Assessing Perturbations of a Fluorescent Lipid in a DPPC Bilayer with Molecular Dynamics

Abstract

Fluorescent lipid analogs are a valuable tool for studying membranes, and in recent years a wide variety of fluorescence techniques have contributed significantly to our understanding of lateral heterogeneity in both model and cell membranes. Despite their usefulness, it is often overlooked that these fluorescent molecules are extrinsic to the system of interest, and a meaningful interpretation of data, e.g. properties of nanoscopic domains, local motion and order of the probe environment, or Forster resonance energy transfer, can benefit from understanding probe location within the bilayer, and how the probe itself affects the native membrane state. We have conducted molecular dynamics simulations to investigate perturbations in a DPPC membrane of a family of commonly-used fluorescent lipids: the indocarbocyanine chromophore DiI attached to two alkyl chains, which vary in length and degree of unsaturation. In particular, we report on the order and dynamics of DPPC as a function of distance from the probe molecule, as well as the influence of probe acyl chains on the location and dynamics of the DiI chromophore.