Backbone dynamics of a short PU.1 ETS domain

Journal of Molecular Biology

Volumn 292, Issue 5, 1999, Pages 1083-1093

  Jia, Xin ^a   Lee, Larry K ^b   Light, James ^a   Palmer III, Arthur G ^b   Assa Munt, Nuria ^a  

^a BURNHAM INSTITUTE   (United States)

^b Columbia University ^*  (United States)

Author keywords

Model free formalism; NMR relaxation; Protein dynamics; Protein secondary structure; Protein protein interaction

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CRYSTAL STRUCTURE; DNA PROTEIN COMPLEX; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE;

EID: 0033536686     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3123     Document Type: Article

References (65)

1. Altieri A. S., Hinton D. P., Byrd R. A. Association of biomolecular systems via pulsed field gradient NMR self diffusion measurements. J. Am. Chem. Soc. 117:1995;7566-7567.
2. Aurora R., Rose G. D. Helix capping. Protein Sci. 7:1998;21-38.
3. Batchelor A. H., Piper D. E., Brousse F. C., Mcknight S. L., Wolberger C. The structure of GABPα/β: an ets domain-ankyrin repeat heterodimer bound to DNA. Science. 279:1998;1037-1041.
4. Brass A. L., Kehrli E., Eisenbeis C. F., Storb U., Singh H. Pip, a lymphoid-restricted IRF, contains a regulatory domain that is important for autoinhibition and ternary complex formation with the Ets factor PU.1. Genes Dev. 10:1996;2335-2347.
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. Carr P. A., Erickson H. P., Palmer A. G. III. Backbone dynamics of homologous fibronectin type III cell adhesion domains from fibronectin and tenascin. Structure. 5:1997;949-959.
7. Cavanagh J., Fairbrother W. J., Palmer A. G. III, Skelton N. J. Protein NMR Spectroscopy. Principles and Practice. 1996;Academic Press, New York.
8. 1H NMR spectroscopy. Biochemistry. 29:1990;7387-7401.
9. Craig M. L., Tsodikov O. V., McQuade K. L., Schlax P. E. Jr, Capp M. W., Saecker R. M., Record M. T. Jr. DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol. 283:1998;741-756.
10. Crepieux P., Coll J., Stehelin D. The ets family of proteins: weak modulators of gene expression in the quest for transcriptional partners. Crit. Rev. Oncogene. 5:1994;615-638.
11. Donaldson L. W., Petersen J. M., Graves B. J., Mcintosh L. P. Solution structure of the Ets domain from murine Ets-1: a winged helix-turn-helix DNA binding motif. EMBO J. 15:1996;125-134.
12. Dubin S. B., Clark N. A., Benedek G. B. Measurement of the rotational diffusion coefficient of lysozyme in solution. J. Chem. Phys. 54:1971;5158-5164.
13. Eisenbeis C., Singh H., Storb U. PU. 1 is a component of a multiprotein complex which binds an essential site in the murine immunoglobulin λ2-4 enhancer. Mol. Cell Biol. 13:1993;6452-6461.
14. Eisenbeis C., Singh H., Storb U. Pip, a novel IRF family member, is a lymphoid-specific, PU. 1-dependent transcriptional activator. Genes Dev. 9:1995;1377-1387.
15. Escalante C. R., Yie J., Thanos D., Aggarwal A. K. Structure of IRF-1 with bound DNA reveals determinants of interferon regulation. Nature. 391:1998;103-106.
16. 15N NMR relaxation. Biochemistry. 33:1994;5984-6003.
17. Farrow N. A., Zhang O., Forman-Kay J. D., Kay L. E. Comparison of backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer. Biochemistry. 34:1995;868-878.
18. Furui J., Uegaki K., Yamazaki T., Shirakawa M., Swindells M. B., Harada H., Taniguchi T., Kyogoku Y. Solution structure of the IRF 2 DNA binding domain: a novel subgroup of the winged helix-turn-helix family. Structure. 6:1998;491-500.
