Molecular dynamics of the pathogenic KCNQ2 variant G256W reveals mechanisms of channel dysfunction in epileptic encephalopathy

Brain potassium channels containing the subunit KCNQ2 are essential for regulating electrical signals contributing to sensation, learning, memory and motor control. De novo KCNQ2 variants are among the more common Mendelian causes of early-life epilepsy and neurodevelopmental impairment. Some patients with KCNQ2 variants are affectedby KCNQ2 developmental and epileptic encephalopathy (KCNQ2 DEE) characterized by seizures and developmental delays. Children with KCNQ2 DEE exhibit a range of impairment patterns that appear to be correlated with specific consequences of the variant for protein function. Here, we used all-atom molecular dynamics to analyze KCNQ2 G256W, a pathogenic missense variant located in the pore turret. G256W subunit simulations showed migration of the hydrophobic W256 side chain toward the lipid membrane. This movement affected overall turret structure and mobility prominently involving K255. We identified hydrogen bonding interactions in the wild type KCNQ2 turret region forming a network that extended to the selectivity filter, with N258, H260 and K283 as key residues. Simulations comparing WT and G256W tetrameric channels exhibited more conformationally unstable ion selectivity filters for G256W subunits. We analyzed how different stoichiometries of wild type and G256W subunits, as expected in heterozygous individuals, impacted dynamics and compared the G256W results to three additional turret-selectivity filter network variants. Our results provide support for an integral role of the KCNQ2 turret in selectivity filter stability. The majority of severe KCNQ2 DEE variants are clustered near the selectivity filter. Our study provides insights that may be broadly applicable to this clinically important allele subgroup.