The importance of being flexible: The case of basic region leucine zipper transcriptional regulators

Current Protein and Peptide Science

Volumn 10, Issue 3, 2009, Pages 244-269

  Miller, Maria ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

bZIP proteins; Induced protein folding; Intrinsic disorder; Molecular recognition motifs; Transcription control

Indexed keywords

ACTIVATING TRANSCRIPTION FACTOR 1; ACTIVATING TRANSCRIPTION FACTOR 2; ACTIVATING TRANSCRIPTION FACTOR 3; ACTIVATING TRANSCRIPTION FACTOR 4; ACTIVATING TRANSCRIPTION FACTOR 6; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; CCAAT ENHANCER BINDING PROTEIN ALPHA; CCAAT ENHANCER BINDING PROTEIN BETA; CCAAT ENHANCER BINDING PROTEIN DELTA; CCAAT ENHANCER BINDING PROTEIN EPSILON; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; CYCLIC AMP RESPONSIVE ELEMENT MODULATOR; DNA BINDING PROTEIN; PROTEIN C FOS; PROTEIN C JUN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 1; TRANSCRIPTION FACTOR FOSB; TRANSCRIPTION FACTOR FRA 1; TRANSCRIPTION FACTOR FRA 2; TRANSCRIPTION FACTOR JUNB; TRANSCRIPTION FACTOR JUND; TRANSCRIPTION FACTOR MAFB; TRANSCRIPTION FACTOR MAFF; TRANSCRIPTION FACTOR MAFG; TRANSCRIPTION FACTOR MAFK; TRANSCRIPTION FACTOR NF E2; TRANSCRIPTION FACTOR NRF2; X BOX BINDING PROTEIN 1; DNA;

AMINO ACID SEQUENCE; ARTIFICIAL NEURAL NETWORK; BIOINFORMATICS; CALORIMETRY; CIRCULAR DICHROISM; COMPUTER PROGRAM; DIMERIZATION; DROSOPHILA; EUKARYOTIC CELL; FLUORESCENCE SPECTROSCOPY; GENE EXPRESSION REGULATION; GENETIC ANALYSIS; HUMAN; HYDRODYNAMICS; MACHINE LEARNING; MAMMAL CELL; MOLECULAR RECOGNITION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; RAMAN SPECTROMETRY; REVIEW; STRUCTURE ACTIVITY RELATION; TRANSACTIVATION; TRANSCRIPTION REGULATION; X RAY CRYSTALLOGRAPHY; ANIMAL; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; TRANSCRIPTION INITIATION;

EUKARYOTA; MAMMALIA;

AMINO ACID SEQUENCE; ANIMALS; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; DNA; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTIONAL ACTIVATION;

EID: 69449092251     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920309788452164     Document Type: Review

References (217)

1. Dunker, A.K.; Obradovic, Z. The protein trinity - linking function and disorder. Nat. Biotechnol., 2001, 19, 805-806.
2. Uversky, V.N. Natively unfolded proteins: a point where biology waits for physics. Protein Sci., 2002, 11, 739-756.
3. Fukuchi, S.; Homma, K.; Minezaki, Y.; Nishikawa, K. Intrinsically disordered loops inserted into the structural domains of human proteins. J. Mol. Biol., 2006, 355, 845-857.
4. Dyson, H.J.; Wright, P.E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol., 2005, 6, 197-208.
5. Dunker, A.K.; Brown, C.J.; Lawson, J.D.; Iakoucheva, L.M.; Obradovic, Z. Intrinsic disorder and protein function. Biochemistry, 2002, 41, 6573-6582.
6. Wright, P.E.; Dyson, H.J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol,, 1999, 293, 321-331.
7. Radivojac, P.; Iakoucheva, L.M.; Oldfield, C.J.; Obradovic, Z.; Uversky, V.N.; Dunker, A.K. Intrinsic disorder and functional proteomics. Biophys. J., 2007, 92, 1439-1456.
8. Dyson, H.J.; Wright, P.E. Unfolded proteins and protein folding studied by NMR. Chem. Rev., 2004, 104, 3607-3622.
9. Receveur-Brechot, V.; Bourhis, J.M.; Uversky, V.N.; Canard, B.; Longhi, S. Assessing protein disorder and induced folding. Proteins, 2006, 62, 24-45.
10. Tompa, P. Intrinsically unstructured proteins. Trends Biochem. Sci., 2002, 27, 527-533.
11. Uversky, V.N.; Oldfield, C.J.; Dunker, A.K. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J. Mol. Recognit., 2005, 18, 343-384.
12. Dyson, H.J.; Wright, P.E. Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol., 2002, 12, 54-60.
13. Fink, A.L. Natively unfolded proteins. Curr. Opin. Struct. Biol., 2005, 15, 35-41.
14. Tompa, P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett., 2005, 579, 3346-3354.
15. Dunker, A.K.; Cortese, M.S.; Romero, P.; Iakoucheva, L.M.; Uversky, V.N. Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J., 2005, 272, 5129-5148.
16. Vucetic, S.; Brown, C.J.; Dunker, A.K.; Obradovic, Z. Flavors of protein disorder. Proteins, 2003, 92, 573-584.
17. Lobley, A.; Swindells, M.B.; Orengo, C.A.; Jones, D.T. Inferring function using patterns of native disorder in proteins. PLoS. Comput. Biol., 2007, 3, e162
18. Uversky, V.N.; Gillespie, J.R.; Fink, A.L. Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins, 2000, 41, 415-427.
19. Prilusky, J.; Felder, C.E.; Zeev-Bon-Mordehai, T.; Rydberg, E.H.; Man, O.; Beckmann, J.S.; Silman, I.; Sussman, J.L. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformaties., 2005, 21, 3435-3438.
20. Coeytaux, K.; Poupon, A. Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics., 2005, 21, 1891-1900.
21. Liu, J.; Rost, B. NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res., 2003, 31, 3833-3835.
22. Linding, R.; Russell, R.B.; Neduva, V.; Gibson, T.J. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res., 2003, 31, 3701-3708.
