Supplementary Fig. 5: Replicate simulation of peptide translocation through aerolysin.
From: Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore
(a,b) Force exerted on the peptide during the two SMD simulations versus the z coordinate of the peptide’s CoM. Hereafter Run 1 refers to the simulation reported in the main text whereas Run 2 refers to the replicate simulation. Instantaneous SMD forces are shown in gray; and their running average (5 Å window) is shown in black. (c) The z coordinate of the peptide’s CoM versus simulation time for Run 1 and Run 2; the two dependences follow closely one another. (d,e) Relative residual current versus the CoM coordinate of RR7, RR6, RR5 and RR4 peptides for Run 1 (d) and Run 2 (e). The peptides’ coordinates were derived from the conformations of RR7 sampled during the SMD simulation. The currents were computed using the steric exclusion model and averaged using a 10 Å running average. (f) Simulated versus experimental average relative currents produced by the arginine peptides within the sensing region of aerolysin. (g-i) Same as d-f but for GR7, AR7, TR7, HR7, and RR7 peptides; the experimental values are reproduced from Fig. 1. For panels f & i, the average simulated current was calculated from 130 relative residual current values for runs 1 and 2, corresponding to the presence of arginine peptides in the sensing region. For panels g & h, the currents were averaged using a 10 Å (50 values) running average.
