Biomolecular condensate microstructure couples molecular and mesoscale properties

Abstract Biomolecular condensates, including those formed by prion-like low complexity domains (LCDs) of proteins, are typically maintained by networks of molecular interactions. Such collective interactions give rise to the rich array of material behaviors underlying condensate function. Previous work has uncovered distinct LCD conformations in condensates versus dilute phases, and recently, single-component LCD condensates have been predicted to exhibit microstructures with “small-world” networks—where molecular nodes are highly clustered and connected via short pathlengths. However, a framework linking single-molecule properties, condensate microstructure, and macroscopic material properties remains elusive. Here, we combine molecular simulation and graph-theoretic analysis to reveal how molecular features encode condensate microstructure, which impacts molecule-scale conformations and droplet-scale material properties. Using a residue-resolution coarse-grained model, we probe condensates comprising natural LCD sequences and generalize our findings by varying composition and patterning in binary sequences of hydrophobic and polar residues. We show that non-blocky sequences form condensates with small-world internal networks featuring “hubs”—molecules responsible for global connectivity—and “cliques”, molecular clusters bound by persistent short-ranged associations. Cliques localize near interfaces without a secondary phase transition, suggesting a role in mediating molecular partitioning and condensate aging by tuning interfacial material properties. Moreover, we demonstrate that network smallworldness predicts droplet surface tension. We also track single-molecule structure and dynamics inside condensates, revealing that internal heterogeneity at the single-molecule level is systematically encoded by network topology. Collectively, our work establishes multiscale structure–property relationships in LCD condensates, providing general principles for designing and interpreting condensates with complex internal organization and material properties. Competing Interest Statement The authors have declared no competing interest. Footnotes HP model simulations have been removed and replaced with simulations of binary sequences comprising tyrosine (Y) and serine (S) using the Mpipi model; simulations are conducted at a conserved distance from each system's critical temperature; graph-theoretic analyses are now performed using an updated energetic criterion to reflect long-lived intermolecular associations within interaction networks; analysis of the surface tension of LCD and YS condensates is included; a new Figure 1 describing sequence features, phase diagrams, and surface tensions is included; Figures 2--5 have been updated with results from new simulations; the text has been reoriented to emphasize the presence of multiscale relations in condensates bridging single-molecule phenomena, mesoscale organization, and macroscopic material properties; title updated; author list updated; Supplemental files included.