Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein

Journal of Proteome Research

Volumn 7, Issue 10, 2008, Pages 4465-4474

  Bressan, Gustavo C ^a,b   Silva, Julio C ^a,c   Borges, Julio C ^b   Passos, Dario O Dos ^a   Ramos, Carlos H I ^b   Torriani, Iris L ^a,c   Kobarg, Jörg ^a,b  

^a LABORATÓRIO NACIONAL DE LUZ SÍNCROTRON   (Brazil)

^b UNIVERSITY OF CAMPINAS   (Brazil)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Circular dichroism; Hydrodynamic characterization; Intrinsically unstructured protein (iup); Limited proteolysis; Protein protein interaction; SAXS

Indexed keywords

CD30 ANTIGEN; RECOMBINANT ANTIGEN; RNA; HABP4 PROTEIN, HUMAN; MYOGENIC FACTOR; PROTEINASE K;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL STRAIN HEK293; CIRCULAR DICHROISM; HUMAN; HUMAN CELL; PLASTICITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RADIATION SCATTERING; RNA BINDING; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; AMINO ACID SEQUENCE; CELL LINE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SMALL ANGLE SCATTERING;

AMINO ACID SEQUENCE; CELL LINE; ENDOPEPTIDASE K; HUMANS; MODELS, MOLECULAR; MYOGENIC REGULATORY FACTORS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SCATTERING, SMALL ANGLE; SIGNAL TRANSDUCTION;

EID: 55949137920     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr8005342     Document Type: Article

References (64)

