PREDICTED STRUCTURE OF THE EXTRACELLULAR REGION OF LIGAND-GATED ION-CHANNEL RECEPTORS SHOWS SH2-LIKE AND SH3-LIKE DOMAINS FORMING THE LIGAND-BINDING SITE

Fast synaptic neurotransmission is mediated by ligand-gated ion-channe l (LGIC) receptors, which include receptors for acetylcholine, seroton in, GABA, glycine, and glutamate. LGICs are pentamers with extracellul ar ligand-binding domains and form integral membrane ion channels that are selective for cations (acetylcholine and serotonin 5HT(3) recepto rs) or anions (GABA(A) and glycine receptors and the invertebrate glut amate-binding chloride channel). They form a protein superfamily with no sequence similarity to any protein of known structure. Using a 1D-3 D structure mapping approach, we have modeled the extracellular ligand -binding domain based on a significant match with the SH2 and SH3 doma ins of the biotin repressor structure. Refinement of the model based o n knowledge of the large family of SH2 and SH3 structures, sequence al ignments, and use of structure templates for loop building, allows the prediction of both monomer and pentamer models. These are consistent with medium-resolution electron microscopy structures and with experim ental structure/function data from ligand-binding, antibody-binding, m utagenesis, protein-labeling and subunit-linking studies, and glycosyl ation sites. Also, the predicted polarity of the channel pore calculat ed from electrostatic potential maps of pentamer models of superfamily members is consistent with known ion selectivities. Using the glycine receptor alpha 1 subunit, which forms homopentamers, the monomeric an d pentameric models define the agonist and antagonist (strychnine) bin ding sites to a deep crevice formed by an extended loop, which include s the invariant disulfide bridge, between the SH2 and SH3 domains. A d etailed binding site for strychnine is reported that is in strong agre ement with known structure/function data. A site for interaction of th e extracellular ligand-binding domain with the activation of the M2 tr ansmembrane helix is also suggested.