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Updated: Sep 10, 2025
Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses
Published on: February 25, 2011
Basis for selective drug evasion of an aminoglycoside-resistance ribosomal RNA modification
Debayan Dey1, Jacob M Mattingly2,3, Natalia Zelinskaya1
1Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
Abstract:
Aminoglycosides disrupt the fidelity of bacterial protein synthesis, but their potent antibacterial activity is threatened by multiple resistance mechanisms, including methylation of their ribosomal RNA (rRNA) binding site. However, the impact of one such resistance-conferring methylation on N1 of helix 44 nucleotide A1408 (m1A1408) is highly variable with some aminoglycosides retaining significant potency. Here, we examine bacterial susceptibility to diverse aminoglycosides, determine high-resolution electron cryomicroscopy structures of m1A1408-modified 70S ribosome-aminoglycoside complexes, and perform molecular dynamics simulations to decipher the key determinants of such "resistance evasion." Collectively, these analyses reveal how some aminoglycosides adapt their conformation to accommodate m1A1408, including the roles of specific ring substituents, balancing ligand strain and maintaining favorable interactions, as well as interactions made by additional functional groups that compensate for those disrupted by the modification. This work provides design principles that can guide future rational development of aminoglycosides refractory to resistance conferred by rRNA modifications.
Insights
Some aminoglycosides overcome bacterial resistance by adapting their structure to bind modified ribosomal RNA (rRNA). This study reveals how specific chemical modifications allow these drugs to evade resistance, guiding future antibiotic development.
Area of Science:
- Microbiology
- Structural Biology
- Drug Discovery
Background:
- Aminoglycosides are crucial antibiotics targeting bacterial protein synthesis.
- Bacterial resistance, often via ribosomal RNA (rRNA) methylation, reduces aminoglycoside efficacy.
- Methylation at A1408 (m1A1408) variably impacts aminoglycoside potency.
Purpose of the Study:
- To investigate bacterial susceptibility to aminoglycosides in the presence of m1A1408.
- To elucidate the structural basis of aminoglycoside "resistance evasion" at high resolution.
- To identify design principles for developing novel aminoglycosides resistant to rRNA modification.
Main Methods:
- Bacterial susceptibility testing against diverse aminoglycosides.
- High-resolution cryo-electron microscopy (cryo-EM) of modified ribosome-aminoglycoside complexes.
- Molecular dynamics (MD) simulations to analyze molecular interactions.
Main Results:
- Observed variable potency of aminoglycosides against the m1A1408 modification.
- Determined cryo-EM structures revealing how some aminoglycosides adapt conformation.
- MD simulations identified key structural adaptations, including substituent roles and compensatory interactions.
Conclusions:
- Specific aminoglycosides can evade resistance conferred by m1A1408 through conformational adaptation.
- Ligand strain, substituent effects, and compensatory interactions are critical for maintaining potency.
- Findings provide a foundation for designing next-generation aminoglycosides effective against resistant bacteria.
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