Interactions of phospholipid bilayers with several classes of amphiphilic alpha-helical peptides: insights from coarse-grained molecular dynamics simulations

Abstract

In this article, we focus on several types of interactions between lipid membranes and alpha-helical peptides, based on the distribution of hydrophobic and hydrophilic residues along the helix. We employ a recently proposed coarse-grained model MARTINI and test its ability to capture diverse types of behavior. MARTINI provides useful insights on the formation of barrel-stave and toroidal pores and on the relation between these two mechanisms. Amphipathic nonspanning peptides are also described with sufficient accuracy. The picture is not as clear for fusion and transmembrane peptides. For each class of peptides, we calculate the potential of mean force (PMF) for peptide translocation across the lipid bilayer and demonstrate that each class has a distinct shape of PMF. The reliability of these calculations, as well as wider implications of the results, is discussed.