Protein-guided RNA dynamics during early ribosome assembly

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Ribosome biogenesis is essential for protein synthesis.
• The precise order of protein binding to ribosomal RNA is critical for 30S subunit assembly.
• The role of early-binding proteins in modulating RNA structure for subsequent protein interactions remains unclear.

Purpose of the Study:

• To investigate the real-time dynamics of early protein-RNA interactions during 30S ribosome assembly.
• To elucidate the structural mechanisms by which ribosomal protein S4 influences 16S ribosomal RNA conformation.
• To understand how protein binding dictates the hierarchy of protein addition in ribosome biogenesis.

Main Methods:

• Single-molecule fluorescence resonance energy transfer (smFRET) to observe real-time protein-RNA interactions.
• Utilizing three-colour FRET to monitor multiple dynamic aspects of the complex.
• Employing molecular dynamics (MD) simulations to complement experimental observations.

Main Results:

• Observed dynamic initial complexes between Escherichia coli ribosomal protein S4 and 16S 5' domain RNA.
• Identified a stable non-native intermediate preceding the formation of the native complex.
• Demonstrated that S4 alters RNA helix dynamics, promoting a conformational switch essential for ordered protein addition.

Conclusions:

• Non-native RNA structures can facilitate protein recognition by providing a low free-energy pathway.
• Protein-guided dynamics play a key role in enforcing the hierarchical assembly of the 30S ribosome.
• These findings offer a new perspective on induced fit mechanisms in RNA-protein interactions.