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. 2014 Feb 21;42(8):4813–4822. doi: 10.1093/nar/gku159

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Figure 2. — The model. In our model, ribosomes arrive at translation start site with rate , and release proteins with rate . During elongation, translating ribosomes wait for their cognate tRNAs at position i and simultaneously unwind the base pairings located at position i + L/2 (L = 42 nt). (A) shows the structure that the first ribosome encounters (the first ribosome is blue). (B) shows the structure that the third ribosome encounters. mRNA secondary structure is weakened due to the constraints of ribosomes. In our model, we assume that different ribosomes might encounter the structure with different folding strength at the same site because the pattern of mRNA folding might be changed when ribosomes have bound to mRNA (see text for details).

Inline graphic — The model. In our model, ribosomes arrive at translation start site with rate , and release proteins with rate . During elongation, translating ribosomes wait for their cognate tRNAs at position i and simultaneously unwind the base pairings located at position i + L/2 (L = 42 nt). (A) shows the structure that the first ribosome encounters (the first ribosome is blue). (B) shows the structure that the third ribosome encounters. mRNA secondary structure is weakened due to the constraints of ribosomes. In our model, we assume that different ribosomes might encounter the structure with different folding strength at the same site because the pattern of mRNA folding might be changed when ribosomes have bound to mRNA (see text for details).