Table 1.
Kinetic network parameters.
| Transition | States | Forward rate | Backward rate | Source | ||
|---|---|---|---|---|---|---|
|
| ||||||
| Cognate | Mismatch | Cognate | Mismatch | |||
|
| ||||||
| Bulk entry to secondary pore | bulk – H | 0.75 μs−1 M−1 | 3.8 μs−1 | MSM/Exp.[40] | ||
| bulk – F | 1.35 μs−1 M−1 | 0.55 μs−1 | MSM/Exp.[40] | |||
| bulk – T | 1.42 μs−1 M−1 | 0.18 μs−1 | MSM/Exp.[40] | |||
| Secondary pore dynamics | H – F | 6.8 μs−1 | 1.2 μs−1 | MSM | ||
| F – T | 5.2 μs−1 | 1.5 μs−1 | MSM | |||
| T – G | 0.76 μs−1 | 0.28 μs−1 | MSM | |||
| F – G | 2.8 μs−1 | 0.58 μs−1 | MSM | |||
| E site binding | G – E | 3.4 μs−1 | 1.8 μs−1 | MSM | ||
| Active site binding | E – A | 13.1 μs−1 | 0.08 μs−1 | 25.8 μs−1 | MD[18] | |
| Trigger loop closing | A – C | 150 s−1 | 15–150 sc−1 | 5 s−1 | 5–4,450 s−1 | MD[41]/Exp.[17] |
| NTP incorporation | C – R | 35 s−1 | 0.7 s−1 | 0 | 0 | Exp.[15, 40] |
Transitions and associated kinetic rates used in kinetic network model. If no rate is given for mismatch bases, the rates for cognate bases were applied. Rates estimated directly from MD have a lower limit of about 0.25 μs−1 based on the total aggregate simulation time used for constructing the MSM model.