1. Schwab, U.; Stein, H.; Gerdes, J.; Lemke, H.; Kirchner, H.; Schaadt, M.; Diehl, V. Production of a monoclonal antibody specific for Hodgin and Sternberg-Reed cells of Hodgkin's disease and a subset of normal lymphoid cells. Nature 1982, 299, 65-67.
2. Hansen, H.; Lemke, H.; Bredfeldt, G.; Könnecke, I.; Havsteen, B. The Hodgkin-associated Ki-1 antigen exists in an intracellular and a membrane-bound form. Biol. Chem. Hoppe-Seyler 1989, 370, 409-416.
3. Hansen, H.; Bredfeldt, G.; Havsteen, B.; Lemke, H. Protein kinase activity of the intracellular but not the membrane-associated form of the Ki-1 antigen (CD30). Res. Immunol. 1990, 141, 13-31.
4. Kobarg, J.; Schnittger, S.; Fonatsch, C.; Lemke, H.; Bowen, M. A.; Buck, F.; Hansen, H. P. Characterization, mapping and partial cDNA sequence of the 57 kDa intracellular Ki-1 antigen. Exp. Clin. Immunogenet. 1997, 14, 273-280.
5. Rohde, D.; Hansen, H.; Hafner, M.; Lange, H.; Mielke, V.; Hansmann, M. L.; Lemke, H. Cellular localization and processing of the two molecular forms of the Hodgkin-associated Ki-1 (CD30) antigen. Am. J. Pathol. 1992, 140, 473-482.
6. Huang, L.; Grammatikakis, N.; Yoneda, M.; Banerjee, S. D.; Toole, B. P. Molecular characterization of a novel intracellular hyaluro-an-binding protein. J. Biol. Chem. 2000, 275, 29829-29839.
7. Lemos, T. A.; Passos, D. O.; Nery, F. C.; Kobarg, J. Characterization of a new family of proteins that interact with the C-terminal region of the chromatin-remodeling factor CHD-3. FEBS Lett. 2003, 533, 14-20.
8. Lemos, T. A.; Kobarg, J. CGI-55 interacts with nuclear proteins and co-localizes to p80-coilin positive-coiled bodies in the nucleus. Cell Biochem. Biophys. 2006, 44, 463-74.
9. Nery, F. C; Rui, E.; Kuniyoshi, T. M.; Kobarg, J. Evidence for the interaction of the regulatory protein Ki-1/57 with p53 and its interacting proteins. Biochem. Biophys. Res. Commun. 2006, 341, 847-855.
10. Passos, D. O.; Bressan, G. G; Nery, F. C; Kobarg, J. Ki-1/57 interacts with PRMT1 and is a substrate for arginine methylation. FEBS J. 2006, 273, 3946-61.
11. Nery, F. C; Passos, D. O.; Garcia, V. S.; Kobarg, J. Ki-1/57 interacts with RACK1 and is a substrate for the phosphorylation by phorbol 12-myristate 13-acetate activated protein kinase C. J. Biol. Chem. 2004, 279, 11444-11455.
12. Nery, F. C; Bressan, G. C; Alborghetti, M. R.; Passos, D. O.; Kuniyoshi, T. M.; Ramos, C. H. I.; Oyama, S.; Kobarg, J. A spectroscopic analysis of the interaction between the human regulatory proteins RACK1 and Ki-1/57. Biol. Chem. 2006, 387, 577- 582.
13. Dunker, A. K.; Brown, C. J.; Lawson, J. D.; Iakoucheva, L. M.; Obradović, Z. Intrinsic disorder and protein function. Biochemistry 2002, 41, 6573-6582.
14. Dyson, H. J.; Wright, P. E. Intrinsically unstructured proteins and their functions. Nat. Rev., Mol. Cell. Biol. 2005, 6, 197-208.
15. Tompa, P.; Fuxreiter, M. Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem. Sci. 2008, 33, 2-8.
16. Dunker, A. K.; Lawson, I. D.; Brown, C. J.; Williams, R. M.; Romero, P.; Oh, J. S.; Oldfield, C. J.; Campen, A. M.; Ratliff, C. M.; Hipps, K. W. Intrinsically disordered protein. J. Mol. Graph. Model. 2001, 19, 26-59.
17. Schulz, G. E. Nucleotide binding proteins. In Molecular Mechanism of Biological Recognition; Balaban, M., Ed.; Elsevier/North-Holland: New York, 1979; pp 79-94.
18. Iakoucheva, L. M.; Brown, C. J.; Lawson, J. D.; Obradovic, Z.; Dunker, A. K. Intrinsic disorder in cell-signalling and cancer- associated proteins. J. Mol. Biol. 2002, 323, 573-584.
19. Cheng, Y.; LeGall, T.; Oldfield, C. J.; Mueller, J. P.; Van, Y. Y. J.; Romero, P.; Cortese, M. S.; Uversky, V. N.; Dunker, A. K. Rational drug design via intrinsically disordered protein. Trends Biotechnol. 2006, 24, 435-442.
20. Tompa, P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett. 2005, 579, 3346- 54.
21. Tompa, P. Intrinsically unstructured proteins. Trends Biochem. Sci. 2002, 27, 527-33.
22. Uversky, V. N.; Gillespie, J. R.; Fink, A. L. Why are "natively unfolded" proteins unstructured under physiologic conditions. Proteins 2000, 41, 415-27.
23. Uversky, V. N. What does it mean to be natively unfolded. Eur. J. Biochem. 2002, 269, 2-12.
24. Dyson, H. J.; Wright, P. E. Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 2002, 12, 54-60.
25. Li, X.; Romero, P.; Rani, M.; Dunker, A. K.; Obradovic, Z. Predicting protein disorder for N-, C-, and internal regions. Genome Informatics 1999, 10, 30-40.
26. Romero, P.; Obradovic, Z.; Li, X.; Garner, E.; Brown, C; Dunker, A. K. Sequence complexity of disordered protein. Proteins: Struct. Fund. Gen. 2001, 42, 38-48.
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 of life. J. Mol. Biol. 2004, 337, 635-645.
28. McGuffin, L. J.; Bryson, K.; Jones, D. T. The PSIPRED protein structure prediction server. Bioinformatics 2000, 16, 404-405.
29. Longhi, S.; Receveur-Bréchot, V.; Karlin, D.; Johansson, K.; Darbon, H.; Bhella, D.; Yeo, R.; Finet, S.; Canard, B. The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphopro- tein. J. Biol. Chem. 2003, 278, 18638-48.
30. Moncoq, K.; Broutin, I.; Craescu, C. T.; Vachette, P.; Ducruix, A.; Durand, D. SAXS study of the PIR domain from the Grbl4 molecular adaptor: a natively unfolded protein with a transient structure primer. Biophys. J. 2004, 87, 4056-64.
