Carpenter, Timothy S.; Lau, Edmond Y.; Lightstone, Felice C.
A Role for Loop F in Modulating GABA Binding Affinity in the GABA(A) Receptor
JOURNAL OF MOLECULAR BIOLOGY, 422:310-323, SEP 14 2012

The brain's major inhibitory neuroreceptor is the ligand-gated ion channel gamma-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 alpha(1)beta(2)gamma(2) subtype is one of the most prevalent GABARs, the less populous alpha(6)beta(3)delta 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: alpha F65, alpha R132, beta L99, beta E155, beta R/K196, beta Y205, and beta R207. Residue substitution at position beta 196 (arginine in alpha(6)beta(3)delta, lysine in alpha(1)beta(2)gamma(2) 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 alpha(6)beta(3)delta receptor. Free energy calculations confirm that the alpha(6)beta(3)delta binding pocket has an increased affinity for GABA. Thus, the possible role for loop F across the GABAR family is to modulate GABA affinity. Published by Elsevier Ltd.

DOI:10.1016/j.jmb.2012.05.025

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