Abstract

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. ### Competing Interest Statement The authors have declared no competing interest. MEXT JSPS Kakenhi, 19H05645, 21H05249, 21H05282, 25K09590 RIKEN pioneering projects, Biology of Intracellular Environments, Glycolipidologue Initiative RIKEN incentive projects MEXT, JPMXP1020200101, JPMXP1122714694, JPMXP1020230327