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Figure 1 | BMC Biophysics

Figure 1

From: Origin of multiple intersubunit rotations before EF-G-catalyzed ribosomal translocation through the mRNA with a downstream secondary structure

Figure 1

Model of tRNA-mRNA translocation in the ribosome at saturating concentration of EF-G.GTP (see text for detailed description). In the model, State I, State C0, State C and State F1 (inside boxes) have a low L1-tRNA FRET efficiency (0.2) in the smFRET experiment of Kim et al. [11], State H, State H1, State H2, State F2, State F3 and State POST have a high L1-tRNA FRET efficiency (0.8), while the L1-tRNA FRET efficiency becomes zero at State 0. In the presence of the downstream mRNA secondary structure, the effective-transition probability P E <1. If no downstream mRNA secondary structure is present, P E =1. Since here we only focus on the dynamics of the intersubunit rotations after the ribosomal complex transits to the hybrid state (State H), we need only to choose values of rate constants k 4, k 5, k 6, k 7, k 8, k 9 and k d . As discussed in the main text, their values are taken as follows: k 4 = 0.8 s−1, k 5 = 35 s−1, k 6 is very large, k 7 = 1.8 s−1, k 8 = 0.2 s−1, k 9 = 250 s−1, and k d =5 s−1.

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