Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.01.29.702704

Dual Effect of RNA-like Polyelectrolytes on Stability and Dynamics of Biomolecular Condensates: A Tale of Competitive Short and Long-range Interactions

Sharma, D.·Roy, S.·HAZRA, M. K.
View original source ↗Export metadata ↓

Abstract

Heterotypic biomolecular condensates underpin the spatiotemporal organization of cellular components and enable precise biological regulation. These condensates frequently comprise proteins and RNA at variable stoichiometries, with RNA acting as a key modulator through its ability to engage in both long-range electrostatic and short-range specific interactions. How such RNA-like components regulate condensate stability and dynamics across distinct interaction regimes, however, remains unclear. Here, we examine the role of RNA-like polyelectrolytes in tuning the stability and material properties of heterotypic condensates formed by designed short peptide sequences spanning a continuum from long-range electrostatics-to short-range hydrophobic interactions. By systematically strengthening short-range hydrophobic interactions while varying polyelectrolyte composition, we uncover a dual, regime-dependent role of RNA-like species. In electrostatics-dominated condensates, excessive polyelectrolyte concentration rapidly destabilizes droplets due to enhanced long-range repulsive interactions while the droplets retain stability until intermediate polyelectrolyte concentration fairly well. In contrast, in strongly hydrophobic condensates, polyelectrolytes function as multivalent sticker hubs, stabilizing condensates through favourable peptide- polyelectrolyte interactions. Polyelectrolyte enrichment within condensates is nonlinear with respect to mixing fraction and saturates at largest cluster mole fractions of [~]0.2-0.25. Condensate dynamics reflect this interplay: polyelectrolyte diffusivity is 20-40% higher in electrostatics dominated systems than in hydrophobic ones, while in extremely hydrophobic condensates, polyelectrolytes diffuse [~]50% more slowly than peptides, indicative of scaffold-like behaviour. Together, these results reveal tuneable and opposing roles of RNA-like polyelectrolytes in shaping condensate stability, dynamics, and morphology across diverse interaction regimes.

Source connections

Explore related subjects

biophysicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sharma, D., Roy, S., HAZRA, M. K.. 2026-01-30. Dual Effect of RNA-like Polyelectrolytes on Stability and Dynamics of Biomolecular Condensates: A Tale of Competitive Short and Long-range Interactions. https://doi.org/10.64898/2026.01.29.702704

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Mechanism of molecular recognition revealed through dynamic drug binding pathways to SARS-CoV-2 main protease

Characterization of drug-binding pathways remains experimentally limited by transient intermediates and computationally challenging due to long timescales intractable for conventional molecular dynamics. To address these challenges, we combined solution NMR titrations with weighted ensemble (WE) enhanced sampling simulations to resolve atomistic pathways of nirmatrelvir binding to the SARS-CoV-2 main protease. NMR titration revealed residue-dependent heterogeneity spanning fast, intermediate, and slow exchange regimes. WE simulations complement the NMR by providing insights into unassigned residues and adding time-resolved and three-dimensional structural context. We map key interactions along two distinct binding pathways, provide dynamic explanations for residues involved in resistance, and capture unique backbone conformations compared to those sampled in unbound or bound states. Our comprehensive binding model is consistent with a combined conformational selection and induced fit mechanism in which early transient contacts are made with residues E47 and L50 and allosteric motions are centered around residue V204 of the distal domain. This synergistic application of WE and titration NMR enables a more comprehensive characterization of drug binding than either method alone, providing an integrated framework that may have broader applicability to defining structure-kinetic relationships and guiding design of next-generation inhibitors.

biophysics↗
bioRxiv2026

Fibers and Glasses are Competing Material States in FUS Protein Condensation

Dense, well-ordered material states of proteins form the amyloid fibers that are a hallmark of neurodegenerative disease in the brain. Beyond forming amyloid fibers, some of these proteins can also adopt other material states termed condensates which are initially liquid-like but evolve to a soft, glassy phase. Fiber growth requires a large supply of monomers and, thus, it is often speculated that fibers emerge from within a dense condensate as it ages and its microscopic dynamics slow into a glassy state. Here, we use the well-established model system Fused in Sarcoma (FUS) to directly observe, quantify and theoretically describe fiber growth and its interplay with condensates. We report the discovery that fibers grow overwhelmingly in the dilute phase surrounding the condensates while the condensates concurrently evolve to a glassy arrested solid. The resulting protein fibers and glassy condensates are both distinct solid-like phases that coexist but do not directly interconvert. Taken together, these findings reveal that there are two competitive aging pathways in FUS condensation that are linked through phase separation kinetics.

biophysics↗
bioRxiv2026

A Minimally Perturbative DARPin Probe for Quantitative Fluorescence Imaging of the Human TCR-CD3 Complex

Fluorescence microscopy is a powerful tool for dissecting the molecular mechanisms of T-cell antigen recognition in living cells, but its quantitative insight critically depends on non-perturbative, high-quality probes. Here, we repurpose a small (~15 kDa) CD3epsilon-binding DARPin (designed ankyrin repeat proteins) to a fluorescent label for T-cell receptor (TCR)/CD3 complexes on primary human CD8+ T-cells, with the aim of generating a powerful tool for quantitative analysis, single-molecule tracking, and advanced imaging of TCR dynamics. We show that the DARPin binds CD3{varepsilon} with high affinity and selectivity and using single molecule tracking and brightness analysis, we characterize the TCR-CD3 diffusion behavior and show that the DARPin binds to both CD3epsilon; subunits. Importantly, labeling preserves antigen sensitivity: on supported lipid bilayers presenting cognate pMHC, T-cells remain responsive, assemble synapses, form TCR microclusters, and initiate signaling similar to unlabeled controls. We further demonstrate compatibility with lattice light-sheet microscopy for volumetric imaging of T-cell - APC interactions in living cells. Together, these results establish DARPins as versatile, minimally perturbative probes for high resolution, quantitative studies of T cell synapse organization and signaling.

biophysics↗