Structural light microscopy - single molecule spectroscopy
Interfacing a large set of tools with our home-built highly sensitive equipment allows us to study structure and dynamics of even heterogeneous biological systems in 4D.
The Lemke group combines advanced microscopy with modern chemical biology tools to elucidate the nature of naturally unfolded proteins in biological systems and disease mechanisms.
Previous and current research
Currently, more than 50,000 protein structures with atomic resolution are available from the protein databank and this number is rapidly growing. However, even if all 3D protein structures were available, our view of the molecular building blocks of cellular function would still be rather incomplete, as we now know that many proteins are intrinsically disordered (unfolded in their native state). Interestingly, the estimated percentage of intrinsically disordered proteins (IDPs) grows with the complexity of the organism (prokaryotes 5% and eukaryotes 50%). In a modern view of systems biology, these disordered proteins are believed to be multi-functional signalling hubs central to the interactome (the whole set of molecular interactions in the cell). Their ability to adopt multiple conformations is considered a major driving force behind their evolution and enrichment in eukaryotes.
While the importance of IDPs in biology is now well established, many strategies for probing protein structure are incompatible with molecular disorder and the highly dynamic nature of those systems. In complex biological systems, the situation is further complicated by the mosaic of molecular states and reaction systems, where unexpected phenotypes might arise where proteins behave differently to the average. One example are Prion proteins, where misfolding of only subpopulations of proteins can trigger a drastic signalling cascade leading to completely new phenotypes. Conventional ensemble experiments are only able to measure the average behaviour of such a system and can easily lead to the generation of false or insufficient models. Single molecule and superresolution techniques - which directly probe the distribution of molecular events - can help to overcome this by revealing important mechanisms that otherwise remain obscured. In particular, single molecule fluorescence studies allow probing of molecular structures and dynamics at near atomic scale with exceptional time resolution.
Future projects and goals
Recent studies have shown that even the building blocks of some of the most complex and precise machines with a critical role in the survival of the cell are built from IDPs rather than ‘structured’ proteins. A prominent example is the nuclear pore complexe (NPC), which, with an approximate molecular weight of 120 megaDalton, constitutes the largest molecular machine in the cell. Malfunctions of this machinery are linked to diseases ranging from leukemia to HIV. e NPC is built from hundreds of proteins and can regulate the transport of 1000 proteins per second in a single pore. But how such floppy protein networks are formed and maintain high specificity, high exchange rates, low error rates and diversity at the same time, challenges our views on how nature designs biological machineries.
Examples such as the NPC, but also DNA packing (Chromatin) and epigenetic mechanisms call for new approaches in biology. Consequently, we aim to: i) combine protein engineering tools with diverse high/superresolution and single molecule fluorescence techniques to explore the physical and molecular rationale behind the fundamental role of IDPs; ii) extend the spectrum of chemical biology and protein engineering tools to overcome limitations in single molecule fluorescence studies – with one of our primary strategies to genetically encode unnatural amino acids; iii) continue to develop new methods and recruit techniques from other disciplines (such as microfluidics) to meet our goals.