The GET insertase exhibits conformational plasticity and induces membrane thinning - The Molecular Dynamics Dataset

The molecular dynamics simulation systems.

List of files: 

1. SimulationSystems.pdf: List of all simulation systems reported and their compositions
2. ProteinComplex.pdb: The initial model for the hsGet2ΔN-Get1/Get3 complex used in simulations was constructed based on the cryo-EM structure (PDB accession 6SO5). Missing residues (except the terminal ones) were modeled using Modeller.
3. prod.mdp: The GROMACS molecular dynamics parameters (mdp) file used for all simulations
4. toppar.zip: The Charmm36(m) force field parameter and topology set used for all simulations generated by CHARMM-GUI.
5. Compressed  (zip) files containing simulations inputs and trajectories

1-PC.zip
2-1:4_PI:PC.zip
3-1:4_PE:PC.zip
4-1:4_PS:PC.zip
5-1:4_CL:PC.zip
6-1:4_chol:PC.zip
7-1:1:1:1_PC:PI:PS:PE.zip
8-1:1:1:1:1:1_PC:PDPC:PS:PI:PE:chol.zip

Each zip file contains the following files:

1. System_0ns.pdb: The initial configuration used for the simulations generated using CHARMM-GUI and equilibrated following the CHARMM-GUI equilibration protocol
2. index.ndx: GROMACS index file
3. topol.top: GROMACS topology file
4. prod0.tpr, prod1.tpr, prod2.tpr:  GROMACS run topology files (tpr) for each repeat
5. prod0.gro, prod1.gro, prod2.gro: The final configuration after 3 μs production runs for each repeat
6. noW_0ns.pdb: The initial configuration without the water molecules.
7. noW_0.xtc, noW_1.xtc, noW_2.xtc: The 3 μs processed production trajectories. The water molecules were removed, and the trajectories were subsampled at 1 ns intervals.