Role of intrinsically disordered protein regions/domains in transcriptional regulation

Life Sciences

Volumn 84, Issue 7-8, 2009, Pages 189-193

  Garza, Anna S ^a   Ahmad, Nihal ^b   Kumar, Raj ^c  

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

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c Geisinger Health Geisinger Commonwealth School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SIGNAL TRANSDUCTION; TRANSACTIVATION; TRANSCRIPTION REGULATION;

ANIMALS; HUMANS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 58249105355     PISSN: 00243205     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.lfs.2008.12.002     Document Type: Review

References (80)

1. Adkins J., and Lumb K. Intrinsic structural disorder and sequence features of the cell cycle inhibitor p57Kip2. Proteins 46 1 (2002) 1-7
2. Auton M., and Bolen D.W. Predicting the energetics of osmolyte-induced protein folding/unfolding. Proceedings of the National Academy of Sciences of the United States of America 102 42 (2005) 15065-15068
3. Bain D.L., Franden M.A., McManaman J.L., Takimoto G.S., and Horwitz K.B. The N-terminal region of the human progesterone A-receptor. Structural analysis and the influence of the DNA binding domain. Journal of Biological Chemistry 275 10 (2000) 7313-7320
4. Baldwin R., and Rose G. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends in Biochemical Sciences 24 2 (1999) 77-83
5. Baskakov I., Kumar R., Srinivasan G., Ji Y., Bolen D., and Thompson E. Trimethylamine N-oxide-induced cooperative folding of an intrinsically unfolded transcription-activating fragment of human glucocorticoid receptor. Journal of Biological Chemistry 274 16 (1999) 10693-10696
6. Bienkiewicz E., Adkins J., and Lumb K. Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1). Biochemistry 41 3 (2002) 752-759
7. Campbell K.M., Terrell A.R., Laybourn P.J., and Lumb K.J. Intrinsic structural disorder of the C-terminal activation domain from the bZIP transcription factor Fos. Biochemistry 39 10 (2000) 2708-2713
8. Cheng Y., LeGall T., Oldfield C.J., Mueller J.P., Van Y.Y., Romero P., Cortese M.S., Uversky V.N., and Dunker A.K. Rational drug design via intrinsically disordered protein. Trends in Biotechnology 24 10 (2006) 435-442
9. Cheng Y., Oldfield C.J., Meng J., Romero P., Uversky V.N., and Dunker A.K. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry 46 47 (2007) 13468-13477
10. Crivici A., and Ikura M. Molecular and structural basis of target recognition by calmodulin. Annual Reviews of Biophysics and Biomolecular Structure 24 (1995) 85-116
11. Crowhurst K.A., and Forman-Kay J.D. Aromatic and methyl NOEs highlight hydrophobic clustering in the unfolded state of an SH3 domain. Biochemistry 42 29 (2003) 8687-8695
12. De Guzman R.N., Martinez-Yamout M., Dyson H.J., and Wright P.E. Interaction of the TAZ1 domain of the CREB-binding protein with the activation domain of CITED2: regulation by competition between intrinsically unstructured ligands for non-identical binding sites. Journal of Biological Chemistry 279 4 (2004) 3042-3049
13. De Guzman R., Goto N., Dyson H., and Wright P. Structural basis for cooperative transcription factor binding to the CBP coactivator. Journal of Molecular Biology 355 5 (2006) 1005-1013
14. Dunker A.K., and Obradovic Z. The protein trinity-linking function and disorder. Nature Biotechnology 19 9 (2001) 805-806
15. Dunker A., and Uversky V. Signal transduction via unstructured protein conduits. Nature Chemical Biology 4 4 (2008) 229-230
16. Dunker A.K., Garner E., Guilliot S., Romero P., Albrecht K., Hart J., Obradovic Z., Kissinger C., and Villafranca J.E. Protein disorder and the evolution of molecular recognition: theory, predictions and observations. Pacific Symposium on Biocomputation (1998) 473-484
