Phosphorylation of Intrinsically Disordered Regions Within the Genome

Chromatin-binding proteins participate in the remodelling and maintenance of genomic structure. These proteins are particularly enriched in Intrinsically Disordered Regions (IDR) - regions with structural diversity and high flexibility. In addition to hindering high-resolution modelling, the disorder of these regions also makes them particularly susceptible to post-translational modifications. Through the application of Metadynamics Molecular Dynamics simulations to two chromatin-binding proteins - H1 and HP1, we identify the molecular mechanisms of their functioning and the effects of their phosphorylation. H1 Linker Histones (LH) are composed of a structured globular domain and unstructured terminal domains. However, structural studies of H1-nucleosome binding have been limited to the globular domain. Through a metadynamics setup that biases the IDP's secondary structure and its interactions with DNA, we demonstrate that the long unstructured C-terminal domain bridges DNA through flexible loops. Subsequently, we demonstrate that the flexibility of these loops within the nucleosome can be significantly modulated through Ser/Thr phosphorylation and in-turn tune oligonucleosome compaction. Heterochromatin Protein 1 (HP1) binds to the H3 tails of nucleosomes and plays an important role in gene regulation through the formation of heterochromatin. The protein consists of intrinsically disordered terminals together with a central hinge region that bridges two structured domains. Using metadynamics simulations, we demonstrate the capability of phosphorylation to modulate the inter-molecular interactions of HP1's disordered N-terminal domain with the H3 histone. Further, with HP1 implicated in the formation of phase-separating droplets within the genome, we demonstrate the effectivity of phosphorylation to amplify the intra-molecular disordered contacts hypothesised to underpin such events.