Structural dynamics in the CENP-A nucleosome impacted by protein-protein interactions with centromere protein N ^†

Noncanonical nucleosomes at the centromere contain the histone variant CENP-A, playing a crucial role in chromosome segregation. CENP-A is highly regulated and its centromeric organization is partially regulated by the centromere protein N (CENP-N). Despite its importance, the protein–protein interactions within the complex formed between CENP-A nucleosomes and CENP-N remain poorly understood at a molecular level. Here, we employ the SIRAH coarse-grained molecular dynamics (MD) simulations to investigate the binding interface and structural rearrangements of proteins in the CENP-A nucleosome complexed with CENP-N. We aim to assess the stability of the CENP-A nucleosome and the change in its plasticity upon the CENP-N binding. By the set of µ s-long MDs, we reveal enhanced flexibility in the N-terminal region of CENP-A and stabilization of its RG loop in the complex with CENP-N. This is demonstrated to have rather minor effects on the overall stability of the nucleosome and changing its compactness. Nevertheless, the data suggest the binding of CENP-N allosterically changes the conformational states of CENP-A and impacts its interactions with other proteins in the histone core. A distance-based contact map analysis further elucidates key residues mediating the interaction between CENP-A and CENP-N, while umbrella sampling simulations quantify their binding free energy, which remains challenging to measure experimentally.