The human ether-à-go-go–related gene (hERG) potassium channel (Kv11.1) plays a critical role in regulating heart rhythm. Its dysfunction due to loss of function mutations or the unintentional drug-induced block can lead to fatal cardiac arrhythmias, making it a key target for both therapeutic modulation and drug safety. The hERG channel exhibits very rapid inactivation that is unique from other potassium channels. While the selectivity filter is known to be involved in this process, the series of structural transitions that lead to rapid inactivation remain unclear. CnERG1 is a toxin produced by the Centruroides noxius scorpion that causes high-affinity but incomplete block of wild-type hERG current. In contrast, CnERG1 completely blocks the inactivation-deficient S631A hERG mutant, suggesting a binding mechanism that is dependent on inactivation gating.
Here we used cryo-EM structures of CnERG1 bound to both wild-type and S631A hERG channels as templates for molecular dynamics simulations to explore the dynamics of toxin binding to the channels. CnERG1 remains stably bound in both structures across simulations, held by strong salt bridge and hydrogen bonding interactions between key residues. There are also distinct structural fluctuations in the upper filter region in the toxin-bound structures compared to the apo state. These differences suggest that subtle rearrangements of the hERG residues F627, G628 and N629, characterised by asymmetric constriction and rotation of backbone carbonyls, differentiate the filter between activated and early inactivated states. Further simulations of CnERG1 and an inactivated hERG complex suggest it can restore the selectivity filter to a conductive-like state. These findings indicate that the toxin occludes conduction but stabilises the hERG selectivity filter in a conductive conformation. This work highlights the utility of toxins as a molecular probe for understanding the conformational dynamics of ion channels.