Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
Fig 6
Log-probability of the sliding and rotation coordinates.
The colors represents the negative log-probability weighted by kBT in kcal/mol. (A) The polyCG sequence shows that most conformations lie along a straight line having a slope of approximately 360 degree over 10 bps, indicating the ideal screw-like rotation of DNA. (B) The polyCG-601 histogram also shows a straight line but the diffusion is now more limited. (C) For the 601 sequence we find 5 distinct basins corresponding to conformations shifted by 5 bps relative to each other. Within each basin, small screw-like rotation of DNA is also observed. (D-K) Some snapshots corresponding to states pointed in A, B, and C. (D, E) The nucleotide that is located at the center in the initial configuration is colored in red. (F, G, H) Two TTAAA motifs are represented with spheres. The beads corresponding to residues A and T are colored in red and blue respectively. (I, J, K) All the positioning “TA” motifs that are shown in bold in Table 1 are colored in red.