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Mol. Cell. Biol. doi:10.1128/MCB.01491-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Screening for PTB Domain Binding Partners and Ligand Specificity Using Proteome-Derived NPxY Peptide Arrays

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada, M5G 1X5; Department of Molecular and Medical Genetics, University of Toronto

	Abstract

Modular interaction domains that recognize peptide motifs in target proteins can impart selectivity in signaling pathways. PTB domains are components of cytoplasmic docking proteins that bind cell surface receptors through NPxY motifs. We have employed a library of human proteome-derived NxxY sequences to explore PTB domain specificity and function. SPOTS peptide arrays were used to create a comprehensive matrix of receptor motifs that were probed with a set of ten diverse PTB domains. This approach confirmed that individual PTB domains have selective and distinct recognition properties, and provided a means to explore over 2500 potential PTB domain-NxxY interactions. The results correlated well with previously known associations between full-length proteins, and predicted novel interactions, as well as consensus binding data for specific PTB domains. Using the Ret, MuSK and ErbB2 receptor tyrosine kinases (RTKs), we show that interactions of these receptors with PTB domains predicted to bind by the NxxY arrays do occur in cells. Proteome-based peptide arrays can therefore identify networks of receptor interactions with scaffold proteins that may be physiologically relevant.

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