IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Fukuchi, Satoshi ^a   Amemiya, Takayuki ^b   Sakamoto, Shigetaka ^c   Nobe, Yukiko ^b   Hosoda, Kazuo ^a   Kado, Yumiko ^b   Murakami, Seiko D ^b   Koike, Ryotaro ^b   Hiroaki, Hidekazu ^b   Ota, Motonori ^b  

^a MAEBASHI INSTITUTE OF TECHNOLOGY   (Japan)

^b NAGOYA UNIVERSITY   (Japan)

^c HOLONICS Corporation   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANDROGEN RECEPTOR; GLUCOCORTICOID RECEPTOR; INTRINSICALLY DISORDERED PROTEIN;

ACETYLATION; ARTICLE; BACTERIAL STRAIN; CORRELATION COEFFICIENT; INTRINSICALLY DISORDERED PROTEINS WITH EXTENSIVE ANNOTATIONS AND LITERATURE; METHYLATION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN MODIFICATION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; AMINO ACID SEQUENCE; BIOINFORMATICS; CLUSTER ANALYSIS; EXPERIMENTAL TEST; INTRINSICALLY DISORDERED PROTEINS WITH EXTENSIVE ANNOTATIONS AND LITERATURE DATABASE; PREDICTION; PROTEIN DEFECT; RELIABILITY; SEQUENCE HOMOLOGY; CHEMISTRY; INTERNET; METABOLISM;

DATABASES, PROTEIN; INTERNET; INTRINSICALLY DISORDERED PROTEINS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN INTERACTION MAPS;

EID: 84891765095     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1010     Document Type: Article

References (39)

