NMR studies of translocation of the Zif268 protein between its target DNA Sites

Biochemistry

Volumn 49, Issue 37, 2010, Pages 7998-8005

  Takayama, Yuki ^a   Sahu, Debashish ^a   Iwahara, Junji ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; DISSOCIATION; DNA; GENES; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; RATE CONSTANTS; ZINC;

CORRELATION SPECTRA; DIRECT TRANSFER; DISSOCIATION RATE CONSTANT; DNA CONCENTRATION; DNA MOLECULES; FAST ACQUISITION; HETERONUCLEAR; NMR CHEMICAL SHIFTS; NMR SPECTROSCOPY; NMR STUDIES; PROTEIN TRANSFER; RESIDUAL DIPOLAR COUPLINGS; SECOND-ORDER RATE CONSTANTS; TARGET SITES; TIME-SCALES; ZINC FINGER DOMAINS;

PROTEINS;

DNA; OCTAMER TRANSCRIPTION FACTOR 1; PROTEIN HOXD9; PROTEIN ZIF268; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN; PROTEIN;

ARTICLE; BINDING AFFINITY; DISSOCIATION CONSTANT; GENE TARGETING; NITROGEN NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN TRANSPORT; PROTON NUCLEAR MAGNETIC RESONANCE; SIGNAL TRANSDUCTION; CHEMISTRY; GENE TRANSLOCATION; GENETICS; HUMAN; METABOLISM; NUCLEAR MAGNETIC RESONANCE IMAGING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; DNA; HUMANS; MAGNETIC RESONANCE IMAGING; MAGNETIC RESONANCE SPECTROSCOPY; PROTEINS; TRANSLOCATION, GENETIC; ZINC FINGERS;

EID: 77956572160     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi100962h     Document Type: Article

References (61)

