DOI: 10.6084/m9.figshare.31314325
title: Molecular dynamics of the pathogenic <i>KCNQ2</i> variant G256W reveals mechanisms of channel dysfunction in epileptic encephalopathy

description: Brain potassium channels containing the subunit KCNQ2 are essential for regulating electrical signals contributing to sensation, learning, memory and motor control. De novo <i>KCNQ2</i> variants are among the more common Mendelian causes of early-life epilepsy and neurodevelopmental impairment. Some patients with <i>KCNQ2</i> variants are affectedby <i>KCNQ2</i> developmental and epileptic encephalopathy (<i>KCNQ2</i> DEE) characterized by seizures and developmental delays. Children with <i>KCNQ2</i> 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 <i>KCNQ2</i> DEE variants are clustered near the selectivity filter. Our study provides insights that may be broadly applicable to this clinically important allele subgroup. A serious childhood illness, called <i>KCNQ2</i> developmental and epileptic encephalopathy, usually arises from single amino acid substitutions, or missense variants. This paper provides insight into how such a local change can profoundly disrupt the function of a large oligomeric channel protein containing over 3,400 residues. Molecular dynamics simulations of the pathogenic KCNQ2 pore domain variant, G256W, revealed that W256 changed the structure and flexibility of the pore domain turret and altered the ion selectivity filter. These findings shed light on the functional impact of KCNQ2 pathogenic variants and may help illuminate general mechanisms underlying severe KCNQ2 variants that occur commonly near the ion pore. <b>Abbreviations:</b> CaM: calmodulin; <i>KCNQ2</i> DEE: <i>KCNQ2</i> developmental and epileptic encephalopathy; MD: molecular dynamics; PGD: pore gating domain; PIP2: phosphatidylinositol 4,5-bisphosphate; POPC: 1-palmitoyl-2-oleoylphosphatidylcholine; RMSD: root mean square deviation; RMSE: root mean square error; RMSF: root mean square fluctuation; SASA: solvent accessible surface area; SD: standard deviation; SF: selectivity filter; SLFNE: self-limited familial neonatal epilepsy; VMD: visual molecular dynamics; VSD: voltage-sensing domain; WT: wild type