Glutathione Transport by the Malaria Parasite's Chloroquine Resistance Transporter, PfCRT

This dataset contains the input structures and representative output frames from a series of molecular dynamics (MD) simulations of the Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT). The data is organized into two main directories: structures and PfCRT-trajectories.

The structures directory contains the initial component files used for system preparation. This includes the protein models for the two PfCRT variants: the HB3 (WT) variant, predicted by AlphaFold3 (hb3_af3.pdb), and the 7G8 variant (7g8.pdb), where a missing loop was resolved using MOE with PDB ID 6UKJ as a template. It also contains the GSH (gsh.pdb, gsh.psf) and GSSG (gssg.pdb, gssg.psf) ligand structures that were used for docking and the MD simulations. Finally, the solvated and neutralized docked poses used as the starting point for each production simulation are also provided (ionized.pdb and ionized.psf).

The PfCRT-trajectories directory contains snapshots from each production simulation run, specifically the initial structure at 0 ns (first.pdb) and the final structure at 200 ns (last.pdb). The simulations were performed for two different variants (7G8 and HB3), two different ligand states (gsd and gsh), with five independent replicates (rep1 to rep5) for each docked pose.

The codes are available at: https://github.com/payamkelich/PfCRT