Biomolecular condensates formed through liquid-liquid phase separation (LLPS) are implicated in various pathologies, often via aberrant aggregation within the condensed phase. Highly charged biomolecules, such as RNA or the Hero proteins, can function as ATP-free chaperones to modulate these condensates; yet, the precise molecular mechanisms remain elusive. While our previous coarse-grained (CG) simulations provided initial hypotheses (Tan et al. JACS Au 2023), they lacked the resolution to capture atomic-level interactions and secondary structure dynamics. Here, we employ large-scale all-atom molecular dynamics to investigate this mechanism with atomic precision. Building on our CG results, we constructed multiple models of condensates containing TDP-43 and Hero11, each comprising ∼2.5 million atoms, alongside smaller single-chain or dimer systems representing the dilute phase. Our simulations reveal that Hero11 decreases the density of the TDP-43 condensate, facilitating the entry of water and ions. Hero11 disrupts the native TDP-43 interaction network, primarily by competing with intermolecular contacts that stabilize a partially folded α-helix within TDP-43. This competitive binding results in a measurable decrease in the stability of the α-helix. As a consequence of these altered interactions, the diffusion of both TDP-43 and ions is significantly enhanced in the presence of Hero11. These results provide a detailed, atomistic mechanism for how highly charged proteins can fluidize condensates and regulate their material properties, offering key insights into preventing pathological phase transitions.
Tan et al. (Sun,) studied this question.