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. 2018 Apr 21;114(10):2336–2351. doi: 10.1016/j.bpj.2018.03.025

Figure 9.

Figure 9

Atomistic MD simulation of HP1 binding to dinucleosome system. (A) The final structure of a 30-ns atomistic MD simulation is shown. DNA is in light gray. Histone tails are in red and the other parts of histone proteins in pink. The CD of HP1 is in light green. The CSD of HP1 is in dark blue or cyan. Arginine and lysine in hinge region (K69-G120) of one of HP1 are in dark green. These regions are also indicated by arrows. The other parts of HP1 are in yellow. (B) A close-up view of interactions between HP1 hinge region and DNA is shown. Hydrogen bonds are shown by cyan dotted lines. Molecules are shown by cartoon model, except around the hydrogen bonding part, which is shown by stick model. For visibility, some important atoms are colored differently. Oxygen atoms are in red and nitrogen in blue. Hydrogen atoms are in white and phosphorus in orange. (C) The number of hydrogen bonds between HP1 hinge region and DNA is given. The hinge region we analyzed is one at a central and upper part in (A), whose arginine and lysine are colored by dark green. To see this figure in color, go online.