Journal
PHYSICAL BIOLOGY
Volume 5, Issue 1, Pages -Publisher
IOP PUBLISHING LTD
DOI: 10.1088/1478-3975/5/1/016002
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Funding
- NIGMS NIH HHS [GM063732, R01 GM063732-05, R01 GM063732-04, R01 GM063732] Funding Source: Medline
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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.
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