Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
Department of Cell and Molecular Biology, Faculty of Science, University of Tehran, Tehran, Iran
High Density Lipoprotein (HDL) is a lipid-protein complex which is responsible to transport cholesterol and triglyceride molecules due to the inability of these compounds to dissolve in aqueous environment such as bloodstream. Among renowned probable structures, belt like structure is the most common shape which is proposed to this vital bimolecular complex. In this structure, the protein scaffold encompasses the lipid bilayer and a planar circular structure is formed. Several HDL simulations with embedded components in lipid section were performed. Here we applied a series of molecular dynamics simulations using MARTINI coarse grain force field to investigate an HDL model with pore of different radiuses in bilayer section instead of embedding components. The results of such studies revealed the probable structural modes in HDL configurations. In addition, totally 2.5 µs simulations lead to study the ratio of lipids to protein in HDL conformation and determine the structural shape of HDL and stability of each model due to atomic interactions. Furthermore, we proposed new conformation for HDL in its initial steps of constructing outside of cells and in peripheral tissues.