Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics
Fig 2
High correlation between the predictions of the MP-SMTM model and measured data for E. coli.
(A) Termination rate in steady state (predicted by the model) and protein abundance (empirical data); (B) Local initiation rate (as estimated for the model) and protein abundance (empirical data); (C) Mean ribo-seq read count and mean simulated occupancy. (D) Ribosomal density profiles for both simulation (average occupancy per codon) and ribo-seq (average read count per codon). In (A), (B) and (D) mRNAs with level lower than 0.2 were omitted from this analysis to avoid discretization errors of the simulation. In (A), (B) and (C) each point represents a single mRNA type. (All terms in this figure are defined in the Methods section, sub-sections System parameters, Prediction of protein synthesis rate and Additional terminology).