Table 1.
Summary of Gltph simulation systems reported in this study
| System | Monomer | Substrate | Na1 | Na2 | Na3 | Simulation time (ns) |
|---|---|---|---|---|---|---|
| S1-a | apo | – | – | – | – | 40 |
| S1-b | apo | – | – | – | – | 40 |
| S1-c | apo | – | – | – | – | 40 |
| S2-a | Na1-bound | – | + | – | – | 50 |
| S2-b | Na1-bound | – | + | – | – | 50 |
| S2-c | Na1-bound | – | + | – | – | 50 |
| S3-a | Substrate-bound | + | – | – | – | 30 |
| S3-b | Substrate-bound | + | – | – | – | 30 |
| S3-c | Substrate-bound | + | – | – | – | 30 |
| S4-a | Substrate/Na1-bound | + | + | – | – | 30 |
| S4-b | Substrate/Na1-bound | + | + | – | – | 30 |
| S4-c | Substrate/Na1-bound | + | + | – | – | 30 |
| Na3-a∗ | – | – | – | + | 20 | |
| Na3-b∗ | – | – | – | + | 20 | |
| Na3-c∗ | – | – | – | + | 20 | |
| Na3-d∗ | – | – | – | + | 20 | |
| Na3-e∗ | – | – | – | + | 20 | |
| Na3-f† | – | – | – | + | 20 | |
| Na3-g† | – | – | – | + | 20 | |
| Na3-h† | – | – | – | + | 20 | |
| Na3-i† | – | – | – | + | 20 | |
| Na3-j† | – | – | – | + | 20 | |
| Na1-boundD405N‡ | – | + | – | – | 30 | |
| Na1/Na3-bound§ | – | + | – | + | 20 | |
| Na1/Na3-bound¶ | – | + | – | + | 20 | |
| Fully bound | + | + | + | + | 20 |
Note that the systems were all simulated as trimers. However, individual monomers within the same trimer might have different bound states.
∗
This simulation system is adopted from the equilibrated structure of the Na1-bound state at 50 ns (system S2-a).
†
The equilibrated structure of the Na1-bound state at 40 ns (system S2-a) is used as the starting point.
‡
In this simulation system, Asp405 in TM8 was mutated to asparagine.
§
Na3 is in the putative binding site in this simulation system.
¶
Na3 is in the intermediate binding site in this simulation system.