Figure 4: Impact of acetylation of H3K56 on the lesion-containing NCPs.

Compared to unacetylatedK56, K56ac (A) significantly weakens the DNA-histone/histone-histone interactions, (B) causes both nearby DNA and the H3 αN helix to be more dynamic, (C) causes the nearby DNA to become distanced from the histones and away from the other gyre, (D) causes the minor groove to be more enlarged.

(A) The hydrogen bonds between the H3 αN helix and the DNA (left panel) as well as the hydrogen bonds of R81 with the surrounding residues (right panel) are given for lesion-containing NCPs. Details concerning all hydrogen bond acceptor-donor pairs are listed in Tables S2–3.

(B) K56ac enhances the dynamics of the DNA near the nucleosome entry-exit region, the αN helix of H3, and the α3- and αC- helices of H2A. The RMSFs of the heavy atoms of the residues are shown by color; higher values correspond to larger fluctuations (red) and lower values to smaller fluctuations (blue) as indicated in the spectrum bar. Their corresponding RMSF values are also given in Figure S3. Only half of the DNA (SHL > 0) and histones (H3, H4) near the end of the DNA are displayed for clarity.

(C) Superposition of the best representative structures of Lesion-H3K56 (light-blue) and Lesion-H3K56ac (red) NCPs reveals that the DNA at the region highlighted as orange is markedly distanced from the H3 αN helix by the presence of K56ac, mainly by moving away from the other gyre. Two views illustrating that the lesion-containing DNA is pulled away from the center of the NCP and away from the other gyre. The ensemble averaged shortest distances between the DNA and the helical axis of H3 αN are plotted, showing that the enhanced distanced DNA segment is mainly observed at BPs 9–15, with an increased distance of up to ~7 Å.

(D) Minor groove widths were calculated by measuring the pairwise P-P distance for lesion-containing and lesion-free NCPs. When compared to the lesion-free NCPs, the lesion with its damaged dG displaced into the minor groove enlarges the minor groove width, and even more so in the presence of K56ac, particularly at P12-P8* and P13-P9* across the damaged dG. The numbering scheme: “P10” refers to the P atom at BP10 on the strand Chain I and “P10*” refers to the P atom at BP10 on the strand Chain J. A distance 5.8 Å was subtracted to account for van der Waals radius of the P atom.¹¹⁰