Figure 11.

Docking experiments within predicted ISO binding cavities as indicated by AziISO photolabeled residues in the α₁β₃γ_2L GABA_A receptor. The 3 suggested transmembrane domain binding cavities within the α+/β− (A) and β+/α− (B) interfaces and the α+/γ− intrasubunit/intersubunit cavity (C). All residues that face cavities were made flexible, whereas the backbone structure remained rigid during docking experiments. The gray Connolly surface/mesh dotted representations are of 5 ISO and 5 AziISO in the highest scored poses predicted by AutoDockVina (33). Green spheres indicate the Cα atoms of residues photolabeled by AziISO in the α₁β₃γ_2L GABA_A receptors and are labeled accordingly. The left panel includes a transmembrane domain view of the docking experiments for each unique interface from the synaptic cleft [only 1 of 2 β+/α− interfaces (B) shown]. The bottom panel includes the aligned α₁-, β₃-, and γ_2L-subunit sequences that span the M1–M3 helices, with photolabeled residues colored in green.