Figure 1.

Overall structures and protected DNA regions in the PANS and the octasome. Distributions of the minimal distance d_min from the DNA basepair to the histone core are shown for the disome (A), tetrasome (B), hexasome (C), and octasome (D) structures obtained in the MD simulations. The basepairs are classified as follows: protected (d_min < d_pro = 15 Å for all the snapshots); accessible (d_min > d_pro for all the snapshots); and transient. Here d_pro is a minimal distance separating histones atoms from the DNA atoms in a realistic complex of the nucleosome with a nuclear factor. Minimal, median, and maximal d_min values are shown by solid lines, 25th and 75th percentiles are shown by dashed lines. Black marks with labels indicate basepair positions. Colored lines connect centers of mass of the histone heterodimers (purple dots); the distances are specified in Å; the color scheme is the same for all the structures. Additional images (Fig. S4; Movie S1) and representative snapshots (in PDB format) are provided in the Supporting Material. To see this figure in color, go online.