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= The human SH3 domain specificity map reveals a wide variety of novel non-canonical peptide-binding specificities =
Joan Teyra 1+, Haiming Huang 1,3+, Shobhit Jain 1,2, Taehyung Kim 1,2, Xinyu Guan 4, Aiping Dong 4, Yanli Liu 4,5, Jinrong Min 4,5, Yufeng Tong 4, Philip M. Kim 1,2,3, Gary D. Bader 1,2,3 and Sachdev S. Sidhu 1,3,*

== Abstract ==
SH3 domains are small protein modules that mediate protein-protein interactions in many eukaryotic signal transduction pathways, including cell growth regulation, endocytosis and cytoskeleton control. Canonically, SH3 domains are thought to act via physical binding to poly-proline-containing linear regions in proteins. Although these binding preferences have been confirmed for the majority of SH3 domains tested thus far, a growing number of studies have revealed exceptions, suggesting alternative molecular mechanisms of protein recognition are possible. To identify them, we have comprehensively surveyed the specificity landscape of human SH3 domains, for the first time in an unbiased manner using peptide-phage display combined with deep sequencing. We obtained results for 117 domains of 320 attempted and these reveal that a large fraction of SH3 domains are non-canonical and collectively recognize a wide variety of peptide motifs, most of them previously unknown (47 of 51). Structural analysis of two SH3 domains with distinct non-canonical specificities confirms novel peptide-binding modes through an extended surface at the SH3 specificity site. In sum, our results constitute a significant contribution towards a complete understanding of the mechanisms underlying SH3-mediated cellular responses.

== Supplementary Information ==

 * [[attachment:HumanSH3TableS1.xlsx|S1]] - Summary of Human SH3 domains analyzed in phage display screen
 * [[attachment:HumanSH3TableS2.xlsx|S2]] - Summary of phage clonal ELISA results
 * [[attachment:HumanSH3FigureS3.docx|S3]] - Summary of ITC data
 * [[attachment:HumanSH3TableS4.doc|S4]] - Data collection and refinement statistics (molecular replacement)
 * [[attachment:HumanSH3FigureS5.docx|S5]] - Comparison of SH3 domain specificity classes between our peptide phage-based work and chip-based work from Carducci et al

== Data ==
 * [[attachment:PWM.zip|PWM files]] - Position weight matrices of SH3 domains
 * [[attachment:PWM.zip|Logo images]] - Logos of SH3 domains

== Author Information ==
1 The Donnelly Centre <<BR>>
2 Department of Computer Science, University of Toronto, Toronto, ON, Canada M5S 3E1 <<BR>>
3 Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A4 <<BR>>
4 Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G 1L7 <<BR>>
5 Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada <<BR>>
* To whom correspondence should be addressed. Email: sachdev.sidhu@utoronto.ca <<BR>>
+ JT and HH contributed equally to the study <<BR>>