Table 1.
Summary of Simulations
| Protein | Bilayer Composition | Particles or Atoms | Duration (μs) |
|---|---|---|---|
| CG Simulations | |||
| Kinase WTa | PC:PS 70:30 | 30,240 | 10 × 3.0 |
| Kinase WTa | PC:PS 60:40 | 33,100 | 10 × 3.0 |
| Kinase WTa | PC:PS:PIP2 90:5:5 | 33,070 | 10 × 3.0 |
| Kinase mutant P1a | PC:PS:PIP2 90:5:5 | 33,070 | 10 × 3.0 |
| Kinase mutant P2a | PC:PS:PIP2 90:5:5 | 33,070 | 10 × 3.0 |
| Kinase mutant P1+P2a | PC:PS:PIP2 90:5:5 | 33,060 | 10 × 3.0 |
| Kinase WTa | PC:PS:PIP3 83:15:2 | 33,080 | 10 × 3.0 |
| TM + JM-small (20 residues) | PC:PS:PIP2 90:5:5 | 82,375 | 1 × 3.0 |
| TM + JM (40 residues) | PC:PS:PIP2 90:5:5 | 135,280 | 1 × 3.0 |
| TM + JM + kinase WT | PC:PS:PIP2 90:5:5 | 164,018 | 3 × 3.0 |
| TM + JM + kinase mutant P1 | PC:PS:PIP2 90:5:5 | 163,576 | 3 × 3.0 |
| TM + JM + kinase mutant P2 | PC:PS:PIP2 90:5:5 | 163,963 | 3 × 3.0 |
| TM + JM + kinase mutant P1+P2 | PC:PS:PIP2 90:5:5 | 164,003 | 3 × 3.0 |
| Atomistic Simulations | |||
| TM + JM + kinase WT mode1 | PC:PS:PIP2 90:5:5 | 863,343 | 0.1 |
| TM + JM + kinase WT mode2 | PC:PS:PIP2 90:5:5 | 867,120 | 0.1 |
Summary of the simulations performed. CG, coarse-grained; WT, wild-type; JM, juxtamembranes; PC, phosphatidylcholine; PS, phosphatidylserine; PIP2, phosphatidyl inositol 4,5-bisphosphate; PIP3, phosphatidylinositol (3,4,5)-trisphosphate. See also Figures 1 and S1 for descriptions of the simulation systems.
a
Simulations in which the kinases domain is not “tethered” via the TM and JM regions.