Binding of a neurotransmitter to its membrane receptor opens an integral ion conducting pore. However, prolonged exposure to the neurotransmitter drives the receptor to a refractory state termed desensitization, which plays an important role in shaping synaptic transmission. Despite intensive research in the past, the structural mechanism of desensitization is still elusive. Using mutagenesis and voltage clamp in an oocyte expression system, we provide several lines of evidence supporting a novel hypothesis that uncoupling between binding and gating machinery is the underlying mechanism for ␣7 nicotinic receptor (nAChR) desensitization. First, the decrease in gate tightness was highly correlated to the reduced desensitization. Second, nonfunctional mutants in three important coupling loops (loop 2, loop 7, and the M2-M3 linker) could be rescued by a gating mutant. Furthermore, the decrease in coupling strength in these rescued coupling loop mutants reversed the gating effect on desensitization. Finally, coupling between M1 and hinge region of the M2-M3 linker also influenced the receptor desensitization. Thus, the uncoupling between N-terminal domain and transmembrane domain, governed by the balance of coupling strength and gate tightness, underlies the mechanism of desensitization for the ␣7 nAChR.The Cys-loop receptor family of ligand-gated ion channels are allosteric proteins (1-4). Binding of neurotransmitter to the receptor binding site located in the N-terminal domain induces conformational changes (5), which propagate to the transmembrane domain (M1-M4) 3 through the interface between these two domains to open the gate, which is formed by M2 domains (see Fig. 1A). Coupling through this interface is mainly mediated by noncovalent interactions between loops 2 and 7 (Cysloop) from N-terminal domain and M2-M3 linker from the transmembrane domain (see Fig. 1B) (6, 7). In addition, pre-M1 and M1 is the only covalent linkage between N-terminal domain and transmembrane domain, which also play a role in controlling channel gating (7). However, agonist binding does not guarantee channel opening. With prolonged exposure to neurotransmitters, most receptors are driven to a refractory state, termed desensitization (8). At the single channel level, desensitization appears as long-lasting nonconducting states (9). Desensitization is a widespread phenomenon in most ligand-gated ion channels. It plays an important role in shaping synaptic transmission (10, 11). Desensitization of the Cys-loop receptor family has been well characterized kinetically. It involves dramatic increase in binding affinity to agonists (12, 13) and closure of the ion conducting pathway (9) with little structural change in transmembrane domain (14). It is an intrinsic property of the receptors (15).Previous studies have identified numerous factors that can influence desensitization. For example, desensitization is dependent on agonists (16) and receptor subtypes (17, 18). Mutations of a residue in the binding pocket (19) or between two binding loops...