The Free energy profile of a nucleosome core particle through the molecular dynamics simulation

Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi

The nucleosomes are the basic unit of eucaryotic chromosome structure. It has recently been discovered that chromatine remodeling complexes peel the nucleosomal DNA away from the histone octomer(the remodeling). The change in the translational and rotational positioning permits access to the binding site of the nucleosomal DNA by proteins involved in gene expression, DNA replication and repair. The free energy profile in the process of the remodeling should provide important clues to clarify the mechanism of the protein binding to the nucleosomal DNA. We perform the molecular dynamics simulation starting from the high-resolution structure of a nucleosome core particle including explicit water and ions. After the equilibration of the nucleosome core particle, we pull the ends of nucleosomal DNA to peel it away from the histone core and obtain the free energy profile.