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The Functional Interaction Trap: A Novel Strategy to Study Specific Protein-Protein Interactions

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Methods in Proteome and Protein Analysis

Part of the book series: Principles and Practice ((PRINCIPLES))

Abstract

Protein-protein interactions play a central role in almost all aspects of the living cell, and understanding these interactions holds the key to understanding a host of cellular processes. Whether it is an enzyme modifying its substrate, the assembly of subunits of a multiprotein complex, the recognition and binding of a specific ligand, or the polymerization of monomeric subunits such as those of actin, protein-protein interactions are essential for regulating and organizing virtually all physiological responses. Much recent research has focused on understanding these interactions in detail, and while progress has been rapid in many areas, it is clear that new tools to study specific protein-protein interactions are sorely needed. For example, our ability to identify actual or potential protein-protein interactions has outpaced our ability to validate the functional significance of those interactions, or of post-translational modifications that might result from those interactions. In this article we will discuss the Functional Interaction Trap (FIT) approach [13, 44], a novel proteomic tool designed to elucidate the physiological outputs that are mediated by specific protein-protein interactions or post-translational modifications in cellular signaling. We will also discuss in detail a specific application of the FIT approach, where it is used to dissect the functional consequences of tyrosine phosphorylation of specific substrates in the cell.

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References

  1. Arndt KM, Pelletier JN, Müller KM, Alb er T, Michnick SW, Plückthun A (2000) A heterodimeric coiled-coil peptide pair selected in vivo from a designed library-versuslibrary ensemble. J. Mol. Biol. 295, 627–639

    Article  PubMed  CAS  Google Scholar 

  2. Belshaw PJ, Ho SN, Crabtree GR, Schreiber SL (1996) Controlling protein association and subcellular localization with a synthetic ligand that induces heterodimerization of proteins. Proc. Nat. Acad. Sci. USA 93, 4604–4607

    Article  PubMed  CAS  Google Scholar 

  3. Bouton AH, Riggins RB, Bruce-Staskal PJ (2001) Functions of the adapter protein Cas: signal convergence and the determination of cellular responses. Oncogene 20, 6448–6458

    Article  PubMed  CAS  Google Scholar 

  4. Brizuela L, Braun P, LaBaer J (2001) FLEXGene repository: from sequenced genomes to gene repositories for high-throughput functional biology and proteomics. Mol. Biochem. Parasitol. 118, 155–65

    Google Scholar 

  5. Brown JL, Stowers L, Baer M, Trejo J, Coughlin S, Chant J (1996) Human Ste20 homologue hPAK1 links GTPases to the JNK MAP kinase pathway. Curr. Biol. 6, 598–605

    Google Scholar 

  6. Bruckner K, Klein R (1998) Signaling by Eph receptors and their ephrin ligands. Curr Opin Neurobiol 8, 375–382

    Article  PubMed  CAS  Google Scholar 

  7. Buday L (1999) Membrane-targeting of signaling molecules by SH2/SH3 domain-containing adaptor proteins. Biochim Biophys Acta 1422, 187–204

    Article  PubMed  CAS  Google Scholar 

  8. Chen X, Vinkemeier U, Zhao Y, Jeruzalmi D, Darnell JEJ, Kuriyan J (1998) Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA. Cell 93, 827–839

    Article  PubMed  CAS  Google Scholar 

  9. Druker BJ (2002) Inhibition of the Bcr-Abl tyrosine kinase as a therapeutic strategy for CML. Oncogene 21, 8541–8546

    Article  PubMed  CAS  Google Scholar 

  10. Druker BJ, Talpaz M, Resta DJ, Peng B, Buchdunger E, Ford JM, Lydon NB, Kantarjian H, Capdeville R, Ohno-Jones S, Sawyers CL (2001) Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N. Engl. J. Med. 344, 1084–1086

    Google Scholar 

  11. Feller SM (2001) Crk family adaptors-signalling complex formation and biological roles. Oncogene 20, 6348–6371

    Article  PubMed  CAS  Google Scholar 

  12. Franco R, Ferre S, Agnati L, Torvinen M, Gines S, Hillion J, Casado V, Lledo P, Zoli M, Lluis C, Fuxe K (2000) Evidence for adenosine/dopamine receptor interactions: indications for heteromerization. Neuropsychopharmacology 23 (4 Suppl), S50–59

    Article  PubMed  CAS  Google Scholar 

  13. Fujiwara K, Poikonen K, Aleman L,Valtavaara M, Saksela K, Mayer BJ (2002) A single-chain antibody/epitope system for functional analysis of protein-protein interactions. Biochemistry 41, 12729–12738

    Google Scholar 

  14. Ho SN, Biggar SR, Spencer DM, Schreiber SL, Crabtree GR (1996) Dimeric ligands define a role for transcriptional activation domains in reinitiation. Nature 382, 822–826

    Article  PubMed  CAS  Google Scholar 

  15. Hochhaus A, Kreil S, Corbin AS, La Rosee P, Muller MC, Lahaye T, Hanfstein B, Schoch C, Cross NC, Berger U, Gschaidmeier H, Druker BJ, Hehlmann R (2002) Molecular and chromosomal mechanisms of resistance to imatinib (STI571) therapy. Leukemia 16, 2190–2196