23. Ferron, F.; Longhi, S.; Canard, B.; Karlin, D. A practical overview of protein disorder prediction methods. Proteins, 2006, 65, 1-14.
24. Bourhis, J.M.; Canard, B.; Longhi, S. Predicting protein disorder and induced folding: from theoretical principles to practical applications. Curr. Protein Pept. Sci., 2007, 8, 135-149.
25. Oldfield, C.J.; Cheng, Y.; Cortese, M.S.; Brown, C.J.; Uversky, V.N.; Dunker, A.K. Comparing and combining predictors of mostly disordered proteins. Biochemistry, 2005, 44, 1989-2000.
26. Liu, J.; Rost, B. Comparing function and structure between entire proteomes. Protein Sci., 2001, 10, 1970-1979.
27. Ward, J.J.; Sodhi, J.S.; McGuffin, L.J.; Buxton, B.F.; Jones, D.T. Prediction and functional analysis of native disorder in proteins from the three kingdoms offife. J. Mol. Biol., 2004, 337, 635-645.
28. Chen, J.W.; Romero, P.; Uversky, V.N.; Dunker, A.K. Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorder. J. Proteome. Res., 2006, 5, 888-898.
29. Minezaki, Y.; Homma, K.; Kinjo, A.R.; Nishikawa, K. Human Transcription Factors Contain a High Fraction of Intrinsically Disordered Regions Essential for Transcriptional Regulation. J. Mol. Biol., 2006, 359, 1137-1149.
30. Romero, P.R.; Zaidi, S.; Fang, Y.Y.; Uversky, V.N.; Radivojac, P.; Oldfield, C.J.; Cortese, M.S.; Sickmeier, M.; LeGall, T.; Obradovic, Z.; Dunker, A.K. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc. Natl. Acad. Sci.USA, 2006, 103, 8390-8395.
31. Gunasekaran, K.; Tsai, C.J.; Kumar, S.; Zanuy, D.; Nussinov, R. Extended disordered proteins: targeting function with less scaffold. Trends Biochem. Sci., 2003, 28, 81-85.
32. Oldfield, C.J.; Cheng, Y.; Cortese, M.S.; Romero, P.; Uversky, V.N.; Dunker, A.K. Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry, 2005, 44, 12454-12470.
33. Sugase, K.; Dyson, H.J.; Wright, P.E. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature, 2007, 447, 1021-1025.
34. Verkhivker, G.M.; Bouzida, D.; Gehlhaar, D.K.; Rejto, P.A.; Freer, S.T.; Rose, P.W. Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding. Proc. Natl. Acad. Sci. USA, 2003, 100, 5148-5153.
35. Wang, J.; Verkhivker, G.M. Energy landscape theory, funnels, specificity, and optimal criterinh of biomolecular binding. Phys. Res. Lett., 2003, 90, 188101
36. Levy, Y.; Cho, S.S.; Onuchic, J.N.; Wolynes, P.G. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J. Mol. Biol., 2005, 346, 1121-1145.
37. Wang, J.; Lu, Q.; Lu, H.P. Single-molecule dynamics reveals cooperative binding-folding in protein recognition. PLoS. Comput. Biol., 2006, 2, e78
38. Wang, J.; Xu, L.; Wang, E. Optimal specificity and function for flexible biomolecular recognition. Biophys. J., 2007, 92, L109-L111
39. Lu, Q.; Lu, H.P.; Wang, J. Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics. Phys. Rev. Lett., 2007, 98, 128105
40. Demchenko, A.P. Recognition between flexible protein molecules: induced and assisted folding. J. Mol. Recognit., 2001, 14, 42-61.
41. Shoemaker, B.A.; Portman, J.J.; Wolynes, P.G. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc. Natl. Acad. Sci. USA, 2000, 97, 8868-8873.
42. Sturtevant, J.M. Heat capacity and entropy changes in processes involving proteins. Proc. Natl. Acad. Sci. USA, 1977, 74, 2236-2240.
43. Duan, Y.; Wilkosz, P.; Rosenberg, J.M. Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases. J. Mol. Biol., 1996, 264, 546-555.
44. Spolar, R.S.; Record, M.T., Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science, 1994, 263, 777-784.
45. Dunitz, J.D. Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions. Chem. Biol., 1995, 2, 709-712.
46. Hilser, V.J.; Thompson, E.B. Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc. Natl. Acad. Sci. USA, 2007, 104, 8311-8315.
47. Mohan, A.; Oldfield, C.J.; Radivojac, P.; Vacic, V.; Cortese, M.S.; Dunker, A.K.; Uversky, V.N. Analysis of molecular recognition features (MoRFs). J. Mol. Biol., 2006, 362, 1043-1059.
48. Puntervoll, P.; Linding, R.; Gemünd, C.; Chabanis-Davidson, S.; Mattingsdal, M.; Cameron, S.; Martin, D.M.A.; Ausiello, G.; Brannetti, B.; Costantini, A.; Ferre, F.; Maselli, V.; Via, A.; Cesareni, G.; Diella, F.; Superti-Furga, G.; Wyrwicz, L.; Ramu, C.; McGuigan, C.; Gudavalli, R.; Letunic, I.; Bork, P.; Rychlewski, L.; Küster, B.; Helmer-Citterich, M.; Hunter, W.N.; Aasland, R.; Gibson, T.J. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res., 2003, 31, 3625-3630.
49. Neduva, V.; Linding, R.; Su-Angrand, I.; Stark, A.; de Masi, F.; Gibson, T.J.; Lewis, J.; Serrano, L.; Russell, R.B. Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS. Biol., 2005, 3, e405
50. Apic, G.; Russell, R.B. A shortcut to peptides to modulate platelets. Nat. Chem. Biol., 2007, 3, 83-84.
51. Csizmok, V.; Bokor, M.; Banki, P.; Klement, E.; Medzihradszky, K.F.; Friedrich, P.; Tompa, K.; Tompa, P. Primary contact sites in intrinsically unstructured proteins: the case of calpastatin and microtubule-associated protein 2. Biochemistry, 2005, 44, 3955-3964.
