Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88

Area of Science:

• Microbiology
• Biochemistry
• Structural Biology

Background:

• Proline-rich antimicrobial peptides (PrAMPs) are known to inhibit bacterial protein biosynthesis.
• They primarily target the polypeptide exit tunnel (PET) near the peptidyl transferase center of bacterial ribosomes.
• Apidaecin-derived peptides, such as Api137, are optimized PrAMPs that trap release factors (RFs) to inhibit translation.

Purpose of the Study:

• To elucidate the detailed mechanisms by which Api137 and its analog Api88 inhibit bacterial protein synthesis.
• To investigate potential alternative or additional binding sites and modes of action beyond RF-trapping.

Main Methods:

• Cryo-electron microscopy (cryo-EM) for structural determination.
• Functional assays to assess translation inhibition.
• Molecular dynamic (MD) simulations to analyze peptide-ribosome interactions.

Main Results:

• Api137 binds to two distinct sites within the PET, including a novel site near the tunnel exit, enabling RF-independent translation repression.
• Api88, a C-terminally amidated analog, binds to the same sites as Api137 and an additional third pocket.
• Api88 likely inhibits translation through mechanisms independent of RF-trapping.

Conclusions:

• Apidaecin-derived PrAMPs employ multimodal mechanisms to inhibit bacterial ribosomes.
• Minor structural modifications in PrAMPs lead to distinct binding modes and inhibitory functions.
• These peptides represent a promising class for developing novel antibacterial agents.