Membrane-Associated Proteins and Peptides

This chapter discusses the practical aspects of setting up molecular dynamics simulations for membrane-associated proteins and peptides. Special emphasis lies on the analysis of such systems. The main focus is the association between a cationic peptide and an anionic lipid bilayer—a peptide/lipid—bilayer system—but the extension onto more complicated systems is discussed. Topology files for selected lipids and several new analysis tools relevant for protein—membrane simulations are presented, the most important ones of which are: g_helixaxis, to calculate the axis of a helix and its angle with the bilayer; g_arom, to calculate aromatic order parameters; and g_under, to calculate which lipids interact with the protein. A procedure is explained to calculate properties involving peptide-interacting lipids only, as opposed to all lipids.