Skip to main content

Characterization of Protein-Protein Interactions

Application to the Understanding of Peroxisome Biogenesis

  • Protocol
Pichia Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 389))

Abstract

With the approaching completion of the Pichia pastoris genome, a greater emphasis will have to be placed on the proteome and the protein-protein interactions between its constituents. This chapter discusses methods that have been used for the study of such interactions among both soluble and membrane-associated proteins in peroxisome biogenesis. The procedures are equally applicable to other cellular processes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Faber, K. N., Heyman, J. A., and Subramani, S. (1998) Two AAA family peroxins, PpPex1p and PpPex6p, interact with each other in an ATP-dependent manner and are associated with different subcellular membranous structures distinct from peroxisomes. Mol Cell Biol 18, 936–943.

    CAS  PubMed  Google Scholar 

  2. Snyder, W. B., Koller, A., Choy, A. J., and Subramani, S. (2000) The peroxin Pex19p interacts with multiple, integral membrane proteins at the peroxisomal membrane. J Cell Biol 149, 1171–1177.

    Article  CAS  PubMed  Google Scholar 

  3. Hazra, P. P., Suriapranata, I., Snyder, W. B., and Subramani, S. (2002) Peroxisome remnants in pex3Δ cells and the requirement of Pex3p for interactions between the peroxisomal docking and translocation subcomplexes. Traffic 3, 560–74.

    Article  CAS  PubMed  Google Scholar 

  4. Graham, T. T. (2004) Unit 8: Protein labeling and immunoprecipitation. 8.5 Immunoprecipitation. In Short protocols in cell biology: a compendium of methods from Current Protocols in Cell Biology (ed. Bonifacio, J.S., Dasso, M., Harford, M., Lippincott-Schwartz, J., and Yamada, K.M., eds.), pp. 8–17. John Wiley & Sons, Hoboken, NJ, USA, pp. 8–17.

    Google Scholar 

  5. Gavin, A. C., Bosche, M., Krause, R., et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147.

    Article  CAS  PubMed  Google Scholar 

  6. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., and Séraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030–1032.

    Article  CAS  PubMed  Google Scholar 

  7. Puig, O., Caspary, F., Rigaut, G., et al. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218–229.

    Article  CAS  PubMed  Google Scholar 

  8. Higgins, D. R., Busser, K., Comiskey, J., Whittier, P. S., Purcell, T. J., and Hoeffler, J. P. (1998) Small vectors for expression based on dominant drug resistance with direct multicopy selection. Methods Mol. Biol. 103, 41–53.

    CAS  PubMed  Google Scholar 

  9. Miller, J. and Stagljar, I. (2004) Using the yeast two-hybrid system to identify interacting proteins. Methods Mol. Biol. 261, 247–262.

    CAS  PubMed  Google Scholar 

  10. McAlister-Henn, L., Gibson, N., and Panisko, E. (1999) Applications of the yeast two-hybrid system. Methods 19, 330–337.

    Article  CAS  PubMed  Google Scholar 

  11. Hu, J. C., Kornacker, M. G., and Hochschild, A. (2000) Escherichia coli one-and two-hybrid systems for the analysis and identification of protein-protein interactions. Methods 20, 80–94.

    Article  CAS  PubMed  Google Scholar 

  12. Dove, S. L., Joung, J. K., and Hochschild, A. (1997) Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 386, 627–630.

    Article  CAS  PubMed  Google Scholar 

  13. Joung, J. K., Ramm, E. I., and Pabo, C. O. (2000) A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc. Natl. Acad. Sci. USA 97, 7382–7387.

    Article  CAS  PubMed  Google Scholar 

  14. Karimova, G., Pidoux, J., Ullmann, A., and Ladant, D. (1998) A bacterial twohybrid system based on a reconstituted signal transduction pathway. Proc. Natl. Acad. Sci. USA 95, 5752–5756.

    Article  CAS  PubMed  Google Scholar 

  15. Shaywitz, A. J., Dove, S. L., Kornhauser, J. M., Hochschild, A., and Greenberg, M. E. (2000) Magnitude of the CREB-dependent transcriptional response is determined by the strength of the interaction between the kinase-inducible domain of CREB and the KIX domain of CREB-binding protein. Mol. Cell. Biol. 20, 9409–9422.

    Article  CAS  PubMed  Google Scholar 

  16. Jobling, M. G. and Holmes, R. K. (2000) Identification of motifs in cholera toxin A1 polypeptide that are required for its interaction with human ADP-ribosylation factor 6 in a bacterial two-hybrid system. Proc. Natl. Acad. Sci. USA 97, 14,662–14,667.

    Article  CAS  PubMed  Google Scholar 

  17. Ghys, K., Fransen, M., Mannaerts, G. P., and Van Veldhoven, P. P. (2002) Functional studies on human Pex7p: subcellular localization and interaction with proteins containing a peroxisome-targeting signal type 2 and other peroxins. Biochem. J 365, 41–50.

    Article  CAS  PubMed  Google Scholar 

  18. Fransen, M., Brees, C., Ghys, K., et al. (2002) Analysis of mammalian peroxin interactions using a non-transcription-based bacterial two-hybrid Assay. Mol. Cell. Proteomics 1, 243–252.

    Article  CAS  PubMed  Google Scholar 

  19. Dautin, N., Karimova, G., and Ladant, D. (2003) Human immunodeficiency virus (HIV) type 1 transframe protein can restore activity to a dimerization-deficient HIV protease variant. J. Virol. 77, 8216–8226.

    Article  CAS  PubMed  Google Scholar 

  20. Johnsson, N. and Varshavsky, A. (1994) Split ubiquitin as a sensor of protein interactions in vivo. Proc. Natl. Acad. Sci. USA 91, 10,340–10,344.

    Article  CAS  PubMed  Google Scholar 

  21. Fetchko, M. and Stagljar, I. (2004) Application of the split-ubiquitin membrane yeast two-hybrid system to investigate membrane protein interactions. Methods 32, 349–362.

    Article  CAS  PubMed  Google Scholar 

  22. Thaminy, S., Miller, J., and Stagljar, I. (2004) The split-ubiquitin membrane-based yeast two-hybrid system. Methods Mol. Biol. 261, 297–312.

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Leon, S., Suriapranata, I., Yan, M., Rayapuram, N., Patel, A., Subramani, S. (2007). Characterization of Protein-Protein Interactions. In: Cregg, J.M. (eds) Pichia Protocols. Methods in Molecular Biology, vol 389. Humana Press. https://doi.org/10.1007/978-1-59745-456-8_16

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-456-8_16

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-429-6

  • Online ISBN: 978-1-59745-456-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics