Monte Carlo simulation of chromatin stretching.
We present Monte Carlo (MC) simulations of the stretching of a single chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-Hückel electrostatics and uses a two-angle zigzag model for the geometry of the linker DNA connecting the nucleosomes. The latter are represented by flat disks interacting via an attractive Gay-Berne potential. Our results show that the stiffness of the chromatin fiber strongly depends on the linker DNA length. Furthermore, changing the twisting angle between nucleosomes from 90 degrees to 130 degrees increases the stiffness significantly. An increase in the opening angle from 22 degrees to 34 degrees leads to softer fibers for small linker lengths. We observe that fibers containing a linker histone at each nucleosome are stiffer compared to those without the linker histone. The simulated persistence lengths and elastic moduli agree with experimental data. Finally, we show that the chromatin fiber does not behave as an isotropic elastic rod, but its rigidity depends on the direction of deformation: Chromatin is much more resistant to stretching than to bending.
Aumann
Frank
F
Division Biophysics of Macromolecules, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
Lankas
Filip
F
Caudron
Maïwen
M
Langowski
Jörg
J
D002843:Chromatin / Q000737:chemistry* / Q000648:ultrastructure*; D019245:Compressive Strength; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004548:Elasticity; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D013314:Stress, Mechanical; D013718:Tensile Strength
D002843:Chromatin; D004247:DNA