Table 1.
The molecular composition of different MD simulations performed in our study.
| Bilayer | No. of lipids | No. of waters | No. of PIs | No. of counter ions | Distance of TIRAP from the membrane surface (Å) | Total no. of molecules (excluding protein) |
|---|---|---|---|---|---|---|
| DPPC | 284 | 18,825 | 4 (PIP2) | 18 Na+ | 5 | 19,131 |
| DPPC | 284 | 24,537 | 4 (PIP2) | 18 Na+ | 10 | 24,843 |
| DPPC | 284 | 32,537 | 4 (PIP2) | 18 Na+ | 15 | 32,843 |
| DPPC | 288 | 25,592 | – | 2 Cl− | 5 | 25,882 |
| DPPC | 288 | 25,515 | – | 2 Cl− | 5 | 25,805 |
| DPPC | 284 | 22,834 | 4 (PIP3) | 26 Na+ | 5 | 23,148 |
| DPPCa | 284 | 22,854 | 4 (PIP2) | 26 Na+ | 5 | 23,168 |
All simulations were performed for a duration of 100 ns.
aMD simulation system containing the lysine-to-alanine mutant of TIRAP.
DPCC, dipalmitoylphosphatidylcholine; MD, molecular dynamics; PI, phosphatidylinositol; PIP2, PI 4,5-bisphosphate; PIP3, PI (3,4,5)-trisphosphate; TIRAP, toll/interleukin 1 receptor domain-containing adaptor protein.