Exploring membrane and protein dynamics with dissipative particle dynamics.

In this chapter, we review recent approaches and results when studying membrane and protein dynamics by means of dissipative particle dynamics (DPD). First, we introduce and discuss DPD as a method, for example, the choice of the thermostat, which is of interest when constructing a DPD code. Then, we review important results on pure membranes and lipid-water systems that have been obtained with DPD.

Dynamic structure formation of peripheral membrane proteins.

Using coarse-grained membrane simulations we show here that peripheral membrane proteins can form a multitude of higher-order structures due to membrane-mediated interactions. Peripheral membrane proteins characteristically perturb the lipid bilayer in their vicinity which supports the formation of protein assemblies not only within the same but surprisingly also across opposing leaflets of a bilayer. In addition, we also observed the formation of lipid-protein domains on heteregeneous membranes.

On the role of acylation of transmembrane proteins.

Acylation is a frequent means to ensure membrane association of a variety of soluble proteins in living cells. However, many transmembrane proteins are palmitoylated, indicating that this posttranslational modification may also serve as a means to regulate protein trafficking. Based on coarse-grained membrane simulations, we find that protein acylation significantly alters the tilting of transmembrane proteins with respect to the bilayer normal.