FuzDB: Database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D228-D235

  Miskei, Marton ^a   Antal, Csaba ^a   Fuxreiter, Monika ^a  

^a UNIVERSITY OF DEBRECEN   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; FUZZY SYSTEM; HUMAN; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PROTEIN ASSEMBLY; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEIN UNFOLDING; REGULATORY MECHANISM; STRUCTURE ACTIVITY RELATION; BIOLOGY; CHEMISTRY; METABOLISM; MOLECULAR MODEL; PROCEDURES; SOFTWARE; WEB BROWSER;

CARRIER PROTEIN; MULTIPROTEIN COMPLEX; PROTEIN; PROTEIN BINDING;

CARRIER PROTEINS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; WEB BROWSER;

EID: 85016050879     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1019     Document Type: Article

References (30)

1. Oldfield, C.J. and Dunker, A.K. (2014) Intrinsically disordered proteins and intrinsically disordered protein regions. Annu. Rev. Biochem., 83, 553-584.
2. Wright, P.E. and Dyson, H.J. (2015) Intrinsically disordered proteins in cellular signalling and regulation. Nat. Rev. Mol. Cell Biol., 16, 18-29.
3. van der Lee, R, Buljan, M., Lang, B., Weatheritt, R.J., Daughdrill, G.W., Dunker, A.K., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D.T. et al. (2014) Classification of intrinsically disordered regions and proteins. Chem. Rev., 114, 6589-6631.
4. Wright, P.E. and Dyson, H.J. (2009) Linking folding and binding. Curr. Opin. Struct. Biol., 19, 31-38.
5. van Leeuwen, H.C., Strating, M.J., Rensen, M., de Laat, W. and van der Vliet, P.C. (1997) Linker length and composition influence the flexibility of Oct-1 DNA binding. EMBO J., 16, 2043-2053.
6. Yu, H., Chen, J.K., Feng, S., Dalgarno, D.C., Brauer, A.W. and Schreiber, S.L. (1994) Structural basis for the binding of proline-rich peptides to SH3 domains. Cell, 76, 933-945.
7. Rezaei-Ghaleh, N., Blackledge, M. and Zweckstetter, M. (2012) Intrinsically disordered proteins: from sequence and conformational properties toward drug discovery. Chembiochem, 13, 930-950.
8. Bernado, P., Mylonas, E., Petoukhov, M.V., Blackledge, M. and Svergun, D.I. (2007) Structural characterization of flexible proteins using small-angle X-ray scattering. J. Am. Chem. Soc., 129, 5656-5664.
9. Marsh, J.A. and Forman-Kay, J.D. (2011) Ensemble modeling of protein disordered states: experimental restraint contributions and validation. Proteins, 80, 556-572.
10. Tompa, P. and Fuxreiter, M. (2008) Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem. Sci., 33, 2-8.
11. Fuxreiter, M. (2012) Fuzziness: linking regulation to protein dynamics. Mol. Biosyst., 8, 168-177.
12. Sharma, R., Raduly, Z., Miskei, M. and Fuxreiter, M. (2015) Fuzzy complexes: specific binding without complete folding. FEBS Lett., 589, 2533-2542.
13. Wu, H. and Fuxreiter, M. (2016) The structure and dynamics of higher-order assemblies: amyloids, signalosomes and granules. Cell, 165, 1055-1066.
14. Milles, S., Mercadante, D., Aramburu, I.V., Jensen, M.R., Banterle, N., Koehler, C., Tyagi, S., Clarke, J., Shammas, S.L., Blackledge, M. et al. (2015) Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors. Cell, 163, 734-745.
15. 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.
16. Potenza, E., Di Domenico, T., Walsh, I. and Tosatto, S.C. (2015) MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. Nucleic Acids Res., 43, D315-D320.
17. Fukuchi, S., Amemiya, T., Sakamoto, S., Nobe, Y., Hosoda, K., Kado, Y., Murakami, S.D., Koike, R., Hiroaki, H. and Ota, M. (2014) IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners. Nucleic Acids Res., 42, D320-D325.
18. Varadi, M., Kosol, S., Lebrun, P., Valentini, E., Blackledge, M., Dunker, A.K., Felli, I.C., Forman-Kay, J.D., Kriwacki, R.W., Pierattelli, R. et al. (2014) pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. Nucleic Acids Res., 42, D326-D335.
19. Mittag, T., Orlicky, S., Choy, W.Y., Tang, X., Lin, H., Sicheri, F., Kay, L.E., Tyers, M. and Forman-Kay, J.D. (2008) Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor. Proc. Natl. Acad. Sci. U.S.A., 105, 17772-17777.
20. Oates, M.E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M.J., Xue, B., Dosztanyi, Z., Uversky, V.N., Obradovic, Z., Kurgan, L. et al. (2013) D(2)P(2): database of disordered protein predictions. Nucleic Acids Res., 41, D508-D516.
21. Fuxreiter, M. and Tompa, P. (2012) Fuzzy complexes: a more stochastic view of protein function. Adv. Exp. Med. Biol., 725, 1-14.
22. Lukhele, S., Bah, A., Lin, H., Sonenberg, N. and Forman-Kay, J.D. (2013) Interaction of the eukaryotic initiation factor 4E with 4E-BP2 at a dynamic bipartite interface. Structure, 21, 2186-2196.
23. Kurzbach, D., Schwarz, T.C., Platzer, G., Hofler, S., Hinderberger, D. and Konrat, R. (2014) Compensatory adaptations of structural dynamics in an intrinsically disordered protein complex. Angew. Chem., 53, 3840-3843.
24. Morales, R.A., MacRaild, C.A., Seow, J., Krishnarjuna, B., Drinkwater, N., Rouet, R., Anders, R.F., Christ, D., McGowan, S. and Norton, R.S. (2015) Structural basis for epitope masking and strain specificity of a conserved epitope in an intrinsically disordered malaria vaccine candidate. Sci. Rep., 5, 10103.
25. Bourhis, J.M., Receveur-Brechot, V., Oglesbee, M., Zhang, X., Buccellato, M., Darbon, H., Canard, B., Finet, S. and Longhi, S. (2005) The intrinsically disordered C-terminal domain of the measles virus nucleoprotein interacts with the C-terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded. Protein Sci., 14, 1975-1992.
26. Lee, G.M., Pufall, M.A., Meeker, C.A., Kang, H.S., Graves, B.J. and McIntosh, L.P. (2008) The affinity of Ets-1 for DNA is modulated by phosphorylation through transient interactions of an unstructured region. J. Mol. Biol., 382, 1014-1030.
27. Vise, P.D., Baral, B., Latos, A.J. and Daughdrill, G.W. (2005) NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain. Nucleic Acids Res., 33, 2061-2077.
28. Stott, K., Watson, M., Howe, F.S., Grossmann, J.G. and Thomas, J.O. (2010) Tail-mediated collapse of HMGB1 is dynamic and occurs via differential binding of the acidic tail to the A and B domains. J. Mol. Biol., 403, 706-722.
29. Schwarten, M., Solyom, Z., Feuerstein, S., Aladag, A., Hoffmann, S., Willbold, D. and Brutscher, B. (2013) Interaction of nonstructural protein 5A of the hepatitis C virus with Src homology 3 domains using noncanonical binding sites. Biochemistry, 52, 6160-6168.
30. Andresen, C., Helander, S., Lemak, A., Fares, C., Csizmok, V., Carlsson, J., Penn, L.Z., Forman-Kay, J.D., Arrowsmith, C.H., Lundstrom, P. et al. (2012) Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding. Nucleic Acids Res., 40, 6353-6366.