Fig. 8: Plasticity of the histone octamer in NCP and its effects on the nucleosomal DNA dynamics.
From: Histone dynamics mediate DNA unwrapping and sliding in nucleosomes
a–d Present data for NCPtt145 simulations. a 2D projections of histone α2-helices’ Cα-atoms (α2-Cα-atoms) on the plane perpendicular to the superhelical axis for MD snapshots vs. X-ray structure. b Same as (a), but for the two MD snapshots with the maximum RMSD as measured by positions of α2-Cα-atoms. c Variation of RMSD with simulation time measured for α2-Cα-atoms positions with respect to the initial X-ray structure and a cryo-EM structure of a “squeezed” NCP (PDB ID 6FQ6)25. d RMSD calculated for Cα-atoms of the H2A α2-helices as a function of simulation time. Insets show inward bending of the helix associated with higher average RMSD. e Average DNA fluctuations for one half of the nucleosomal DNA compared for NCP147 simulations (<8 µs) and NCPfixed147 simulations with restrained histone folds. f Distance between Cα-atoms of H3L82 and H3V81 residues. Thick lines in (d) and (f) show signal smoothed with Savitzky-Golay filter.
