Atomistic simulations reveal sub-μs contact dynamics in MUT-16 condensates.

Phase separation of proteins gives rise to biomolecular condensates, which function as membraneless organelles that spatially and temporally organize cellular functions. Such condensates are often formed by intrinsically disordered regions of proteins (IDRs), whose multivalent and transient interactions govern condensate structure and dynamics. However, elucidating the molecular determinants of these interactions at atomistic resolution remains challenging. Here, we present a total of 10 {micro}s of atomistic molecular dynamics simulations of a phase-separated condensate formed by the foci-forming region (FFR) of MUT-16. MUT-16 serves as a scaffold of the Mutator foci germ granules in Caenorhabditis elegans and is essential for transposon silencing. MUT-16 FFR is enriched in polar uncharged (Gln, Asn), charged, aromatic, and Pro residues, raising the question of how these amino acids interact within condensates. We find that most contacts are short lived, typically breaking within a few nanoseconds (ns), with a median life time of 9.8 ns. A smaller fraction persist for much longer timescales (> 100 ns). We characterized the relative contributions of different amino acids and specific interaction types, including hydrogen bonding, cation-{pi} interactions,{pi} -{pi} stacking, and salt bridges and theirs dynamics. We further examined the roles of water and ions in modulating condensate interactions, including ion-mediated bridging between similarly charged residues. Our results reveal that salt bridges, cation-{pi} interactions, Na+ ions, and water in the condensate are key determinants of contact dynamics in MUT-16 FFR condensates. In parallel, we show that these condensates exhibit upper-critical solution temperature (UCST) phase behavior in vitro, providing a coherent framework to explain both the loss of Mutator foci at elevated temperatures in vivo and the scaffolding role of MUT-16 at lower temperatures.