Brownian dynamics simulation of the effect of histone modification on nucleosome structure.
Using Brownian dynamics we simulate the effect of histone modification, such as phosphorylation, acetylation, and methylation, on nucleosome structure by varying the interaction force between DNA and the histone octamer. The simulation shows that the structural stability of nucleosome is very sensitive to the interaction force, and the DNA unwrapping from the modified histone octamer usually occurs turn by turn. Furthermore, the effects of temperature and DNA break as well as the competition between modified and normal histone octamers are investigated, with the simulation results being in agreement with the experimental observation that phosphorylated nucleosomes near DNA breaks are more easily depleted. Though the simulation study may only give a coarse grained view of the DNA unwrapping process for the modified histone octamer, it may provide insight into the mechanism of DNA repair.
Li
Wei
W
Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
Dou
Shuo-Xing
SX
Xie
Ping
P
Wang
Peng-Ye
PY
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; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000648:ultrastructure*; D011485:Protein Binding
D006657:Histones; D009707:Nucleosomes; D004247:DNA