Edited by F. Anne StephensonAllosteric modulators of pentameric ligand-gated ion channels are thought to act on elements of the pathways that couple agonist binding to channel gating. Using ␣42 nicotinic acetylcholine receptors and the ␣42-selective positive modulators 17-estradiol (EST) and desformylflustrabromine (dFBr), we have identified pathways that link the binding sites for these modulators to the Cys loop, a region that is critical for channel gating in all pentameric ligand-gated ion channels. Previous studies have shown that the binding site for potentiating EST is in the C-terminal (post-M4) region of the ␣4 subunit. Here, using homology modeling in combination with mutagenesis and electrophysiology, we identified the binding site for potentiating dFBr on the top half of a cavity between the third (M3) and fourth transmembrane (M4) ␣-helices of the ␣4 subunit. We found that the binding sites for EST and dFBr communicate with the Cys loop, through interactions between the last residue of post-M4 and Phe 170 of the conserved FPF sequence of the Cys loop, and that these interactions affect potentiating efficacy. In addition, interactions between a residue in M3 (Tyr 309 ) and Phe 167 , a residue adjacent to the Cys loop FPF motif, also affect dFBr potentiating efficacy. Thus, the Cys loop acts as a key control element in the allosteric transduction pathway for potentiating EST and dFBr. Overall, we propose that positive allosteric modulators that bind the M3-M4 cavity or post-M4 region increase the efficacy of channel gating through interactions with the Cys loop.The ␣42 nicotinic acetylcholine receptor (nAChR) 2 belongs to the superfamily of pentameric ligand-gated ion channels (pLGICs). In humans, this superfamily comprises the Cys loop receptors (including muscle and neuronal nAChRs, 5-HT 3 , GABA A , and glycine receptors), which mediate all fast central nervous system synaptic inhibition and much of fast peripheral excitation. Cys loop receptor subunits assemble as a pentamer of identical (homomeric channels) or different (heteromeric channels) subunits around a central ion channel. The individual subunits have a large extracellular N-terminal domain (ECD) that consists of 10 -strands (1-10) folded into a -sandwich and a transmembrane domain (TMD) with four transmembrane ␣ helices (M1-M4) connected by linkers (M1-M2, M2-M3, and M3-M4), as well as intracellular domains and a highly variable extracellular C-terminal (post-M4) region (1). There are 2-5 neurotransmitter binding sites at subunit interfaces within the ECD, and these sites are functionally coupled to the transmembrane ion channel located ϳ50 Å away. In the nAChR, the subunit contributing the principal face of the agonist binding site (an ␣ subunit) couples agonist-triggered agonist binding site movements to channel gating (2, 3). The coupling is achieved at the ECD-TMD interface by a principal pathway that couples the pre-M1 region in the ECD to the M2-M3 linker through the 1-2 loop (4) and the canonical FPF motif of the 6-...