17. Dunker A.K., Obradovic Z., Romero P., Garner E.C., and Brown C.J. Intrinsic protein disorder in complete genomes. Genome Informatics 11 (2000) 161-171
18. Dunker A., Lawson J., Brown C., Williams R., Romero P., Oh J., Oldfield C., Campen A., Ratliff C., Hipps K., Ausio J., Nissen M., Reeves R., Kang C., Kissinger C., Bailey R., Griswold M., Chiu W., Garner E., and Obradovic Z. Intrinsically disordered protein. Journal of Molecular Graphic Model 19 1 (2001) 26-59
19. Dunker A., Brown C., Lawson J., Iakoucheva L., and Obradović Z. Intrinsic disorder and protein function. Biochemistry 41 21 (2002) 6573-6582
20. Dunker A.K., Cortese M.S., Romero P.O., Iakoucheva L.M., and Uversky V.N. Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS Journal 272 20 (2005) 5129-5148
21. Dyson H., and Wright P. Coupling of folding and binding for unstructured proteins. Current Opinion in Structural Biology 12 1 (2002) 54-60
22. Dyson H., and Wright P. Intrinsically unstructured proteins and their functions. Nature Reviews in Molecular and Cellular Biology 6 3 (2005) 197-208
23. Ebert M., Bae S., Dyson H., and Wright P. NMR relaxation study of the complex formed between CBP and the activation domain of the nuclear hormone receptor coactivator ACTR. Biochemistry 47 5 (2008) 1299-1308
24. Eliezer D. Characterizing residual structure in disordered protein States using nuclear magnetic resonance. Methods in Molecular Biology 350 (2007) 49-67
25. Fink A. Natively unfolded proteins. Current Opinion in Structural Biology 15 1 (2005) 35-41
26. Flaugh S., and Lumb K. Effects of macromolecular crowding on the intrinsically disordered proteins c-Fos and p27(Kip1). Biomacromolecules 2 2 (2001) 538-540
27. Hernández M., Avila J., and Andreu J. Physicochemical characterization of the heat-stable microtubule-associated protein MAP2. European Journal of Biochemistry 154 1 (1986) 41-48
28. Iakoucheva L., Brown C., Lawson J., Obradović Z., and Dunker A. Intrinsic disorder in cell-signaling and cancer-associated proteins. Journal of Molecular Biology 323 3 (2002) 573-584
29. Iakoucheva L., Radivojac P., Brown C., O'Connor T., Sikes J., Obradovic Z., and Dunker A. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Research 32 3 (2004) 1037-1049
30. Issaeva N., Friedler A., Bozko P., Wiman K.G., Fersht A.R., and Selivanova G. Rescue of mutants of the tumor suppressor p53 in cancer cells by a designed peptide. Proceedings of the National Academy of Sciences of the United States of America 100 23 (2003) 13303-13307
31. Jonker H.R., Wechselberger R.W., Boelens R., Folkers G.E., and Kaptein R. Structural properties of the promiscuous VP16 activation domain. Biochemistry 44 3 (2005) 827-839
32. Kriwacki R., Hengst L., Tennant L., Reed S., and Wright P. Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. Proceedings of the National Academy of Sciences of the United States of America 93 21 (1996) 11504-11509
33. Kumar R., and Thompson E. The structure of the nuclear hormone receptors. Steroids 64 5 (1999) 310-319
34. Kumar R., and Thompson E. Transactivation functions of the N-terminal domains of nuclear hormone receptors: protein folding and coactivator interactions. Molecular Endocrinology 17 1 (2003) 1-10
35. Kumar R., Baskakov I.V., Srinivasan G., Bolen D.W., Lee J.C., and Thompson E.B. Interdomain signaling in a two-domain fragment of the human glucocorticoid receptor. Journal of Biological Chemistry 274 35 (1999) 24737-24741
36. Kumar R., Lee J., Bolen D., and Thompson E. The conformation of the glucocorticoid receptor af1/tau1 domain induced by osmolyte binds co-regulatory proteins. Journal of Biological Chemistry 276 21 (2001) 18146-18152
37. Kumar R., Volk D., Li J., Lee J., Gorenstein D., and Thompson E. TATA box binding protein induces structure in the recombinant glucocorticoid receptor AF1 domain. Proceedings of the National Academy of Sciences of the United States of America 101 47 (2004) 16425-16430
