The Lemke group uses an interdisciplinary approach to elucidate the nature of naturally disordered proteins in biological systems and disease mechanisms at the single molecule level.
Previous and current research
Currently, more than 100 000 protein structures with atomic resolution are available from the protein databank. However, even if all 3D protein structures were available, our view of the molecular building blocks of cellular function would still be 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 (eukaryotes ≈ 50%). Their ability to adopt multiple conformations is considered a major driving force behind their evolution and enrichment in eukaryotes.
Most common strategies for probing protein structure are incompatible with the highly dynamic nature of molecular disorder, so that 50% of the proteome remains “dark”, or invisible. In contrast, single molecule and super-resolution techniques, which directly probe the distribution of molecular events, can reveal important mechanisms that otherwise remain obscured. In particular, highly time-resolved advanced fluorescence tools allow probing of molecular structures and dynamics at near atomic scale down to picosecond resolution. While such experiments are now possible in the natural environment of the entire cell, single molecule fluorescence studies in vitro and in vivo suffer from several limitations such as low throughput and the need for site-specific labelling with special fluorescent dyes. In particular the latter one has become a major bottle neck in state of the art fluorescence.
Besides developing new spectroscopy and microscopy methods, we are utilising a large spectrum of chemical biology and protein engineering tools to overcome these limitations. Our bioengineering efforts allow us to reprogram cells in a way that enables the custom tailoring of proteins with diverse probes, such as dyes and post-translational modifications. This will ultimately enable us to transform living organisms into ideal test beds for molecular, biophysical, and even physiochemical studies of molecular function. Our chemical biology tools also present an ideal interface between the life and material sciences. Furthermore, microfluidics and its potential to miniaturise lab efforts and increase throughput of single molecule science is an area we explore efficiently.
Future projects and goals
Recent studies have shown that even the building blocks with an absolutely critical role in cell survival are largely built from IDPs. For example, many nucleoporins are central to nucleocytoplasmic transport, but also in oncogenesis, chromatin organisation, epigenetic mechanisms, and transcription. Furthermore, viruses extensively use reprogramming of critical IDPs to gain access to, and modify, cellular genomes. How multifunctionality can be encoded into protein disorder is a central question in biology that we aim to answer, as well as integrating our knowledge about such biopolymers towards a better understanding of the life sciences, better drug design, and exploration for bio-inspired material sciences.
Figure 1: We innovate new tools, and combine those with our home-built, highly sensitive single molecule and super-resolution equipment to study structure and dynamics of heterogeneous biological systems and pathways, such as viral host pathogen mechanisms and nuclear pore complexes in 4D, and how malfunction of those can lead to disease. We also aim to explore the potential of these IDP biopolymers for novel applications in the life and material sciences.