Amphipathic membrane-active peptides recognize and stabilize ruptured membrane pores: exploring cause and effect with coarse-grained simulations.

Induction of membrane pores has been suggested as the common molecular action by which a variety of amphipathic membrane-active peptides cause damage to cells. In this study, we have performed coarse-grained molecular dynamics simulations to establish two clear molecular processes that seem critical for the activity of amphipathic peptides. They are (i) the recognition and (ii) the stabilization of ruptured membrane pores. By considering 12 structurally different peptide types, we reveal that peptide secondary structure content, hydrophobicity, and length are important physicochemical factors that allow amphipathic peptides to aggregate in and stabilize ruptured membrane pores. The simulated inner diameters of peptide-stabilized membrane pores are in good agreement with available experimental data. However, the orientations of α-helical peptides in the membrane pore were found to be quite dispersed. This supports recent challenges to the traditional depictions to peptide orientations in the classical toroidal and barrel-stave pore models.