52. Namba, K. Roles of partly unfolded conformations in macromolecular self-assembly. Genes Cells, 2001, 6, 1-12.
53. Blundell, T.L.; Fernandez-Recio, J. Cell biology: brief encounters bolster contacts. Nature, 2006, 444, 279-280.
54. Han, J.D.; Bertin, N.; Han, T.; Goldberg, D.S.; Berriz, G.F.; Zhang, L.V.; Dupuy, D.; Walhour, A.J.; Cusick, M.E.; Roth, F.P.; Vidal, M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 2004, 430, 88-93.
55. Singh, G.P.; Ganapathi, M.; Dash, D. Role of intrinsic disorder in transient interactions of hub proteins. Proteins: Struct.Funct. Bioinformatics, 2007, 66, 761-765.
56. Iakoucheva, L.M.; Radivojac, P.; Brown, C.J.; O'Connor, T.R.; Sikes, J.G.; Obradovic, Z.; Dunker, A.K. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res., 2004, 32, 1037-1049.
57. Eisenhaber, B.; Eisenhaber, F. Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure? Curr. Protein Pept. Sci., 2007, 8, 197-203.
58. Ptashne, M.; Gann, A. Transcriptional activation by recruitment. Nature, 1997, 386, 569-577.
59. Sigler, P.B. Transcriptional activation. Acid blobs and negative noodles. Nature, 1988, 333, 210-212.
60. Frankel, A.D.; Kim, P.S. Modular structure of transcription factors: implications for gene regulation. Cell, 1991, 65, 717-719.
61. Uesugi, M.; Nyanguile, O.; Lu, H.; Levine, A.J.; Verdine, G.L. Induced alpha helix in the VP16 activation domain upon binding to a human TAF. Science, 1997, 277, 1310-1313.
62. Ayed, A.; Mulder, F.A.; Yi, G.S.; Lu, Y.; Kay, L.E.; Arrowsmith, C.H. Latent and active p53 are identical in conformation. Nat. Struct. Biol., 2001, 8, 756-760.
63. Grossmann, J.G.; Sharff, A.J.; O'Hare, P.; Luisi, B. Molecular shapes of transcription factors TFIIB and VP16 in solution: implications for recognition. Biochemistry, 2001, 40, 6267-6274.
64. Liu, J.; Perumal, N.B.; Oldfield, C.J.; Su, E.W.; Uversky, V.N.; Dunker, A.K. Intrinsic disorder in transcription factors. Biochemistry, 2006, 45, 6873-6888.
65. Struhl, K. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell, 1999, 98, 1-4.
66. Levine, M.; Tjian, R. Transcription regulation and animal diversity. Nature, 2003, 424, 147-151.
67. Michelson, A.M. Deciphering genetic regulatory codes: a challenge for functional genomics. Proc. Natl. Acad. Sci. USA, 2002, 99, 546-548.
68. Amoutzias, G.; Veron, A.; Weiner, J.; III, Robinson-Rechavi, M.; Bornberg-Bauer, E.; Oliver, S.; Robertson, D. One Billion Years of bZIP Transcription Factor Evolution: Conservation and Change in Dimerization and DNA-Binding Site Specificity. Mol. Biol. Evol., 2007, 24, 827-835.
69. Hurst, H.C. Transcription factors 1: bZIP proteins. Protein Profile., 1995, 2, 101-168.
70. Chinenov, Y.; Kerppola, T.K. Close encounters of many kinds: Fos-Jun interactions that mediate transcription regulatory specificity. Oncogene, 2001, 20, 2438-2452.
71. Landschulz, W.H.; Johnson, P.F.; Mcknight, S.L. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science, 1988, 240, 1759-1764.
72. Landschulz, W.H.; Johnson, P.F.; Mcknight, S.L. The DNA binding domain of the rat liver nuclear protein C/EBP is bipartite. Science, 1989, 243, 1681-1688.
73. Ellenberger, T.E.; Brandl, C.J.; Struhl, K.; Harrison, S.C. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell, 1992, 71, 1223-1237.
74. Glover, J.N., Harrison, S.C. Crystal structure of the heterodimeric bZIP transcription factor c-Fos- c-Jun bound to DNA. Nature, 1995, 373, 257-261.
75. Fujii, Y.; Shimizu, T.; Toda, T.; Yanagida, M.; Hakoshima, T. Structural basis for the diversity of DNA recognition by bZIP transcription factors. Nat. Struct. Biol., 2000, 7, 889-893.
76. Schumacher, M.A.; Goodman, R.H.; Brennan, R.G. The structure of a CREB bZIP somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding. J. Biol. Chem., 2000, 275, 35242-35247.
77. Miller, M.; Shuman, J.D.; Sebastian, T.; Dauter, Z.; Johnson, P.F. Structural basis for DNA recognition by the basic region leucine zipper transcription factor CCAAT/enhancer-binding protein alpha. J. Biol. Chem., 2003, 278, 15178-15184.
78. Wolberger, C. Transcription factor structure and DNA binding. Curr. Opin. Struct. Biol., 1993, 3, 3-10.
79. Cho, Y.; Gorina, S.; Jeffrey, P.D.; Pavletich, N.P. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science, 1994, 265, 346-355.
80. 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, 1990, 347, 575-578.
81. Krylov, D.; Olive, M.; Vinson, C. Extending dimerization interfaces: the bZIP basic region can form a coiled coil. EMBO J., 1995, 14, 5329-5337.
82. Patel, L.R.; Curran, T.; Kerppola, T.K. Energy transfer analysis of Fos-Jun dimerization and DNA binding. Proc. Natl. Acad. Sci. USA, 1994, 91, 7360-7364.
83. Garvie, C.W.; Wolberger, C. Recognition of specific DNA sequences. Mol. Cell, 2001, 8, 937-946.
84. Vinson, C.R.; Hai, T.; Boyd, S.M. Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: prediction and rational design. Genes Dev., 1993, 7, 1047-1058.