    Article  PubMed  CAS  Google Scholar 

  16. Hunter T (2000) Signaling-2000 and beyond. Cell 100, 113–127

    Article  PubMed  CAS  Google Scholar 

  17. Hunter T, Sefton BM (1980) Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc Natl Acad Sci, USA 77, 1311–1315

    Google Scholar 

  18. Klemke RL, Leng J, Molander R, Brooks PC, Vuori K, Cheresh DA (1998) CAS/Crk coupling serves as a “molecular switch” for induction of cell migration. J. Cell Biol. 140, 961–972

    Article  PubMed  CAS  Google Scholar 

  19. Klinghoffer RA, Sachsenmaier C, Cooper JA, Soriano P (1999) Src family kinases are required for integrin but not PDGFR signal transduction. EMBO 118, 2459–2471

    Google Scholar 

  20. Koleske AJ, Gifford AM, Scott ML, Nee M, Bronson RT, Miczek KA, Baltimore D (1998) Essential roles for the Abl and Arg tyrosine kinases in neurulation. Neuron 21, 1259–1272

    Article  PubMed  CAS  Google Scholar 

  21. Kullander K, Klein, R. (2002) Mechanisms and functions of Eph and ephrin signalling. Nat Rev Mol Cell Biol 3, 475–486

    Article  PubMed  CAS  Google Scholar 

  22. Kuriyan J, Cowburn D (1997) Modular peptide recognition domains in eukaryotic signaling. Annu. Rev. Biophys. Biomol. Struct. 26, 259–288

    Google Scholar 

  23. Leaman DW, Pisharody S, Flickinger TW, Commane MA, Schlessinger J, Kerr IM, Levy DE, Stark GR (1996) Roles of JAKs in activation of STATs and stimulation of cfos gene expression by epidermal growth factor. Mol. Cell. Biol. 16, 369–375

    Google Scholar 

  24. Lee FJS, Xue S, Pei L, Vukusic B, Chery N, Wang Y, Wang YT, Niznik HB, Liu F (2002) Dual regulation of NMDA receptor functions by direct protein-protein interactions with the dopamine D1 receptor. Cell 111, 219–230

    Article  PubMed  CAS  Google Scholar 

  25. Lee SP, O’Dowd BF, Ng GY, Varghese G, Akil H, Mansour A, Nguyen T, George SR (2000) Inhibition of cell surface expression by mutant receptors demonstrates that D2 dopamine receptors exist as oligomers in the cell. Mol Pharmacol 58, 120–128

    PubMed  CAS  Google Scholar 

  26. Liu F, Wan Q, Pristupa ZB, Yu XM, Wang YT, Niznik HB (2000) Direct protein-protein coupling enables cross-talk between dopamine D5 and gamma-aminobutyric acid A receptors. Nature 403, 274–280

    Article  PubMed  CAS  Google Scholar 

  27. Lupas A (1996) Coiled coils: new structures and new functions. Trends Biochem Sci 21, 375–382

    PubMed  CAS  Google Scholar 

  28. Manning BD, Cantley LC (2002) Hitting the target: emerging technologies in the search for kinase substrates. Sci STKE 2002(162), PE49

    Google Scholar 

  29. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S (2002) The protein kinase complement of the human genome. Science 298, 1912–1934

    Article  PubMed  CAS  Google Scholar 

  30. Marshall CJ (1995) Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80, 179–185

    Article  PubMed  CAS  Google Scholar 

  31. Mayer BJ (2001) SH3 domains: complexity in moderation. J. Cell Sci. 114, 1253–1263

    PubMed  CAS  Google Scholar 

  32. Mayer BJ, Hirai H, Sakai R (1995) Evidence that SH2 domains promote processive phosphorylation by protein-tyrosine kinases. Curr. Biol. 5, 296–305

    Google Scholar 

  33. Mayer BJ, Jackson PK, Van Etten RA, Baltimore D (1992) Point mutations in the abl SH2 domain coordinately impair phosphotyrosine binding in vitro and transforming activity in vivo. Mol. Cell. Biol. 12, 609–618

    Google Scholar 

  34. Panetti TS (2002) Tyrosine phosphorylation of paxillin, FAK, and p130Cas: effects on cell spreading and migration. Front. Biosci. 7, d143–150

    Article  PubMed  CAS  Google Scholar 

  35. Pawson T, Nash P (2000) Protein-protein interactions define specificity in signal transduction. Genes Dey. 14, 1027–1047

    CAS  Google Scholar 

  36. Pawson T, Scott JD (1997) Signaling through scaffold, anchoring, and adaptor proteins. Science 278, 2075–2080

    Article  PubMed  CAS  Google Scholar 

  37. Pellicena P, Miller WT (2002) Coupling kinase activation to substrate recognition in Src-family tyrosine kinases. Front. Biosci. 7, d256–267

    Article  PubMed  CAS  Google Scholar 

  38. Pellicena P, Miller WT (2001) Processive phosphorylation of p 1 30Cas by Src depends on SH3-polyproline interactions. J. Biol. Chem. 276, 28190–28196

