Side chain flexibility and the pore dimensions in the GABAA receptor

Permeation of ions through open channels and their accessibility to pore-targeting drugs depend on the pore cross-sectional dimensions, which are known only for static X-ray and cryo-EM structures. Here, we have built homology models of the closed, open and desensitized α 1 β 2 γ 2 GABA A receptor (GABA A R). The models are based, respectively, on the X-ray structure of α 3 glycine receptor (α 3 GlyR), cryo-EM structure of α 1 GlyR and X-ray structure of β 3 GABA A R. We employed Monte Carlo energy minimizations to explore how the pore lumen may increase due to repulsions of flexible side chains from a variable-diameter electroneutral atom (an expanding sphere) pulled through the pore. The expanding sphere computations predicted that the pore diameter averaged along the permeation pathway is larger by approximately 3 Å than that computed for the models with fixed sidechains. Our models predict three major pore constrictions located at the levels of −2′, 9′ and 20′ residues. Residues around the −2′ and 9′ rings are known to form the desensitization and activation gates of GABA A R. Our computations predict that the 20′ ring may also serve as GABA A R gate whose physiological role is unclear. The side chain flexibility of residues −2′, 9′ and 20′ and hence the dimensions of the constrictions depend on the GABA A R functional state.