Tetrapeptides Remodel FUS and A1 LCD Condensates without Disrupting Network Topology

Abstract

Biomolecular condensates are stabilized by the collective action of short, low-affinity interactions distributed across intrinsically disordered protein sequences, precisely the interaction grammar that short peptides are chemically designed to engage. This conceptual alignment makes tetrapeptides and other minimal sequence fragments natural candidates for condensate modulation: they are readily synthesized, chemically tunable across a vast combinatorial space, and small enough to partition into the dense phase without the steric constraints that limit larger molecules. Yet whether short peptides act as passive occupants of the condensate milieu or as active, sequence-specific perturbants of its internal architecture remains an open question. Here, we use Mpipi coarse-grained molecular dynamics simulations to characterize how a combinatorial library of tetrapeptides drawn from a low-dimensional sequence space actively perturbs two prototypical LCD condensates: hnRNPA1-LCD and FUS-LCD. We find that tetrapeptide partitioning into the condensate is governed primarily by aromatic hydrophobicity, which drives exponential increases in uptake, while charge plays a more delicate secondary role. Also, the spatial mode of perturbation is controlled not by peptide composition alone but by the host protein’s aromatic sequence architecture: the same tetrapeptides produce discrete, hotspot-concentrated disruptions in A1-LCD where charged and aromatic residues are clustered, and diffuse, sequence-wide perturbations in FUS-LCD where aromatics are regularly spaced. This architectural dependence is confirmed by binding–disruption alignment analysis, where spatial coupling between peptide binding and contact remodeling is strong in A1-LCD and collapses in FUS-LCD. Despite this local remodeling, the condensates’ hub–clique network topology remains invariant across all conditions, indicating it is an emergent collective property of the condensed state rather than a tunable structural feature.