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, which plays a crucial role in chromosome segregation. CENP-A is highly regulated, including that by the centromere protein N (CENP-N). Despite its importance, the protein–protein interactions within the CENP-A nucleosome–CENP-N complex remain poorly understood at the molecular level. Here, we employ SIRAH coarse-grained molecular dynamics (MD) simulations to investigate dynamic mechanisms through which CENP-N binding to CENP-A nucleosome modulates structural changes of histones, contributing to the regulation processes. Using a set of μs-long MDs, we reveal enhanced flexibility in the N-terminal region of CENP-A and the stabilization of its RG loop in the complex with CENP-N, thus reshaping the conformational structure of the CENP-A protein. We characterize these allosteric changes and analyze their influence on histone–DNA contacts. Moreover, we demonstrate that they have rather minor effects on the overall stability of the nucleosome and its compactness. 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.