A Designed Peptide Chip: Protein Fingerprinting Technology with a Dry Peptide Array and Statistical Data Mining

  • Kenji Usui
  • Kin-ya Tomizaki
  • Hisakazu Mihara
Part of the Methods in Molecular Biology™ book series (MIMB, volume 570)


There has recently been increased interest in the potential for microarray technologies to study protein networks in a whole cell system within a single experiment. Protein-detecting microarrays are composed of numerous agents immobilized within a tiny area on solid surfaces to capture targeted proteins and to detect interactions in a high-throughput fashion. In this chapter, in order to extend the usability of peptide microarrays, we describe a novel dry peptide microarray format to obtain protein fingerprint (PFP) data sets and a statistical PFP data manipulation technique to quantitatively analyze targeted proteins.

Key words

Protein-detecting chip designed peptide dry peptide array fluorimetric assay statistical data mining 


  1. 1.
    Kambhampati, D. (2003) Protein Microarray Technology. Wiley-VCH, Weinheim.CrossRefGoogle Scholar
  2. 2.
    Fung, E. T. (2004) Protein Arrays: Methods and Protocols; Methods in Molecular Biology vol 264. Humana Press, New Jersey.Google Scholar
  3. 3.
    Tomizaki, K.-Y., Usui, K., Mihara, H. (2005) Protein-detecting microarrays: Current accomplishments and requirements. ChemBioChem 6, 782–799.PubMedCrossRefGoogle Scholar
  4. 4.
    Kodadek, T. (2001) Protein microarrays: Prospects and problems. Chem. Biol. 8, 105–115.PubMedCrossRefGoogle Scholar
  5. 5.
    Uttamchandani, M., Wang, J., Yao, S. Q. (2006) Protein and small molecule microarrays: Powerful tools for high-throughput proteomics. Mol. BioSyst. 2, 58–68.PubMedCrossRefGoogle Scholar
  6. 6.
    Usui, K., Tomizaki, K.-Y., Ohyama, T., Nokihara, K., Mihara, H. (2006) A novel peptide microarray for protein detection and analysis utilizing a dry peptide array system. Mol. Biosyst. 2, 113–121.PubMedCrossRefGoogle Scholar
  7. 7.
    Takahashi, M., Nokihara, K., Mihara, H. (2003) Construction of a protein-detection system using a loop peptide library with a fluorescence label. Chem. Biol. 10, 53–60.PubMedCrossRefGoogle Scholar
  8. 8.
    Usui, K., Takahashi, M., Nokihara, K., Mihara, H. (2004) Peptide arrays with designed alpha-helical structures for characterization of proteins from FRET fingerprint patterns. Mol. Divers. 8, 209–218.PubMedCrossRefGoogle Scholar
  9. 9.
    Usui, K., Ojima, T., Takahashi, M., Nokihara, K., Mihara, H. (2004) Peptide arrays with designed secondary structures for protein characterization using fluorescent fingerprint patterns. Biopolymers 76, 129–139.PubMedCrossRefGoogle Scholar
  10. 10.
    Usui, K., Ojima, T., Tomizaki, K.-Y., Mihara, H. (2005) A designed glycopeptide array for characterization of sugar-binding proteins toward a glycopeptide chip technology. NanoBiotechnology 1, 191–200.CrossRefGoogle Scholar
  11. 11.
    Usui, K., Tomizaki, K.-Y., Mihara, H. (2006) Protein-fingerprint data mining of a designed alpha-helical peptide array. Mol. Biosyst. 2, 417–420.PubMedCrossRefGoogle Scholar
  12. 12.
    Usui, K., Tomizaki, K.-Y., Mihara, H. (2007) Screening of alpha-helical peptide ligands controlling a calcineurin-phosphatase activity. Bioorg. Med. Chem. Lett. 17, 167–171.PubMedCrossRefGoogle Scholar
  13. 13.
    Chan, W. C., White, P. D. (2000) Fmoc solid phase peptide synthesis: A practical approach. New York, Oxford University Press.Google Scholar
  14. 14.
    Wahler, D., Badalassi, F., Crotti, P., Reymond, J. L. (2002) Enzyme fingerprints of activity, and stereo- and enantioselectivity from fluorogenic and chromogenic substrate arrays. Chemistry 8, 3211–3228.PubMedCrossRefGoogle Scholar
  15. 15.
    Cox, J. A., Comte, M., Fitton, J. E., DeGrado, W. F. (1985) The interaction of calmodulin with amphiphilic peptides. J. Biol. Chem. 260, 2527–2534.PubMedGoogle Scholar
  16. 16.
    O'Neil, K. T., DeGrado, W. F. (1990) How calmodulin binds its targets: sequence independent recognition of amphiphilic alpha-helices. Trends. Biochem. Sci. 15, 59–64.PubMedCrossRefGoogle Scholar
  17. 17.
    Maulet, Y., Cox, J. A. (1983) Structural changes in melittin and calmodulin upon complex formation and their modulation by calcium. Biochemistry 22, 5680–5686.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Kenji Usui
    • 1
  • Kin-ya Tomizaki
    • 2
  • Hisakazu Mihara
    • 1
  1. 1.Graduate School of Bioscience and BiotechnologyTokyo Institute of TechnologyYokohamaJapan
  2. 2.Innovative Materials and Processing Research Center and Department of Materials ChemistryRyukoku UniversitySetaJapan

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