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Additional data: Kinase-phosphatase cycles drive self-sustained oscillations of protein condensates

Year: 2026
Type: article
Abstract: Kinase-phosphatase cycles drive self-sustainedoscillations of protein condensates: additional trajectories Additional trajectories of Zippo, E., Qiao, L., Dormann, D., Speck, T., Schmid, F., Stelzl, L.S. Kinase-phosphatase cycles drive self-sustainedoscillations of protein condensates, bioRxiv (2026), https://doi.org/10.64898/2026.10.27.762139 This record complements the main record of the paper, https://doi.org/10.5281/zenodo.24088578, which contains thesimulation inputs and outputs, the analyses, the code, the movies and the trajectories of the runs shown in the movies.Folder names, run names and conventions are the same as in the main record; see its `README.md`. ## Trajectories Trimmed copies of the full MD trajectories (`*_dump.gsd`), with the same names plus `_trimmed`: - all the particles: positions, images and particle types in every frame (so the pSer of every chain can be followed in time); no velocities- one frame every 10⁶ steps (10 ns, every 5th frame of the original)- continuations of a run: `_20us_` and `_40us_` start at 20 µs and 40 µs The full trajectories are kept by the authors and are available on request. | Folder | Runs | Time ||---|---|---|| `droplet_200-tdp43-lcd/sim_ness_200-tdp43-lcd_2-ck1d-open_24-pp3_fr01/` | active droplet, 2 CK1δ, 24 PP3, replica 1 | 0–30 µs || `droplet_200-tdp43-lcd/sim_ness_200-tdp43-lcd_3-ck1d-open_12-pp3_fr01/` | active droplet, 3 CK1δ, 12 PP3, replica 1 | 0–60 µs || `droplet_200-tdp43-lcd/sim_ness_200-tdp43-lcd_3-ck1d-open_18-pp3_fr01/` | active droplet, 3 CK1δ, 18 PP3, replica 3 | 0–40 µs || `droplet_200-tdp43-lcd/sim_ness_200-tdp43-lcd_4-ck1d-open_14-pp3_fr01/` | active droplet, 4 CK1δ, 14 PP3, replica 1 | 0–50 µs || `droplet_200-tdp43-lcd/sim_ness_200-tdp43-lcd_4-ck1d-open_20-pp3_fr01/` | active droplet, 4 CK1δ, 20 PP3, replica 1 | 0–60 µs || `droplet_200-tdp43-lcd/sim_dmu0_200-tdp43-lcd_2-ck1d-open_24-pp3_fr01/` | passive droplet (Δμ = 0), 2 CK1δ, 24 PP3, replica 1 | 0–30 µs || `droplet_200-tdp43-lcd/sim_200-tdp43-lcd_5-ck1d-open_fr01/` | droplet with 5 CK1δ only, replica 1 | 0–10 µs || `condensate_structure/` | droplets of 200 LCD chains with 5 CK1δ or 5 PP3, 0 or 1257 pSer, no reactions | 0–5 µs || `ostwald_ripening/` | two droplets of 400 LCD chains in total, 4 CK1δ and 48 PP3, active (`sim11_`) and passive (`sim11_eq_`), replica 11 | 0–5 µs | All droplet runs contain 200 TDP-43 LCD chains at 250 K (CALVADOS3); active runs: Δμ_k = −40 kJ/mol, Δμ_p = +8 kJ/mol.The inputs, logs, reaction files and analyses of these runs are in the main record (`simulations/` and `analysis/`). ## Reading the trajectories The files are GSD files (HOOMD-blue); they can be read with the `gsd` Python package, MDAnalysis or OVITO: ```pythonimport gsd.hoomdwith gsd.hoomd.open('..._dump_trimmed.gsd', 'r') as traj: frame = traj[0] frame.particles.position, frame.particles.typeid, frame.configuration.step``` Units: lengths in nm, time step 0.01 ps (10⁸ steps = 1 µs). The bead type `SEP` is phosphoserine. ## Licence CC BY 4.0, https://creativecommons.org/licenses/by/4.0/
DOI: 10.5281/zenodo.24103646
Language: English
Open Access status: green
OpenAlex ID: W7225728252
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