Nucleotide-Specific RNA Conformations and Dynamics as Precursors to Ribonucleoprotein Condensates.

Area of Science:

• Biophysics
• Structural Biology
• Molecular Biology

Background:

• Ribonucleoprotein (RNP) condensates are crucial in cellular processes, but the internal RNA structure remains poorly understood.
• Understanding RNA conformation within these dynamic assemblies is key to elucidating their function and associated pathologies.

Purpose of the Study:

• To characterize the conformational changes and structural organization of RNA within RNP condensates.
• To investigate the influence of polybasic peptides on RNA structure and dynamics in phase-separated systems.

Main Methods:

• Utilized contrast-variation solution X-ray scattering (SAXS) to specifically probe RNA structures within protein-RNA complexes.
• Employed ensemble-based structural modeling and coarse-grained molecular dynamics simulations.
• Applied these methods to poly-U, poly-A RNA, and trinucleotide repeat sequences (CAG, CUG) with and without peptides.

Main Results:

• Observed distinct RNA structural changes and dynamics upon interaction with polybasic peptides under varying salt concentrations.
• Detected enhanced RNA association and positional ordering of poly-A RNA within phase-separated RNP mixtures at lower salt concentrations.
• Demonstrated that peptides promote RNA association and positional ordering for CAG and CUG repeat motifs.

Conclusions:

• Polybasic peptides significantly influence RNA structure and organization within RNP condensates.
• The findings reveal sequence-specific RNA ordering, particularly for poly-A and repeat motifs, driven by peptide interactions.
• This study provides critical insights into the structural basis of RNA within dynamic cellular compartments.