Supporting data for "UBE2J2 sensitizes the ERAD ubiquitination cascade to changes in membrane lipid saturation"

This dataset contains all the data needed to recreate the MD simulations and analysis described in the paper 'UBE2J2 sensitizes the ERAD ubiquitination cascade to changes in membrane lipid saturation'. All steps are detailed in Bash and SLURM scripts. All path definitions have been adapted to the folder structure described below, although we may have missed some, so please double-check. The folder structure is as follows: supporting_data ├─ simulations └─ <system> ├─sysbuilder └─postprocess └─<replicate> ├─ structures├─ scripts └─analysis ├─ mdp_files└─ packmem The 'simulations' folder contains data for molecular dynamics (MD) simulations. The system folder can be ER, 10SFA or 60SFA, indicating the corresponding lipid composition. The "sysbuilder" folder contains the necessary files and instructions to generate the simulation system. This process is detailed in gen_topology_insane.sh. The 'postprocess' folder contains the processed trajectories after the water molecules have been removed and the periodic boundary conditions (PBC) artefacts resolved. This process is detailed in supporting_data/scripts/jobscript_postprocess.sbatch. To reduce file size, the timestep of the uploaded trajectories was increased from 1 ns to 10 ns. The original trajectories can be obtained from the authors upon reasonable request. The simulation files are stored in the rep1-rep10 subfolders. The 'structures' subfolder contains the input structure. The 'scripts' subfolder contains all the scripts used to perform the simulations and analyse the results. The 'params' subfolder contains all the simulation parameter files (MDP files) and the Martini3 parameters used for packmem.