Studying Protein Aggregation in the Context of Liquid-liquid Phase Separation Using Fluorescence and Atomic Force Microscopy, Fluorescence and Turbidity Assays, and FRAP.

Liquid-liquid phase separation (LLPS) underlies the physiological assembly of many membrane-less organelles throughout the cell. However, dysregulation of LLPS may mediate the formation of pathological aggregates associated with neurodegenerative diseases. Here, we present complementary experimental approaches to study protein aggregation within and outside the context of LLPS in order to ascertain the impact of LLPS on aggregation kinetics. Techniques described include imaging-based approaches [fluorescence microscopy, atomic force microscopy (AFM), fluorescence recovery after photobleaching (FRAP)] as well as plate reader assays [Thioflavin-T (ThT) fluorescence intensity and turbidity]. Data and conclusions utilizing these approaches were recently reported for the low complexity domain (LCD) of the transactive response DNA binding protein of 43 kDa (TDP-43).