1. Härd, T. (1999) NMR studies of protein-nucleic acid complexes: structures, solvation, dynamics and coupled protein folding Q. Rev. Biophys. 32, 57-98
2. Bonvin, A. M., Boelens, R., and Kaptein, R. (2005) NMR analysis of protein interactions Curr. Opin. Chem. Biol. 9, 501-508
3. Iwahara, J. and Clore, G. M. (2006) Detecting transient intermediates in macromolecular binding by paramagnetic NMR Nature 440, 1227-1230
4. Iwahara, J. and Clore, G. M. (2006) Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy J. Am. Chem. Soc. 128, 404-405
5. Iwahara, J., Zweckstetter, M., and Clore, G. M. (2006) NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA Proc. Natl. Acad. Sci. U.S.A. 103, 15062-15067
6. 1H paramagnetic relaxation enhancement J. Am. Chem. Soc. 126, 12800-12808
7. Sahu, D., Clore, G. M., and Iwahara, J. (2007) TROSY-based z-exchange spectroscopy: application to the determination of the activation energy for intermolecular protein translocation between specific sites on different DNA molecules J. Am. Chem. Soc. 129, 13232-13237
8. Doucleff, M. and Clore, G. M. (2008) Global jumping and domain-specific intersegment transfer between DNA cognate sites of the multidomain transcription factor Oct-1 Proc. Natl. Acad. Sci. U.S.A. 105, 13871-13876
9. Clore, G. M. and Iwahara, J. (2009) Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes Chem. Rev. 109, 4108-4139
10. Baumgartel, K., Genoux, D., Welzl, H., Tweedie-Cullen, R. Y., Koshibu, K., Livingstone-Zatchej, M., Mamie, C., and Mansuy, I. M. (2008) Control of the establishment of aversive memory by calcineurin and Zif268 Nat. Neurosci. 11, 572-578
11. Beckmann, A. M. and Wilce, P. A. (1997) Egr transcription factors in the nervous system Neurochem. Int. 31, 477-510 discussion 517-476.
12. Bozon, B., Davis, S., and Laroche, S. (2003) A requirement for the immediate early gene zif268 in reconsolidation of recognition memory after retrieval Neuron 40, 695-701
13. Hall, J., Thomas, K. L., and Everitt, B. J. (2001) Cellular imaging of zif268 expression in the hippocampus and amygdala during contextual and cued fear memory retrieval: selective activation of hippocampal CA1 neurons during the recall of contextual memories J. Neurosci. 21, 2186-2193
14. Jones, M. W., Errington, M. L., French, P. J., Fine, A., Bliss, T. V., Garel, S., Charnay, P., Bozon, B., Laroche, S., and Davis, S. (2001) A requirement for the immediate early gene Zif268 in the expression of late LTP and long-term memories Nat. Neurosci. 4, 289-296
15. Mokin, M. and Keifer, J. (2005) Expression of the immediate-early gene-encoded protein Egr-1 (zif268) during in vitro classical conditioning Learn. Mem. 12, 144-149
16. 2 zinc finger proteins Annu. Rev. Biophys. Biomol. Struct. 29, 183-212
17. Beerli, R. R., Segal, D. J., Dreier, B., and Barbas, C. F., 3rd (1998) Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks Proc. Natl. Acad. Sci. U.S.A. 95, 14628-14633
18. Wu, H., Yang, W. P., and Barbas, C. F., III (1995) Building zinc fingers by selection: toward a therapeutic application Proc. Natl. Acad. Sci. U.S.A. 92, 344-348
19. Christy, B. and Nathans, D. (1989) DNA binding site of the growth factor-inducible protein Zif268 Proc. Natl. Acad. Sci. U.S.A. 86, 8737-8741
20. Yang, W. P., Wu, H., and Barbas, C. F., III (1995) Surface plasmon resonance based kinetic studies of zinc finger-DNA interactions J. Immunol. Methods 183, 175-182
21. Turk, J. A. and Smithrud, D. B. (2003) Synthesis and evaluation of peptidomimetics that bind DNA Bioorg. Med. Chem. 11, 2355-2365
22. Elrod-Erickson, M. and Pabo, C. O. (1999) Binding studies with mutants of Zif268. Contribution of individual side chains to binding affinity and specificity in the Zif268 zinc finger-DNA complex J. Biol. Chem. 274, 19281-19285
23. Greisman, H. A. and Pabo, C. O. (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites Science 275, 657-661
24. Hamilton, T. B., Borel, F., and Romaniuk, P. J. (1998) Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1 Biochemistry 37, 2051-2058
25. Rebar, E. J. and Pabo, C. O. (1994) Zinc finger phage: affinity selection of fingers with new DNA-binding specificities Science 263, 671-673
26. Shi, Y. and Berg, J. M. (1995) A direct comparison of the properties of natural and designed zinc-finger proteins Chem. Biol. 2, 83-89
27. Swirnoff, A. H. and Milbrandt, J. (1995) DNA-binding specificity of NGFI-A and related zinc finger transcription factors Mol. Cell. Biol. 15, 2275-2287
28. Elrod-Erickson, M., Benson, T. E., and Pabo, C. O. (1998) High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition Structure 6, 451-464
29. Pavletich, N. P. and Pabo, C. O. (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A Science 252, 809-817
