(416b) Realistic Lipid Membrane Modeling with All-Atom Molecular Dynamics Simulations

Lipids constitute structural building blocks for cell membranes. These serve as barriers between the cell and its surroundings as well as between compartments within the cell. Lipid diversity is great across organisms and even within cell compartments. This variety results in different mechanical and structural properties in the membrane that directly impact the molecules that interact with this interface. Lipids can influence the function of both membraned-bound and peripheral proteins, serving as active modulators in various cellular processes. Computational approaches are increasingly used to predict interactions between biomolecules. Molecular dynamics simulations, based on statistical mechanics, have become a powerful tool to study the natural interaction between biomolecules. Typical membrane models in simulations are made of a single lipid species to provide a hydrophobic environment for the membrane for the study of protein dynamics. Over the past few years, all-atom models have use binary or ternary lipid mixtures to account for lipid diversity in the cell. However, given that lipid composition greatly affects the mechanical properties of the membrane, it is crucial to select an appropriate mixture of lipid species that are characteristic to a particular organism or compartment in the cell. Here, we focus on important considerations when selecting lipid species for a membrane model, and the effects of membrane size and simulation time on the mechanical and structural properties of these model bilayers at the atomistic level. We present a systematic study to determine the minimum membrane patch size when simulating complex lipid bilayers, examining membrane properties and their trend with respect to membrane size. Finally, we present some examples where membrane composition modulates interactions with other biomolecules.