TABLE 1.
vSGLT and PutP MD trajectories
The frames from the last 100 ns of each trajectory are used for the analysis. The root mean square deviations (r.m.s.d.) were calculated against the starting model for each simulation.
| Transporter | Starting Sc binding mode | Length of the trajectories | r.m.s.d. of the Cα in TMs | Movement of substrate Sc |
|---|---|---|---|---|
| ns | Å | |||
| vSGLT | Sub-pocket 1, near Na2 | 250 | 1.3 ± 0.1 | Moves within sub-pocket 1 |
| Sub-pocket 2, between Tyr-263 and Ser-368 | 238 | 1.2 ± 0.1 | Moves within sub-pockets 2 and 3 | |
| Sub-pocket 3, right below Tyr-263 | 213 | 1.6 ± 0.2 | Moves within sub-pockets 2 and 3 | |
| PutP | Sub-pocket 1, near Na2 | 118 | 2.8 ± 0.1 | Moves within sub-pocket 1 |
| Sub-pocket 2, between Tyr-248 and Cys-344 | 108 | 2.0 ± 0.1 | Moves within sub-pocket 2 | |
| Sub-pocket 3, right below Tyr-248 | 500 | 2.9 ± 0.1 | Moves within sub-pocket 3 |