Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries

Molecules. 2011 Jan 28;16(2):1211-39. doi: 10.3390/molecules16021211.

Abstract

Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Bacteriophage M13 / genetics*
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Peptide Library*
  • Peptides / chemistry*
  • Peptides / genetics
  • RNA, Ribosomal / chemistry*
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal, 16S / chemistry*
  • RNA, Ribosomal, 16S / genetics
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics
  • Surface Plasmon Resonance

Substances

  • Peptide Library
  • Peptides
  • RNA, Ribosomal
  • RNA, Ribosomal, 16S
  • Recombinant Fusion Proteins