An associative memory Hamiltonian model for DNA and nucleosomes
Fig 4
Nucleosome model and unwrapping analysis.
(a) A detailed representation of the nucleosome core particle (PDB ID: 1KX5 [59]) (left) and the corresponding coarse-grained WEChroM representation (right). In the left figure, the upper half of the nucleosome particle is shown as solid while the lower half is transparent for clear visualization. The DNA nucleotides in close contact with amino acids are defined as “contact DNA” and subject to the AMH potential modeling histones-to-DNA interactions (black circle). In our model, contact DNA interacts with the histone octamer’s center of mass (Ucenter, represented by the red arrow in the figure). Contact DNA also interacts with neighboring contact DNA (Uneighbor, represented by the black arrows inside the indigo dashed circle). (b) Free energy of partial DNA unwrapping for a system composed of the histone octamer plus 223-bp of DNA; WEChroM model (blue) and 3SPN-AICG model (orange). Simulation data shown for the 3SPN-AICG mode are extracted from ref. [38], figure 8. Examples of nucleosome configurations are shown for end-to-end distances of roughly 45 Å (left), 107 Å (right), 330 Å (outside) (c) Free energy of partial nucleosome unwrapping for a system composed of the histone octamer plus 147-bp of DNA; WEChroM model. (d) Nucleosome AMH energy of the partial nucleosome unwrapping for the 147-bp WEChroM model. Example nucleosome configurations are shown for end-to-end distances of 76 Å (left), 142 Å (middle), 221 Å (right).