Membrane-associated proteins and peptides

Abstract

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. © 2008 Humana Press.