Phosphorylation-regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor

Abstract

Site-specific phosphorylation of disordered proteins is often considered a marker of protein activity, yet it remains unclear how phosphorylation alters the conformational dynamics of disordered protein chains, such as those in the nuclear receptor superfamily. In the case of the disordered human glucocorticoid receptor N-terminal domain (GR NTD), a negatively charged region known as core activation function 1 (AF1c) features three phosphorylation sites, regulating its function and intracellular localization. Deletion of this sequence dramatically reduces the GR transcriptional activation ability in cell experiments. By developing a circuit topology-based fold analysis approach, combined with atomistic simulations, we reveal that site-specific phosphorylation facilitates the formation of nonlocal contacts, leading to the emergence of disordered compact topologies with significant entanglement, which are distinct from solvent-exposed topologies. While we observe that the topological buildup of solvent-exposed states is similar across different phosphovariants, it depends on the exact phosphorylation site for the disordered topologically compact states. This study thus reveals the complex regulatory role of the GR phosphorylation and introduces a unique analysis framework that can be broadly applied to studying the topological dynamics of disordered proteins.