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Nucleotide-specific RNA conformations and dynamics within ribonucleoprotein condensates.

Tong Wang1, Qingyue Hu1, Scout Fronhofer1

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Area of Science:

  • Biophysics
  • Structural Biology
  • Molecular Biology

Background:

  • Ribonucleoprotein (RNP) condensates are crucial in cellular processes but the RNA structure within them remains unclear.
  • Understanding RNA's role in RNP condensate formation is key to deciphering their physiological and pathological roles.

Purpose of the Study:

  • To investigate the structural changes of single-stranded RNA (poly-A, poly-U, poly-C) interacting with polybasic peptides.
  • To characterize RNA conformation during the formation of RNP coacervate mixtures under varying salt conditions.
  • To elucidate nucleotide-specific dynamics within RNP condensates using molecular dynamics simulations.

Main Methods:

  • Contrast-variation solution X-ray scattering to specifically probe RNA structures within protein-RNA complexes.
  • Ensemble-based structural modeling to analyze RNA conformational changes.
  • Coarse-grained molecular dynamics simulations to study nucleotide-specific dynamics in RNP condensates.

Main Results:

  • RNA structural changes were observed, influenced by peptide charge screening and base interactions.
  • At lower salt concentrations, poly-A RNA in phase-separated RNP mixtures showed subtle ordering.
  • Adenine-rich condensates behaved as stable solutions, while uracil-rich condensates exhibited compositional fluctuations.

Conclusions:

  • RNA sequence significantly impacts the molecular mechanisms of RNA-protein phase separation.
  • The study provides insights into how RNA structure and dynamics contribute to RNP condensate formation and properties.
  • This work advances the understanding of the structural basis for RNA's role in phase separation.