1. Dunker, A.K., Brown, C.J., Lawson, J.D., Iakoucheva, L.M. and Obradovic, Z. (2002) Intrinsic disorder and protein function. Biochemistry, 41, 6573-6582.
2. Dunker, A.K., Lawson, J.D., Brown, C.J., Williams, R.M., Romero, P., Oh, J.S., Oldfield, C.J., Campen, A.M., Ratliff, C.M., Hipps, K.W. et al. (2001) Intrinsically disordered protein. J. Mol. Graph. Model., 19, 26-59.
3. Dyson, H.J. and Wright, P.E. (2005) Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol., 6, 197-208.
4. Tompa, P. (2005) The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett., 579, 3346-3354.
5. Uversky, V.N. and Dunker, A.K. (2010) Understanding protein non-folding. Biochim. Biophys. Acta, 1804, 1231-1264.
6. Fukuchi, S., Hosoda, K., Homma, K., Gojobori, T. and Nishikawa, K. (2011) Binary classification of protein molecules into intrinsically disordered and ordered segments. BMC Struct. Biol., 11, 29.
7. Minezaki, Y., Homma, K., Kinjo, A.R. and Nishikawa, K. (2006) Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. J. Mol. Biol., 359, 1137-1149.
8. Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F. and Jones, D.T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 337, 635-645.
9. Iakoucheva, L.M., Brown, C.J., Lawson, J.D., Obradovic, Z. and Dunker, A.K. (2002) Intrinsic disorder in cell-signaling and cancer-associated proteins. J. Mol. Biol., 323, 573-584.
10. Sickmeier, M., Hamilton, J.A., LeGall, T., Vacic, V., Cortese, M.S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V.N. et al. (2007) DisProt: the database of disordered proteins. Nucleic Acids Res., 35, D786-D793.
11. Di Domenico, T., Walsh, I., Martin, A.J. and Tosatto, S.C. (2012) MobiDB: a comprehensive database of intrinsic protein disorder annotations. Bioinformatics, 28, 2080-2081.
12. 2: database of disordered protein predictions. Nucleic Acids Res., 41, D508-D516.
13. Fukuchi, S., Sakamoto, S., Nobe, Y., Murakami, S.D., Amemiya, T., Hosoda, K., Koike, R., Hiroaki, H. and Ota, M. (2012) IDEAL: intrinsically disordered proteins with extensive annotations and literature. Nucleic Acids Res., 40, D507-D511.
14. Dinkel, H., Michael, S., Weatheritt, R.J., Davey, N.E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A. et al. (2012) ELM-the database of eukaryotic linear motifs. Nucleic Acids Res., 40, D242-D251.
15. Fuxreiter, M., Simon, I., Friedrich, P. and Tompa, P. (2004) Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J. Mol. Biol., 338, 1015-1026.
16. Lobanov, M.Y., Shoemaker, B.A., Garbuzynskiy, S.O., Fong, J.H., Panchenko, A.R. and Galzitskaya, O.V. (2010) ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Res., 38, D283-D287.
17. Mohan, A., Oldfield, C.J., Radivojac, P., Vacic, V., Cortese, M.S., Dunker, A.K. and Uversky, V.N. (2006) Analysis of molecular recognition features (MoRFs). J. Mol. Biol., 362, 1043-1059.
18. Wright, P.E. and Dyson, H.J. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol., 293, 321-331.
19. Kriwacki, R.W., Hengst, L., Tennant, L., Reed, S.I. and Wright, P.E. (1996) Structural studies of p21Waf1/Cip1/Sdi1 in the free and CDK2-bound state: conformational disorder mediates binding diversity. Proc. Natl Acad. Sci. USA, 93, 11504-11509.
20. Haynes, C., Oldfield, C.J., Ji, F., Klitgord, N., Cusick, M.E., Radivojac, P., Uversky, V.N., Vidal, M. and Iakoucheva, L.M. (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput. Biol., 2, e100.
21. Patil, A. and Nakamura, H. (2006) Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Lett., 580, 2041-2045.
22. Rose, P.W., Bi, C., Bluhm, W.F., Christie, C.H., Dimitropoulos, D., Dutta, S., Green, R.K., Goodsell, D.S., Prlic, A., Quesada, M. et al. (2013) The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res., 41, D475-D482.
23. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
24. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
25. Jones, D.T. and Ward, J.J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins, 53(Suppl. 6), 573-578.
26. Uversky, V.N., Gillespie, J.R. and Fink, A.L. (2000) Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins, 41, 415-427.
27. Martin, J.A., Witzell, J., Blumenstein, K., Rozpedowska, E., Helander, M., Sieber, T.N. and Gil, L. (2013) Resistance to Dutch ELM disease reduces presence of xylem endophytic fungi in ELMs (Ulmus spp.). PLoS One, 8, e56987.
28. Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z. et al. (2008) BioMagResBank. Nucleic Acids Res., 36, D402-D408.
29. Ota, M., Koike, R., Amemiya, T., Tenno, T., Romero, P.R., Hiroaki, H., Dunker, A.K. and Fukuchi, S. (2013) An assignment of intrinsically disordered regions of proteins based on NMR structures. J. Struct. Biol., 181, 29-36.
30. Matthews, B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
31. UniProt Consortium. (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
32. Levine, A.J. (1997) p53, the cellular gatekeeper for growth and division. Cell, 88, 323-331.
33. McKenna, N.J., Lanz, R.B. and O'Malley, B.W. (1999) Nuclear receptor coregulators: cellular and molecular biology. Endocr. Rev., 20, 321-344.
34. Bhaumik, S.R., Smith, E. and Shilatifard, A. (2007) Covalent modifications of histones during development and disease pathogenesis. Nat. Struct. Mol. Biol., 14, 1008-1016.
35. Fontes, M.R., Teh, T., Jans, D., Brinkworth, R.I. and Kobe, B. (2003) Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha. J. Biol. Chem., 278, 27981-27987.
36. Clevers, H. and Nusse, R. (2012) Wnt/beta-catenin signaling and disease. Cell, 149, 1192-1205.
37. Ferreon, J.C., Martinez-Yamout, M.A., Dyson, H.J. and Wright, P.E. (2009) Structural basis for subversion of cellular control mechanisms by the adenoviral E1A oncoprotein. Proc. Natl Acad. Sci. USA, 106, 13260-13265.
38. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
39. Finn, R.D., Clements, J. and Eddy, S.R. (2013) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.