Divergent evolution of a protein-protein interaction revealed through ancestral sequence reconstruction and resurrection

Abstract

The postsynaptic density extends across the postsynaptic dendritic spine with Discs large (DLG) as the most abundant scaffolding protein. DLG dynamically alters the structure of the postsynaptic density, thus controlling the function and distribution of specific receptors at the synapse. PDZ domains make up one of the most abundant protein interaction domain families in animals. One important interaction governing postsynaptic architecture is that between the PDZ3 domain from DLG and cysteinerich interactor of PDZ3 (CRIPT). However, little is know regarding functional evolution of the PDZ3:CRIPT interaction. Here, we subjected PDZ3 and CRIPT to ancestral sequence reconstruction, resurrection and biophysical experiments. We show that the PDZ3:CRIPT interaction is an ancient interaction, which was present in the last common ancestor of Eukaryotes, and that high affinity is maintained in most extant animal phyla. However, affinity is low in nematodes and insects, raising questions about the physiological function of the interaction in species from these animal groups. Our findings demonstrate how an apparently established proteinprotein interaction involved in cellular scaffolding in bilaterians can suddenly be subject to dynamic evolution including possible loss of function.

Evolution of affinity between p53 and MDM2 across the animal kingdom demonstrates high plasticity of motif-mediated interactions

“…In addition, interactions of this type are often hijacked by viral proteins (37), potentially imposing additional selection pressure. While we here attempted to pinpoint historical amino acid substitutions shaping the affinity between the p53TAD binding motif and MDM2, as done for other short motifs (38), conformational heterogeneity among the bound conformations of p53TAD is also likely contributing to the variation in affinity. Such structural plasticity, previously observed in evolution of protein-protein interactions (36, 39), is likely connected to general frustration of binding involving disordered regions, where several possible conformations compete and where none is perfectly optimized (40).…”