A metadynamic approach to understand the recognition mechanism of the histone H3 tail with the ATRX_ADD domain

The binding affinity between the histone 3 (H3) tail and the ADD domain of ATRX (ATRX_ADD) increases with the subsequent addition of methyl groups on lysine 9 on H3. To improve our understanding of how the difference in methylation state affects binding between H3 and the ATRX_ADD, we adopted a metadynamic approach to explore the recognition mechanism between the two proteins and identify the key intermolecular interactions that mediate this protein-peptide interaction (PPI). The non-methylated H3 peptide is recognized only by the PHD finger of ATRX_ADD while mono-, di-, and trimethylated H3 is recognized by both the PHD and GATA-like zinc finger of the domain. Furthermore, water molecules play an important role in orienting the lysine 9 anchor towards the GATA-like zinc finger, which results in stabilizing the lysine 9 binding pocket on ATRX_ADD. We compared our computational results against experimentally determined NMR and X-ray structures by demonstrating the RMSD, order parameter S² and hydration number of the complex. The metadynamics data provide new insight into roles of water-bridges and the mechanisms through which K9 hydration stabilizes the H3K9me3:ATRX_ADD PPI, providing context for the high affinity demonstrated between this protein and peptide.