Replication Data for: Chain Length Dependence of poly-Lysine - poly-Uridine Condensate Structure and Properties

Simulated condensates with peptide:RNA ratios of 0.5 to 2 show that excess negative charge disrupts condensation more than an equivalent positive charge excess, attributed to uridine’s larger monomer size (and hence lower charge density) relative to lysine. This charge density difference also drives a mild, chain-length-dependent enrichment of poly-U at the condensate interface. Conformational entropy calculations show greater conformational restriction at the interface than in the bulk, an effect that grows with chain length and is more pronounced for poly-U than for poly-K. Free-energy calculations (PMFs) show that K–U attraction weakens while K–K and U–U repulsion strengthens with increasing chain length; this shift causes shorter chains to form more, shorter-lived inter-chain contacts, while longer chains form fewer, longer-lived contacts sustained by a greater number of alternative contact points between already-connected chains.

Together, these results provide residue-to-network-level insight into how chain length tunes poly-K – poly-U condensate structure and properties. This work was supported by the Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy – EXC 2033 – 390677874 – RESOLV. A.W. acknowledges support from the Alexander von Humboldt Foundation through a fellowship for postdoctoral researchers.

Dataset Description Files contained in the dataset: File-S1.csv, File-S2.csv, File-S3.csv, File-S4.txt, Kx-Ux.tar, K26-U.tar, polyK-U.tar, KE-controls.tar and single_chains.tar (see file description below for full contents). Data types and required software: Trajectory files (.xtc) with reference structures (.pdb, ref.pdb): openable with GROMACS, MDAnalysis, MDTraj, VMD, or PyMOL. Simulations were run using the OpenMM-based CALVADOS coarse-grained simulation framework.

Force field parameter file (File-S1.csv): plain-text CSV, openable with any spreadsheet application or text editor; contains a compiled version of the CALVADOS protein and RNA force field parameters (masses, λ, σ, ε, charges). Parameter values are given in standard OpenMM units (mass in daltons, length in nm, energy in kJ/mol, charge in units of the elementary charge e). Experimental data files (File-S2.csv, File-S3.csv, File-S4.txt): plain-text CSV/TXT, openable with any spreadsheet application or text editor.

File content description: File-S1.csv: A compiled version of the CALVADOS protein and CALVADOS RNA force field parameters (mass, λ (stickiness, unitless), σ, ε, and charge per bead type for amino acids and RNA nucleotides). See the LICENCE section below regarding the licence and modifications applying to this file. The CALVADOS package can be found at github.com/KULL-Centre/CALVADOS.

The CALVADOS protein parameters can be found at github.com/KULL-Centre/_2024_Cao_CALVADOSCOM. File-S2.csv: Experimental optical density (OD500, unitless absorbance value) measurements for phase-separation assays, taken immediately after mixing (0 min incubation), for poly-K:poly-U mixtures at a 1:1 monomer ratio across poly-U lengths U15–U35. File-S3.csv: Same as File-S2.csv, but measured after 15 min incubation at room temperature.

File-S4.txt: Commercial polyK chain-length distribution (chain length given in number of lysine residues, unitless count), adapted from Le Vay et al., 2021, Angewandte Chemie (ESI-MS data), used to define the polydisperse poly-K ensemble used in simulations. K26-U.tar: K26 peptide paired with poly-U of varying length (U10–U35); 8 replicas per condition. KE-controls.tar: Charge-matched and connectivity controls: K35-E35, K35-EG35.

Each contains ref.pdb plus 8 replicas. Kx-Ux.tar: Chain-length series of monodisperse K/U condensates (x = 10, 15, 20, 25, 30, 35). Each subfolder contains ref.pdb plus 8 replica trajectories (run0.xtc–run7.xtc). polyK-U.tar: Polydisperse poly-K (matched to the experimental ESI-MS chain-length distribution) paired with monodisperse poly-U (U10–U35); 8 replicas per condition. single_chains.tar: Isolated single-chain reference simulations: K10–K35 and U10–U35, each with ref.pdb and a single trajectory (run.xtc).

Naming convention: Kx-Ux: condensate system of poly-lysine (Kx) and poly-uridine (Ux), where x is the number of residues/nucleotides per chain (10–35, in steps of 5). Ex / (EG)x: poly-glutamate and glutamate-glycine control chains of length x, used to test the role of monomer charge density vs. topology (see manuscript). run0.xtc–run7.xtc: 8 independent replica trajectories per system. ref.pdb: reference structure/topology for the corresponding trajectory set.

Dataset generation date(s): 01.09.2026 Dataset versions: v1 Reproducing the results: All results can be reproduced from the provided simulation trajectories following the protocols described in the Methods section of the related publication. Analysis scripts can be provided upon request. Methodological Information All methods used to generate and analyse the data — simulation setup and parameters (CALVADOS-3/CALVADOS-RNA force fields, slab geometry, equilibration and production protocols, replica counts), analysis protocols (density profile fitting, conformational entropy, PMF/RDF, small-world network analysis, contact autocorrelation functions), and experimental procedures (turbidity assays, ESI-MS) — are described in full in the Methods section of the related publication.