Fig. 1: Overview of NCP structure and dynamics.
From: Histone dynamics mediate DNA unwrapping and sliding in nucleosomes
a NCP and its reference axes (z - superhelical, y - dyad). White arrows on DNA strands show 5′-3″ direction. Spheres highlight the proximal and distal ends of the double helix. Superhelical locations (SHL) are shown for the proximal half of the DNA (SHL < 0). Proximal H3-H4/H2A-H2B dimers are in the front (z > 0). Key arginines inserted in DNA minor grooves are shown in dark blue. b NCP in a simulation box with solvent. c, d Dynamics of NCP with truncated and with full-length histone tails (NCPtt145 and NCP147 systems, respectively). Overlay of MD snapshots spaced 0.1 µs apart. e Sequences of the core histones and their secondary structure features: α-helices, β-strands, loops, flexible histone tails, etc. For simulations with truncated histone tails, the respective positions are marked with black triangle. Positively and negatively charged residues are highlighted in blue and red, respectively. Key arginines are highlighted with dark blue frames. Black asterisk - H2B residues absent in the recombinant protein.
