Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides

Abstract

Biological membranes are important cell structures that play important role in the transport of the ions and other molecules into and out of the cell and regulate the signaling pathway. They are composed of lipid bilayer, integral and peripheral proteins. The ionic channels, enzymes and most of the membrane receptors belong to integral proteins that span the membrane and contact by their hydrophobic part with hydrophobic interior of the lipid bilayer. These hydrophobic interactions are crucial for the effect of peptide on a lipid bilayer matrix and vice versa. The study of the mechanisms of these interactions is important for understanding the functioning of the peptides in a membrane. However the study of native biomembrane is rather complicated due to its complexity and inhomogeneity. Therefore model lipid bilayers and short peptides can be used as a model for study of the protein–lipid interactions. In this chapter we review the current state of the art in experimental and molecular dynamics simulation study of the short peptide–membrane interactions. As an example we consider in more detail the application of molecular dynamic simulations on the study of interaction of a model lysine-flanked α-helical peptides P24, LA12, L24 and its analogues A24, I24, and V24 with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both in a gel and in a liquid-crystalline state. We have shown that these peptides cause disordering of the lipid bilayer in the gel state and small changes in a liquid-crystalline state. The peptides affect ordering of the surrounding lipids depending on the helix stability, the amount of dihedral angles in trans conformation and the number of transitions between trans and gauche conformation. It has been found the tendency of Lys-flanked peptides to compensate the positive mismatch between peptide and membrane hydrophobic core by tilting. In some cases the tilt was replaced by superhelical double-twisted structure. The rest of helices were bend or produced kink in addition to the tilt. The lipid structural state around the peptide has been also analyzed.