Fig. 1
Time evolution of ribosome ensembles in termination of translation a. Cartoon visualization of the pathway from free release complex to peptide release. Compact class 1 release factor (RF) binds to RF-free ribosomal release complex (RC0) and forms the RC·RFcompact complex with compounded rate constant ka·[RFfree]. Stop codon recognition induces conformational change in the RF which brings the ribosome from the RC·RFcompact to the RC·RFextended complex with rate constant kconf. The ester bond between the peptide and the P-site tRNA is hydrolyzed with rate constant khydr. b Predicted dynamics of peptide release with conformational change in RF1. We solved the ordinary differential equations associated with termination according to the scheme in a with association rate constant ka = 45 µM−1s−1, [RF1free] = 3 µM, kconf = 18 s−1 and khydr = 2 s−1 (Supplementary Fig. 2) and plotted the fractions of ribosomes in RC0, RC·RFcompact and RC·RFextended forms (y-axis) as functions of time (x-axis). Green dot lines, RC0; red solid lines, RC·RFcompact; blue dash lines, RC·RFextended. c Predicted dynamics of peptide release with conformational change in RF2. The fractions of ribosomes in different release complexes were obtained in the same way as b with the rate constants ka = 17 µM−1 s−1, [RF2free] = 3 µM, kconf = 11 s−1 and khydr = 2.7 s−1 (Supplementary Fig. 3). d, e The populations of release complexes containing compact conformation and extended conformation of RF1 (d) and RF2 (e) at the 24 ms, 60 ms and long incubation time points as obtained by time-resolved cryo-EM after 3D classification of the particle images
