R05: A Supramolecular Chemical Biology Approach to Studying Protein-RNA-Based Regulatory Switches

Biological systems often rely on switch-like all-or-nothing responses. These regulatory switches are based on feedback loops or molecular cooperativity. Understanding the underlying mechanisms has important implications, from preventing dysregulation in disease to the design of new switches for synthetic biology applications. We will study such mechanisms from the point of view of physical chemistry and polymer science. Our model system is a biological switch relevant to neurodegenerative diseases. We have previously shown that the RNA-binding protein HNRNPH can regulate RNA splicing in a switch-like manner: small changes in its cellular concentration (in diseases caused by nuclear aggregation) have a strong impact on those splicing events. The underlying molecular principles are not yet understood. Here, we propose to investigate the biophysical determinants of HNRNPH-mediated regulation through interdisciplinary efforts combining functional genomics (biology), the synthesis and characterization of artificial biomimetic polymer assembly platforms (supramolecular chemistry), and computational modelling on multiple scales (physics). In the first funding period, we will focus on three objectives. We will determine the role of folding and unfolding of G-quadruplex (G4) structures in cooperative HNRNPH binding and splicing regulation (Objective 1). We will investigate how multivalent interactions between HNRNPH and RNA contribute to cooperativity (Objective 2). More generally, we will study how generic polymer concepts such as network formation, specific versus non-specific binding, and bridging and looping, can impact protein–RNA interaction and assembly (Objective 3). Overall, we aim to understand how system complexity and multi-scale and multi-component ensemble behaviour contribute to cooperativity in RNA regulation.

Schematic overview of this project.
Pol Besenius

Department of Chemistry, JGU

Julian König

Institute of Molecular Biology

Friederike Schmid

Institute of Physics, JGU

Department of Physics, Mathematics and Computer Science