Fig. 5.
Revised predictions of tclear,NO· and NO· consumption distribution as a function of [O2]. Using the updated model structure (with an [O2]-dependent translation rate) with parameters trained on WT [NO·] curves measured at 0, 5, 10, 20, and 50 μM O2 (optimization “stage 4”), 50 μM DPTA NONOate treatment was simulated for WT E. coli under [O2] ranging from 0 to 50 μM. (A) The resulting tclear,NO· was predicted (dashed black line) and compared with experimental measurements (open circles; mean of at least three independent experiments with error bars representing the SEM). (B) Comparison of predicted and measured [NO·] at 2.5 ± 0.5 μM O2. The dashed black line represents the simulation at 2.5 μM O2 using the best-fit parameter set, where the dark gray shading (too narrow to see) represents prediction uncertainty (range of viable parameter sets with ER < 10) at 2.5 μM O2, and light gray shading represents the range of simulation results for [O2] conditions spanning 2–3 μM O2, to account for the ±0.5 μM O2 experimental uncertainty in the hypoxic chamber O2 meter. The experimental data (solid red line) are mean of three independent experiments, with light red shading representing the SEM. (C) Predicted distribution of cumulative NO· detoxification (up to time tclear,NO·) for transfer to the gas phase, autoxidation, and combined Hmp- and NorV-mediated detoxification. (D) Individual contributions of Hmp and NorV to cumulative NO· detoxification. Predictions (dashed lines) were obtained using the best-fit parameter set, with shading (which is very small) representing prediction uncertainty (range of viable parameter sets with ER < 10).