85. Vinson, C.; Myakishev, M.; Acharya, A.; Mir, A.A.; Moll, J.R.; Bonovich, M. Classification of human B-ZIP proteins based on dimerization properties. Mol. Cell Biol., 2002, 22, 6321-6335.
86. Fassler, J.; Landsman, D.; Acharya, A.; Moll, J.R.; Bonovich, M.; Vinson, C. B-ZIP proteins encoded by the Drosophila genome: evaluation of potential dimerization partners. Genome Res., 2002, 12, 1190-1200.
87. Ryu, T.; Jung, J.; Lee, S.; Nam, H.J.; Hong, S.W.; Yoo, J.W.; Lee, D.K.; Lee, D. bZIPDB: a database of regulatory information for human bZIP transcription factors. BMC. Genomics, 2007, 8, 136
88. Blank, V.; Andrews, N.C. The Maf transcription factors: regulators of differentiation. Trends Biochem. Sci., 1997, 22, 437-441.
89. Motohashi, H.; O'Connor, T.; Katsuoka, F.; Engel, J.D.; Yamamoto, M. Integration and diversity of the regulatory network composed of Maf and CNC families of transcription factors. Gene, 2002, 294, 1-12.
90. Richards, J.P.; Bachinger, H.P.; Goodman, R.H.; Brennan, R.G. Analysis of the structural properties of cAMP-responsive element-binding protein (CREB) and phosphorylated CREB. J. Biol. Chem., 1996, 271, 13716-13723.
91. Nagadoi, A.; Nakazawa, K.; Uda, H.; Okuno, K.; Maekawa, T.; Ishii, S.; Nishimura, Y. Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain. J. Mol. Biol., 1999, 287, 593-607.
92. Kusunoki, H.; Motohashi, H.; Katsuoka, F.; Morohashi, A.; Yamamoto, M.; Tanaka, T. Solution structure of the DNA-binding domain of MafG. Nat. Struct. Biol., 2002, 9, 252-256.
93. Yoshida, C.; Tokumasu, F.; Hohmura, K.I.; Bungert, J.; Hayashi, N.; Nagasawa, T.; Engel, J.D.; Yamamoto, M.; Takeyasu, K.; Igarashi, K. Long range interaction of cis-DNA elements mediated by architectural transcription factor Bach1. Genes Cells, 1999, 4, 643-655.
94. Williamson, E.A.; Xu, H.N.; Gombart, A.F.; Verbeek, W.; Chumakov, A.M.; Friedman, A.D.; Koeffler, H.P. Identification of transcriptional activation and repression domains in human CCAAT/enhancer-binding protein epsilon. J. Biol. Chem., 1998, 273, 14796-14804.
95. Smith, J.L.; Freebern, W.J.; Collins, I.; De Siervi, A.; Montano, I.; Haggerty, C.M.; McNutt, M.C.; Butscher, W.G.; Dzekunova, I.; Petersen, D.W.; Kawasaki, E.; Merchant, J.L.; Gardner, K. Kinetic profiles of p300 occupancy in vivo predict common features of promoter structure and coactivator recruitment. Proc. Natl. Acad. Sci. USA, 2004, 101, 11554-11559.
96. Wagner, E.F. AP-1 - Introductory remarks. Oncogene, 2001, 20, 2334-2335.
97. Yoon, M.K.; Shin, J.; Choi, G.; Choi, B.S. Intrinsically unstructured N-terminal domain of bZIP transcription factor HY5. Proteins, 2006, 65, 856-866.
98. Sharma, N.; Lopez, D.I.; Nyborg, J.K. DNA binding and phosphorylation induce conformational alterations in the kinase-inducible domain of CREB. Implications for the mechanism of transcription function. J. Biol. Chem., 2007, 282, 19872-19883.
99. Romero, P.; Obradovic, Z.; Li, X.; Garner, E.C.; Brown, C.J.; Dunker, A.K. Sequence complexity of disordered protein. Proteins, 2001, 42, 38-48.
100. Miller, M. Phospho-Dependent Protein Recognition Motifs Contained in C/ EBP Family of Transcription Factors: in Silico, Studies. Cell Cycle, 2006, 5, 2501-2508.
101. Vucetic, S.; Obradovic, Z.; Vacic, V.; Radivojac, P.; Peng, K.; Iakoucheva, L.M.; Cortese, M.S.; Lawson, J.D.; Brown, CJ.; Sikes, J.G.; Newton, C.D.; Dunker, A.K. DisProt: a database of protein disorder. Bioinformatics., 2005, 21, 137-140.
102. Leturric, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P.; Bork, P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res., 2002, 30, 242-244.
103. Podust, L.M.; Krezel, A.M.; Kim, Y. Crystal structure of the CCAAT box/ enhancer-binding protein beta activating transcription factor-4 basic leucine zipper heterodimer in the absence of DNA. J. Biol. Chem., 2001, 276, 505-513.
104. Thompson, K.S.; Vinson, C.R.; Freire, E. Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4. Biochemistry, 1993, 32, 5491-5496.
105. Krylov, D.; Mikhailenko, I.; Vinson, C. A thermodynamic scale for leucine zipper stability and dimerization specificity: e and g interhelical interactions. EMBO J., 1994, 13, 2849-2861.
106. Sosnick, T.R.; Jackson, S.; Wilk, R.R.; Englander, S.W.; DeGrado, W.F. The role of helix formation in the folding of a fully alpha-helical coiled coil. Proteins, 1996, 24, 427-432.
107. d'Avignon, D.A.; Bretthorst, G.L.; Holtzer, M.E.; Holtzer, A. Site-specific thermodynamics and kinetics of a coiled-coil transition by spin inversion transfer NMR. Biophys. J., 1998, 74, 3190-3197.
108. Dragan, A.I.; Privalov, P.L. Unfolding of a leucine zipper is not a simple two-state transition. J. Mol. Biol., 2002, 321, 891-908.
