Fig. 3.

Lipids recede from the hydrophilic inner surface of the transmembrane $\beta$-sheet formed by PLY oligomers in pore conformation. Shown are three snapshots from an all-atom MD simulation of an arc-shaped PLY pentamer embedded in a DOPC bilayer with 30% cholesterol, as seen from above (A–C) and along the transmembrane $\beta$-sheet (D–F). After water (red dots) is drawn to the inner face of the $\beta$-sheet (purple strands), the lipid molecules recede and form an open membrane edge that allows free exchange of lipids between the upper and lower leaflets (B and E). Water influx expands the gap into a membrane pore between the protein and the nascent bilayer edge. See SI Appendix, Figs. S6 and S7 for monomer and trimer simulations, respectively, and Movie S1.