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In silicio stretching of chromatin
Biomolecules · Submitted 21 Sep 2005
abstract compiled · 2026-09-23 · no language-model review
The authors' main claim 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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The abstract, sentence by sentence
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.
background contribution method result interpretation main claim
| # | sentence | role | the authors' own work | states the main conclusion | strength |
|---|---|---|---|---|---|
| s0 | We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. | contribution 0.92 | 0.96 | 0.04 | asserted 0.92 |
| s1 | 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. | method 1.00 | 0.72 | 0.02 | asserted 1.00 |
| s2 | The latter are represented by flat disks interacting via an attractive Gay-Berne potential. | method 1.00 | 0.40 | 0.02 | asserted 0.99 |
| s3 | Our results show that the stiffness of the chromatin fiber strongly depends on the linker DNA length. | result 1.00 | 0.96 | 0.33 | asserted 1.00 |
| s4 | Furthermore, changing the twisting angle between nucleosomes from 90 deg to 130 deg increases the stiffness significantly. | result 1.00 | 0.95 | 0.11 | asserted 1.00 |
| s5 | An increase in the opening angle from 22 deg to 34 deg leads to softer fibers for small linker lengths. | result 1.00 | 0.93 | 0.05 | asserted 1.00 |
| s6 | We observe that fibers containing a linker histone at each nucleosome are stiffer compared to those without the linker histone. | result 1.00 | 0.94 | 0.08 | asserted 1.00 |
| s7 | The simulated persistence lengths and elastic moduli agree with experimental data. | result 0.90 | 0.89 | 0.11 | asserted 0.98 |
| s8 | 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. | result 0.96 | 0.95 | 0.47 | asserted 1.00 |
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Original 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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