In the ionotropic glutamate receptor, the global conformational changes induced by partial agonists are smaller than those induced by full agonists. However, in the pentameric ligand-gated ion channel receptor family, the structural basis of partial agonism is not understood. This study investigated whether full and partial agonists induce different conformation changes in the glycine receptor chloride channel (GlyR). A substituted cysteine accessibility analysis demonstrated previously that glycine binding induced an increase in surface accessibility of all residues from Arg 271 to Lys 276 in the M2-M3 domain of the homomeric ␣1 GlyR. Here we compare the surface accessibility changes induced by the full agonist, glycine, and the partial agonist, taurine. In GlyRs incorporating the A272C, S273C, L274C, or P275C mutation, the reaction rate of the cysteine-specific compound, methanethiosulfonate ethyltrimethylammonium, depended on how strongly the receptors were activated but was agonist-independent. Reaction rates could not be compared in the R271C and K276C mutant GlyRs because methanethiosulfonate ethyltrimethylammonium did not modify the extremely small currents induced by saturating taurine or equivalent low glycine concentrations. The results indicate that bound taurine and glycine molecules impose identical conformational changes to the M2-M3 domain. We therefore conclude that the higher efficacy of glycine is due to an increased ability to stabilize a common activated configuration.The glycine receptor chloride channel (GlyR) 1 mediates fast inhibitory neurotransmission in the vertebrate central nervous system (1, 2). It belongs to the family of pentameric ligandgated ion channels (LGICs) that includes the nicotinic acetylcholine receptor (nAChR) as its prototypical member (3). Each subunit incorporates a large N-terminal extracellular domain and four ␣-helical membrane-spanning domains. The second membrane-spanning (M2) domains curve radially so as to form a tapering, water-filled pore with a hydrophobic barrier (or channel gate) at either its mid-point (4) or intracellular boundary (5). The N-terminal domains contain the agonist-binding sites and a disulfide loop that is an invariant feature of LGIC receptors (6). Agonists binding in the N-terminal domain initiate conformational changes that propagate as a wave toward the channel gate (7). Different agonists induce these conformational changes with different efficacies (where efficacy is the ability of an agonist to open the channel once bound to the receptor). If the efficacy of an agonist is sufficiently low, it will behave as a partial agonist (8). The structural basis of differential agonist efficacy is not yet understood for any member of the LGIC family.Partial agonism could be caused by one, or a combination, of the following two sharply contrasting mechanisms. First, it is possible that different agonists induce different structural changes throughout the protein. A clear example of this has been characterized recently (9 -11) in the ionotropic g...