Speaker
Description
With the increase of the available computational resources, and software acceleration of molecular dynamics, there is a drive to enlarge the simulated systems as well. Complex biological systems such as the cell membrane contain up to hundreds of various phospholipids, in the form of an asymmetric bilayer. However, the vast majority of molecular dynamics simulations of membrane proteins still use a basic symmetric POPC membrane. In contrast, simulation groups that focus on membrane simulations have built several cell membranes models of varying complexity – containing up to 60 lipids in the mixture. Which raises the question: is it more useful to increase the simulation complexity – the number of lipids in the mixture, or to take advantage of the available resources of a different way, such as using simpler models, but longer simulations with more replicas?
To compare the properties of lipid mixtures of various complexity, we built 7 different membrane models, based on both experimental studies and simulation convenience. A transmembrane segment of TLR2 protein was inserted into the model membranes, to describe the effects of the various membrane compositions.
We observe that in the membrane-only models, cholesterol plays a crucial role in the membrane thickness and fluidity, while other lipids contribute largely to the charge density of the membrane. The studied protein reacts to the different thickness of the membranes by either changing the angle between the transmembrane and juxtamembrane domains or the tilt of the protein with respect to the membrane normal.
