Abstract
Peptide recognition modules (PRMs) play critical roles in cellular processes, including differentiation, proliferation and cytoskeleton organization. PRMs normally bind to short linear motifs in protein ligands, and by so doing recruit proteins into signaling complexes. Based on the binding specificity profile of a PRM, one can predict putative natural interaction partners by searching genome databases. Candidate interaction partners can in turn provide clues to assemble potential in vivo protein complexes that the PRM may be involved with. Combinatorial peptide libraries have proven to be effective tools for profiling the binding specificities of PRMs. Herein, we describe high-throughput methods for the expression and purification of PRM proteins and the use of peptide-phage libraries for PRM specificity profiling. These high-throughput methods greatly expedite the study of PRM families on a genome-wide scale.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Pawson, T. & Scott, J. D. (1997). Signaling through scaffold, anchoring, and adaptor proteins. Science 278, 2075–80.
Lowenstein, E. J., Daly, R. J., Batzer, A. G., Li, W., Margolis, B., Lammers, R., Ullrich, A., Skolnik, E. Y., Bar-Sagi, D. & Schlessinger, J. (1992). The SH2 and SH3 domain-containing protein GRB2 links receptor tyrosine kinases to ras signaling. Cell 70, 431–42.
Tong, A. H., Drees, B., Nardelli, G., Bader, G. D., Brannetti, B., Castagnoli, L., Evangelista, M., Ferracuti, S., Nelson, B., Paoluzi, S., Quondam, M., Zucconi, A., Hogue, C. W., Fields, S., Boone, C. & Cesareni, G. (2002). A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295, 321–4.
Tonikian, R., Zhang, Y., Sazinsky, S. L., Currell, B., Yeh, J. H., Reva, B., Held, H. A., Appleton, B. A., Evangelista, M., Wu, Y., Xin, X., Chan, A. C., Seshagiri, S., Lasky, L. A., Sander, C., Boone, C., Bader, G. D. & Sidhu, S. S. (2008). A specificity map for the PDZ domain family. PLoS Biol 6, e239.
Huang, H., Li, L., Wu, C., Schibli, D., Colwill, K., Ma, S., Li, C., Roy, P., Ho, K., Songyang, Z., Pawson, T., Gao, Y. & Li, S. S. (2008). Defining the specificity space of the human SRC homology 2 domain. Mol Cell Proteomics 7, 768–84.
Li, L., Wu, C., Huang, H., Zhang, K., Gan, J. & Li, S. S. (2008). Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. Nucleic Acids Res 36, 3263–73.
Song, E., Gao, S., Tian, R., Ma, S., Huang, H., Guo, J., Li, Y., Zhang, L. & Gao, Y. (2006). A high efficiency strategy for binding property characterization of peptide-binding domains. Mol Cell Proteomics 5, 1368–81.
Rodriguez, M., Li, S. S., Harper, J. W. & Songyang, Z. (2004). An oriented peptide array library (OPAL) strategy to study protein-protein interactions. J Biol Chem 279, 8802–7.
Tonikian, R., Xin, X., Toret, C. P., Gfeller, D., Landgraf, C., Panni, S., Paoluzi, S., Castagnoli, L., Currell, B., Seshagiri, S., Yu, H., Winsor, B., Vidal, M., Gerstein, M. B., Bader, G. D., Volkmer, R., Cesareni, G., Drubin, D. G., Kim, P. M., Sidhu, S. S. & Boone, C. (2009). Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol 7, e1000218.
Machida, K., Thompson, C. M., Dierck, K., Jablonowski, K., Karkkainen, S., Liu, B., Zhang, H., Nash, P. D., Newman, D. K., Nollau, P., Pawson, T., Renkema, G. H., Saksela, K., Schiller, M. R., Shin, D. G. & Mayer, B. J. (2007). High-throughput phosphotyrosine profiling using SH2 domains. Mol Cell 26, 899–915.
Liu, B. A., Jablonowski, K., Raina, M., Arce, M., Pawson, T. & Nash, P. D. (2006). The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling. Mol Cell 22, 851–68.
Stiffler, M. A., Chen, J. R., Grantcharova, V. P., Lei, Y., Fuchs, D., Allen, J. E., Zaslavskaia, L. A. & MacBeath, G. (2007). PDZ domain binding selectivity is optimized across the mouse proteome. Science 317, 364–9.
Tonikian, R., Zhang, Y., Boone, C. & Sidhu, S. S. (2007). Identifying specificity profiles for peptide recognition modules from phage-Âdisplayed peptide libraries. Nat Protoc 2, 1368–86.
Acknowledgments
This work was supported by grant from the CIHR (MOP-93684) to S.S.S. We thank Andreas Ernst for figure preparation.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Huang, H., Sidhu, S.S. (2011). Studying Binding Specificities of Peptide Recognition Modules by High-Throughput Phage Display Selections. In: Cagney, G., Emili, A. (eds) Network Biology. Methods in Molecular Biology, vol 781. Humana Press. https://doi.org/10.1007/978-1-61779-276-2_6
Download citation
DOI: https://doi.org/10.1007/978-1-61779-276-2_6
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-275-5
Online ISBN: 978-1-61779-276-2
eBook Packages: Springer Protocols