Allosteric control of the ribosome by small-molecule antibiotics

Nat Struct Mol Biol. 2012 Sep;19(9):957-63. doi: 10.1038/nsmb.2360. Epub 2012 Aug 19.


Protein synthesis is targeted by numerous, chemically distinct antibiotics that bind and inhibit key functional centers of the ribosome. Using single-molecule imaging and X-ray crystallography, we show that the aminoglycoside neomycin blocks aminoacyl-transfer RNA (aa-tRNA) selection and translocation as well as ribosome recycling by binding to helix 69 (H69) of 23S ribosomal RNA within the large subunit of the Escherichia coli ribosome. There, neomycin prevents the remodeling of intersubunit bridges that normally accompanies the process of subunit rotation to stabilize a partially rotated ribosome configuration in which peptidyl (P)-site tRNA is constrained in a previously unidentified hybrid position. Direct measurements show that this neomycin-stabilized intermediate is incompatible with the translation factor binding that is required for distinct protein synthesis reactions. These findings reveal the functional importance of reversible intersubunit rotation to the translation mechanism and shed new light on the allosteric control of ribosome functions by small-molecule antibiotics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / pharmacology*
  • Crystallography, X-Ray
  • Escherichia coli / chemistry
  • Escherichia coli / drug effects*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Neomycin / chemistry
  • Neomycin / pharmacology*
  • Protein Biosynthesis / drug effects
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism*
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / metabolism
  • RNA, Transfer, Amino Acyl / metabolism*
  • Ribosome Subunits, Large, Bacterial / chemistry
  • Ribosome Subunits, Large, Bacterial / drug effects*
  • Ribosome Subunits, Large, Bacterial / metabolism
  • Ribosome Subunits, Small, Bacterial / chemistry
  • Ribosome Subunits, Small, Bacterial / drug effects
  • Ribosome Subunits, Small, Bacterial / metabolism


  • Anti-Bacterial Agents
  • Escherichia coli Proteins
  • RNA, Bacterial
  • RNA, Ribosomal
  • RNA, Transfer, Amino Acyl
  • Neomycin