Selectivity Filter Dynamics Define Ion Conductance and Selectivity Differences in CNG and HCN Channels

ABSTRACT Cyclic nucleotide‐gated (CNG) channels and hyperpolarization‐activated cyclic nucleotide‐gated (HCN) channels are key members of the cyclic nucleotide‐activated ion channel family that translate intracellular cyclic nucleotide binding into electrical signals. Functionally, CNG channels drive large inward currents in photoreceptors and olfactory sensory neurons, whereas HCN channels are best known for their roles in pacemaker activity in the heart and the regulation of neuronal excitability. Despite their considerable sequence similarity and conserved overall architecture, these channels exhibit striking differences in ion conductance, K + selectivity, and voltage dependence. Here, we performed microsecond‐timescale atomistic molecular dynamics (MD) simulations to directly compare the ion conduction mechanisms of HCN and CNG channels, using the prototypical K + ‐selective channel MthK as a reference. Our simulations reproduced key features observed in single‐channel patch‐clamp electrophysiology and revealed that distinct selectivity filter architectures and dynamic behaviors are the primary determinants underlying the divergence in ion conductance and K + selectivity between HCN and CNG channels. Together, these results provide a mechanistic framework for understanding the physiological roles of these channels and pave the way for the rational design of cation channels with tailored functional properties.