dorsal/arxiv
View SchemaIn silicio stretching of chromatin
| Authors | Frank Aumann, Filip Lankas, Maiwen Caudron, Jörg Langowski |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0509024 |
| URL | https://arxiv.org/abs/q-bio/0509024 |
Abstract
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag 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 deg to 130 deg increases the stiffness significantly. An increase in the opening angle from 22 deg to 34 deg 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.
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"abstract": "We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm\nchromatin fiber. The model approximates the DNA by a flexible polymer chain\nwith Debye-H\\\"uckel electrostatics and uses a two-angle zig-zag model for the\ngeometry of the linker DNA connecting the nucleosomes. The latter are\nrepresented by flat disks interacting via an attractive Gay-Berne potential.\nOur results show that the stiffness of the chromatin fiber strongly depends on\nthe linker DNA length. Furthermore, changing the twisting angle between\nnucleosomes from 90 deg to 130 deg increases the stiffness significantly. An\nincrease in the opening angle from 22 deg to 34 deg leads to softer fibers for\nsmall linker lengths. We observe that fibers containing a linker histone at\neach nucleosome are stiffer compared to those without the linker histone. The\nsimulated persistence lengths and elastic moduli agree with experimental data.\nFinally, we show that the chromatin fiber does not behave as an isotropic\nelastic rod, but its rigidity depends on the direction of deformation:\nchromatin is much more resistant to stretching than to bending.",
"arxiv_id": "q-bio/0509024",
"authors": [
"Frank Aumann",
"Filip Lankas",
"Maiwen Caudron",
"J\u00f6rg Langowski"
],
"categories": [
"q-bio.BM",
"q-bio.GN"
],
"title": "In silicio stretching of chromatin",
"url": "https://arxiv.org/abs/q-bio/0509024"
},
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