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Eukaryotic DNA exists within a structure called chromatin. Chromatin and its basic unit, the nucleosome, are highly dynamic structures. The nucleosome core particle is formed by an octamer of histone proteins and 145-147 base pairs of wrapped DNA. Nucleosome dynamics regulate the accessibility of DNA to molecular machines and facilitate nuclear protein interactions. While experimental studies of nucleosome dynamics provide a static snapshots of dynamically stable states, additional methods, such as molecular modeling, are essential to interpret the indirect data. We use molecular dynamics (MD) simulations to describe nucleosome dynamics and mechanisms underlying its epigenetic regulation. Recent rapid improvements in computational capabilities have enabled the modeling of atomistic nucleosome dynamics on a multi-microsecond timescale.

Here we describe recent advances in MD simulations of nucleosomes.  MD simulations have provided mechanistic insights into the interplay between DNA dynamics and histone core dynamics within nucleosomes. The role of histone bending in DNA sliding and unwinding has been described, as well as how the presence of histone variants or peptide binding can influence nucleosome dynamics. These findings enhance our understanding of the structural and dynamic complexity of nucleosomes, particularly in the context of epigenetic regulation.