Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins

Protein-protein interactions drive many cellular processes. Some protein interactions are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of two paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have subtly different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and characterizing the SH3 domains freed from their protein context, we find that few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the pre-duplication SH3 domains and examined, moving back in time, how t..., The data published in this dataset was collected by multiple methods. Among the methods used are DHFR Protein-fragment Complementation Assay, cytometry, ancestral sequence reconstruction with IQ-TREE and FastML, protein structure prediction with AlphaFold2 and AlphaFold Multimer, molecular docking with Haddock2.4, orthology analysis and coevolution predictions with EVCouplings. See the README.md file and the method section of the paper Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins for more details. File S1 : Tables S1 - S12 File S2 : Detailled protocols FiguresS : Figures S1 - S10 DataS1 : DHFR PCA results DataS2 : Phylogeny and sequence alignment DataS3 : AlphaFold results DataS4 : Molecular docking input and output files DataS5: Orthology input and motif conservation results DataS6: EVCouplings output Please refer to Lemieux et al. 2023 for details on the data collection and transformation., All files can be opened with either R, a text editor, Excel or ChimeraX., This README file was generated on 2023-09-19 by Pascale Lemieux. # GENERAL INFORMATION 1. Title of Dataset: Data from : Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins 2. Author Information A. Principal Investigator Contact Information Name: Christian Landry Institution: Université Laval, Québec CA Email: [e-mail] B. Associate or Co-investigator Contact Information Name: Pascale Lemieux Institution: Université Laval, Québec, CA Email: [e-mail] 3. Date of data collection (single date, range, approximate date): 2020-2023 4. Information about funding sources that supported the collection of the data: Canadian Institutes of Health Research (CIHR) Foundation grant 387697 and a HFSP grant (RGP0034/2018) to CRL SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to publications that cite or use ...