38. Kumar R., Betney R., Li J., Thompson E., and McEwan I. Induced alpha-helix structure in AF1 of the androgen receptor upon binding transcription factor TFIIF. Biochemistry 43 11 (2004) 3008-3013
39. Liu J., Perumal N., Oldfield C., Su E., Uversky V., and Dunker A. Intrinsic disorder in transcription factors. Biochemistry 45 22 (2006) 6873-6888
40. Marianayagam N.J., and Jackson S.E. The folding pathway of ubiquitin from all-atom molecular dynamics simulations. Biophysical Chemistry 111 2 (2004) 159-171
41. Mark W., Liao J., Lu Y., Ayed A., Laister R., Szymczyna B., Chakrabartty A., and Arrowsmith C. Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNA interactions?. Journal of Molecular Biology 345 2 (2005) 275-287
42. Mayor U., Guydosh N.R., Johnson C.M., Grossmann J.G., Sato S., Jas G.S., Freund S.M., Alonso D.O., Daggett V., and Fersht A.R. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421 6925 (2003) 863-867
43. McCarney E.R., Kohn J.E., and Plaxco K.W. Is there or isn't there? The case for (and against) residual structure in chemically denatured proteins. Critical Reviews in Biochemistry and Molecular Biology 40 4 (2005) 181-189
44. McEwan I., Dahlman-Wright K., Ford J., and Wright A. Functional interaction of the c-Myc transactivation domain with the TATA binding protein: evidence for an induced fit model of transactivation domain folding. Biochemistry 35 29 (1996) 9584-9593
45. Minezaki Y., Homma K., Kinjo A., and Nishikawa K. Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. Journal of Molecular Biology 359 4 (2006) 1137-1149
46. Mittag T., and Forman-Kay J.D. Atomic-level characterization of disordered protein ensembles. Current Opinion in Structural Biology 17 1 (2007) 3-14
47. Mohan A., Oldfield C.J., Radivojac P., Vacic V., Cortese M.S., Dunker A.K., and Uversky V.N. Analysis of molecular recognition features (MoRFs). Journal of Molecular Biology 362 5 (2006) 1043-1059
48. Namba K. Roles of partly unfolded conformations in macromolecular self-assembly. Genes Cells 6 1 (2001) 1-12
49. Ng K.P., Potikyan G., Savene R.O., Denny C.T., Uversky V.N., and Lee K.A. Multiple aromatic side chains within a disordered structure are critical for transcription and transforming activity of EWS family oncoproteins. Proceedings of the National Academy of Sciences of the United States of America 104 2 (2007) 479-484
50. Oldfield C.J., Cheng Y., Cortese M.S., Brown C.J., Uversky V.N., and Dunker A.K. Comparing and combining predictors of mostly disordered proteins. Biochemistry 44 37 (2005) 12454-12470
51. Oldfield C.J., Meng J., Yang J.Y., Yang M.Q., Uversky V.N., and Dunker A.K. Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics 9 Suppl 1 (2008) S1
52. Receveur-Bréchot V., Bourhis J.M., Uversky V.N., Canard B., and Longhi S. Assessing protein disorder and induced folding. Proteins 62 1 (2006) 24-45
53. Romero P.O., Obradovic Z., and Dunker A.K. Sequence data analysis for long disordered regions prediction in the calcineurin family. Genome Informatics 8 (1997) 110-124
54. Romero P.O., Obradovic Z., Kissinger C., Villafranca J.E., and Dunker A.K. Identifying disordered regions in protein from amino acid sequences. Proceeding of International Conference of Neural Network (1997) 90-95
55. Romero P., Obradovic Z., Kissinger C., Villafranca J., Garner E., Guilliot S., and Dunker A. Thousands of proteins likely to have long disordered regions. Pacific Symposium on Biocomputing (1998) 437-448
56. Romero P., Obradovic Z., and Dunker A. Natively disordered proteins: functions and predictions. Applied Bioinformatics 3 2-3 (2004) 105-113
57. Schulz G.E. Nucleotide binding proteins. Molecular Mechanism of Biological Recognition (1979) 79-94
