Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes
Fig 5
Results of the interpenetration and scoring algorithm and example structures for scoring K30HUb into 5NL0.
The sketch-map projection (A) colored according to ISA score exhibits distinct regions with fitting (green, low score) and non-fitting (red, high score) conformations. The histogram of scores has a skew to lower scores (B). In (C) and (D) exemplary HUb clusters are rendered within the nucleosome of 5NL0, their location in sketch-space is annotated in (A). Both (C) and (D) visualize the DNA as tubes and the core histones as a transparent blue surface. The HUb structure bundles are rendered using their secondary structure and colored accordingly. In (C) the K30HUb cluster with the lowest ISA score is shown. Using this cluster the HUb chromatosome complex could easily be used as input for further simulations. In (D) a cluster with an ISA score of 150 is shown. This cluster can be taken as an example of a high-score cluster, that does only slightly intersects with the DNA linkers.