General overview of the three replicas (REP) of 300-ns MD simulations of PTx2–hNaV1.7 activated VSD II and IV as a part of the full channel. (A–F) Panels A–C show activated VSD II, and panels D–F show activated VSD IV. The lipid membrane is represented as a gray box, with the extracellular- and intracellular-facing sides labeled as “EX” and “IN,” respectively. PTx2–VSD binding sites are highlighted by yellow circles. (A and D) Conformational changes of the toxin–VSD complex following the 300-ns-long molecular dynamics simulation for each replica. (B and E) Distribution of all toxin–VSD interaction types encountered during the MD simulations, computed by dividing the sum of a specific interaction type by the sum of all interactions across all MD simulation frames. (C and F) Time series of the RMSD of PTx2–VSD complex, VSD, toxin’s binding region, and PTx2 backbone atoms compared to the initial structures. The plotted values represent the moving averages calculated over intervals of 5 ns each. The MD simulation equilibration period is shown as a light green box.