31. Bernadó, P.; Mylonas, E.; Petoukhov, M. V.; Blackledge, M.; Svergun, D. I. Structural characterization of flexible proteins using small-angle X-ray scattering. J. Am. Chem. Soc. 2007, 129, 5656- 64.
32. Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S.; Wilkins, M. R.; Appel, R. D.; Bairoch, A. In Protein Identification and Analysis Tools on the ExPASy Server, Walker, J. M, Ed.; The Proteomics Protocols Handbook; Humana Press: Totowa, NJ, 2005; pp 571-607.
33. Kirste, R. G.; Oberthür, R. C. In Small Angle X-Ray Scattering; Glatter, O., Kratky, O., Eds.; Academic Press: New York, 1982; pp 387-431.
34. Feigin, L. A.; Svergun, D. I. Structure analysis by small-angle X-ray and neutron scattering, Plenum Press: New York, 1987; pp 59- 104.
35. Beaucage, G.; Rane, S.; Sukumaran, S.; Satkowski, M. M.; Schechtman, L. A.; Doi, Y. Persistence Length of Isotactic Polyfhydroxyl butyrate). Macromolecules 1997, 30, 4158-4162.
36. Svergun, D. I. solution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 1999, 76, 2879-2886.
37. Svergun, D. I.; Petoukhov, M. V.; Koch, M. H. Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 2001, 80, 2946-2953.
38. Svergun, D. I.; Koch, M. H. J. Small-angle scattering studies of biological macromolecules in solution. Rep. Prog. Phys. 2003, 66, 1735-1782.
39. Volkov, V. V.; Svergun, D. I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 2003, 36, 860-864.
40. Bourhis, J. M.; Receveur-Bréchot, V.; Oglesbee, M.; Zhang, X.; Buccellato, M.; Darbon, H.; Canard, B.; Finet, S.; Longhi, S. Protein Sci. 2005, 14, 1975-1992.
41. Receveur-Bréchot, V.; Bourhis, J. M.; Uversky, V. N.; Canard, B.; Longhi, S. Assessing protein disorder and induced folding. Proteins 2006, 62, 24-45.
42. Laue, T. Biophysical studies by ultracentrifugation. Curr. Opin. Struct. Biol. 2001, 11, 579-583.
43. Lebowitz, J.; Lewis, M. S.; Schuck, P. Modern analytical ultracentrifugation in protein science: A tutorial review. Protein Sci. 2002, 11, 2067-2079.
44. Denning, D. P.; Uversky, V.; Patel, S. S.; Fink, A. L.; Rexach, M. The Saccharomyces cerevisiae nucleoporin Nup2p is a natively unfolded protein. J. Biol. Chem. 2002, 277, 33447-55.
45. Heaton, J. H.; Dlakic, W. M.; Dlakic, M.; Gelehrter, T. D. Identification and cDNA cloning of a novel RNAbinding protein that interacts with the cyclic nucleotideresponsive sequence in the type-1 plasminogen activator inhibitor mRNA. J. Biol. Chem. 2001, 276, 3341-3347.
46. Luo, P.; Baldwin, R. L. Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry 1997, 36, 8413-21.
47. Oldfield, C. J.; Cheng, Y.; Cortese, M. S.; Romero, P.; Uversky, V. N.; Dunker, A. K. Coupled folding and binding with α helix-forming molecular recognition elements. Biochemistry 2005, 44, 12454-70.
48. Jeong, H.; Mason, S. P.; Barabasi, A. L.; Oltvai, Z. N. Lethality and centrality in protein networks. Nature 2001, 411, 41-42.
49. Han, J. D.; Benin, N.; Hao, T.; Goldberg, D. S.; Berriz, G. F.; Zhang, L. V.; Dupuy, D.; Walhout, 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.
50. Patil, A.; Nakamura, H. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Lett. 2006, 580, 2041-2045.
51. Cavalcanti, L. P.; Torriani, I. L.; Plivelic, T. S.; Oliveira, C. L. P.; Kellermann, G.; Neuenschwander, R. Two new sealed sample cells for small angle X-ray scattering from macromolecules in solution and complex fluids using synchrotron radiation. R. Rev. Sci. Inst. 2004, 75, 4541-4546.
52. Orthaber, D.; Bergmann, A.; Glatter, O. J. Appl. Crystallogr. 2000, 33, 218-255.
53. Mylonas, E.; Svergun, D. I. Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering. J. Appl. Cryst. 2001, 40, 245-249.
54. Guinier, A.; Fournet, G. In Small angle scattering of X-rays; Translated by Walker, C. B.; Yudowitch, K. L.; John Wiley & Sons: New York, 1955; pp 5-78.
55. Glatter, O.; Kratky, O. Small Angle X-Ray Scattering, Academic Press: New York, 1982; pp 17-50.
56. Debye, P. J. Molecular-weight determination by light scattering. Phys. Colloid. Chem. 1947, 51, 18-32.
57. Calmettes, P.; Durand, D.; Desmadril, M.; Minard, P.; Receveur, V.; Smith, J. C. How random is a highly denatured protein. Biophys. Chem. 1994, 53, 105-114.
58. Perez, J.; Vachette, P.; Russo, D.; Desmadril, M.; Durand, D. Heat-induced unfolding of neocarzinostatin, a small all-beta protein investigated by small-angle X-ray scattering. J. Mol. Biol. 2001, 308, 721-743.
59. Svergun, D. I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Cryst. 1992, 25, 495-503.
60. Flory, P. J. Statistical Mechanics of Chain Molecules; Interscience Publishers: New York, 1969.
61. Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys. J. 2000, 78, 1606-19.
62. Schuck, P.; Perugini, M. A.; Gonzales, N. R.; Howlett, G. J.; Schubert, D. Size-Distribution Analysis of Proteins by Analytical Ultracentrifugation: Strategies and Application to Model Systems. Biophys. J. 2002, 82, 1096-1111.
63. Moraes, K. C; Quaresma, A. J.; Maehnss, K.; Kobarg, J. Identification and characterization of proteins that selectively interact with isoforms of the mRNA binding protein AUF1 (hnRNP D). Biol. Chem. 2003, 384, 25-37.
64. DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific: Palo Alto, CA, 2002.