Tan, C.; Jung, J.; Sugita, Y.

Biomolecular condensates formed by intrinsically disordered proteins (IDPs) rely on a balance of sequenceencoded interactions and secondary-structure elements. TDP-43, a disease-associated protein, undergoes liquid-liquid phase separation (LLPS) through its low-complexity domain, whereas Hero11 has been proposed to modulate its condensate properties. However, the molecular mechanisms by which Hero11 affects the internal organization and dynamics of TDP-43 condensates remain unknown. Here, using multimicrosecond explicit-solvent all-atom simulations spanning single chains to ~100-chain condensates, we show that the TDP-43 alpha-helix, which is only marginally stable in isolation, becomes a major structural hub within the condensate, forming a percolated helix-helix interaction network whose contact lifetimes are substantially longer than those of the surrounding disordered contacts. Hero11 selectively dismantles this network: it binds preferentially near the helical region, reduces the helix-helix coordination number, and shortens helix-helix contact lifetimes. This targeted disruption lowers condensate density, increases both water and ion infiltration, and enhances TDP-43 diffusion within the dense phase. Notably, dimer simulations reveal that the interactions between TDP-43 and Hero11 are too weak to persist under dilute conditions, indicating that the regulatory effect emerges only through multivalent contacts in the condensed phase. These results establish the alpha-helix as a selectively vulnerable structural element within the TDP-43 condensate and provide an atomic-level mechanism for how a highly charged disordered protein can tune condensate material properties by targeting its longest-lived interaction nodes.