109. Zitzewitz, J.A.; Ibarra-Molero, B.; Fishel, D.R.; Terry, K.L.; Matthews, C.R. Preformed secondary structure drives the association reaction of GCN4-p1, a model coiled-coil system. J. Mol. Biol., 2000, 296, 1105-1116.
110. Fuxreiter, M.; Simon, I.; Friedrich, P.; Tompa, P. Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J. Mol. Biol., 2004, 338, 1015-1026.
111. Lamb, P.; Mcknight, S.L. Diversity and specificity in transcriptional regulation: the benefits of heterotypic dimerization. Trends Biochem. Sci., 1991, 16, 417-422.
112. Vinson, C.; Acharya, A.; Taparowsky, E.J. Deciphering B-ZIP transcription factor interactions in vitro and in vivo. Biochim. Biophys. Acta., 2006, 1759, 4-12.
113. Alber, T. Structure of the leucine zipper. Curr. Opin. Genet. Dev., 1992, 2, 205-210.
114. Grigoryan, G.; Keating, A.E. Structure-based prediction of bZIP partnering specificity. J. Mol. Biol., 2006, 355, 1125-1142.
115. Fong, J.H.; Keating, A.E.; Singh, M. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biol., 2004, 5, R11
116. Harbury, P.B.; Zhang, T.; Kim, P.S.; Alber, T. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science, 1993, 262, 1401-1407.
117. Newman, J.R.; Keating, A.E. Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science, 2003, 300, 2097-2101.
118. Deppmann, C.D.; Acharya, A.; Rishi, V.; Wobbes, B.; Smeekens, S.; Taparowsky, E.J.; Vinson, C. Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs. Nucleic Acids Res., 2004, 32, 3435-3445.
119. Parkin, S.E.; Baer, M.; Copeland, T.D.; Schwartz, R.C.; Johnson, P.F. Regulation of CCAAT/enhancer-binding protein (C/EBP) activator proteins by heterodimerization with C/EBPgamma (Ig/EBP). J. Biol. Chem., 2002, 277, 23563-23572.
120. O'Neil, K.T.; Shuman, J.D.; Ampe, C.; DeGrado, W.F. DNA-induced increase in the alpha-helical content of C/EBP and GCN4. Biochemistry, 1991, 30, 9030-9034.
121. Bracken, C.; Carr, P.A.; Cavanagh, J.; Palmer, A.G., III Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA. J. Mol. Biol., 1999, 285, 2133-2146.
122. Hollenbeck, J.J.; McClain, D.L.; Oakley, M.G. The role of helix stabilizing residues in GCN4 basic region folding and DNA binding. Protein Sci., 2002, 11, 2740-2747.
123. Kabe, Y.; Goto, M.; Shima, D.; Imai, T.; Wada, T.; Morohashi, K.; Shirakawa, M.; Hirose, S.; Handa, H. The role of human MBF1 as a transcriptional coactivator. J. Biol. Chem., 1999, 274, 34196-34202.
124. Lively, T.N.; Nguyen, T.N.; Galasinski, S.K.; Goodrich, J.A. The basic leucine zipper domain of c-Jun functions in transcriptional activation through interaction with the N terminus of human TATA-binding protein-associated factor-1 (human TAF(II)250). J. Biol. Chem., 2004, 279, 26257-26265.
125. Conkright, M.D.; Canettieri, G.; Screaton, R.; Guzman, E.; Miraglia, L.; Hogenesch, J.B.; Montminy, M. TORCs: transducers of regulated CREB activity. Mol. Cell, 2003, 12, 413-423.
126. Baranger, A.M. Accessory factor-bZIP-DNA interactions. Curr. Opin. Chem. Biol., 1998, 2, 18-23.
127. Miotto, B.; Struhl, K. Differential gene regulation by selective association of transcriptional coactivators and bZIP DNA-binding domains. Mol. Cell Biol., 2006, 26, 5969-5982.
128. Williams, S.C.; Angerer, N.D.; Johnson, P.F. C/EBP proteins contain nuclear localization signals imbedded in their basic regions. Gene Expr., 1997, 6, 371-385.
129. Weis, K. Importins and exportins: how to get in and out of the nucleus. Trends Biochem. Sci., 1998, 23, 185-189.
130. Conti, E.; Izaurralde, E. Nucleocytoplasmic transport enters the atomic age. Curr. Opin. Cell Biol., 2001, 13, 310-319.
131. Fontes, M.R.; Teh, T.; Kobe, B. Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha. J. Mol. Biol., 2000, 297, 1183-1194.
132. Harreman, M.T.; Kline, T.M.; Milford, H.G.; Harben, M.B.; Hodel, A.E.; Corbett, A.H. Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals. J. Biol. Chem., 2004, 279, 20613-20621.
133. Buck, M.; Zhang, L.; Halasz, N.A.; Hunter, T.; Chojkier, M. Nuclear export of phosphorylated C/EBPbeta mediates the inhibition of albumin expression by TNF-alpha. EMBO J., 2001, 20, 6712-6723.
134. Bannister, A.J.; Cook, A.; Kouzarides, T. In vitro DNA binding activity of Fos/Jun and BZLFI but not C/EBP is affected by redox changes. Oncogene, 1991, 6, 1243-1250.
135. Jindra, M.; Gaziova, I.; Uhlirova, M.; Okabe, M.; Hiromi, Y.; Hirose, S. Coactivator MBF1 preserves the redox-dependent AP-1 activity during oxidative stress in Drosophila. EMBO J, 2004, 23, 3538-3547.
136. Metallo, S.J.; Schepartz, A. Certain bZIP peptides bind DNA sequentially as monomers and dimerize on the DNA. Nat. Struct. Biol., 1997, 4, 115-117.
137. Wu, X.; Spiro, C.; Owen, W.G.; McMurray, C.T. cAMP response element-binding protein monomers cooperatively assemble to form dimers on DNA. J. Biol. Chem., 1998, 273, 20820-20827.
138. Pomerantz, J.L.; Wolfe, S.A.; Pabo, C.O. Structure-based design of a dimeric zinc finger protein. Biochemistry, 1998, 37, 965-970.
