Computational characterization of dimerization and ligand binding in biological systems

The self-association of proteins to form dimers or higher-order oligomers is a very common phenomenon in biology. Protein dimerization or oligomerization acts as a control tool for the execution of functions in many biological systems. Three systems were studied by computational methods in this thesis. Cyclic diguanylic acid (CDG) is a ubiquitous messenger involved in bacterial signaling networks. CDG can form an intercalated dimer and bind at the inhibition site of PleD. MD simulations were carried out for the CDG dimer as well as the analogue of CDG (endo-S-CDG) in solution and binding to the PleD protein. It was demonstrated, that dimeric CDG is only marginally stabilized even in high concentration. The results help the fundamental understanding of c-di-GMP and preventing biofilm formation. Insulin is a small protein that plays an eminent role in controlling glucose uptake in cells. Insulin can associate as a dimer which leads to diabetes. The key role of the B24 residue for insulin dimerization was identified. Our work provided an insight for designing analogues of human insulin and thus a therapy for diabetes.