Ribosome-mRNA Interactions During Protein Synthesis
Using a subsystem of the ribosome, including the neighborhood of the decoding center where the A-site mRNA codon base pairs with the tRNA anticodon, we have discovered an interaction surface that hydrogen-bonds to the +1 codon next in line to enter the A site. At the beginning of translocation, the interaction surface is positioned immediately adjacent to the tRNA anticodon, aligning it with the +1 codon in the mRNA. The interaction surface consists of the edges of two stacked rRNA bases—the Watson-Crick edge of 16S/18S C1054 and the Hoogsteen edge of A1196 (E. coli 16S rRNA numbering)—and the guanidinium group of R146 of yeast ribosomal protein Rps3 which pi-stacks with A1196. This C1054-A1196-R146 (CAR) surface H-bonds to the first two nucleotides of the +1 codon 
and this interaction is particularly strong when the codon is GCN. We are currently exploring the sequence dependence of this mRNA-CAR interaction which potentially contributes to GCN-mediated regulation of protein translation..
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Funding: National Institutes of Health
Figure: CAR interaction surface
