Unravelling the mechanism of HP1 eviction from methylated Histone H3: A DFT study suggests a complex salt bridge as the spurring interaction

The highly conserved Heterochromatin Protein 1 (HP1) family of proteins are responsible for many functions in the nucleus of eukaryotic cells. HP1 is a reader of a post-translational modification in Lysine 9 (K9) of Histone 3 (H3): It binds to di- and tri-methylated histone H3K9 via its amino acid aromatic cage consisting of two tyrosines and one tryptophan. Upon Serine 10 (S10) phosphorylation, HP1 loses binding to H3 through a still unknown mechanism. In this work, we constructed a representative molecular system of the HP1-H3 K9me₃S10_phos complex, comprised of the aromatic cage of HP1 (Y24, W45 and Y48) and the R8K9_me3S10 tripeptide by reproducing Cartesian Coordinates from the crystal structure with the PDB code 1KNE.pdb. A single arginine in its charged form was added to the system and allowed to interact with the S10phos. We systematically drew away the single arginine from S10phos within interacting distance with the added arginine and, subsequently, energy optimizations took place. A new electrostatic interaction between the S10_phos, the single arginine and R8 was observed, a “complex salt bridge”, that was able to draw away H3 from HP1. DFT calculations at the DFT-CAM-B3LYP/6–31 + G(d,p) level of theory and basis set were employed to model the system in the gas phase and implicit solvation.