139. Kohler, J.J.; Schepartz, A. Kinetic studies of Fos.Jun.DNA complex formation: DNA binding prior to dimerization. Biochemistry, 2001, 40, 130-142.
140. Kohler, J.J.; Metallo, S.J.; Schneider, T.L.; Schepartz, A. DNA specificity enhanced by sequential binding of protein monomers. Proc. Natl. Acad. Sci. USA, 1999, 96, 11735-11739.
141. Berger, C.; Piubelli, L.; Haditsch, U.; Bosshard, H.R. Diffusion-controlled DNA recognition by an unfolded, monomeric bZIP transcription factor. FEBS Lett., 1998, 425, 14-18.
142. Kim, B.; Little, J.W. Dimerization of a specific DNA-binding protein on the DNA. Science, 1992, 255, 203-206.
143. Williams, S.C.; Baer, M.; Dillner, A.J.; Johnson, P.F. CRP2 (C/EBP beta) contains a bipartite regulatory domain that controls transcriptional activation, DNA binding and cell specificity. EMBO J., 1995, 14, 3170-3183.
144. Hattori, T.; Ohoka, N.; Inoue, Y.; Hayashi, H.; Onozaki, K. C/EBP family transcription factors are degraded by the proteasome but stabilized by forming dimer. Oncogene, 2003, 22, 1273-1280.
145. Lee, S.J.; Sekimoto, T.; Yamashita, E.; Nagoshi, E.; Nakagawa, A.; Imamoto, N.; Yoshimura, M.; Sakai, H.; Chong, K.T.; Tsukihara, T.; Yoneda, Y. The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor. Science, 2003, 302, 1571-1575.
146. Johnson, P.F.; Sterneck, E.; Williams, S.C. Activation domains of transcriptional regulatory proteins. J. Nutr. Biochem., 1993, 4, 386-398.
147. Triezenberg, S.J. Structure and function of transcriptional activation domains. Curr. Opin. Genet. Dev., 1995, 5, 190-196.
148. Gill, G.; Ptashne, M. Negative effect of the transcriptional activator GALA. Nature, 1988, 334, 721-724.
149. O'Hare, P.; Williams, G. Structural studies of the acidic transactivation domain of the Vmw65 protein of herpes simplex virus using 1H NMR. Biochemistry, 1992, 31, 4150-4156.
150. Campbell, K.M.; Terrell, A.R.; Laybourn, P.J.; Lumb, K.J. Intrinsic structural disorder of the C-terminal activation domain from the bZIP transcription factor Fos. Biochemistry, 2000, 39, 2708-2713.
151. Fladvad, M.; Zhou, K.; Moshref, A.; Pursglove, S.; Safsten, P.; Sunnerhagen, M. N and C-terminal sub-regions in the c-Myc trans-activation region and their joint role in creating versatility in folding and binding. J. Mol. Biol., 2005, 346, 175-189.
152. Metz, R.; Bannister, A.J.; Sutherland, J.A.; Hagemeier, C.; O'Rourke, E.C.; Cook, A.; Bravo, R.; Kouzarides, T. c-Fos-induced activation of a TATA-box-containing promoter involves direct contact with TATA-box-binding protein. Mol. Cell Biol., 1994, 14, 6021-6029.
153. Hermann, S.; Berndt, K.D.; Wright, A.P. How transcriptional activators bind target proteins. J. Biol. Chem., 2001, 276, 40127-40132.
154. Schmitz, M.L.; dos Santos Silva, M.A.; Altmann, H.; Czisch, M.; Holak, T.A.; Baeuerle, P.A. Structural and functional analysis of the NF-kappa B p65 C terminus. An acidic and modular transactivation domain with the potential to adopt an alpha-helical conformation. J. Biol. Chem., 1994, 269, 25613-25620.
155. Nerlov, C.; Ziff, E.B. CCAAT/enhancer binding protein-alpha amino acid motifs with dual TBP and TFIIB binding ability cooperate to activate transcription in both yeast and mammalian cells. EMBO J., 1995, 14, 4318-4328.
156. Kovacs, K.A.; Steinmann, M.; Magistretti, P.J.; Halfon, O.; Cardinaux, J.R. CCAAT/enhancer-binding protein family members recruit the coactivator CREB-binding protein and trigger its phosphorylation. J. Biol. Chem., 2003, 278, 36959-36965.
157. Kussie, P.H.; Gorina, S.; Marechal, V.; Elenbaas, B.; Moreau, J.; Levine, A.J.; Pavletich, N.P. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science, 1996, 274, 948-953.
158. Choi, Y.; Asada, S.; Uesugi, M. Divergent hTAFII31-binding motifs hidden in activation domains. J. Biol. Chem., 2000, 275, 15912-15916.
159. Anderson, C.W.; Appella, E. In The p53 Tumor Suppressor Pathway and Cancer, Zanbetti, G.P., Ed.; Posttranslational modificaitons of p53: Upstream signaling. Springer Science+Business Media, Inc., New York, 2005, 95-114.
160. Bannister, A.J.; Brown, H.J.; Sutherland, J.A.; Kouzarides, T. Phosphorylation of the c-Fos and c-Jun HOW motif stimulates its activation capacity. Nucleic Acids Res., 1994, 22, 5173-5176.
161. Du, K.; Montminy, M. CREB is a regulatory target for the protein kinase Akt/PKB. J. Biol. Chem., 1998, 273, 32377-32379.
162. Shanware, N.P.; Trinh, A.T.; Williams, L.M.; Tibbetts, R.S. Coregulated ataxia telangiectasia-mutated and casein kinase sites modulate cAMP-response element-binding protein-coactivator interactions in response to DNA damage. J. Biol. Chem., 2007, 282, 6283-6291.
163. Shuman, J.D.; Sebastian, T.; Kaldis, P.; Copeland, T.D.; Zhu, S.; Smart, R.C.; Johnson, P.F. Cell cycle-dependent phosphorylation of C/EBPβ mediates oncogenic cooperativity between C/EBPO and H-RasV12. Mol. Cell Biol., 2004, 24, 7380-7391.
