Sticking together? Falling apart? Exploring the dynamics of the interactome

Trends in Biochemical Sciences

Volumn 33, Issue 5, 2008, Pages 195-200

  Wilkins, Marc R ^a   Kummerfeld, Sarah K ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; HUMAN; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEOMICS; UPREGULATION;

EVOLUTION, MOLECULAR; PROTEIN INTERACTION MAPPING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; UP-REGULATION;

EID: 43849083417     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2008.03.001     Document Type: Article

References (54)

1. Fields S., and Song O. A novel genetic system to detect protein-protein interactions. Nature 340 (1989) 245-246
2. Rigaut G., et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17 (1999) 1030-1032
3. Ho Y., et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 (2002) 180-183
4. Rain J.C., et al. The protein-protein interaction map of Helicobacter pylori. Nature 409 (2001) 211-215
5. Butland G., et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 (2005) 531-537
6. Li S., et al. A map of the interactome network of the metazoan C. elegans. Science 303 (2004) 540-543
7. Giot L., et al. A protein interaction map of Drosophila melanogaster. Science 302 (2003) 1727-1736
8. LaCount D.J., et al. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438 (2005) 103-107
9. Rual J.F., et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 (2005) 1173-1178
10. Stelzl U., et al. A human protein-protein interaction network: a resource for annotating the. proteome. Cell 122 (2005) 957-968
11. Goh K.I., et al. The human disease network. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 8685-8690
12. Yildirim M.A., et al. Drug-target network. Nat. Biotechnol. 25 (2007) 1119-1126
13. Jonsson P.F., and Bates P.A. Global topological features of cancer proteins in the human interactome. Bioinformatics 22 (2006) 2291-2297
14. Lage K., et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat. Biotechnol. 25 (2007) 309-316
15. Ito T., et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 4569-4574
16. Uetz P., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403 (2000) 623-627
17. Fromont-Racine M., et al. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat. Genet. 16 (1997) 277-282
18. Gavin A.C., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 (2002) 141-147
19. Gavin A.C., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440 (2006) 631-636
20. Krogan N.J., et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440 (2006) 637-643
21. Bertin N., et al. Confirmation of organized modularity in the yeast interactome. PLoS Biol. 5 (2007) e153
22. Cusick M.E., et al. Interactome: gateway into systems biology. Hum. Mol. Genet. 14 (2005) R171-R181
23. Devos D., and Russell R.B. A more complete, complexed and structured interactome. Curr. Opin. Struct. Biol. 17 (2007) 370-377
24. Ruffner H., et al. Human protein-protein interaction networks and the value for drug discovery. Drug Discov. Today 12 (2007) 709-716
25. Jeong H., et al. Lethality and centrality in protein networks. Nature 411 (2001) 41-42
26. Han J.D., et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430 (2004) 88-93
27. Batada N.N., et al. Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol. 4 (2006) e317
28. Batada N.N., et al. Still stratus not altocumulus: further evidence against the date/party hub distinction. PLoS Biol. 5 (2007) e154
29. Kim P.M., et al. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314 (2006) 1938-1941
30. Ekman D., et al. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?. Genome Biol. 7 (2006) R45
31. Singh G.P., et al. Role of intrinsic disorder in transient interactions of hub proteins. Proteins 66 (2007) 761-765
32. Higurashi M., et al. Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci. 17 (2008) 72-78
33. de Lichtenberg U., et al. Dynamic complex formation during the yeast cell cycle. Science 307 (2005) 724-727
34. Komurov K., and White M. Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol. Syst. Biol. 3 (2007) 110
35. Lee I., et al. A probabilistic functional network of yeast genes. Science 306 (2004) 1555-1558
36. Jin G., et al. Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS ONE 2 (2007) e1207
37. Perugini M.A., et al. Insight into the self-association of key enzymes from pathogenic species. Eur. Biophys. J. 34 (2005) 469-476
38. Sopko R., et al. Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21 (2006) 319-330
39. Neverov A.D. Alternative splicing and protein function. BMC Bioinformatics 6 (2005) 266
40. The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449 (2007) 851-861
41. Sadowski I., et al. Noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps. Mol. Cell. Biol. 6 (1986) 4396-4408
42. Seet B.T., et al. Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol. 7 (2006) 473-483
43. Strahl B.D., and Allis C.D. The language of covalent histone modifications. Nature 403 (2000) 41-45
44. Jensen O.N. Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell Biol. 7 (2006) 391-403
45. Batada N.N., et al. Evolutionary and physiological importance of hub proteins. PLoS Comput. Biol. 2 (2006) e88
46. Jensen L.J., et al. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 443 (2006) 594-597
47. de Lichtenberg U., et al. Evolution of cell cycle control: same molecular machines, different regulation. Cell Cycle 6 (2007) 1819-1825
48. Pawson T., and Nash P. Assembly of cell regulatory systems through protein interaction domains. Science 300 (2003) 445-452
49. Lavin M.F., and Gueven N. The complexity of p53 stabilization and activation. Cell Death Differ. 13 (2006) 941-950
50. Dartnell L., et al. Robustness of the p53 networks and biological hackers. FEBS Lett. 579 (2005) 3037-3042
51. Ho E., et al. Interactive three-dimensional visualization and contextual analysis of protein interaction networks. J. Proteome Res. 7 (2008) 104-112
52. Kummerfeld S.K., and Teichman S.A. Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet. 21 (2005) 25-30
53. Rasteiro R., and Pereira-Leal J.B. Multiple domain insertions and losses in the evolution of the Rab prenylation complex. BMC Evol. Biol. 7 (2007) 140
54. Fraser H.B., et al. Evolutionary rate in the protein interaction network. Science 296 (2002) 750-752