Mapping the ρ₁ GABA_C receptor agonist binding pocket: Constructing a complete model

γ-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the mammalian brain. The GABA receptor type C (GABA_C) is a ligand-gated ion channel with pharmacological properties distinct from the GABA_A receptor. To date, only three binding domains in the recombinant ρ₁ GABA_C receptor have been recognized among six potential regions. In this report, using the substituted cysteine accessibility method, we scanned three potential regions previously unexplored in the ρ₁ GABA_C receptor, corresponding to the binding loops A, E, and F in the structural model for ligand-gated ion channels. The cysteine accessibility scanning and agonist/antagonist protection tests have resulted in the identification of residues in loops A and E, but not F, involved in forming the GABA_C receptor agonist binding pocket. Three of these newly identified residues are in a novel region corresponding to the extended stretch of loop E. In addition, the cysteine accessibility pattern suggests that part of loop A and part of loop E have a β-strand structure, whereas loop F is a random coil. Finally, when all of the identified ligand binding residues are mapped onto a three-dimensional homology model of the amino-terminal domain of the ρ₁ GABA_C receptor, they are facing toward the putative binding pocket. Combined with previous findings, a complete model of the GABA_C receptor binding pocket was proposed and discussed in comparison with the GABA_A receptor binding pocket.