Phase separation of protein kinase A regulatory subunits is driven by similar inter- and intra-molecular interactions involving the inhibitory segment

Phase separation of biological macromolecules has emerged as a widespread mechanism for cellular organization, governing the spatiotemporal regulation of biochemical processes including signaling pathways. The regulatory subunit of the cAMP-dependent protein kinase A (PKA) RI phase separates following cAMP-induced kinase activation, thereby restricting and enhancing PKA activity in space and time. The N-terminal dimerization/docking (D/D) domain and the linker region of RI have been identified as necessary and sufficient for phase separation, but their interactions at atomic resolution have remained elusive. We report here a structural investigation of the minimal phase-separating region of RI by nuclear magnetic resonance spectroscopy (NMR) and molecular dynamics (MD) simulations. The intrinsically disordered regions of RI cause broadening of NMR signals throughout the protein indicative of widespread dynamic interactions. Mutation of arginine residues in the RI inhibitory sequence leads to a reduction in signal broadening accompanied by loss of phase separation. Independently, binding of RI to an A-kinase anchoring protein (AKAP) leads to spectral changes that are indicative of a loss of interactions between the D/D domain and the linker region, suggestive of a competition between intramolecular interactions and partner binding. Corroborating the experimental observations, multiscale MD simulations detect pervasive interactions of the folded D/D domain of RI with the intrinsically disordered linker, and the intermolecular interactions in the condensate mirror those found internally in RI dimers. Our results support the view that for PKA RI, homotypic phase separation is underpinned by intermolecular interactions that are similar to intramolecular interactions.