Multi-Domain Interplay Controls Full-Length TDP-43 Phase Separation and Condensate Dynamics

TDP-43 (TAR DNA-binding protein 43) is a 414-amino acid protein with a structured N-terminal domain (NTD), two RNA recognition motifs (RRM1 and RRM2), and a long disordered C-terminal low complexity domain (LCD). TDP-43 forms phase-separated condensates as part of its physiological function in RNA processing. However, aberrant TDP-43 condensation, changes in condensate material properties, and subsequent aggregation are linked to the development of neurodegenerative diseases. Using explicit-solvent, near-atomic resolution coarse-grained simulations we demonstrate how the interplay among different domains drives phase separation of the full-length protein.We directly capture how the secondary structure of a conserved helix in the LCD modulates phase separation, and follow the effect of phosphomimicking mutations on the condensation of full-length TDP-43. C-terminal phosphomimicking mutations rewire the interactions of the LCD by increasing solvation locally and enhancing Na ⁺ binding to the LCD. Our simulations and in vitro experiments emphasize the importance of the aromatic residues in the LCD but also of N-terminal residues 1-101 including the NTD for full-length TDP-43 condensation. With a Gō-type approach we capture not just conformational flexibility but also specific dimer formation through NTD-NTD interactions and how they modulate the phase behavior as well as the dynamic and interfacial properties of full-length TDP-43 condensates.