Selective binding of divalent cations reshapes nucleosome mechanics and unlocks histone tail dynamics

Divalent cations such as Mg2+ and Ca2+ are key modulators of chromatin architecture, yet their atomistic influence on nucleosome structure and histone tail dynamics remains elusive. Here, we present 81 microseconds of all-atom molecular dynamics (MD) simulations to dissect how these ions shape nucleosome dynamics and plasticity. We quantitively mapped the selective binding patterns of Mg2+ and Ca2+ in nucleosomes with and without histone tails, revealing distinct ion–nucleosome interactions. Notably, divalent ion binding reduces inter-gyre electrostatic repulsion, facilitates DNA gyre compaction, and increases nucleosome stiffness, as quantified by estimates of the Young’s modulus and correlated motions within specific DNA regions. Importantly, ion binding weakens histone tail–DNA interactions and enhances tail mobility—particularly that of H3—potentially facilitating access by chromatin regulators and tail-mediated chromatin compaction. These findings reveal a dual role of divalent ions in modulating nucleosome plasticity while reinforcing histone tail dynamics, providing a mechanistic framework for understanding how ionic fluctuations influence gene accessibility and chromatin state. Nucleosome plasticity is critical for many chromatin-related processes. The authors demonstrate how biologically relevant divalent ions reshape nucleosome structure and mechanical stiffness.