Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes
Fig 6
Scores and renders of the six HUb variants in the four chromatosome structures.
In (A) the sketch-map projection is colored according to the ISA score where a specific region exhibits high scores and contains non-fitting HUb conformations. The distribution of scores can be seen in (B), (C), and (E). The clusters with the lowest scores of the parent chromatosomes 5NL0, 5WCU, 4QLC, and the off-dyad structure are shown in (D, F-H), their location annotated in (A). Coloration of renders is in line with Fig 5. Note, that the lowest scoring cluster for 5WCU (F) and 4QLC (G) is the same cluster. Both chromatosomes are structurally very similar, missing the DNA linkers that are present in 5NL0. Also note, how the Ub subunit of the lowest scoring cluster fitted into the off-dyad chromatosome points into a different direction. The off-dyad structure in (H) contains the tail domains of the core histones. In (I), the crystal structure of 1UBQ was colored according to the average per-residue minimal distance to DNA after placing HUb into 5NL0. The possible values range from red (closest) to blue (farthest).