Fig. 4: Enhanced sampling MD simulations of the membrane permeation process of CP1, DP1, and MP1. | Nature Communications

Fig. 4: Enhanced sampling MD simulations of the membrane permeation process of CP1, DP1, and MP1.

From: Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides

Fig. 4

a Graphical abstract of the MD simulations. b Conformational ensembles of CP1, DP1, and MP1 inside, at the interface, and outside the lipid membrane projected onto the first and second principal components (PC1 and PC2), and representative conformations and backbone hydrogen bonding patterns. The percentages of the major conformations are shown in Supplementary Fig. 48. c The two-dimensional free energy profiles against the polar surface area (PSA) and z coordinate. Minima and saddle points in the free-energy profile are connected by red arrows. Stars denote the most stable positions. d The one-dimensional free energy profile of CP1, DP1, and MP1 along the z coordinate.

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