocorticoid receptor DNA-binding domain: comparison of wild type and a mutant with altered specificity. Biochemistry. 36:1997;11188-11197.
7. Brüschweiler R., Liao X., Wright P. E. Long-range motional restrictions in a multidomain zinc-finger protein from aniostropic tumbling. Science. 268:1995;886-889.
8. Brzozowski A. M., Pike A. C. W., Dauter Z., Hubbard R. E., Bonn T., Engström O., Öhman L., Greene G. L., Gustafsson J.-Å., Carlquist M. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature. 389:1997;753-758.
9. Cairns W., Cairns C., Pongratz I., Poellinger L., Okret S. Assembly of glucocorticoid receptor complex prior to DNA binding enhances its specific interaction with a glucocorticoid response element. J. Biol. Chem. 266:1991;11221-11226.
10. Cavanagh J., Fairbrother W. J., Palmer A. G., Skelton N. J. Protein NMR Spectroscopy: Principles and Practice. 1996;Academic Press, London.
11. Clore G. M., Szabo A., Bax A., Kay L. E., Dristoll P. C., Gronenborn A. M. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 112:1990;3989-4991.
12. Dahlman-Wright K., Wright A., Gustafsson J.-Å., Carlstedt-Duke J. Interaction of the glucocorticoid receptor DNA-binding domain with DNA as a dimer is mediated by a short segment of five amino acids. J. Biol. Chem. 266:1991;3107-3112.
13. Danielsen M., Hinck L., Ringold G. M. Two amino acids within the knuckle of the first finger specify DNA response element activation by the glucocorticoid receptor. Cell. 57:1989;1131-1138.
14. Devore J. L. Probability and Statistics for Engineering and the Sciences. 1995;Wadsworth, Inc./International Thomson Publishing Inc. New York.
15. 15N NMR relaxation. Biochemistry. 33:1994;5984-6003.
16. Freedman L. P., Luisi B. F., Korszun Z. R., Basavappa R., Sigler P. B., Yamamoto K. R. The function and structure of the metal coordination sites within the glucocorticoid receptor DNA binding domain. Nature. 334:1988;543-546.
17. Gewirth D. T., Sigler P. B. The basis for half-site specificity explored through a non-cognate steroid receptor-DNA complex. Nature Struct. Biol. 2:1995;386-394.
18. Härd T., Dahlman K., Carlstedy-Duke J., Gustafsson J.-Å., Rigler R. Cooperativity and specificity in the interactions between DNA and the glucocorticoid receptor DNA-binding domain. Biochemistry. 29:1990a;5358-5364.
19. Härd T., Kellenbach E., Boelens R., Maler B. A., Dahlman K., Freedman L. P., Carlstedt-Duke J., Yamamoto K. R., Gustafsson J.-Å., Kaptein R. Solution structure of the glucocorticoid receptor DNA-binding domain. Science. 249:1990b;157-160.
20. 15N]glycine benzyl ester. J. Am. Chem. Soc. 110:1988;2378-2383.
21. Holmbeck S. M. A., Dyson H. J., Wright P. E. DNA-induced conformational changes are the basis for cooperative dimerization by the DNA binding domain of the retinoid X receptor. J. Mol. Biol. 284:1998;533-539.
22. Kay L. E. Pulsed field gradient multi-dimensional NMR methods for the study of protein structure and dynamics in solution. Prog. Biophys. Mol. Biol. 63:1995;277-299.
23. Kay L. E., Torchia D. A., Bax A. Backbone dynamics of proteins as studied by nitrogen-15 invers detected NMR spectroscopy: application to staphylococcal nuclease. Biochemistry. 28:1989;8972-8979.
24. Kumar V., Chambon P. The estrogen receptor binds tightly to its responsive element as a ligand-inducer dimer. Cell. 55:1988;145-156.
25. αnuclear spin relaxation. J. Biol. NMR. 9:1997;287-298.
26. Lefstin J. A., Yamamoto K. R. Allosteric effects of DNA on transcriptional regulators. Nature. 392:1998;885-888.
27. Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104:1982a;4546-4559.
28. Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104:1982b;4559-1570.
29. Lucas P. C., Granner D. K. Hormone response domains in gene transcription. Annu. Rev. Biochem. 61:1992;1131-1173.
30. Luisi B. F., Xu W. X., Otwinowski Z., Freedman L. P., Yamamoto K. R., Sigler P. B. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 352:1991;497-505.
31. Lundbäck T., Härd T. Salt dependence of the free energy, enthalpy and entropy of nonsequence specific DNA binding. J. Phys. Chem. 100:1996a;17690-17695.