58. Shen F., Triezenberg S., Hensley P., Porter D., and Knutson J. Transcriptional activation domain of the herpesvirus protein VP16 becomes conformationally constrained upon interaction with basal transcription factors. Journal of Biological Chemistry 271 9 (1996) 4827-4837
59. Shoemaker B., Portman J., and Wolynes P. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proceedings of the National Academy of Sciences of the United States of America 97 16 (2000) 8868-8873
60. Singh G., and Dash D. Intrinsic disorder in yeast transcriptional regulatory network. Proteins 68 3 (2007) 602-605
61. Sugase K., Dyson H., and Wright P. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447 7147 (2007) 1021-1025
62. Tompa P. Intrinsically unstructured proteins. Trends in Biochemical Sciences 27 10 (2002) 527-533
63. Tompa P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Letters 579 15 (2005) 3346-3354
64. Uversky V. Natively unfolded proteins: a point where biology waits for physics. Protein Science 11 4 (2002) 739-756
65. Uversky V.N. Protein folding revisited. A polypeptide chain at the folding-misfolding-nonfolding cross-roads: which way to go?. Cellular and Molecular Life Sciences 60 9 (2003) 1852-1871
66. Uversky V.N. A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disorders. Journal of Biomolecular and Structural Dynamics 21 2 (2003) 211-234
67. Uversky V., Gillespie J., and Fink A. Why are "natively unfolded" proteins unstructured under physiologic conditions?. Proteins 41 3 (2000) 415-427
68. Uversky V., Oldfield C., and Dunker A. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. Journal of Molecular Recognition 18 5 (2005) 343-384
69. Vacic V., Oldfield C.J., Mohan A., Radivojac P., Cortese M.S., Uversky V.N., and Dunker A.K. Characterization of molecular recognition features, MoRFs, and their binding partners. Journal of Proteome Research 6 6 (2007) 2351-2366
70. Vucetic S., Xie H., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., and Uversky V.N. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. Journal of Proteome Research 6 5 (2007) 1899-1916
71. Wang W., Cherry J.M., Nochomovitz Y., Jolly E., Botstein D., and Li H. Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proceedings of the National Academy of Sciences of the United States of America 102 6 (2005) 1998-2003
72. Ward J., Sodhi J., McGuffin L., Buxton B., and Jones D. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. Journal of Molecular Biology 337 3 (2004) 635-645
73. Wärnmark A., WA, Wright A.P., Gustafsson J.A., and Härd T. The N-terminal regions of estrogen receptor alpha and beta are unstructured in vitro and show different TBP binding properties. Journal of Biological Chemistry 276 49 (2001) 45939-45944
74. Wells M., Tidow H., Rutherford T.J., Markwick P., Jensen M.R., Mylonas E., Svergun D.I., Blackledge M., and Fersht A.R. Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proceedings of the National Academy of Sciences of the United States of America 105 15 (2008) 5762-5767
75. Wen E.Z., and Luo R. Interplay of secondary structures and side-chain contacts in the denatured state of BBA1. Journal of Chemical Physics 121 5 (2004) 2412-2421
76. Williamson J.R. Proteins that bind RNA and the labs who love them. Nature Structural Biology 8 5 (2001) 390-391
77. Wright P., and Dyson H. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology 293 2 (1999) 321-331
78. Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., and Uversky V.N. Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. Journal of Proteome Research 6 5 (2007) 1917-1932
79. Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Uversky V.N., and Obradovic Z. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. Journal of Proteome Research 6 5 (2007) 1882-1898
80. Zor T., De Guzman R., Dyson H., and Wright P. Solution structure of the KIX domain of CBP bound to the transactivation domain of c-Myb. Journal of Molecular Biology 337 3 (2004) 521-534