Figure 5

Model with mRNA circularisation. Sketches of the two possible mRNA conformations, open and circularised, whose transitions depend on the free energy gap ΔG (A). In blue and yellow we have represented the interacting proteins (e.g. PABP and eIF4F) bound at the 3′ and 5′ ends; the black line is the end-to-end distance that is equal to d in the circularised state. We have fixed d = 5 nm in our calculation. Ribosome density computed taking into account mRNA circularisation (continuous line) is then compared to experimental data (triangles, cfr. symbols used in Fig. 1) and the previous model neglecting circularisation (dashed line) (B). The fitted parameters are \({\bar{\alpha }}_{\infty }\mathrm{=(4.7}\pm \mathrm{0.6)}\,{10}^{-3}\) s⁻¹, λ = 7.0 ± 0.6 nm and ε = − 8.3 ± 0.4 (k _B T). End-to-end distance (blue curve, right axis) and calculated probabilities P _c and P _o  = 1 − P _c as a function of the CDS length L (C).