Fig 1.
Simulation systems used and distribution of contact surface area (CSA) between the H3 tail and DNA in an obtained ensemble.
(A) The system was prepared based on two nucleosome crystal structures, 1KX5 and 1ZBB. The linker DNA was extended by 10 bp from that of 1KX5 using the DNA structure of 1ZBB as a reference. Only atoms immersed within a water sphere centered at the root of the H3 tail (a nitrogen atom in the 40th residue) were considered in the simulations to reduce computational costs. All simulations were performed within the water sphere boundary. H3 histone tail, DNA, and histone core regions are shown in magenta, orange and green, respectively. (B) Distribution of CSA between the H3 tail and DNA is plotted as a function of the scaling factor λ for ALSD. See S1 Fig for the K14ac H3 tail.
Fig 2.
Impact of K14ac on H3 tail conformation.
(A) Average α-helical content ratio with the standard error for each residue of unacetylated and K14ac H3 tails. The error bars represent the standard errors calculated from 256 independent trajectories. (B) Rg distributions for unacetylated and K14ac H3 tails.
Fig 3.
Differences in the spatial distributions between the unacetylated and K14ac systems.
Differences in the H3 tails and DNA are shown in the upper and lower panels, respectively. Blue and red contour maps show spatial regions preferred in the unacetylated and K14ac system, respectively. The coloring of the molecules and the nucleosome model are the same as in Fig 1.
Fig 4.
Averaged DNA contact and solvent exposure of lysine, arginine and K14ac residues within the H3 tail.
(A) Contact ratios for side chain terminal atoms of lysine, arginine, and K14ac residues with DNA. (B) Exposure ratios of the atoms to solvent. The error bars represent the standard errors calculated from 256 independent trajectories.