Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions

Trends in Biochemical Sciences

Volumn 33, Issue 1, 2008, Pages 2-8

  Tompa, Peter ^a   Fuxreiter, Monika ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; FORCE; FUZZY COMPLEX; HUMAN; MACROMOLECULE; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

MODELS, MOLECULAR; POLYMORPHISM, GENETIC; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 37749053887     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2007.10.003     Document Type: Article

References (58)

1. Aloy P., and Russell R.B. Ten thousand interactions for the molecular biologist. Nat. Biotechnol. 22 (2004) 1317-1321
2. Aloy P., and Russell R.B. Structural systems biology: modelling protein interactions. Nat. Rev. Mol. Cell Biol. 7 (2006) 188-197
3. Tompa P. Intrinsically unstructured proteins. Trends Biochem. Sci. 27 (2002) 527-533
4. Tompa P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett. 579 (2005) 3346-3354
5. Uversky V.N., et al. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J. Mol. Recognit. 18 (2005) 343-384
6. Dyson H.J., and Wright P.E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6 (2005) 197-208
7. Dunker A.K., et al. Intrinsic protein disorder in complete genomes. Genome Inform. Ser. Workshop Genome Inform. 11 (2000) 161-171
8. Ward J.J., et al. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol. 337 (2004) 635-645
9. Tompa P., et al. Prevalent structural disorder in E. coli and S. cerevisiae proteomes. J. Proteome Res. 5 (2006) 1996-2000
10. Dyson H.J., and Wright P.E. Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 12 (2002) 54-60
11. Hansen J.C., et al. Intrinsic protein disorder, amino acid composition, and histone terminal domains. J. Biol. Chem. 281 (2006) 1853-1856
12. Ng K.P., et al. Multiple aromatic side chains within a disordered structure are critical for transcription and transforming activity of EWS family oncoproteins. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 479-484
13. Ross E.D., et al. Primary sequence independence for prion formation. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 12825-12830
14. Wright P.E., and Dyson H.J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293 (1999) 321-331
15. Graham T.A., et al. Tcf4 can specifically recognize beta-catenin using alternative conformations. Nat. Struct. Biol. 8 (2001) 1048-1052
16. Cliff M.J., et al. Conformational diversity in the TPR domain-mediated interaction of protein phosphatase 5 with Hsp90. Structure 14 (2006) 415-426
17. Fontes M.R., et al. Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha. J. Mol. Biol. 297 (2000) 1183-1194
18. Fontes M.R., et al. Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha. Biochem. J. 375 (2003) 339-349
19. Fowler D.M., et al. Functional amyloid - from bacteria to humans. Trends Biochem. Sci. 32 (2007) 217-224
20. Krishnan R., and Lindquist S.L. Structural insights into a yeast prion illuminate nucleation and strain diversity. Nature 435 (2005) 765-772
21. Tanaka M., et al. The physical basis of how prion conformations determine strain phenotypes. Nature 442 (2006) 585-589
22. Tompa P., et al. Structural disorder throws new light on moonlighting. Trends Biochem. Sci. 30 (2005) 484-489
23. Haarmann C.S., et al. The random-coil 'C' fragment of the dihydropyridine receptor II-III loop can activate or inhibit native skeletal ryanodine receptors. Biochem. J. 372 (2003) 305-316
24. Ma J. Stimulatory and inhibitory functions of the R domain on CFTR chloride channel. News Physiol. Sci. 15 (2000) 154-158
25. Park I.K., and DePaoli-Roach A.A. Domains of phosphatase inhibitor-2 involved in the control of the ATP-Mg-dependent protein phosphatase. J. Biol. Chem. 269 (1994) 28919-28928
26. Bhattacharyya R.P., et al. The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway. Science 311 (2006) 822-826
27. Remenyi A., et al. Docking interactions in protein kinase and phosphatase networks. Curr. Opin. Struct. Biol. 16 (2006) 676-685
28. van Leeuwen H.C., et al. Linker length and composition influence the flexibility of Oct-1 DNA binding. EMBO J. 16 (1997) 2043-2053
29. von Ossowski I., et al. Protein disorder: conformational distribution of the flexible linker in a chimeric double cellulase. Biophys. J. 88 (2005) 2823-2832
