Simulation of conformational changes in proteins

First of all there is the correct folding of the proteins to form functional units. In signaling pathways and regulation association and dissociation processes are of paramount importance. Involved in these processes is often a conformational change of the interacting proteins. These mechanisms can also be found in pathological processes like aggregation.

The timescale of these processes is within the µs to ms range and thus too short to be observed with experimental methods. To get insights in the dynamic processes involved we use molecular dynamics simulation methods. Because of the long timescale, which is 4 orders of magnitude longer than traditional simulations we apply simplified models during our simulation. The models use a 4 atom to 1 bead mapping (c.f. figure 1). The reduced number of interaction points allows much longer timescales und much larger system sizes

Because we are especially interested in the protein aggregation process and conditions, which influence the aggregation we simulate several units of the same protein in one system. Hopefully we can reproduce a specific aggregation mechanism for our system of interest and predict environmental conditions which influence the process.