32. Lundbäck T., Härd T. Sequence specific DNA-binding dominated by dehydration. Proc. Natl Acad. Sci. USA. 93:1996b;4754-4759.
33. Lundbäck T., Zilliacus J., Gustafsson J.-Å., Carlstedt-Duke J., Hård T. Thermodynamics of sequence-sopecific glucocorticoid receptor-DNA interactions. Biochemistry. 33:1994;5955-5965.
34. Mangelsdorf D. J., Thummel C., Beato M., Herrlich P., Schutz G., Umesuno K., Blomberg B., Kastner P., Mark M., Chambon P., Evans R. The nuclear receptor family: the second decade. Cell. 83:1995;835-839.
35. 15N NMR spectroscopy. Eur. J. Biochem. 219:1994;887-896.
36. 13C heteronuclear NMR spectroscopy. J. Am. Chem. Soc. 113:1991;4371-4380.
37. Palmer A. G., Skelton N. J., Chazin W. J., Wright P. E., Rance M. Suppression of cross-correlation between dipolar and anisotropic chemical shift relaxation mechanisms in the measurement of spin-spin relaxation rates. Mol. Phys. 75:1992;699-711.
38. Palmer A. G., Williams J., McDermott A. Nuclear magnetic resonance studies of biopolymer dynamics. J. Phys. Chem. 100:1996;13293-13310.
39. Schurr J. M., Babcock H. P., Fujimoto B. S. A test of the model-free formulas. Effects of anisotropic rotational diffusion and dimerization. J. Magn. Reson. ser. B. 105:1994;211-224.
40. Schwabe J. W. R., Neuhaus D., Rhodes D. Solution structure of the oestrogen receptor. Nature. 348:1990;458-461.
41. Schwabe J. W. R., Chapman L., Finch J. T., Rhodes D. The crystal structure of the oestrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell. 75:1993a;567-578.
42. Schwabe J. W. R., Chapman L., Finch J. T., Rhodes D., Neuhaus D. DNA recognition by the oestrogen receptor: from solution to the crystal. Structure. 1:1993b;187-204.
43. Schwabe J. W. R., Chapman L., Rhodes D. The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation. Structure. 3:1995;201-213.
44. 15N NMR relaxation. J. Am. Chem. Soc. 117:1995;12562-12566.
45. Truss M., Beato M. Steroid hormone receptors: interaction with deoxyribonucleic acid and transcription factors. Endocrine Rev. 14:1993;459-479.
46. Tsai M. J., O'Malley B. W. Molecular mechanisms of action of steroid/thyroid receptor superfamily members. Annu. Rev. Biochem. 63:1994;451-486.
47. Umensono K., Evans R. M. Determinants of target gene specificity for steroid thyroid hormone receptors. Cell. 57:1989;1139-1146.
48. van Tilborg M. The glucocorticoid receptor DNA binding domain: structure and allosteric modulation. PhD thesis. 1998;University of Utrecht.
49. van Tilborg M. A. A., Bonvin A. M. J. J., Hård K., Davis A. L., Maler B., Boelens R., Yamamoto K. R., Kaptein R. Structure refinement of the glucocorticoid receptor DNA-binding domain from NMR data by relaxation matrix calculations. J. Mol. Biol. 247:1995;689-700.
50. van Tilborg P. J. A., Mulder F. A. A., de Backer M. M. E., Nair M., van Heerde E. C., Folkers G., van der Saaga P. T., Karimi-Nejad Y., Boelens R., Kaptein R. Millisecond to microsecond time scale dynamics of the retinoid X and retinoic acid receptor DNA-binding domains and dimeric complex formation. Biochemistry. 38:1999;1951-1956.
51. Woessner D. E. Nuclear spin relaxation in ellipsoids undergoind rotational Brownian motion. J. Chem. Phys. 37:1962;647-654.
52. Wolfram S. The Mathematica Book. 1996;Wolfram Media/Cambridge University Press, Cambridge.
53. 15N-enriched proteins. J. Am. Chem. Soc. 115:1993;7772-7777.
54. Xu W., Alroy I., Freedman L. P., Sigler P. B. Stereochemistry of specific steroid receptor-DNA interactions. Cold Spring Harbor Symp. Quant. Biol. 58:1993;133-139.
55. Zilliacus J., Dahlman-Wright K., Wright A., Gustafsson J.-Å., Carlstedt-Duke J. DNA-binding specificity of mutant glucocorticoid receptor DNA-binding domains. J. Biol. Chem. 266:1991;3101-3106.
56. Zilliacus J., Wright A. P. H., Norinder U., Gustafsson J.-Å., Carlstedt-Duke J. Determinants for DNA-binding site recognition by the glucocorticoid receptor. J. Biol. Chem. 267:1992;24941-24947.