Fig. 3

Lysine acetylations asymmetrically loosen DNA entry and exit ends and alter DNA dynamics. a The distance between DNA ends to the pseudo-dyad was measured for all time steps and distributions shown. In the structures showing which graph corresponds to which DNA end, the CENP-A NCP is shown with CENP-A and H4 in red, CENP-A′ and H4′ in blue, and H2A/H2B monomers in tan. The entry end of DNA unwraps more in the acetyl NCP in blue. b Coarse-grained free energy landscapes are shown for both systems through the projection of PC1^NUC and PC2^NUC of the whole nucleosomal principal component analysis (PCA^NUC). Here it is shown that the acetyl NCP landscape becomes more rugged and frustrated. c From PC1^NUC trajectories, three representative snap shots are shown to illustrate the intra-helical bubble formed in DNA near K79ac that does not occur in unmodified CENP-A. DNA is shown in white, and the L1 loop of CENP-A is marked