Predicting ribosomal frameshifting efficiency. Phys. Biol

Many retroviruses use −1 ribosomal frameshifting as part of the mechanism in translational control of viral protein synthesis. Quantitative prediction of the efficiency of −1 frameshifting is crucial for understanding the viral gene expression. Here we investigate the free energy landscape for a minimal −1 programmed ribosomal frameshifting machinery, including the codon–anticodon base pairs at the slippery site, the downstream messenger RNA structure and the spacer between the slippery site and the downstream structure. The free energy landscape analysis leads to a quantitative relationship between the frameshifting efficiency and the tension force generated during the movement of codon–anticodon complexes, which may occur in the A/T to A/A accommodation process or the translocation process. The analysis shows no consistent correlation between frameshifting efficiency and global stability of the downstream mRNA structure