Brownian dynamics simulation of DNA unrolling from the nucleosome.
Nucleosomes organize chromatin in eukaryotic cells at the lowest scale by wrapping the DNA double helix around a histone octamer. The mechanism by which this structure can be opened, giving access to DNA-processing enzymes, is of fundamental biological importance. Here we describe a new coarse-grained model based on the toroidal geometry of the nucleosome which allows the simulation of nucleosome stretching experiments with a Brownian dynamics algorithm including hydrodynamics. We obtain force-extension curves and calculate energy barriers and kinetic rate constants of the unrolling transition from rupture forces.
Wocjan
T
T
Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany.
Klenin
K
K
Langowski
J
J
D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D002875:Chromosomes / Q000378:metabolism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D011108:Polymers / Q000737:chemistry
D009707:Nucleosomes; D011108:Polymers; D004247:DNA