164. Monje, P.; Hernandez-Losa, J.; Lyons, R.J.; Castellone, M.D.; Gutkind, J.S. Regulation of the transcriptional activity of c-Fos by ERK. A novel role for the prolyl isomerase PIN1. J. Biol. Chem., 2005, 280, 35081-35084.
165. Manke, I.A.; Lowery, D.M.; Nguyen, A.; Yaffe, M.B. BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science, 2003, 302, 636-639.
166. Gardner, K.H.; Montminy, M. Can you hear me now? Regulating transcriptional activators by phosphorylation. Sci. STKE., 2005, 2005, e44
167. Kwong, P.D.; Wyatt, R.; Majeed, S.; Robinson, J.; Sweet, R.W.; Sodroski, J.; Hendrickson, W.A. Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure Fold Des., 2000, 8, 1329-1339.
168. Freedman, S.J.; Sun, Z.Y.; Poy, F.; Kung, A.L.; Livingston, D.M.; Wagner, G.; Eck, M.J. Structural basis for recruitment of CBP/p300 by hypoxia-inducible factor-I alpha. Proc. Natl. Acad. Sci. USA, 2002, 99, 5367-5372.
169. Campbell, K.M.; Lumb, K.J. Structurally distinct modes of recognition of the KIX domain of CBP by Jun and CREB. Biochemistry, 2002, 41, 13956-13964.
170. De Guzman, R.N.; Goto, N.K.; Dyson, H.J.; Wright, P.E. Structural basis for cooperative transcription factor binding to the CBP coactivator. J. Mol. Biol., 2006, 355, 1005-1013.
171. Radhakrishnan, I.; Perez-Alvarado, G.C.; Parker, D.; Dyson, H.J.; Montminy, M.R.; Wright, P.E. Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: a model for activator:coactivator interactions. Cell, 1997, 91, 741-752.
172. Zor, T.; De Guzman, R.N.; Dyson, H.J.; Wright, P.E. Solution structure of the KIX domain of CBP bound to the transactivation domain of c-Myb. J. Mol. Biol., 2004, 337, 521-534.
173. Roach, P.J. Multisite and hierarchal protein phosphorylation. J. Biol. Chem., 1991, 266, 14139-14142.
174. Ilouz, R.; Kowalsman, N.; Eisenstein, M.; Eldar-Finkelman, H. Identification of novel glycogen synthase kinase-3beta substrate-interacting residues suggests a common mechanism for substrate recognition. J. Biol. Chem., 2006, 281, 30621-30630.
175. Kim, J.; Sharma, S.; Li, Y.; Cobos, E.; Palvimo, J.J.; Williams, S.C. Repression and coactivation of CCAAT/enhancer-binding protein epsilon by sumoylation and protein inhibitor of activated STATx proteins. J. Biol. Chem., 2005, 280, 12246-12254.
176. Lise, S.; Jones, D.T. Sequence patterns associated with disordered regions in proteins. Proteins, 2005, 58, 144-150.
177. Fontana, A.; Polverino, d.L.; De, F.; V, Scaramella, E.; Zambonin, M. Probing the partly folded states of proteins by limited proteolysis. Fold. Des., 1997, 2, R17-R26
178. Singh, G.P.; Ganapathi, M.; Sandhu, K.S.; Dash, D. Intrinsic unstructuredness and abundance of PEST motifs in eukaryotic proteomes. Proteins, 2006, 62, 309-315.
179. Hill, C.S.; Treisman, R. Transcriptional regulation by extracellular signals: mechanisms and specificity. Cell, 1995, 80, 199-211.
180. Ciechanover, A.; DiGiuseppe, J.A.; Bercovich, B.; Orian, A.; Richter, J.D.; Schwartz, A.L.; Brodeur, G.M. Degradation of nuclear oncoproteins by the ubiquitin system in vitro. Proc. Natl. Acad. Sci. USA, 1991, 88, 139-143.
181. Ramji, D.P.; Foka, P. CCAAT/enhancer-binding proteins: structure, function and regulation. Biochem. J., 2002, 365, 561-575.
182. Sharrocks, A.D.; Yang, S.H.; Galanis, A. Docking domains and substrate-specificity determination for MAP kinases. Trends Biochem. Sci., 2000, 25, 448-453.
183. Narlikar, G.J.; Fan, H.Y.; Kingston, R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell, 2002, 108, 475-487.
184. Orphanides, G.; Reinberg, D. A unified theory of gene expression. Cell, 2002, 108, 439-451.
185. Merika, M.; Thanos, D. Enhanceosomes. Curr. Opin. Genet. Dev., 2001, 11, 205-208.
186. Chen, L.; Glover, J.N.; Hogan, P.G.; Rao, A.; Harrison, S.C. Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA. Nature, 1998, 392, 42-48.
187. Panne, D.; Maniatis, T.; Harrison, S.C. Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer. EABO J., 2004, 23, 4384-4393.
188. Tahirov, T.H.; Sato, K.; Ichikawa-Iwata, E.; Sasaki, M.; Inoue-Bungo, T.; Shiina, M.; Kimura, K.; Takata, S.; Fujikawa, A.; Morii, H.; Kumasaka, T.; Yamamoto, M.; Ishii, S.; Ogata, K. Mechanism of c-Myb-C/ EBPJβ cooperation from separated sites on a promoter. Cell, 2002, 108, 57-70.
189. Cha-Molstad, H.; Young, D.P.; Kushner, L; Samols, D. The interaction of C-Rel with C/EBPbeta enhances C/EBPbeta binding to the C-reactive protein gene promoter. Mol. Immunol., 2007, 44, 2933-2942.
190. Wolberger, C. Multiprotein-DNA complexes in transcriptional regulation. Annu. Rev. Biophys. Biomol. Struct., 1999, 28, 29-56.
191. Ogata, K.; Sato, K.; Tahirov, T.H. Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar. Curr. Opin. Struct. Biol., 2003, 13, 40-48.
