Membrane-forming phospholipids allosterically modulate native-state prolyl isomerization in a CNG channel

Ion channel activity is intricately linked to the surrounding lipid environment, yet the molecular effects of lipid-mediated regulation remain largely understudied. Here, we show that membrane-forming phospholipids, which are known to modulate the activity of the cyclic nucleotide-gated channel SthK from Spirochaeta thermophila, exhibit effects that extend well beyond the membrane boundary. Using stopped-flow flux assays, we demonstrate that anionic lipids, which are known to promote channel opening, also affect the fast-to-slow activation ratio and the cAMP potency in SthK. Enzymatic catalysis studies confirm that this occurs by altering the cis/trans equilibrium at Pro300 in the apo state. Additionally, cryogenic electron microscopy structures of SthK reveal lipid-dependent conformational changes that propagate from the bundle crossing into the cytosolic domains. All observed effects correlate with the electronegativity of the lipid headgroup, indicating a common underlying mechanism. Our results highlight membrane-forming phospholipids as allosteric regulators of SthK, controlling multiple functional characteristics of the channel.