Predicting ribosomal frameshifting efficiency.
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.
Cao
Song
S
Department of Physics and Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.
Chen
Shi-Jie
SJ
D000926:Anticodon / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D016368:Frameshift Mutation / Q000235:genetics*; D018965:Frameshifting, Ribosomal; D015685:Fusion Proteins, gag-pol / Q000235:genetics; D015967:Gene Expression Regulation, Viral; D015497:HIV-1 / Q000235:genetics; D001351:Infectious bronchitis virus / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010942:Plant Viruses / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*
D000926:Anticodon; D003062:Codon; D015685:Fusion Proteins, gag-pol; D012367:RNA, Viral