Intrinsically Disordered Flanking Regions Increase the Affinity of a Transcriptional Coactivator Interaction across Vertebrates

Interactions between two proteins are often mediated
by a disordered
region in one protein binding to a groove in a folded interaction
domain in the other one. While the main determinants of a certain
interaction are typically found within a well-defined binding interface
involving the groove, recent studies show that nonspecific contacts
by flanking regions may increase the affinity. One example is the
coupled binding and folding underlying the interaction between the
two transcriptional coactivators NCOA3 (ACTR) and CBP, where the flanking
regions of an intrinsically disordered region in human NCOA3 increases
the affinity for CBP. However, it is not clear whether this flanking
region-mediated effect is a peculiarity of this single protein interaction
or if it is of functional relevance in a broader context. To further
assess the role of flanking regions in the interaction between NCOA3
and CBP, we analyzed the interaction across orthologs and paralogs
(NCOA1, 2, and 3) in human, zebra fish, and ghost shark. We found
that flanking regions increased the affinity 2- to 9-fold in the six
interactions tested. Conservation of the amino acid sequence is a
strong indicator of function. Analogously, the observed conservation
of increased affinity provided by flanking regions, accompanied by
moderate sequence conservation, suggests that flanking regions may
be under selection to promote the affinity between NCOA transcriptional
coregulators and CBP.