19. 15N relaxation with monomer/dimer equilibration. J. Mol. Biol. 266:1997;173-194.
20. Gaal T., Ross W., Blatter E. E., Hong T., Jia X., Krishnan V. V., Assa-Munt N., Ebright R. H., Gourse R. L. DNA binding determinants of the α subunit of RNA polymerase: a novel DNA binding domain architecture. Genes Dev. 10:1996;16-26.
21. Ghysdael J., Boureux A. The Ets family of transcriptional regulators. Yaniv M., Ghysdael J. Oncogenes as Transcriptional Regulators. 1997;29-89 Birkhauser Verlag Basel.
22. 13C chemical shifts. J. Biomol. NMR. 4:1994;455-4458.
23. 15N NMR backbone assignments and secondary structure of human interferon-γ Biochemistry. 31:1992;8180-8190.
24. Grzesiek S., Bax A., Hu J.-S., Kaufman J., Palmer I., Stahl S. J., Tjandra N., Wingfield P. T. Refined solution structure and backbone dynamics of HIV-1 Nef. Protein Sci. 6:1997;1248-1263.
25. Karim F. D., Urness L. D., Thummel C. S., Klemsz M. J., McKercher S. R., Celada A., Van Beveren C., Maki R. A., Gunther C. V., Nye J. A. The ETS-domain: a new DNA-binding motif that recognizes a purine-rich core DNA sequence. Genes Dev. 4:1990;1451-1453.
26. Kaufmann E., Knochel W. Five years on the wings of fork head. Mech. Dev. 57:1996;3-20.
27. Klemsz M. J., Maki R. A., Papayannopoulou T., Moore J., Hromas R. Characterizaiton of the ets oncogene family member, fli-1. J. Biol. Chem. 268:1993;5769-5773.
28. Kodandapani R., Pio F., Ni C. Z., Piccialli G., Klemsz M., McKercher S., Maki R. A., Ely K. R. A new pattern for helix-turn-helix recognition revealed by the PU. 1 ets-domain-DNA complex. Nature. 380:1996;456-460.
29. Laudet V., Hanni C., Stehelin D., Duterque-Coquillaud M. Molecular phylogeny of the ETS gene family. Oncogene. 18:1999;1351-1359.
30. αnuclear spin relaxation. J. Biomol. NMR. 9:1997;287-298.
31. Liang H., Mao X., Olejniczak E. T., Nettesheim D. G., Yu L., Meadows R. P., Thompson C. B., Fesik S. W. Solution structure of the ETS domain of Fli-1 when bound to DNA. Nature Struct. Biol. 1:1994;871-875.
32. Liang H., Petros A. M., Meadows R. P., Yoon H. S., Egan D. A., Walter E. K., Holzman T. F., Robins T., Fesik S. W. Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions. Biochemistry. 35:1996;2095-2103.
33. 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;4546-4559.
34. 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.
35. Macleod K., Leprince D., Stehelin D. The ets gene family. Trends Biochem. Sci. 17:1992;251-256.
36. Mandel A. M., Akke M., Palmer A. G. Backbone dynamics of Escherichia coli ribonuclease H1: Correlations with structure and function in an active enzyme. J. Mol. Biol. 246:1995;144-163.
37. Markley J. L., Horseley W. J., Klein M. P. Spin-lattice relaxation in slowly relaxing complex spectra. J. Chem. Phys. 55:1971;3604-3605.
38. Marsden I., Chen Y., Jin C., Liao X. Evidence that the DNA binding specificity of winged helix proteins is mediated by a structural change in the amino acid sequence adjacent to the principal DNA binding helix. Biochemistry. 36:1997;13248-13255.
39. 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.
40. Mo Y., Vaessen B., Jonston K., Marmorstein R. Structures of SAP-1 bound to DNA targets from the E74 and C-fos promoters: insights into DNA sequence discrimination by ets proteins. Mol. Cell. 2:1998;201-212.
41. Moreau-Gachelin F. Spi-1/PU.1: an oncogene of the Ets family. Biochim. Biophys. Acta. 1198:1994;149-163.
