Kinetic Analysis of the Interaction of b/HLH/Z Transcription Factors Myc, Max, and Mad with Cognate DNA

Biochemistry

Volumn 49, Issue 12, 2010, Pages 2627-2635

  Ecevit, Ozgur ^a   Khan, Mateen A ^a   Goss, Dixie J ^a  

^a CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARRHENIUS ACTIVATION ENERGY; BASIC HELIX LOOP HELIXES; COMPLEX ASSEMBLY; CONFORMATIONAL CHANGE; DNA BINDING; FASTER RATES; HETERODIMERS; HOMODIMERS; KINETIC ANALYSIS; LEUCINE ZIPPERS; PROTEIN DIMERIZATION; RATE LIMITING; RATE-LIMITING STEPS; STOPPED FLOW; TEMPERATURE DEPENDENCE;

ACTIVATION ENERGY; AMINO ACIDS; BINDING ENERGY; COMPLEXATION; DIMERIZATION; DIMERS; DNA; MONOMERS; RATE CONSTANTS; TRANSCRIPTION; TRANSCRIPTION FACTORS;

GENES;

DNA; HETERODIMER; HOMODIMER; MAX PROTEIN; MONOMER; MYC PROTEIN; PROTEIN MAD1;

ARTICLE; BINDING AFFINITY; CONCENTRATION (PARAMETERS); CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DIMERIZATION; DNA BINDING; KINETICS; POLARIZATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN INTERACTION; TEMPERATURE DEPENDENCE;

AMINO ACID SEQUENCE; BASIC HELIX-LOOP-HELIX LEUCINE ZIPPER TRANSCRIPTION FACTORS; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; DNA; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTO-ONCOGENE PROTEINS C-MYC; TRANSCRIPTION FACTORS;

EID: 77949867499     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi901913a     Document Type: Article

References (47)

