Fig. 3: MD simulations of the pore structure of α-LTX.

a Cartoon representation of the pore structure of α-LTX (residues E21–E360). The pore is represented as an orange surface. Residues facing the pore volume are represented as sticks with labels colored according to their biochemical properties. The pore profiles from the two simulations (residues C91–Y260 for the upper part and the stalk; residues E21–S116 for the membrane protein part) are shown as blue and orange lines, respectively. b Cartoon representation of the Na⁺ and Ca²⁺ positions in the HBD, respectively, obtained from a superposition of many simulation snapshots with an applied electric field. Also, the resulting pore radius is shown together with its standard deviation. c Representative ion trajectories, correspond to typical permeation events of the TMD by Na⁺ and Ca²⁺ ions, with and without an applied electric field. Additionally, shown are ion density profiles obtained by averaging all successful permeation events. d Cartoon representations of simulations of the membrane part with different ions (Na⁺, Ca²⁺, La³⁺, and Cl⁻) with a superposition analogous to b. The Ca²⁺ ionic densities in different slabs in the xy-plane are shown (5 Å and 10 Å widths along z, respectively).