1. cPLA2–Membrane Systems Employed in the Present Study .
| no.
of lipids |
||||||
|---|---|---|---|---|---|---|
| system | Ca2+ | 1% PIP2 | upper leaflet | lower leaflet | total no. of atoms | simulation length |
| 1 | + | – | – | – | 424 425 | 3 replicates × 500 ns |
| 2 | – | – | 400 | 400 | 495 230 | 3 replicates × 500 ns |
| 3 | + | – | 400 | 400 | 495 366 | 3 replicates × 500 ns |
| 4 | – | + | 400 | 400 | 495 388 | 3 replicates × 500 ns |
| 5 | + | + | 400 | 400 | 495 110 | 3 replicates × 500 ns |
a
All systems were simulated using the CHARMM36 force field and built using the CHARMM-GUI Membrane Builder. Membrane compositions were derived from Andreyev et al. Na+ and Cl– ions at 150 mM were added. cPLA2 histidine protonation states were set based on the PROPKA output. The orientation of cPLA2 with respect to the membrane was consistent with the OPM and HDX-MS data.