Data from: 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 the
binding preference changed. Although the closest ancestor of the two
domains had a very similar binding preference as the extant ones, older
ancestral domains displayed a gradual loss of interaction with the modern
interaction partners when inserted in the extant paralogs. Molecular
docking and experimental characterization of the free ancestral domains
showed that their affinity with the proline motifs is likely not the cause
for this loss of binding. Taken together, our results suggest that the SH3
and its host protein could create intramolecular or allosteric
interactions essential for the SH3-dependent PPIs, making domains not
functionally equivalent even when they have the same binding specificity.