Topological Closure Drives Structural Stabilization and Fast Cooperative Dynamics in Crowded Circular Polysomes
Year: 2026
Type: preprint
Abstract: In linear polysomes, excluded-volume interactions among ribosomes can induce dimensional reduction of mRNA. Yet linear architectures allow steric stress to relax at open ends– limiting how strongly crowding can remodel the mRNA’s structure and dynamics. Using coarse-grained molecular-dynamics simulations, we compare circular and linear polysomes over a range of ribosome densities. Circular closure selects a predominantly quasi-planar global conformational ensemble, as indicated by a shape dimensionality d shape ≈ 2 over a range of ribosome densities. Crucially, circular topology and ribosome crowding act cooperatively to suppress structural fluctuations. While closure alone or linear crowding reduces relative global size fluctuations (Δ R g / R g ) only to ≈ 0.16, their combined effect drives this fluctuation down to ≈ 0.07. Within this stabilized architecture, increasing ribosome density drives a distinct in-plane reorganization: the ring becomes more isotropic, global size fluctuations are strongly suppressed, and the scaling exponent increases toward ν ≃ 0.74–0.77, consistent with two-dimensional self-avoiding walk-like value over the accessible finite-size window, 1000 ≤ N ≤ 4969. Closure shortens the radius-of-gyration decorrelation time of circular polysomes by 40-fold relative to matched linear systems, reflecting the topological elimination of free ends. Within this closure-selected ensemble, ribosome crowding further reduces the decorrelation time by up to 20% at the highest density. A fluctuation-informed crossover model links the density dependence of the global scaling exponent to inter-ribosomal subchain statistics. These results distinguish the geometric role of circular closure from the density-dependent steric response that it enables, revealing a confined yet dynamically responsive conformational regime for circular polysomes.
Authors: Hideki Kobayashi, Horacio V. Guzman
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7204937108