General overview of the three replicas (REP) of 1-μs MD simulations of PTx2–hNaV1.7 VSD II in the deactivated and activated states. (A–F) Panels A–C show deactivated VSD II and panels D–F show activated VSD II. 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 in yellow circles. (A and D) Conformational changes of the toxin–VSD complex following the 1-μs long MD simulation for each replica. (B and E) Distribution of all toxin–VSD non-bonded interaction types encountered during the 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 with 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.