1. Duesberg, P. H., Bister, K., and Vogt, P. K. (1977) The RNA of avian acute leukemia virus MC29. Proc. Natl. Acad. Sci. U.S.A. 74, 4320-4324.
2. Gearhart, J., Pashos, E. E., and Prasad, M. K. (2007) Pluripotency redux-advances in stem-cell research. N. Engl. J. Med. 357, 1469-1472.
3. Boult, J. K., Taniere, P., Hallissey, M. T., Campbell, M. J., and Tselepis, C. (2008) Oesophageal adenocarcinoma is associated with a deregulation in the MYC/MAX/MAD network. Br. J. Cancer 98, 1985-1992.
4. MacGregor, D. N., and Ziff, E. B. (1990) Proteins of the Myc network: Essential regulators of cell growth and differentiation. Pediatr. Res. 28, 63-68.
5. Henriksson, M., and Luscher, B. (1996) Regulation of cyclin D2 gene expression by the Myc/Max/Mad network: Myc-dependent TRRAP recruitment and histone acetylation at the cyclin D2 promoter. Adv. Cancer Res. 68, 109-182.
6. Bouchard, C., Dittrich, O., Kiermaier, A., Dohmann, K., Menkel, A., Eilers, M., and Luscher, B. (2001) Regulation of cyclin D2 gene expression by the Myc/Max/Mad network: Myc-dependent TRRAP recruitment and histone acetylation at the cyclin D2 promoter. Genes Dev. 15, 2042-2047.
7. Lin, C. J., Cencic, R., Mills, J. R., Robert, F., and Pelletier, J. (2008) cMyc and eIF4F are components of a feedforward loop that links transcription and translation. Cancer Res. 68, 5326-5334.
8. Eilers, M., and Eisenman, R. N. (2008) Myc's broad reach. Genes Dev. 22, 2755-2766.
9. Okubo, T., Knoepfler, P. S., Eisenman, R. N., and Hogan, B. L. (2005) N-myc plays an essential role during lung development as a dosage-sensitive regulator of progenitor cell proliferation and differentiation. Development 132, 1363-1374.
10. Hopewell, R., Li, L., MacGregor, D., Nerlov, C., and Ziff, E. B. (1995) Regulation of cell proliferation and differentiation by Myc. J. Cell Sci., Suppl. 19, 85-89.
11. Eberhardy, S. R., and Farnham, P. J. (2001) c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism. J. Biol. Chem. 276, 48562-48571.
12. Gomez-Roman, N., Grandori, C., Eisenman, R. N., and White, R. J. (2003) Direct activation of RNA polymerase III transcription by cMyc. Nature 421, 290-294.
13. Lee, T. C., Li, L., Philipson, L., and Ziff, E. B. (1997) Myc represses transcription of the growth arrest gene gas1. Proc. Natl. Acad. Sci. U. S.A. 94, 12886-12891.
14. Amati, B., Littlewood, T. D., Evan, G. I., and Land, H. (1993) The c-Myc protein induces cell cycle progression and apoptosis through dimerization with Max. EMBO J. 12, 5083-5087.
15. Grandori, C., Cowley, S. M., James, L. P., and Eisenman, R. N. (2000) The Myc/Max/Mad network and the transcriptional control of cell behavior. Annu. Rev. Cell Dev. Biol. 16, 653-699.
16. Ayer, D. E., Kretzner, L., and Eisenman, R. N. (1993) Mad: A heterodimeric partner for Max that antagonizes Myc transcriptional activity. Cell 72, 211-222.
17. Hurlin, P. J., Queva, C., Koskinen, P. J., Steingrimsson, E., Ayer, D. E., Copeland, N. G., Jenkins, N. A., and Eisenman, R. N. (1995) Mad3 and Mad4: Novel Max-interacting transcriptional repressors that suppress c-myc dependent transformation and are expressed during neural and epidermal differentiation. EMBO J. 14, 5646-5659.
18. Zervos, A. S., Gyuris, J., and Brent, R. (1993) Mxil, a protein that specifically interacts with Max to bind Myc-Max recognition sites. Cell 72, 223-232.
19. Nair, S. K., and Burley, S. K. (2003) X-raystructures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by protooncogenic transcription factors. Cell 112, 193-205.
20. Choy, B., and Green, M. R. (1993) Eukaryotic activators function during multiple steps of preinitiation complex assembly. Nature 366, 531-536.
21. Li, X. Y., Virbasius, A., Zhu, X., and Green, M. R. (1999) Enhancement of TBP binding by activators and general transcription factors. Nature 399, 605-609.
22. Holmbeck, S. M., Dyson, H. J., and Wright, P. E. (1998) DNA induced conformational changes are the basis for cooperative dimerization by the DNA binding domain of the retinoid X receptor. J. Mol. Biol. 284, 533-539.
23. Shuai, K., Horvath, C. M., Huang, L. H., Qureshi, S. A., Cowburn, D., and Darnell, J. E., Jr. (1994) Interferon activation of the transcription factor Stat91 involves dimerization through SH2-phosphotyrosyl peptide interactions. Cell 76, 821-828.
