Nucleotide-specific RNA conformations and dynamics within ribonucleoprotein condensates.

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.