Table 1.
The pKa prediction of K245 residue over MD trajectories. The pKa prediction was computed over the last 50 ns of simulation and averaged over three replicas (n = 300) for each system: T2Tre2OO-K245+, T2Tre2OO-K2450, T2Tre1CC-K245+, and T2Tre1CC-K2450. The calculation was carried out by considering only the channel and membrane atoms explicitly. K245 total corresponds to the average ± SD of the system protonated and neutral (n = 1200). The pK1/2 value reported by Niemeyer et al. [7] is used as a parameter to compare the pKa of K245 predicted in K245 total for open (T2Tre2OO model) and closed (T2Tre1CC model) states of the fenestrations.
| TASK-2 Simulations | ||||||
|---|---|---|---|---|---|---|
| T2Tre2OO | T2Tre1CC | |||||
| System | Subunit | Average | SD | Average | SD | pK1/2 Experimental |
| K245+ | A | 8.65 | 0.63 | 7.95 | 0.43 | ~8.0 |
| K245+ | B | 8.98 | 0.38 | 7.75 | 0.40 | |
| K2450 | A | 7.27 | 0.37 | 6.86 | 0.35 | |
| K2450 | B | 6.88 | 0.29 | 6.79 | 0.25 | |
| K245 Total | All | 7.93 | 0.98 | 7.34 | 0.63 | |