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Molecules 2011, 16(2), 1211-1239; doi:10.3390/molecules16021211

Selection of Peptides Targeting Helix 31 of Bacterial 16S Ribosomal RNA by Screening M13 Phage-Display Libraries

1
Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
2
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
Current address: Intramural Research Program, NICHD, NIH, Bethesda, MD 20892, USA
§
Current address: Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
||
Current address: Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 5 January 2011 / Revised: 24 January 2011 / Accepted: 25 January 2011 / Published: 28 January 2011
(This article belongs to the Special Issue Phage Display of Combinatorial Libraries)
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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.
Keywords: Helix 31; modified nucleotides; peptides; phage display; 5-methylcytidine; 2-methylguanosine Helix 31; modified nucleotides; peptides; phage display; 5-methylcytidine; 2-methylguanosine
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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Lamichhane, T.N.; Abeydeera, N.D.; Duc, A.-C.; Cunningham, P.R.; Chow, C.S. Selection of Peptides Targeting Helix 31 of Bacterial 16S Ribosomal RNA by Screening M13 Phage-Display Libraries. Molecules 2011, 16, 1211-1239.

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