The binding site in G-protein-linked neurotramsmitter receptors is formed among their membranepning segments. Because the binding site is in the plane of the bilayer and is accessible to charged, water-soluble agonists, it must lie in a crevice open to the extracellular, aqueous medium. Information about the structure of these receptors can be obtained by identifying the residues in the membranesnning segments which face this water-filed crevice Our understanding of the molecular mechanisms of membrane receptor function depends on our knowledge of the molecular structures of receptors and on the assignment of functional roles to structural domains. High-resolution structures of membrane receptors are not yet available, but local structural information obtained by biochemical approaches, such as affinity labeling and mutagenesis, in conjunction with low-resolution structural information obtained by biophysical approaches, has provided some insight into receptor mechanisms and the potential functional roles of specific residues and regions of receptors. Affinity labeling has the advantage that the residues labeled can be inferred to be at the surface, near the residues involved in binding; however, only a few of the residues forming a binding site are likely to be affinity labeled. Mutagenesis has the advantage that any residue can be altered; however, the mutation of residues outside of a binding site can alter binding by long-range perturbation of receptor structure, thus confounding the identification of binding-site residues.The substitution by mutagenesis of cysteines for other residues is generally well tolerated. The characteristics ofthe environment surrounding a native or engineered cysteine can be inferred from the relative rates of reaction of sulfhydrylspecific reagents that differ in polarity, charge, or size. For example, hydrophilic, lipophobic reagents will react much faster with cysteines at the water-accessible surface of the protein than at the lipid/protein interface or in the protein interior. The electrostatic potential and steric constraints around cysteines can be probed with reagents of different charges and sizes.A particularly convenient arena for this approach is in ion channels, which are formed by membrane-spanning segments ofthe proteins. Among the residues in the membrane-spanning segments, only those which face the channel lumen should be water accessible. Cysteines substituted for residues in these surfaces should be accessible to small, highly polar reagents, while cysteines substituted for residues facing away from these surfaces, toward the interior ofthe protein or toward the lipid bilayer, should be inaccessible to such reagents. By determining the functional effects of charged methanethiosulfonate (MTS) derivatives on cysteine-substitution mutants, residues lining the channels of the nicotinic acetylcholine receptor (1), GABAA y-raminobutyrate receptor (2), and the cystic fibrosis transmembrane conductance regulator (3) have been identified. Covalent modification ofs...