Fig. 6

The H2A.B NCP may be even more dynamic without its Nt. a Time evolution of the RMSD of the DNA during the AA-MD simulations of the NtH2A–H2A.B NCP (blue). The RMSD curves of the H2A NCP (black) and the H2A.B NCP (red) are also shown for comparison. b Distribution of the DNA end-to-end distances from the AA-MD simulations of the NtH2A–H2A.B NCP (blue). The distributions of the H2A NCP (black) and the H2A.B NCP (red) are also shown for comparison. A representative structure of the NtH2A–H2A.B NCP that has a peak DNA end-to-end distance of 168 Å is shown in the panel. c Time evolution of the number of the unwrapped DNA base pairs during the AA-MD simulations of the NtH2A–H2A.B NCP (blue). The curves of the H2A NCP (black) and the H2A.B NCP (red) are also shown for comparison. d Average number of contacts of each residue in NtH2A–H2A.B with the DNA during the AA-MD simulations. The Nt and the L2 are labeled. In a–d for each system, average values calculated from the three independent simulations are plotted, and standard deviations are plotted as errors that are represented by shade. In d the contact numbers from the two copies of the same histone in one nucleosome structure are also averaged. e Detailed interactions between the Nt and DNA in the H2A NCP, the H2A.B NCP, and the NtH2A–H2A.B NCP. Args in the Nt are drawn in licorice. The base pairs in contact with the Nt are colored in pink