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Using Peptide Array to Identify Binding Motifs and Interaction Networks for Modular Domains

  • Shawn S.-C. Li
  • Chenggang Wu
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 570)

Abstract

Specific protein–protein interactions underlie all essential biological processes and form the basis of cellular signal transduction. The recognition of a short, linear peptide sequence in one protein by a modular domain in another represents a common theme of macromolecular recognition in cells, and the importance of this mode of protein–protein interaction is highlighted by the large number of peptide-binding domains encoded by the human genome. This phenomenon also provides a unique opportunity to identify protein–protein binding events using peptide arrays and complementary biochemical assays. Accordingly, high-density peptide array has emerged as a useful tool by which to map domain-mediated protein–protein interaction networks at the proteome level. Using the Src-homology 2 (SH2) and 3 (SH3) domains as examples, we describe the application of oriented peptide array libraries in uncovering specific motifs recognized by an SH2 domain and the use of high-density peptide arrays in identifying interaction networks mediated by the SH3 domain. Methods reviewed here could also be applied to other modular domains, including catalytic domains, that recognize linear peptide sequences.

Key words

Peptide arrays oriented peptide array library (or OPAL) SPOT celluspots domains src-homology 2 (or SH2) src-homology 3 (SH3) specificity linear motif protein–protein interaction (or PPI) interaction network 

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Copyright information

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

Authors and Affiliations

  • Shawn S.-C. Li
    • 1
  • Chenggang Wu
    • 1
  1. 1.Department of Biochemistry and the Siebens–Drake Medical Research Institute, Schulich School of Medicine and DentistryUniversity of Western OntarioLondonCanada

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