A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions

The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome-nucleosome attraction in the presence of multivalent cations (Mg(H2O)(6)(2)(+) or Co(NH3)(6)(3)(+)) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP-NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.

Automated summary

Researchers have developed a coarse-grained model of the nucleosome core particle (NCP) using a systematic bottom-up approach. The model accurately reproduces the known structural features of the NCP and provides a realistic description of nucleosome-nucleosome attraction in the presence of multivalent cations. This model opens up possibilities for rigorous modeling of chromatin fibers.