Related Experiment Video
Updated: Jun 18, 2026
10:27
Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
Published on: July 8, 2019
Aminoglycoside activity observed on single pre-translocation ribosome complexes
Michael B Feldman1, Daniel S Terry, Roger B Altman
1Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York, USA.
Nature Chemical Biology
|December 1, 2009
Summary
Aminoglycoside antibiotics disrupt ribosome function by altering RNA dynamics. Single-molecule methods reveal distinct effects for each drug, explaining their varied inhibition profiles and impact on protein synthesis.
Area of Science:
- Molecular Biology
- Biochemistry
- Microbiology
Background:
- Aminoglycoside antibiotics target bacterial ribosomes, inhibiting protein synthesis.
- Previous studies focused on structural interactions, but mechanisms for differing drug effects remain unclear.
- Understanding these mechanisms is crucial for developing new antibiotics.
Purpose of the Study:
- To elucidate the distinct mechanisms by which aminoglycosides inhibit ribosome function.
- To investigate the relationship between aminoglycoside-induced dynamic changes and translocation inhibition.
- To demonstrate the utility of single-molecule fluorescence resonance energy transfer (smFRET) in studying antibiotic action.
Main Methods:
- Employed single-molecule fluorescence resonance energy transfer (smFRET) to monitor ribosome dynamics.
- Studied interactions of various aminoglycosides with functional pre-translocation ribosome complexes.
- Correlated observed dynamic changes with inhibition of elongation factor G (EF-G)-catalyzed translocation.
Main Results:
- High-affinity aminoglycoside binding remodels intrinsic dynamic processes within the ribosome's decoding site.
- These dynamic alterations are unique for each aminoglycoside and correlate with translocation inhibition.
- Neomycin exhibits secondary binding sites, causing additional perturbations that enhance translocation inhibition.
Conclusions:
- Distinct ribosome dynamics induced by chemically similar aminoglycosides explain their varied inhibitory effects.
- smFRET is a powerful tool for dissecting the molecular mechanisms of antibiotic action.
- These findings provide a mechanistic basis for aminoglycoside-induced pleiotropic effects on translation.
Related Concept Videos
01:25Inhibitors of Bacterial Protein Synthesis
Aminoglycosides constitute a highly potent class of bactericidal antibiotics that exert their antimicrobial effects by targeting the bacterial ribosome, specifically disrupting protein synthesis. These polycationic molecules consist of amino-modified sugars linked via glycosidic bonds to an aminocyclitol core such as 2-deoxystreptamine or streptamine. Their strong positive charges facilitate tight binding to the negatively charged phosphate backbone of ribosomal RNA (rRNA), primarily at the 16S...
02:07Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
01:20Cotranslational Protein Translocation
Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
02:53Ribosomal RNA Synthesis
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
02:53Ribosomal RNA Synthesis
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...