Magainins are natural peptides that selectively kill bacteria at concentrations that are harmless to animal cells. Due to a positive charge and distinct hydrophobic moment, magainins in the α-helical conformation interact favorably with bacterial membrane lipids. These interactions lead to the formation of large openings in the membrane and to the cell's death. The openings (toroidal pores) are supramolecular structures consisting of lipid and peptide molecules. A computer model of the pore in a bacterial membrane was constructed (see Figure) for the study of the molecular basis for magainin selectivity and specificity. Details of the construction and the preliminary equilibration of the pore model are given in this paper.
Figure Stages of PORE construction. a A side view and b the top view of E6 cluster (see text for details). The coloring scheme of lipid molecules is described in the caption to Fig. 5. c The top view of the magainin pore built of five M2a molecules (in purple and gold), five EG4E clusters, and five E6 clusters. d The top view of the lamellar part of PORE. The size of the hole in the bilayer center matches the size of the supramolecular complex shown in c. e The pore (c) is now placed in the central part of the bilayer (d)