Protein-interaction mapping in search of effective drug targets

BioEssays

Volumn 27, Issue 9, 2005, Pages 958-969

  Chaudhuri, Amitabha ^a   Chant, John ^a  

^a GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BEVACIZUMAB; BORTEZOMIB; CETUXIMAB; DIACYLGLYCEROL; EPIDERMAL GROWTH FACTOR RECEPTOR; ERLOTINIB; GEFITINIB; GROWTH FACTOR RECEPTOR BOUND PROTEIN 2; IMATINIB; INOSITOL TRISPHOSPHATE; INSULIN RECEPTOR SUBSTRATE 1; KINESIN; LEUCINE ZIPPER PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE KINASE 7; PEGAPTANIB; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE; PHOSPHATIDYLINOSITOL 4,5 BISPHOSPHATE; PHOSPHOLIPASE C GAMMA; PLATELET DERIVED GROWTH FACTOR; PLATELET DERIVED GROWTH FACTOR RECEPTOR; PROTEIN KINASE B; PROTEIN P110; RAS PROTEIN; ROFECOXIB; SOS PROTEIN; STRESS ACTIVATED PROTEIN KINASE; TUMOR NECROSIS FACTOR RECEPTOR; UNINDEXED DRUG;

BIOINFORMATICS; CELL HYBRIDIZATION; DRUG PROTEIN BINDING; DRUG SCREENING; DRUG TARGETING; ENZYME ACTIVATION; ENZYME INACTIVATION; ENZYME INHIBITION; FEEDBACK SYSTEM; HIGH THROUGHPUT SCREENING; IMMUNOPRECIPITATION; MASS SPECTROMETRY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RECEPTOR BLOCKING; REVIEW; SIGNAL TRANSDUCTION;

ANIMALS; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; HUMANS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; SUBSTRATE SPECIFICITY;

EID: 26244460198     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20284     Document Type: Review

References (72)

1. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. 1999. From molecular to modular cell biology. Nature 402:C47-C52.
2. Buday L, Downward J. 1993. Epidermal growth factor regulates p21ras through the formation of a complex of receptor, Grb2 adapter protein, and Sos nucleotide exchange factor. Cell 73:611-620.
3. Gale NW, Kaplan S, Lowenstein EJ, Schlessinger J, Bar-Sagi D. 1993. Grb2 mediates the EGF-dependent activation of guanine nucleotide exchange on Ras. Nature 363:88-92.
4. Shpakov AO, Pertseva MN. 2000. Structural and functional characterization of insulin receptor substrate proteins and the molecular mechanisms of their interaction with insulin superfamily tyrosine kinase receptors and effector proteins. Membr Cell Biol 13:455-484.
5. Eungdamrong NJ, Iyengar R. 2004. Modeling cell signaling networks. Biology of the Cell 96:355-362.
6. Bhalla US, Ram PT, Iyengar R. 2002. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297:1018-1023.
7. Ferrell JE Jr. 2002. Self-perpetuating states in signal transduction. Positive feedback, double negative feedback and bistability. Curr Opin Cell Biol 14:140-148.
8. Parker PJ, Murray-Rust J. 2004. PKC at a glance. J Cell Sci 117:131-132.
9. Scheid MP, Woodgett JR. 2000. Protein kinases: Six degrees of separation? Current Biol 10:R191-R194.
10. Rodriguez-Viciana P, Warne PH, Dhand R, Vanhaesebroeck B, et al. 1994. Phosphatidylinositol-3-OH kinase as a direct target of Ras. Nature 370:527-532.
11. Rodriguez-Viciana P, Warne PH, Vanhaesebroeck B, Waterfield MD, Downward J. 1996. Activation of phosphoinositide 3-kinase by interaction with Ras and by point mutation. EMBO J 15:2442-2451.
12. Tari AM, Lopez-Berestein G. 2001. GRB2: a pivotal protein in signal transduction. Semin Oncol 28:142-147.
13. Nimnual A, Bar-Sagi D. 2002. The two hats of SOS. Sci STKE 145: PE36.
14. Kazalauskas A, Kashishian A, Cooper JA, Valius M. 1992. GTPase-activating protein and phosphatidylinositol 3-kinase bind to distinct region of platelet-derived growth factor receptor beta subunit. Mol Cell Biol 12:2532-2544.
15. Maruta H, Burgess AW. 1994. Regulation of the Ras signaling network. Bioessays 16:489-496.
16. Verhey KJ, Meyer D, Deehan R, Blenis J, et al. 2001. Cargo of kinesin identified as JIP scaffolding proteins and associated signaling molecules. J Cell Biol 152:959-970.
17. Goldstein LSB. 2001. When Worlds collide-Trafficking in JNK. Science 291:2102-2103.
18. Pawson T, Nash P. 2003. Assembly of cell regulatory systems through protein interaction domains. Science 300:445-452.
19. Venter JC, Adams MD, Myers EW, Li PW, et al. 2001. The sequence of the human genome. Science 291:1304-1351.
20. Lander ES, Linton LM, Birren B, Nusbaum C, et al. Initial sequencing and analysis of the human genome. Nature 409:860-921.
21. Ivan M, Kondo K, Yang H, Kim W, et al. 2001. HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing. Science 292:464-468.
22. Jaakkola P, Mole DR, Tian YM, Wilson MI, et al. 2001. Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. Science 292:468-472.
23. Collette Y, Gilles A, Pontarotti P, Olive D. 2003. A co-evolution perspective of the TNFSF and TNFRSF families in the immune system. Trends Immunol 24:387-394.
24. Marengere LE, Songyang Z, Gish GD, Schaller MD, et al. 1994. SH2 domain specificity and activity modified by a single residue. Nature 369: 502-505.
25. Pawson T. 2004. Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 116: 191-203.
26. Fields S, Song O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340:245-246.
27. Uetz P, Giot L, Cagney G, Mansfield TA, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.
28. Ito T, Chiba T, Ozawa R, Yoshida M, et al. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569-4574.
29. Rain JC, Selig L, De Reuse H, Battaglia V, et al. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409:211-215.
30. Giot L, Bader JS, Brouwer C, Chaudhuri A, et al. 2003. A protein interaction map of Drosophila melanogaster. Science 302:1727-1736.
31. Li S, Armstrong CM, Bertin N, Ge H, et al. 2004. A map of the interactome network of the metazoan C. elegans. Science 303:540-543.
32. Formstecher E, Aresta S, Collura V, Hamburger A, et al. 2005. Protein interaction mapping: A Drosophila case study. Genome Res 15:376-384.
33. Gavin AC, Bosche M, Krause R, Grandi P, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147.
34. Ho Y, Gruhler A, Heilbut A, Bader GD, et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183.
35. Bouwmeester T, Bauch A, Ruffner H, Angrand PO, et al. 2004. A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 6:97-105.
36. Blagoev B, Ong SE, Kratchmarova I, Mann M. 2003. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 22:1139-1145.
37. von Mering C, Krause R, Snel B, Cornell M, et al. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-403.
