DNA replication and repair

We are eager to learn about the mechanisms of the replication machinery, in particular the key players like helicases, polymerases and primases (see sketch of E.coli replication fork on the right side). Several diseases are strongly correlated with malfunctions in DNA replication and repair. Most likely some of these key players simply malfunction on a molecular basis. Thus it is important to establish suitable assays to study their function and malfunction in great detail, potentially leading to ideas of treatment.

Other recent studies have unambiguously linked several cancers to viral infections. Interestingly, although viruses hijack most of the cellular biomachines in order to self-replicate, most of them encode their own specific helicase. We are interested in understanding and comparing viral and eukaryotic helicases on a mechanistic single-molecule level. Future studies can then lead to a drug development for specifically targeting viral helicases.

Protein degradation

Living cells precisely control all three different levels of information bearing biopolymers - DNA, RNA and proteins (central dogma of biology). While the degradation machineries for RNA and DNA are fairly well understood, the actual function of the protein degradation machinery is poorly understood on a molecular mechanistic basis. In principle, these machines have to mechanically unfold their target proteins, before they can finally degrade the unstructured polypeptide chain (see sketch on the left hand side). The mechanical unfolding most likely requires large conformational changes inferred from crystal structures with different cofactors. Although the substrate between protein degradation enzymes and helicases is different some of these machines are exhibiting a very similar tertiary and quaternary structure. We are interested in establishing a single-molecule assay to test the function of these protein unfolding machines in detail and further compare it to structurally similar helicases.