Predicting affinities of protein-lipid interactions using molecular simulations

Abstract

Membrane proteins are bound and regulated by lipids and sterols from the surrounding bilayer, and understanding the nature of these interactions is vital for understanding the biological function of the protein. Molecular dynamics (MD) simulations, especially using coarse-grained methods (CG), are routinely used to identify these binding interactions. We are increasingly interested in determining not only if and where a particular lipid binds a protein, but also the affinity of the interaction and whether a certain lipid type selectively binds.