38. Bader GD, Hogue CW. 2002. Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 20:991-997.
39. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, et al. 2001. Global analysis of protein activities using proteome chips. Science 293:2101-2105.
40. Sidhu SS, Fairbrother WJ, Deshayes K. 2003. Exploring protein-protein interactions with phage display. Chembiochem 4:14-25.
41. Tong AH, Drees B, Nardelli G, Bader GD, et al. 2002. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295:321-324.
42. Thaminy S, Miller J, Stagljar I. 2004. The split-ubiquitin membrane-based yeast two-hybrid system. Methods Mol Biol 261:297-312.
43. Barrios-Rodiles M, Brown KR, Ozdamar B, Bose R, et al. 2005. High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307:1621-1625.
44. Ozdamar B, Bose R, Barrios-Rodiles M, Wang HR, et al. 2005. Regulation of the polarity protein Par6 by TGFbeta receptors controls epithelial cell plasticity. Science 307:1603-1609.
45. Bader JS, Chaudhuri A, Rothberg JM, Chant J. 2004. Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 22:78-85.
46. Salwinski L, Eisenberg D. 2003. Computational methods of analysis of protein-protein interactions. Curr Opin Struc Biol 13:377-382.
47. Jansen R, Gerstein M. 2004. Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol 7:535-545.
48. Schwikowski B, Uetz P, Fields S. 2000. A network of protein-protein interactions in yeast. Nat Biotechnol 18:1257-1261.
49. Ge H, Liu Z, Church GM, Vidal M. 2001. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29:482-486.
50. Deane CM, Salwinski L, Xenarios I, Eisenberg D. 2002. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 1:349-356.
51. Sprinzak E, Sattath S, Margalit H. 2003. How reliable are experimental protein-protein interaction data? J Mol Biol 327:919-923.
52. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2003. Evolutionary rate in the protein interaction network. Science 296:750-752.
53. Pagel P, Mewes HW, Frishman D. 2004. Conservation of protein-protein interactions-lessons from ascomycota. Trends Genet 20:72-76.
54. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, et al. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449-453.
55. Barabasi AL, Oltvai ZN. 2004. Network biology: understanding the cell's functional organization. Nat Rev Genet 5:101-113.
56. Maslov S, Sneppen K. 2002. Specificity and stability in topology of protein networks. Science 296:910-913.
57. Jeong H, Mason SP, Barabasi A-L, Oltvai ZN. 2001. Lethality and centrality in protein networks. Nature 411:41-42.
58. Frantz S. 2004. 2003 approvals: a year of innovation and upward trends. Nature Rev Drug Disc 3:103-105.
59. Frantz S. 2005. 2004 approvals: the demise of the blockbuster? Nature Rev Drug Disc 4:93-94.
60. Muhsin M, Graham J, Kirkpatrick P. 2004. Bevacizumab. Nature Rev Drug Disc 3:995-996.
61. Fine SL, Martin DF, Kirkpatrick P. 2005. Pegaptanib sodium. Nature Rev Drug Disc 4:187-188.
62. Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, et al. 2004. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. New Eng J Med 350:2129-2139.
63. Paez JG, Janne PA, Lee JC, Tracy S, et al. 2004. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 304:1497-1500.
64. Olson MK 2004. Are novel drugs more risky for patients than less novel drugs? J Health Econ 23:1135-1138.
65. Melinikova I, Golden J. 2004. Apoptosis-targeting therapies. Nature Rev Drug Disc 3:905-906.
66. Cappuzzo F, Magrini E, Ceresoli GL, Bartolini S, et al. 2004. Akt phosphorylation and gefitinib efficacy in patients with advanced non-small-cell lung cancer. J Natl Cancer Inst 96:1133-1141.
67. Sumitomo M, Asano T, Asakuma J, Asano T, et al. 2004. ZD1839 modulates paclitaxel response in renal cancer by blocking paclitaxel-induced activation of the epidermal growth factor receptor-extracellular signal-regulated kinase pathway. Clin Cancer Res 10:794-801.
68. Schurmann A, Mooney AF, Sanders LC, Sells MA, et al. 2000. p21-Activated kinase 1 phosphorylates the death agonist bad and protects cells from apoptosis. Mol Cell Biol 20:453-461.
69. Cotteret S, Jaffer ZM, Beeser A, Chernoff J. 2003. p21-Activated kinase 5 (Pak5) localizes to mitochondria and inhibits apoptosis by phosphorylating BAD. Mol Cell Biol 23:5526-5539.
70. Gnesutta N, Qu J, Minden A. 2001. The serine/threonine kinase PAK4 prevents caspase activation and protects cells from apoptosis. J Biol Chem 276:14414-14419.
71. Zheng TS, Schlosser SF, Dao T, Hingorani R, et al. 1998. Caspase-3 controls both cytoplasmic and nuclear events associated with Fas-mediated apoptosis in vivo. Proc Natl Acad Sci USA 95:13618-13623.
72. Thomas DA, Du C, Xu M, Wang X, Ley TJ. 2000. DFF45/ICAD can be directly processed by granzyme B during the induction of apoptosis. Immunity 12:621-632.