title: The impact of aminoglycosides on the dynamics of translation elongation.
abstract: Inferring antibiotic mechanisms on translation through static structures has been challenging, as biological systems are highly dynamic. Dynamic single-molecule methods are also limited to few simultaneously measurable parameters. We have circumvented these limitations with a multifaceted approach to investigate three structurally distinct aminoglycosides that bind to the aminoacyl-transfer RNA site (A site) in the prokaryotic 30S ribosomal subunit: apramycin, paromomycin, and gentamicin. Using several single-molecule fluorescence measurements combined with structural and biochemical techniques, we observed distinct changes to translational dynamics for each aminoglycoside. While all three drugs effectively inhibit translation elongation, their actions are structurally and mechanistically distinct. Apramycin does not displace A1492 and A1493 at the decoding center, as demonstrated by a solution nuclear magnetic resonance structure, causing only limited miscoding; instead, it primarily blocks translocation. Paromomycin and gentamicin, which displace A1492 and A1493, cause significant miscoding, block intersubunit rotation, and inhibit translocation. Our results show the power of combined dynamics, structural, and biochemical approaches to elucidate the complex mechanisms underlying translation and its inhibition.
authors: Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
authors: Albert
authors: A
authors: Tsai
authors: Sotaro
authors: S
authors: Uemura
authors: Magnus
authors: M
authors: Johansson
authors: Elisabetta Viani
authors: EV
authors: Puglisi
authors: R Andrew
authors: RA
authors: Marshall
authors: Colin Echeverría
authors: CE
authors: Aitken
authors: Jonas
authors: J
authors: Korlach
authors: Måns
authors: M
authors: Ehrenberg
authors: Joseph D
authors: JD
authors: Puglisi
mesh_terms: D000617:Aminoglycosides / Q000494:pharmacology*; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D005839:Gentamicins / Q000494:pharmacology; D009328:Nebramycin / Q000031:analogs & derivatives / Q000494:pharmacology; D009690:Nucleic Acid Conformation; D010303:Paromomycin / Q000494:pharmacology; D010441:Peptide Chain Elongation, Translational / Q000187:drug effects*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000378:metabolism; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry / Q000378:metabolism
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D005839:Gentamicins; D012336:RNA, Ribosomal, 16S; D012346:RNA, Transfer, Amino Acyl; D009328:Nebramycin; C011666:apramycin; D010303:Paromomycin