Rewiring protein binding specificity in paralogous DRG/DFRP complexes

Abstract

The Developmentally Regulated GTP-binding (DRG) proteins are an ancient subfamily of GTPases implicated in the regulation of translation and cell growth. In eukaryotes, there are two paralogs: DRG1 and DRG2, both of which have a conserved binding partner called DRG family regulatory protein 1 and 2 (DFRP1 and DFRP2), respectively. These binding partners are required for the function of DRGs, including their stabilisation at the protein level. Moreover, DFRPs interact with their respective DRG via a conserved region called the DFRP domain. Despite being highly similar, DRG1 and DRG2 have strict binding specificity for their respective DFRP. Using AlphaFold generated structure models of the human DRG/DFRP complexes, we have biochemically characterised their interactions and identified interface residues involved in determining specificity. This analysis revealed that as few as five mutations in DRG1 can switch its binding from DFRP1 to DFRP2. We show how two DRG1 residues in the core of the interface are most important for specifying the interaction with DFRP1 over DFRP2. We also demonstrate that whilst DFRP1 can stimulate the GTPase activity of DRG1, DFRP2 binding cannot. Overall, this work provides new insight into the structural determinants responsible for the binding specificities of the DRG:DFRP translation factor complexes, which are known to be essential for normal development in mice and humans.