An ion permeable state of the Glycine Receptor captured by Molecular Dynamics
The dataset presented here is supporting the article "An ion permeable state of the Glycine Receptor captured by Molecular Dynamics" (Cerdan et. al., Structure). Are available the two DCD trajectories, related to Figure 2 and Figure S2: - Trajectories/MD-open_protein_membrane_skip20.dcd - Trajectories/MD-open-replica_protein_membrane_skip20.dcd and the the corresponding topology file: - Trajectories/protein_membrane.psf leading to the MD-open structure: - MD-open.pdb that we characterized as a model for the active state of the Glycine Receptor alpha 1 (See Main Text for details). Only the protein and the membrane are available in these DCD files and a step size of 20 is applied in respect to the original trajectories. Additionally, we provide a short (10ns) all-atom DCD trajectory of the free permeation of a chloride anion ("name CLA and resid 129"), related to Movie S1 and Movie S2: - Trajectories/permeation.dcd and its corresponding topology file: - Trajectories/permeation.psf Visualization can be achieved with various software, for example VMD. See all details in our article.
Steps to reproduce
Molecular Dynamics simulations where carried out with NAMD2.12 starting from the Glycine Receptor alpha 1 with glycine bound cryo-EM structure (PDB: 3JAE). See all details in our article.