MD simulations data for the molecular mechanism of ICA-105574 based activation of hERG channels

The dataset is a collection of molecular dynamics (MD) simulation trajectories generated using GROMACS software, initial structure (gro and pdb format) and topology files (tpr) used for performing MD simulations to investigate the therapeutic potential of ICA-105574, a hERG activator, in severe hERG mutations (A561V, G628S, L779P) associated with LQT2.

Details about different ZIP files

Wild type: WT

SQT mutations: S631A, N588K

LQT mutations: G628S, A561V

ICA-105574 bound trajectories: WT-ICA, G628S-ICA and A561V-ICA.

LQT mutation: L779P (MD simulations using only CNBHD in the wild type (WT) and mutation (MUT).

MDP-PLUMED: MDP files for running different steps in simulations using gromacs

Files in each folder:

SYSTEM_Charmm-Gui_Output.pdb : Output file generated using charmm-gui protocol. The file contains: Protein embedded in POPC bilayer with water and KCl (200mM).

Structure.gro: Structure after minimisation with K+ placed manually (KWKWK configuration) inside the selectivity filter to prevent inactivation.

R1 and R2: Two replica of trajectories. The trajectories are saved with frames at every 1ns for convenience. Full trajectories with frames saved at every 10ps are available upon request.

md.tpr: The file represents the topology parameters used for the production run. The number of steps and the starting structure may differ depending upon the individual equilibration and final length of the production run for different replica.