Atomic-level characterization of protein-lipid interactions using molecular dynamics simulations

Peripheral membrane proteins are structurally diverse proteins that are involved in fundamental cellular processes. Their activity of these proteins is frequently modulated through their interaction with cellular membranes, and as a result techniques to study the interfacial interaction between peripheral proteins and the membrane are in high demand. Due to the fluid nature of the membrane and the reversibility of protein–membrane interactions, the experimental study of these systems remains a challenging task. Molecular dynamics (MD) simulations offer a suitable approach to study protein–lipid interactions with high spatial and temporal resolution. Here, we present a summary of recent applications of MD simulations to study the interaction of different classes of membrane proteins with lipid bilayers at the atomic level. Specific systems studied include membrane-bound cytochrome P450 (CYP) enzymes, a class membrane proteins involved in the metabolism of a wide range of molecules, the hemagglutinin fusion peptide (HAfp), a small peptide that mediates the fusion process of the influenza virus to a host cell, and the T-cell immunoglobulin and mucin domain (Tim) proteins, involved in the mechanism of lipid recognition by T-cells