FIGURE 1.

(a) Basic residues in the nucleosome core particle. Crystal structure of the nucleosome core particle (Protein DataBank ID 1kx5) (4). Basic residues, lysine (dark gray) and arginine (black), present in the histone octamer assembly are shown. Strong salt-bridge interactions are formed between basic histone side chains and the phosphate backbone of nucleosomal DNA. (b) Snapshot of cold sites in the nucleosome. Cold sites are those histone residues that maintain more of their contacts throughout simulations than other residues. In discrete molecular dynamics simulations of histone-octamer assembly, we observe that these sites are present within the core of the nucleosome. A and B are aligned for comparison of cold sites against regions rich in basic lysine and arginine residues. Bold arrow indicates the nucleosomal dyad axis of symmetry.