30. Rock R.S., et al. A flexible domain is essential for the large step size and processivity of myosin VI. Mol. Cell 17 (2005) 603-609
31. Fuxreiter M., et al. Structural disorder imparts plasticity on linear motifs. Bioinformatics 23 (2007) 950-956
32. Mohan A., et al. Analysis of molecular recognition features (MoRFs). J. Mol. Biol. 362 (2006) 1043-1059
33. Zor T., et al. Roles of phosphorylation and helix propensity in the binding of the KIX domain of CREB-binding protein by constitutive (c-Myb) and inducible (CREB) activators. J. Biol. Chem. 277 (2002) 42241-42248
34. Selenko P., et al. Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Mol. Cell 11 (2003) 965-976
35. Yu H., et al. Structural basis for the binding of proline-rich peptides to SH3 domains. Cell 76 (1994) 933-945
36. Schwarz-Linek U., et al. High affinity streptococcal binding to human fibronectin requires specific recognition of sequential f1 modules. J. Biol. Chem. 279 (2004) 39017-39025
37. Gill G., et al. A glutamine-rich hydrophobic patch in transcription factor Sp1 contacts the dTAFII110 component of the Drosophila TFIID complex and mediates transcriptional activation. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 192-196
38. Phylip L.H., et al. The potency and specificity of the interaction between the IA3 inhibitor and its target aspartic proteinase from Saccharomyces cerevisiae. J. Biol. Chem. 276 (2001) 2023-2030
39. Iakoucheva L.M., et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 32 (2004) 1037-1049
40. Prakash S., et al. An unstructured initiation site is required for efficient proteasome-mediated degradation. Nat. Struct. Mol. Biol. 11 (2004) 830-837
41. Tompa P., and Csermely P. The role of structural disorder in the function of RNA and protein chaperones. FASEB J. 18 (2004) 1169-1175
42. Lindner R.A., et al. Mouse Hsp25, a small shock protein. The role of its C-terminal extension in oligomerization and chaperone action. Eur. J. Biochem. 267 (2000) 1923-1932
43. Proudfoot N.J., et al. Integrating mRNA processing with transcription. Cell 108 (2002) 501-512
44. Sigalov A.B. Multichain immune recognition receptor signaling: different players, same game?. Trends Immunol. 25 (2004) 583-589
45. Sigalov A., et al. Homooligomerization of the cytoplasmic domain of the T cell receptor zeta chain and of other proteins containing the immunoreceptor tyrosine-based activation motif. Biochemistry 43 (2004) 2049-2061
46. Pometun M.S., et al. Quantitative observation of backbone disorder in native elastin. J. Biol. Chem. 279 (2004) 7982-7987
47. Rauscher S., et al. Proline and glycine control protein self-organization into elastomeric or amyloid fibrils. Structure 14 (2006) 1667-1676
48. Hope I.A., et al. Structural and functional characterization of the short acidic transcriptional activation region of yeast GCN4 protein. Nature 333 (1988) 635-640
49. Sigler P.B. Transcriptional activation. Acid blobs and negative noodles. Nature 333 (1988) 210-212
50. Neduva V., and Russell R.B. Linear motifs: evolutionary interaction switches. FEBS Lett. 579 (2005) 3342-3345
51. Kriwacki R.W., et al. Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 11504-11509
52. Borg M., et al. Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 9650-9655
53. Baker J.M., et al. CFTR regulatory region interacts with NBD1 predominantly via multiple transient helices. Nat. Struct. Mol. Biol. 14 (2007) 738-745
54. Melcher K. The strength of acidic activation domains correlates with their affinity for both transcriptional and non-transcriptional proteins. J. Mol. Biol. 301 (2000) 1097-1112
55. Ferreira M.E., et al. Mechanism of transcription factor recruitment by acidic activators. J. Biol. Chem. 280 (2005) 21779-21784
56. Vaynberg J., et al. Structure of an ultraweak protein-protein complex and its crucial role in regulation of cell morphology and motility. Mol. Cell 17 (2005) 513-523
57. Radhakrishnan I., et al. Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: a model for activator:coactivator interactions. Cell 91 (1997) 741-752
58. Bourhis J.M., et al. 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 (2005) 1975-1992