Molecular dynamics investigation of Cl− transport through the closed and open states of the 2α12β2γ2 GABAA receptor

- Homology models are embedded into a lipid bilayer to perform MD simulation.
- Some structural features of the GABAAR are explored by performing MD simulations.
- ABF simulation is used to evaluate the energy barriers for the Cl− permeation.

The α1β2γ2 gamma-aminobutyric type A receptor (GABAAR) is one of the most widely expressed GABAAR subtypes in the mammalian brain. GABAARs belonging to the Cys-loop superfamily of ligand-gated ion channels have been identified as key targets for many clinical drugs, and the motions that govern the gating mechanism are still not well understood. In this study, an open-state GABAAR was constructed using the structure of the glutamate-gated chloride channel (GluCl), which has a high sequence identity to GABAAR. A closed-state model was constructed using the structure of the nicotinic acetylcholine receptor (nAChR). Molecular dynamics simulations of the open-state and closed-state GABAAR were performed. We calculated the electrostatic potential of the two conformations, the pore radius of the two ion channels and the root-mean-square fluctuation. We observed the presence of two positively charged girdles around the ion channel and found flexible regions in the GABAAR. Then, the free-energy of chloride ion permeations through the closed-state and open-state GABAAR has been estimated using adaptive biasing force (ABF) simulation. For the closed-state GABAAR, we observed two major energy barriers for chloride ion translocation in the transmembrane domain (TMD). For the open-state GABAAR, there was only one energy barrier formed by two Thr261 (α1), two Thr255 (β2) and one Thr271 (γ2). By using ABF simulation, the overall free-energy profile is obtained for Cl− transporting through GABAAR, which gives a complete map of the ion channel of Cl− permeation.