5'-initiation rate and scanning rate impact on 5'-UTR translation under repressing conditions (Model 3). (A) For constant 60S subunit joining (30 nt/s), translation elongation and termination rates (calculated by Gilchrist and Wagner, ), the average 5'-polysome sizes were calculated for different scanning rates (5, 15, 30, 100 nt/s) under different 5'-initiation rates (from 0.0145 to 0.29 s-1). The repressing ternary complex binding rate was predicted by the simplified model. GCN4 mRNA translation is simulated for 60 minutes, and the results are averaged over the time period of 10-60 min. Each point represents an average of 50 such replicates. And the error bars denote 1 standard deviation. Some error bars are too short to be seen. Data in C and D were averaged in the same way. (B) Average 5'-polysome size was plotted against the ratio a
relative to its nominal value. Simulation results at scanning rate of 5 nt/s from A were used. (C) uORF1 translation rate is calculated for different 5'-initiation rates at each scanning rate. (D) The probability that the 5'-end is unoccupied and available to receive an initiating ribosome is calculated for different 5'-initiation rates at different scanning rates.