Protein Context Shapes the Specificity of SH3 Domain-Mediated
ARTICLE https://doi.org/10.1038/s41467-021-21873-2 OPEN Protein context shapes the specificity of SH3 domain-mediated interactions in vivo Ugo Dionne1,2,3,4,5, Émilie Bourgault3,4,5,6,13, Alexandre K. Dubé 3,4,5,6,7,13, David Bradley3,4,5,6,7,13, François J. M. Chartier 1,2,3,13, Rohan Dandage3,4,5,6,7, Soham Dibyachintan3,4,6,7,8, Philippe C. Després 3,4,5,6, Gerald D. Gish9, N. T. Hang Pham3,10, Myriam Létourneau3,10, ✉ ✉ Jean-Philippe Lambert 1,2,11, Nicolas Doucet3,10, Nicolas Bisson 1,2,3,12 & Christian R. Landry 3,4,5,6,7 1234567890():,; Protein–protein interactions (PPIs) between modular binding domains and their target pep- tide motifs are thought to largely depend on the intrinsic binding specificities of the domains. The large family of SRC Homology 3 (SH3) domains contribute to cellular processes via their ability to support such PPIs. While the intrinsic binding specificities of SH3 domains have been studied in vitro, whether each domain is necessary and sufficient to define PPI speci- ficity in vivo is largely unknown. Here, by combining deletion, mutation, swapping and shuffling of SH3 domains and measurements of their impact on protein interactions in yeast, we find that most SH3s do not dictate PPI specificity independently from their host protein in vivo. We show that the identity of the host protein and the position of the SH3 domains within their host are critical for PPI specificity, for cellular functions and for key biophysical processes such as phase separation.
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