42. 1H resonance assignments and secondary structure of the carbon monoxide complex of soybean leghemoglobin determined by homonuclear two-dimensional and three-dimansional NMR spectroscopy. Eur. J. Biochem. 219:1994;611-626.
43. Mosteller F., Tukey J. W. Data Analysis and Regression. A Second Course in Statistics. 1997;Addison-Wesley, Reading.
44. Muchmore D. C., McIntosh L. P., Russell C. B., Dahlquist F. W. Expression and labelling of proteins for proton and nitrogen-15 nuclear magnetic resonance. Methods Enzymol. 177:1989;44-73.
45. Noggle J. H., Schirmer R. E. The Nuclear Overhauser Effect: Chemical Applications. 1971;Academic Press, New York.
46. Ortiz M. A., Light J., Maki R. A., Assa-Munt N. Mutaiton anaylsis of the Pip interaction domain reveals critical residues for protein-protein interactions. Proc. Natl Acad. Sci. USA. 96:1999;2740-2745.
47. Overdier D. G., Porcella A., Costa R. H. The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino acid residues adjacent to the recognition helix. Mol. Cell Biol. 14:1994;2755-2766.
48. 13C heteronuclear NME spectroscopy. J. Am. Chem. Soc. 113:1991;4371-4380.
49. Perkel J. M., Atchison M. L. A two-step mechanism for recruitment of Pip by PU.1. J. Immunol. 160:1998;241-252.
50. Pongubala J., Nagulapalli S., Klemsz M., McKercher S., Maki R., Atchison M. PU. 1 recruits a second nuclear factor to a site important for immunoglobulin κ3′ enhancer activity. Mol. Cell Biol. 12:1992;368-378.
51. Press W. H., Flannery B. P., Teukolsky S. A., Vetterling W. T. Numerical Recipes. The Art of Scientific Computing. 1986;Cambridge University Press.
52. Richardson J. S., Richardson D. C. Amino acid preferences for specific locations at the ends of α helices. Science. 240:1988;1648-1652.
53. Seale J. W., Srinivasan R., Rose G. D. Sequence determinations of the capping box, a stabilizing motif at the N-termini of α-helices. Protein Sci. 3:1994;1741-1745.
54. Shaka A. J., Barker P. B., Freeman R. Computer-optimized decoupling scheme for wideband applications and low-level operation. J. Magn. Reson. 64:1985;547-552.
55. Sharrocks A. D., Brown A. L., Ling Y., Yates P. R. The ETS-domain transcription factor family. Int. J. Biochem. Cell Biol. 29:1997;1371-1387.
56. Spolar R. S., Record M. T. Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:1994;777-784.
57. Srinivasan P. R., Lichter R. L. Nitrogen-15 nuclear magnetic resonance spectroscopy. Evaluation of chemical shift references. J. Magn. Reson. 28:1977;227-234.
58. States D. J., Haberkorn R. A., Ruben D. J. A two-dimensional nuclear Overhauser experiment with pure absorption phase in four quadrants. J. Magn. Reson. 48:1982;286-292.
59. Teller D. C., Swanson E., de Haen C. The translational friction coefficient of proteins. Methods Enzymol. 61:1979;103-124.
60. Weiss M. A., Ellenberger T., Wobbe C. R., Lee J. P., Harrison S. C., Struhl K. Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA. Nature. 347:1990;575-578.
61. Wishart D. S., Sykes B. D. Chemical shifts as a tool for structure determination. Methods Enzymol. 239:1994;363-393.
62. Wüthrich K. NMR of Proteins and Nucleic Acids. 1986;John Wiley & Sons, New York. p. 167.
63. 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli. J. Biomol. NMR. 9:1997;167-180.
64. Zhang H., Zhao D., Revington M., Lee W., Jia X., Arrowsmith C., Jardetzky O. The solution structure of the trp repressor-operator DNA complex. J. Mol. Biol. 238:1994;592-614.
65. Zhao D., Arrowsmith C. H., Jia X., Jardetzky O. Refinement of the solution structures of the E. colitrp holo- and aporepressor. J. Mol. Biol. 229:1993;735-746.