Brownian dynamics simulation of directional sliding of histone octamers caused by DNA bending.
Chromatin-remodeling complexes such as SWI/SNF and RSC of yeast can perturb the structure of nucleosomes in an ATP-dependent manner. Experimental results prove that this chromatin remodeling process involves DNA bending. We simulate the effect of DNA bending, caused by chromatin-remodeling complexes, on directional sliding of histone octamers by Brownian dynamics simulation. The simulation results show that, after a DNA loop being generated at the side of a nucleosome, the histone octamer slides towards this DNA loop until the loop disappears. The DNA loop size is an important factor affecting the process of directional sliding of the histone octamer.
Li
Wei
W
Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China.
Dou
Shuo-Xing
SX
Xie
Ping
P
Wang
Peng-Ye
PY
D016880:Anisotropy; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004058:Diffusion; D006657:Histones / Q000737:chemistry* / Q000648:ultrastructure*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009038:Motion; D009690:Nucleic Acid Conformation
D006657:Histones; D004247:DNA