FIGURE 2.

Localization of kinked basepair steps during the MD simulation of the whole nucleosome core particle (WholeNCP-DNA), represented here by 1000 equidistant snapshots. The solid lines (shown here to guide the eye), correspond to the kinks in the original structure identified by Richmond and Davey (14). We adopt a slightly more relaxed definition of a kink (open circles): roll <−11.8°; twist > 40°; and slide > 1.25 Å. Solid circles represent kinks at t = 0. The dashed line represents a region that has been identified as a spot of DNA distortion (biochemical kink).