Modeling and Stability Analysis of Truncated High Density Lipoprotein (HDL) System Using Martini Coarse Grain Technique

Abstract

Lipoproteins are biochemical compounds containing both proteins and lipids. These particles carry chemicals like cholesterol and triglycerides that are not soluble in aqueous solutions. This paper presents modeling of lipoprotein system using coarse grain molecular dynamics technique and stability analysis of this system in a water solution like blood. A high density lipoprotein (HDL) that consists of two annular monomers is modeled. Also there are lipid bilayers located in center of the rings, so the whole HDL and lipid bilayers are called lipoprotein system. First, all atom model is provided and then coarse-grain model is obtained using MARTINI technique. Modeling of the system in all atom and coarse-grain is performed by VMD and simulation is executed by NAMD. System is simulated for 400ns with time step of 20fs in NPT ensemble. System temperature assumed similar to normal human body temperature. Finally the structure shape and stability of system were considered and results were analyzed.

Analytical investigation of non-Fickian receptor-mediated endocytosis

“…Molecular dynamics simulations can reveal detailed observations at this scale. The application of this technique on studies such as assembly of high density proteins (HDL) [7][8], penetration of peptides into living cell [6] and homo-oligomerization of integrin proteins on the membrane [9] have showed the ability of this method to model and further understanding of nano-scale biological processes.…”