30. Elrod-Erickson, M., Rould, M. A., Nekludova, L., and Pabo, C. O. (1996) Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions Structure 4, 1171-1180
31. Kim, C. A. and Berg, J. M. (1996) A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA Nat. Struct. Biol. 3, 940-945
32. 2 zinc finger/TATA box complexes Structure 9, 717-723
33. Wolfe, S. A., Greisman, H. A., Ramm, E. I., and Pabo, C. O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code J. Mol. Biol. 285, 1917-1934
34. Iwahara, J., Wojciak, J. M., and Clubb, R. T. (2001) Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment J. Biomol. NMR 19, 231-241
35. Cavanagh, J., Fairbrother, W. J., Palmer, A. G., III, Rance, M., and Skelton, N. J. (2007) Protein NMR Sprectroscopy: Principles and Practice, 2 nd ed., Elsevier Academic Press, Burlington, MA.
36. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe - a multidimensional spectral processing system based on Unix pipes J. Biomol. NMR 6, 277-293
37. Johnson, B. A. and Blevins, R. A. (1994) NMRView - a computer-program for the visualization and analysis of NMR data J. Biomol. NMR 4, 603-614
38. Ottiger, M., Delaglio, F., and Bax, A. (1998) Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra J. Magn. Reson. 131, 373-378
39. Schwieters, C. D., Kuszewski, J. J., and Clore, G. M. (2006) Using Xplor-NIH for NMR molecular structure determination Prog. NMR Spectrosc. 48, 47-62
40. Schwieters, C. D., Kuszewski, J. J., Tjandra, N., and Clore, G. M. (2003) The Xplor-NIH NMR molecular structure determination package J. Magn. Reson. 160, 65-73
41. Shen, Y., Delaglio, F., Cornilescu, G., and Bax, A. (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44, 213-223
42. Deschamps, M. and Campbell, I. D. (2006) Cooling overall spin temperature: protein NMR experiments optimized for longitudinal relaxation effects J. Magn. Reson. 178, 206-211
43. Heirer, E., Norsett, S. P., and Wanner, G. (1991) Solving Ordinary Differential Equations I: Nonstiff Problems, Springer, Berlin.
44. Brewer, D., Barenco, M., Callard, R., Hubank, M., and Stark, J. (2008) Fitting ordinary differential equations to short time course data Philos. Trans. R. Soc. London, Ser. A 366, 519-544
45. Tjoa, I. B. and Biegler, L. T. (1991) Simultaneous solution and optimization strategies for parameter-estimation of differential-algebraic equation systems Ind. Eng. Chem. Res. 30, 376-385
46. Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (2007) Numerical Recipies: The Art of Scientific Computing, 3 rd ed., Cambridge University Press, New York.
47. Bevington, P. R. and Robinson, D. K. (2003) Data Reduction and Error Analysis, 3 rd ed., McGraw-Hill, Boston, MA.
48. Cornilescu, G., Delaglio, F., and Bax, A. (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology J. Biomol. NMR 13, 289-302
49. Clore, G. M. and Garrett, D. S. (1999) R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures J. Am. Chem. Soc. 121, 9008-9012
50. 1H relaxation optimization in TROSY NMR spectroscopy J. Am. Chem. Soc. 124, 12898-12902
51. Schanda, P. and Brutscher, B. (2005) Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds J. Am. Chem. Soc. 127, 8014-8015
52. Berg, O. G., Winter, R. B., and von Hippel, P. H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory Biochemistry 20, 6929-6948
53. Cho, S. and Wensink, P. C. (1997) DNA binding by the male and female doublesex proteins of Drosophila melanogaster J. Biol. Chem. 272, 3185-3189
54. Fried, M. G. and Crothers, D. M. (1984) Kinetics and mechanism in the reaction of gene regulatory proteins with DNA J. Mol. Biol. 172, 263-282
55. Lieberman, B. A. and Nordeen, S. K. (1997) DNA intersegment transfer, how steroid receptors search for a target site J. Biol. Chem. 272, 1061-1068
56. Ruusala, T. and Crothers, D. M. (1992) Sliding and intermolecular transfer of the lac repressor: kinetic perturbation of a reaction intermediate by a distant DNA sequence Proc. Natl. Acad. Sci. U.S.A. 89, 4903-4907
57. 15N longitudinal decay and chemical exchange rates of systems in slow equilibrium J. Biomol. NMR 4, 727-734
58. Li, Y. and Palmer, A. G., 3rd (2009) TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins J. Biomol. NMR 45, 357-360
59. Kristie, T. M. and Sharp, P. A. (1990) Interactions of the Oct-1 POU subdomains with specific DNA sequences and with the HSV alpha-trans-activator protein Genes Dev. 4, 2383-2396
60. Vuzman, D., Azia, A., and Levy, Y. Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails, J. Mol. Biol. 396, 674-684.
61. Kubosaki, A., Tomaru, Y., Tagami, M., Arner, E., Miura, H., Suzuki, T., Suzuki, M., Suzuki, H., and Hayashizaki, Y. (2009) Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation Genome Biol. 10, R41