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Significance The cation-versus-anion selectivity of pentameric ligand-gated ion channels cannot always be predicted on the basis of their amino acid sequences alone. Indeed, the relationship between amino acid sequence and function contains subtle elements that have eluded prior investigation. Here, we found that ion–ion interactions between the passing ions and ionized side chains in the first turn of the M2 α-helices dominate the permeation free-energy landscape, but we also found that the mere presence of an ionized residue in the first turn of M2 does not ensure that its charge is “felt” by permeating ions. Instead, there seems to be a requirement for a proper conformation for a charged side chain to exert its effect on selectivity.

Identifying the elusive link between amino acid sequence and charge selectivity in pentameric ligand-gated ion channels