Skip to main content

Fabrication of Protein Function Microarrays for Systems-Oriented Proteomic Analysis

  • Protocol
Chemical Genomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 310))

Abstract

Protein microarrays have many potential applications in high-throughput analysis of protein function. However, simple, reproducible, and robust methods for array fabrication are required. Here we discuss the background to different routes to array fabrication and describe in detail one approach in which the purification and immobilization procedures are combined into a single step, dramatically simplifying the array fabrication process. We illustrate this approach by reference to the creation of an array of p53 variants, and discuss methods for assay and data analysis on such arrays.

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 109.00
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. Mulder, N. J., Apweiler, R., Attwood, T. K., et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucl. Acid Res. 31, 315–318.

    Article  CAS  Google Scholar 

  2. Wise, E. Y., Yew, W. S., Babbitt, P. C., Gerlt, J. A., and Rayment, I. (2002) Homologous (β/α)8-barrel enzymes that catalyze unrelated reactions: orotidine 5′-monophosphate decarboxylase and 3-keto-l-gulonate 6-phosphate decarboxylase. Biochemistry 41, 3861–3869.

    Article  PubMed  CAS  Google Scholar 

  3. Schmidt, D. M. Z., Mundorff, E. C., Dojka, M., et al. (2003) Evolutionary potential of (β/α)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry 42, 8387–8393.

    Article  PubMed  CAS  Google Scholar 

  4. The Genome International Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.

    Article  Google Scholar 

  5. MacBeath, G. (2002) Protein microarrays and proteomics. Nat. Genet. 32, 526–532.

    Article  PubMed  CAS  Google Scholar 

  6. Boutell, J. M., Hart, D. J., Gobder, B. L. J., Kozlowski, R. Z., and Blackburn, J. M. (2004) Analysis of the effect of clinically relevant mutations on p53 function using protein microarray technology. Proteomics 4, 1950–1958.

    Article  PubMed  CAS  Google Scholar 

  7. Kodadek, T. (2001) Protein microarrays: prospects and problems. Chem. Biol. 8, 105–115.

    Article  PubMed  CAS  Google Scholar 

  8. Predki, P. (2004) Functional protein microarrays: ripe for discovery. Curr. Opin. Chem. Biol. 8, 8–13.

    Article  PubMed  CAS  Google Scholar 

  9. Zhu, H., Klemic, J. F., Chang, S., et al. (2000) Analysis of yeast protein kinases using protein chips. Nat. Genet. 26, 283–289.

    Article  PubMed  CAS  Google Scholar 

  10. Zhu, H., Bilgin, M., Bangham, R., et al. (2001) Global analysis of protein activities using proteome chips. Science 293, 2101–2105.

    Article  PubMed  CAS  Google Scholar 

  11. Michaud, G. A., Salcius, M., Zhou, F., et al. (2003) Analyzing antibody specificity with whole proteome microarrays. Nat. Biotech. 21, 1509–1512.

    Article  CAS  Google Scholar 

  12. Fang, Y., Lahiri, J., and Picard, L. (2003) G-protein-coupled receptor microarrays for drug discovery. Drug Discovery Today 8, 755–761.

    Article  PubMed  CAS  Google Scholar 

  13. MacBeath, G. and Schreiber, S. L. (2000) Printing proteins as microarrays for highthroughput function determination. Science 289, 1760–1763.

    PubMed  CAS  Google Scholar 

  14. Angenendt, P., Glokler, J., Sobek, J., Lehrach, H., and Cahill, D. J. (2003) Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications. J. Chromatogr. A 1009, 97–104.

    Article  PubMed  CAS  Google Scholar 

  15. Koopmann, J.-O. and Blackburn, J. M. (2003) High affinity capture surface for MALDI compatible protein microarrays. Rapid Commun. Mass Spectrom. 17, 1–8.

    Article  Google Scholar 

  16. Varley, J. M., Evans, D. G. R., and Birch, J. M. (1997) Li-Fraumeni syndrome—a molecular and clinical review. Br. J. Cancer 76, 1–14.

