A Coarse Grained Molecular Dynamics Study of the Formation and Structure of Bicelles

Abstract

Our goal is to study interactions between bicelles and membrane associated proteins by computer simulations. In this preliminary study we have tested different representations of the bicelle lipids within the MARTINI coarse grain (CG) model. Bicelles are lipid disk-shaped systems with properties that are believed to resemble those of a native lipid bilayer. This has made them useful for studies of membrane associated proteins by a range of biophysical techniques, such as circular dichroism, liquid and solid state NMR and in diffraction studies. Bicelles normally consist of two different kinds of lipids, one with short hydrophobic tails and one with longer tails. The structure and composition of a bicelle depends on both the temperature and the ratio between the long and short tailed lipids, also known as the q-factor. The results from the CG molecular dynamics (MD) simulations are compared to NMR data, and by that revealing that this method can account for the experimental observations made of bicelle structures. Furthermore, reversed CG united atom MD simulations using the GROMOS96 force field indicate that the bicelles formed are stable on the time scale simulated. The results from the CG MD of bicelles also underline the importance of choosing a proper mapping of atoms to the CG beads.