Coarse-grained Chromatin Modelling

Our Model: interactive 3d graphic

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Click and drag to rotate, mouse wheel to zoom.
Slide the bar to show coarse-graining:

This graphic demonstrates the coarse-grain mapping of our model [1]. It begins as the all atom structure of a nucleosome 1kx5 pdb [2] with additional linker histone [3] and using the slider you can see how we map it onto the coarse-grained structure, then the minimal structure. Warning: this graphic does require some reasonable computation, it will take several seconds for it to load, it works best on Chrome, and it might not work on mobile. You can use you mouse and scroll wheel to rotate and zoom in. This was created using the three.js javascript library.

[1] Stephen E. Farr, Esmae J. Woods, Jerelle A. Joseph, Adiran Garaizar, Rosana Collepardo-Guevara, Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions, bioRxiv 2020.11.23.391599, DOI: 10.1101/2020.11.23.391599.

[2] Curt A. Davey, David F. Sargent, Karolin Luger, Armin W. Maeder, Timothy J. Richmond, Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9Å Resolution, Journal of Molecular Biology, 2002, DOI:10.1016/S0022-2836(02)00386-8 .

[3] Akshay Sridhar, Stephen E. Farr, Guillem Portella, Tamar Schlick, Modesto Orozco, Rosana Collepardo-Guevara, Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry, Proceedings of the National Academy of Sciences, 2020, DOI:10.1073/pnas.1910044117.

Nucleosome Formation

Nucleosome formation using our CG model. Simulated with LAMMPS, visualised using Ovito.

Force-extension of Chromatin

Force-extension simulations (constant velocity steered molecular dynamics). Simulated with LAMMPS, visualised using Ovito.

Liquid-liquid Phase Separation

LLPS of chromatin: Slab method to setup a coexistence simulation. Simulated with LAMMPS, visualised using Ovito.

LLPS of chromatin: Coexistence simulation. Simulated with LAMMPS, visualised using Ovito.