192. Reeves, R.; Beckerbauer, L. HMGI/Y proteins: flexible regulators of transcription and chromatin structure. Biochim. Biophys. Acta., 2001, 1519, 13-29.
193. Sgarra, R.,;Tessari, M.A.; Di Bernardo, J.; Rustighi, A.; Zago, P.; Liberatori, S.; Armini, A.; Bini, L.; Giancotti, V.; Manfioletti, G. Discovering high mobility group A molecular partners in tumour cells. Proteomics., 2005, 5, 1494-1506.
194. Naar, A.M.; Lemon, B.D.; Tjian, R. Transcriptional coactivator complexes. Annu. Rev. Biochem., 2001, 70, 475-501.
195. Di Poi, N.; Desvergne, B.; Michalik, L.; Wahli, W. Transcriptional repression of peroxisome proliferator-activated receptor beta/delta in murine keratinocytes by CCAAT/enhancer-binding proteins. J. Biol. Chem., 2005, 280, 38700-38710.
196. Conaway, R.C.; Sato, S.; Tomomori-Sato, C.; Yao, T.; Conaway, J.W. The mammalian Mediator complex and its role in transcriptional regulation. Trends Biochem. Sci., 2005, 30, 250-255.
197. Starita, L.M.; Parvin, J.D. The multiple nuclear flanctions of BRCAl: transcription, ubiquitination ana DNA repair. Curr. Opin. Cell Biol., 2003, 15, 345-350.
198. Edmunds, J.W.; Mahadevan, L.C. Cell signaling. Protein kinases seek close encounters with active genes. Science, 2006, 313, 449-451.
199. Pokholok, DK.; Zeitlinger, J.; Hannett, N.M.; Reynolds, D.B.; Young, R.A. Activated signal transduction kinases frequently occupy target genes. Science, 2006, 313, 533-536.
200. Zhang, X.; Odom, D.T.; Koo, S.H.; Conkright, M.D.; Canettieri, G.; Best, J.; Chen, H.; Jenner, R.; Herbolsheimer, E.; Jacobsen, E.; Kadam, S.; Ecker, J.R.; Emerson, B.; Hogenesch, J.B.; Unterman, T.; Young, R.A.; Montminy, M. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc. Natl. Acad. Sci. USA, 2005, 102, 4459-4464.
201. Vries, R.G.; Prudenziati, M.; Zwartjes, C.; Verlaan, M.; Kalkhoven, E.; Zantema, A. A specific lysine in c-Jun is required for transcriptional repression by E1A and is acetylated by p300. EMBO J., 2001, 20, 6095-6103.
202. Cesena, T.I.; Cardinaux, J.R.; Kwok, R.; Schwartz, J. CCAAT/ enhancer-binding protein (C/EBP) beta is acetylated at multiple lysines: acetylation of C/EBP beta at lysine 39 modulates its ability to activate transcription. J. Biol. Chem., 2007, 282, 956-967.
203. Schwartz, C.; Beck, K.; Mink, S.; Schmolke, M.; Budde, B.; Wenning, D.; Klempnauer, K.H. Recruitment of p300 by C/EBPbeta triggers phosphorylation of p300 and modulates coactivator activity. EMBO J., 2003, 22, 882-892.
204. Boulton, S.J. BRCAl-Mediated Ubiquitylation. Cell Cycle, 2006, 5, 1481-1486.
205. Xu, W.; Chen, H.; Du, K.; Asahara, H.; Tini, M.; Emerson, B.M.; Montminy, M.; Evans, R.M. A transcriptional switch mediated by cofactor methylation. Science, 2001, 294, 2507-2511.
206. Mark, W.Y.; Liao, J.C.; Lu, Y.; Ayed, A.; Laister, R.; Szymczyna, B.; Chakrabartty, A.; Arrowsmith, C.H. Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNA interactions? J. Mol. Biol., 2005, 345, 275-287.
207. Lo, C.L.; Chothia, C.; Janin, J. The atomic structure of protein-protein recognition sites. J. Mol. Biol., 1999, 285, 2177-2198.
208. Bateman, A.; Birney, E.; Cerruti, L.; Durbin, R.; Etwiller, L.; Eddy, S.R.; Griffiths-Jones, S.; Howe, K.L.; Marshall, M.; Sonnhammer, E.L. The Pfam protein families database. Nucleic Acids Res., 2002, 30, 276-280.
209. Hai, T.; Hartman, M.G. The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis. Gene, 2001, 273, 1-11.
210. Bailey, D.; O'Hare, P. Transmembrane bZIP Transcription Factors in ER Stress Signaling and the Unfolded Protein Response. Antioxid. Redox. Signal., 2007, 9.
211. Hunger, S.P.; Li, S.; Fall, M.Z.; Naumovski, L.; Cleary, M.L. The proto-oncogene HLF and the related basic leucine zipper protein TEF display highly similar DNA-binding and transcriptional regulatory properties. Blood, 1996, 87, 4607-4617
212. Goodman, R.H.; Smolik, S. CBP/p300 in cell growth, transformation, and development. Genes Dev., 2000, 14, 1553-1577.
213. McManus, K.J.; Hendzel, M.J. CBP, a transcriptional coactivator and acetyltransferase. Biochem. Cell Biol., 2001, 79, 253-266.
214. Lamprecht, C.; Mueller, C.R. D-site binding protein transactivation requires the proline- and acid-rich domain and involves the coactivator p300. J. Biol. Chem., 1999, 274, 17643-17648.
215. Nerlov, C. The C/EBP family of transcription factors: a paradigm for interaction between gene expression and proliferation control. Trends Cell Biol., 2007, 17, 318-324.
216. Yu, X.; Chini, C.C.; He, M.; Mer, G.; Chen, J. The BRCT domain is a phospho-protein binding domain. Science, 2003, 302, 639-642.
217. Hu, Y.F.; Li, R, JunB potentiates function of BRCA1 activation domain 1 (AD1) through a coiled-coil-mediated interaction. Genes Dev., 2002, 16, 1509-1517.