Seeing and Engineering Biomolecular Condensates with Atomic Precision

Phase separation of RNA-binding proteins via multivalent interactions between aromatic/polar-rich disordered domains contributes to the formation of functional cytoplasmic granules and nuclear puncta. These domains have also been identified as players in cancer-causing fusion proteins as well as the nucleators of neuronal inclusions in amyotrophic lateral sclerosis (ALS), frontotemporal dementia, and some forms of Alzheimer’s Disease (AD). We use solution NMR spectroscopy and biophysical methods combined with molecular simulation to see and quantify the residue-by-residue details of interactions along to the pathway from monomer, to liquid-liquid phase separated state, to static aggregates and hydrogels. Pushing current machine learning models of protein structure beyond their training data, we show how integrative approaches are required for challenging problems in dynamic assembly. We combine AlphaFold, molecular simulation, and experiment to define atomic models of the functional helical oligomerization of the conserved region in the C-terminal domain of TDP-43, aggregates of which are the primary hallmark of ALS. We demonstrate how this atomic-level insight into biomolecular phase separation and protein aggregation combined with cellular and organismal studies enable us to understand and engineer condensates and to create new therapeutic avenues including future gene therapies for neurodegenerative diseases.

Bioengineering Rising Star Lecture

Speaker: Nicolas Fawzi, Brown University