Supplementary Fig. 3: MD simulation of open-pore aerolysin system.
From: Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore
(a) Equilibration of the lipid bilayer. During this 0.5 ns simulation, all non-hydrogen atoms of the aerolysin channel were restrained to their initial coordinates while preventing water molecules from entering the lipid-protein interface. The aerolysin channel is shown as a gray cut-away molecular surface, the head groups and tails of the DPhPC lipid bilayer are shown in red and cyan; 1 M KCl solution is not shown. (b) Free equilibration of the aerolysin system. The last frame of the equilibration trajectory was used as the starting structure for subsequent electric field simulations. (c) Root-mean-square deviation (RMSD) of the protein’s alpha-carbon atoms from their initial coordinates during the equilibration simulations. Each data point was averaged over the protein’s 2976 alpha-carbon atoms. (d) The simulated current-voltage curve of the aerolysin nanopore. Each data point derives from an independent MD simulation of the aerolysin system, each lasting from 13 to 37 ns, at the specified transmembrane voltage and 1 M KCl concentration. The average current was obtained by averaging instantaneous ionic current over the course of the MD trajectory. The number of data points used for calculating the average ionic current of each system is as follows: 4521 (-1.2 V), 6193 (-0.5 V), 15084 (-0.25 V), 12733 (-0.1 V), 5914 (0.5 V), 5925 (1 V).