    Google Scholar 

  39. Ponticelli AS, Whitlock CA, Rosenberg N, Witte ON (1982) In vivo tyrosine phosphorylations of the abelson virus transforming protein are absent in its normal cellular homolog. Cell 29, 953–960

    Article  PubMed  CAS  Google Scholar 

  40. Reddy EP, Smith MJ, Srinivasan A (1983) Nucleotide sequence of Abelson murine leukemia virus genome: Structural similarity of its transforming gene product to other one gene products with tyrosine-specific kinase activity. Proc. Natl. Acad. Sci. USA 80, 3623–3627

    Google Scholar 

  41. Rocheville M, Lange DC, Kumar U, Patel SC, Patel RC, Patel YC (2000) Receptors for dopamine and somatostatin: formation of hetero-oligomers with enhanced functional activity. Science 288, 154–157

    Article  PubMed  CAS  Google Scholar 

  42. Roovers K, Assoian RK (2000) Integrating the MAP kinase signal into the G1 phase cell cycle machinery. Bioessays 22, 818–826

    Article  PubMed  CAS  Google Scholar 

  43. Scarselli M, Novi F, Schallmach E, Lin R, Baragli A, Colzi A, Griffon N, Corsini GU, Sokoloff P, Levenson R, Vogel Z, Maggio R (2001) D2/D3 dopamine receptor heterodimers exhibit unique functional properties. J Biol Chem 276, 30308–30314

    Article  PubMed  CAS  Google Scholar 

  44. Sharma A, Antoku S, Fujiwara K, Mayer BJ (2003) Functional interaction trap: A strategy for validating the functional consequences of tyrosine phosphorylation of specific substrates in vivo. Mol Cell Proteomics (in press), published online on 29th September, 2003

    Google Scholar 

  45. Sefton BM, Hunter T, Beemon K, and Eckhart W (1980) Evidence that the phosphorylation of tyrosine is essential for cellular transformation by Rous sarcoma virus. Cell 20, 807–816

    Article  PubMed  CAS  Google Scholar 

  46. Sefton BM, Hunter, T., and Beemon, K. (1980) Relationship of polypeptide products of the transforming gene of Rous sarcoma virus and the homologous gene of vertebrates. Proc Natl Acad Sci, USA 77, 2059–2063

    Google Scholar 

  47. Shokat KM (1995) Tyrosine kinases: modular signaling enzymes with tunable specificities. Chem. Biol. 2, 509–514

    Article  PubMed  CAS  Google Scholar 

  48. Smith JM, Mayer BJ (2002) Abl: mechanisms of regulation and activation. Front. Biosci. 7, d31–42

    PubMed  CAS  Google Scholar 

  49. Thomas SM, Brugge J (1997) Cellular functions regulated by Src family kinases. Ann. Rev. Cell Dev. Biol. 13, 513–609

    Google Scholar 

  50. Tian M, Martin GS (1997) The role of the Src homology domains in morphological transformation by v-src. Mol. Biol. Cell 8, 1183–1193

    Google Scholar 

  51. Turkson J, Jove R (2000) STAT proteins: novel molecular targets for cancer drug discovery. Oncogene 19, 6613–6626

    Article  PubMed  CAS  Google Scholar 

  52. Wang JYJ, Baltimore D (1983) Cellular RNA homologous to the abelson murine leukemia virus transforming gene: expression and relationship to the viral sequence. Mol. Cell. Biol. 3, 773–779

    PubMed  CAS  Google Scholar 

  53. Yano H, Uchida H, Iwasaki T, Mukai M, Akedo H, Nakamura K, Hashimoto S, Sabe H (2000) Paxillin alpha and Crk-associated substrate exert opposing effects on cell migration and contact inhibition of growth through tyrosine phosphorylation. Proc. Natl. Acad. Sci., USA 97, 9076–9081

    Article  PubMed  CAS  Google Scholar 

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Authors
  1. Alok Sharma
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  2. Susumu Antoku
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  3. Bruce J. Mayer
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Editor information

Editors and Affiliations

  1. Technische Fachhochschule Berlin, Seestraße 65, 13347, Berlin, Germany

    Roza Maria Kamp

  2. Instituto de Biomedicina de Valencia, C.S.I.C., Jaime Roig 11, 46010, Valencia, Spain

    Juan J. Calvete

  3. School of Chemistry, Laboratory of Biochemistry, Aristotle University of Thessaloniki, 54006, Thessaloniki, Greece

    Theodora Choli-Papadopoulou

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© 2004 Springer-Verlag Berlin Heidelberg

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Sharma, A., Antoku, S., Mayer, B.J. (2004). The Functional Interaction Trap: A Novel Strategy to Study Specific Protein-Protein Interactions. In: Kamp, R.M., Calvete, J.J., Choli-Papadopoulou, T. (eds) Methods in Proteome and Protein Analysis. Principles and Practice. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-08722-0_11

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  • DOI: https://doi.org/10.1007/978-3-662-08722-0_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-05779-3

  • Online ISBN: 978-3-662-08722-0

  • eBook Packages: Springer Book Archive

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