24. Nair, S. K., and Burley, S. K. (2006) Structural aspects of interactions within the Myc/Max/Mad network. Curr. Top. Microbiol. Immunol. 302, 123-143.
25. Sauve, S., Naud, J. F., and Lavigne, P. (2007) The mechanism of discrimination between cognate and non-specific DNA by dimeric b/ HLH/LZ transcription factors. J. Mol. Biol. 365, 1163-1175.
26. Meier-Andrejszki, L., Bjelic, S., Naud, J. F., Lavigne, P., and Jelesarov, I. (2007) Thermodynamics of b-HLH-LZ protein binding to DNA: The energetic importance of protein-DNA contacts in sitespecific E-box recognition by the complete gene product of the Max p21 transcription factor. Biochemistry 46, 12427-12440.
27. Ferre-D'Amare, A. R., Prendergast, G. C., Ziff, E. B., and Burley, S. K. (1993) Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363, 38-45.
28. Cohen, S. L., Ferre-D'Amare, A. R., Burley, S. K., and Chait, B. T. (1995) Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci. 4, 1088-1099.
29. Hu, J., Banerjee, A., and Goss, D. J. (2005) Assembly of b/HLH/z proteins c-Myc, Max, and Mad1 with cognate DNA: Importance of protein-protein and protein-DNA interactions. Biochemistry 44, 11855-11863.
30. Sha, M., Wang, Y., Xiang, T., van Heerden, A., Browning, K. S., and Goss, D. J. (1995) Interaction of wheat germ protein synthesis initiation factor eIF-(iso)4F and its subunits p28 and p86 with m7GTP and mRNA analogues. J. Biol. Chem. 270, 29904-29909.
31. Kohler, J. J., Metallo, S. J., Schneider, T. L., and Schepartz, A. (1999) DNA specificity enhanced by sequential binding of protein monomers. Proc. Natl. Acad. Sci. U.S.A. 96, 11735-11739.
32. Prendergast, G. C., Lawe, D., and Ziff, E. B. (1991) Association of Myn, the murine homolog of max, with c-Myc stimulates methylation-sensitive DNA binding and ras cotransformation. Cell 65, 395-407.
33. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254.
34. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685.
35. Khan, M. A., Miyoshi, H., Ray, S., Natsuaki, T., Suehiro, N., and Goss, D. J. (2006) Interaction of genome-linked protein (VPg) of turnip mosaic virus with wheat germ translation initiation factors eIFiso4E and eIFiso4F. J. Biol. Chem. 281, 28002-28010.
36. Khan, M. A., and Goss, D. J. (2005) Translation initiation factor (eIF) 4B affects the rates of binding of the mRNA m7G cap analogue to wheat germ eIFiso4F and eIFiso4F.PABP. Biochemistry 44, 4510-4516.
37. Garland, D. L. (1978) Kinetics and mechanism of colchicine binding to tubulin: Evidence for ligand-induced conformational change. Biochemistry 17, 4266-4272.
38. Olsen, K., Christensen, U., Sierks, M. R., and Svensson, B. (1993) Reaction mechanisms of Trp 120 -Phe and wild-type glucoamylases from Aspergillus niger. Interactions with maltooligodextrins and acarbose. Biochemistry 32, 9686-9693.
39. Kohler, J. J., and Schepartz, A. (2001) Kinetic studies of Fos.Jun. DNA complex formation: DNA binding prior to dimerization. Biochemistry 40, 130-142.
40. Metallo, S. J., and Schepartz, A. (1997) Certain bZIP peptides bind DNA sequentially as monomers and dimerize on the DNA. Nat. Struct. Biol. 4, 115-117.
41. Wendt, H., Thomas, R. M., and Ellenberger, T. (1998) DNAmediated folding and assembly of MyoD-E47 heterodimers. J. Biol. Chem. 273, 5735-5743.
42. Rentzeperis, D., Jonsson, T., and Sauer, R. T. (1999) Acceleration of the refolding of Arc repressor by nucleic acids and other polyanions. Nat. Struct. Biol. 6, 569-573.
43. Kim, B., and Little, J. W. (1992) Dimerization of a specific DNAbinding protein on the DNA. Science 255, 203-206.
44. Kohler, J. J., and Schepartz, A. (2001) Effects of nucleic acids and polyanions on dimer formation and DNA binding by bZIP and bHLHZip transcription factors. Bioorg. Med. Chem. 9, 2435-2443.
45. Park, S., Chung, S., Kim, K. M., Jung, K. C., Park, C., Hahm, E. R., and Yang, C. H. (2004) Determination of binding constant of transcription factor myc-max/max-max and E-box DNA: The effect of inhibitors on the binding. Biochim. Biophys. Acta 1670, 217-228.
46. Banerjee, A., Hu, J., and Goss, D. J. (2006) Thermodynamics of protein-protein interactions of cMyc, Max, and Mad: Effect of polyions on protein dimerization. Biochemistry 45, 2333-2338.
47. Halford, S. E., and Marko, J. F. (2004) How do site-specific DNAbinding proteins find their targets? Nucleic Acids Res. 32, 3040-3052.