A Role for Loop F in Modulating GABA Binding Affinity in the GABAA Receptor

The brainʹs major inhibitory neuroreceptor is the ligand-gated ion channel γ‐aminobutyric acid (GABA) type A receptor (GABAR). GABARs exist in a variety of different subunit combinations that act to modulate the physiological behavior of GABAR by altering its pharmacological profile, as well as its affinity for GABA. While the α1β2γ2 subtype is one of the most prevalent GABARs, the less populous α6β3δ subtype has much higher GABA sensitivity. Previous studies identified residues crucial for GABA binding; however, the specific molecular differences responsible for this diverse sensitivity are not known. Furthermore, the role of loop F is a divisive subject, with conflicting evidence for ligand binding function. Using homology modeling, ligand docking, and molecular dynamics simulations, we investigated the GABA binding sites of the two receptor subtypes. Simulations identified seven residues that consistently interacted with GABA in both subtypes: αF65, αR132, βL99, βE155, βR/K196, βY205, and βR207. Residue substitution at position β196 (arginine in α6β3δ, lysine in α1β2γ2) resulted in a shift in GABA binding. However, the major difference between the two binding sites was the magnitude of loop F involvement, with a greater contribution in the α6β3δ receptor. Free energy calculations confirm that the α6β3δ binding pocket has an increased affinity for GABA. Thus, the possible role for loop F across the GABAR family is to modulate GABA affinity.