    Article  PubMed  CAS  Google Scholar 

  17. Birch, J. M., Alston, R. D., McNally, R. J., et al. (2001) Relative frequency and morphology of cancers in carriers of germline TP53 mutations. Oncogene 20, 4621–4628.

    Article  PubMed  CAS  Google Scholar 

  18. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning, A Laboratory Manual, Second ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

    Google Scholar 

  19. Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714–2723.

    Article  PubMed  CAS  Google Scholar 

  20. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248–254.

    Article  PubMed  CAS  Google Scholar 

  21. Ryan, K. M., Phillips, A. C., and Vousden, K. H. (2001) Regulation and function of the p53 tumor suppressor protein. Curr. Opin. Cell Biol. 13, 332–337.

    Article  PubMed  CAS  Google Scholar 

  22. Vogelstein, B., Lane, D., and Levine, A. J. (2000) Surfing the p53 network. Nature 408, 307–310.

    Article  PubMed  CAS  Google Scholar 

  23. Data provided by Amersham Biosciences.

    Google Scholar 

  24. Choi-Rhee, E. and Cronan, J. E. (2003) The biotin carboxylase-biotin carboxyl carrier protein complex of Escherichia coli acetyl-CoA carboxylase. J. Biol. Chem. 278, 30,806–30,812

    Article  PubMed  CAS  Google Scholar 

  25. Cull, M. G. and Schatz, P. J. (2000) Biotinylation of proteins in vivo and in vitro using small peptide tags. Methods Enzymol. 326, 430–440.

    Article  PubMed  CAS  Google Scholar 

  26. Chapman-Smith, A. and Cronan, J. E. (1999) The enzymatic biotinylation of proteins: a posttranslational modification of exceptional specificity. Trends Biochem. Sci. 24, 359–363.

    Article  PubMed  CAS  Google Scholar 

  27. Athappilly, F. K. and Hendrickson, W. A. (1995) Structure of the biotinyl domain of acetylcoenzyme A carboxylase determined by MAD phasing. Structure 3, 1407–1419.

    Article  PubMed  CAS  Google Scholar 

  28. Berliner, E., Mahtani, H. K., Karki, S., et al. (1994) Microtubule movement by a biotinated kinesin bound to streptavidin-coated surface. J. Biol. Chem. 269, 8610–8615.

    PubMed  CAS  Google Scholar 

  29. Lerner, C. G. and Saiki, A. Y. (1996) Scintillation proximity assay for human DNA topoisomerase I using recombinant biotinyl-fusion protein produced in baculovirus-infected insect cells. Anal. Biochem. 240, 185–196.

    Article  PubMed  CAS  Google Scholar 

  30. Parrott, M. B. and Barry M. A. (2001) Metabolic biotinylation of secreted and cell surface proteins from mammalian cells. Biochem. Biophys. Res. Commun. 281, 993–1000

    Article  PubMed  CAS  Google Scholar 

  31. Lue, R. Y., Chen, G. Y., Hu, Y., Zhu, Q., and Yao, S. Q. (2004) Versatile protein biotinylation strategies for potential high-throughput proteomics. J. Am. Chem. Soc. 126, 1055–1062.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Drs. Joe Boutell, Ben Godber, and Mike Dyson for their help in generating the data and the procedures detailed in this chapter, and Dr. Roland Kozlowski for helpful discussion along the way. This work was supported by Procognia Ltd.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Humana Press Inc.

About this protocol

Cite this protocol

Blackburn, J.M., Hart, D.J. (2005). Fabrication of Protein Function Microarrays for Systems-Oriented Proteomic Analysis. In: Zanders, E.D. (eds) Chemical Genomics. Methods in Molecular Biology™, vol 310. Humana Press. https://doi.org/10.1007/978-1-59259-948-6_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-59259-948-6_14

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-399-2

  • Online ISBN: 978-1-59259-948-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics