Figure 6.

Ultra-coarse-grained Simulations Reveal RNA-Dependent Clusters of G3BP1

(A) A G3BP1 dimer is coarse-grained into a two-bead model, with one bead capturing the NTF2 domain and central IDRs and the other bead capturing the RRM and RG-rich region. The RNA is coarse-grained so that each “bead” represents 8–10 nt. The interaction strength between distinct beads is shown.

(B) Analysis of RNA-mediated G3BP1 oligomerization for simulations of G3BP1, WT or ΔRG, with short RNA.

(C) Simulation snapshots illustrate the cooperative nature of oligomerization, demonstrating the coexistence of fully decorated short RNA molecules and predominantly unbound RNA molecules.

(D) Simulations with long RNA yield clusters that form on the RNA and act as crosslinkers between RNA-RNA interactions.

(E) Schematic highlighting the clusters as physical crosslinks.

(F) X-Y cross-sectional slice of a refractive index tomogram of G3BP1-RNA condensates. Scale bar, 10 μm.

(G) Refractive index and total concentration inside G3BP1-RNA condensates (n = 187 condensates).

(H) Concentration of G3BP1 inside versus outside the condensate (n = 437 condensates).

G3BP1-RNA condensates in F-H were formed with 50 ng/μl poly(A) RNA. See also Figure S6 and Video S4.