Molecular contacts between antibiotics and the 30S ribosomal particle

Methods Enzymol. 2006;415:180-202. doi: 10.1016/S0076-6879(06)15012-0.


Crystal structures of complexes between ribosomal particles and antibiotics have pinned down very precisely the discrete binding sites of several classes of antibiotics inhibiting protein synthesis. The crystal structures of complexes between various antibiotics and ribosomal particles show definitively that ribosomal RNAs (rRNAs), rather than ribosomal proteins, are overwhelmingly targeted. The antibiotics are found at messenger RNA or transfer RNA binding sites and, most importantly, at pivot locations that are key for the structural rearrangements during the molecular mechanical steps in initiation, elongation, or termination of protein synthesis. We focus here on the 30S particle. Structurally, the antibiotics interact in many ways with RNA: (i) only with the phosphate groups (streptomycin); (ii) mainly with bases (hygromycin, spectinomycin); (iii) with a mixture of both (paromomycin, Geneticin); (iv) via magnesium ions (tetracycline) or a protein side chain (streptomycin). The antibiotics can mimic base stacking (pactamycin) or form pseudo-base pairing interactions with ribosomal bases (paromomycin and related aminoglycosides). Resistance strategies (mutations or methylations in rRNA or enzymatic modifications of the antibiotics) can generally be understood on the basis of the intermolecular contacts made between the antibiotics and rRNA residues in the crystal structures. In humans, toxicity of ribosomal antibiotics is most likely due, at least in part, to the sensitivity of mitochondrial ribosomes, since mitochondria evolved from a bacterial ancestor. Antibiotic families (e.g., aminoglycosides) form a set of invariant H-bonds to defined rRNA residues. When such residues are conserved in bacteria, but not in eukaryotes, resistance of eukaryotic ribosomes is observed. The structural knowledge, together with comparative genomic analysis, should allow for the development of new broad-spectrum antibiotics with higher selectivity toward bacterial ribosomes and less toxicity on eukaryotic cytoplasmic and mitochondrial ribosomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aminoglycosides / chemistry
  • Aminoglycosides / genetics
  • Aminoglycosides / metabolism
  • Anti-Bacterial Agents / chemistry*
  • Anti-Bacterial Agents / metabolism
  • Crystallography, X-Ray
  • Humans
  • Models, Molecular
  • Molecular Conformation*
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / metabolism
  • Ribosomal Proteins / chemistry*
  • Ribosomal Proteins / metabolism


  • Aminoglycosides
  • Anti-Bacterial Agents
  • Protein Subunits
  • RNA, Ribosomal
  • Ribosomal Proteins