Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• Ribosomes, the cellular machinery for protein synthesis, exhibit dynamic movements.
• Elongation factor G (EF-G) is crucial for productive ribosome translocation.
• In EF-G's absence, ribosomes fluctuate between pre-translocation and hybrid states without mRNA movement.

Purpose of the Study:

• To investigate mechanisms that can induce productive ribosome translocation.
• To identify classes of molecules that can rectify intrinsic ribosome dynamics into directional movement.
• To elucidate the role of the peptidyl transferase A site in antibiotic-induced translocation.

Main Methods:

• Utilizing single-molecule Förster Resonance Energy Transfer (smFRET) to monitor ribosome dynamics.
• Testing the effects of various peptidyl transferase inhibitors on ribosome translocation.
• Analyzing the impact of antibiotic binding site on translocation induction.

Main Results:

• Several peptidyl transferase inhibitors, including sparsomycin, induce productive mRNA translocation.
• Antibiotics binding to the peptidyl transferase A site trigger translocation.
• Antibiotics not occupying the A site fail to induce translocation.
• Translocation-inducing antibiotics rectify intrinsic ribosome thermal dynamics without accelerating intersubunit rotation.

Conclusions:

• The ribosome functions as a Brownian ratchet machine.
• Ligand binding, specifically to the A site, can rectify the ribosome's inherent dynamics into unidirectional translocation.
• This provides a new perspective on ribosome function and regulation.