Figure 2. Fluctuations of intact nucleosomes from ten independent molecular dynamic simulations.

(a) rmsd for histone core and a 127-bp segment of nucleosomal DNA of heavy atoms (red) and linker DNA end-to-end distance (black). The second and fifth simulations exhibit significantly different end-to-end distances compared with the other simulations. The insets in red and green boxes show two simulations with closed and open conformations, respectively. (b,c) Show intermediate snapshots of the fifth and second simulations, which transitioned to a closed or open conformation, respectively.