Fig. 8.

Description of coarse-grained nucleosome model. DNA is represented by the 3SPN.2C model (63), which represents each nucleotide by three sites located at the center-of-mass of the phosphate (brown), sugar (yellow), and base (pink, purple, orange, green). The histone proteins are represented by the AICG model (50), where each amino acid is represented by a single site, located at the center-of-mass of the amino acid side chain. Interactions between the DNA and histones are represented by Coulombic interactions at the level of Debye–Hückel theory. Phosphate sites of DNA are given a charge of −1, whereas protein sites are given a charge of −1, 0, +1 (red, white, and blue, respectively) corresponding to the charge of that amino acid under physiological pH. Nucleosome configurations and DNA–histone contacts in the 3SPN-AICG model arise naturally from a balance between these Coulombic interactions, with no bias toward the observed nucleosome crystal structure (51).