Table 1. Molecular simulation systems evaluated in this study of McsS and MSL1 mechanosensation.
| MscS coarse grained* | MscS all atom† | MSL1coarse grained* | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Closed WT POPC |
Closed WT POPC §d |
Closed WT DMPC |
Closed WT PC:PG |
Open WT POPC |
Open A106V POPC |
Open D67R1 POPC |
Closed WT POPC |
Closed WT DMPC |
Closed WT POPC |
Open WT POPC |
|
| Protein | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| POPC | 2057 | 755 | 0 | 1651 | 686 | 737 | 740 | 755 | 0 | 2001 | 1916 |
| POPG | 0 | 0 | 0 | 407 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| DMPC | 0 | 0 | 768 | 0 | 0 | 0 | 0 | 0 | 768 | 0 | 0 |
| Na+ | 855 | 328 | 340 | 1265 | 328 | 328 | 328 | 314 | 326 | 855 | 855 |
| Cl– | 862 | 335 | 347 | 865 | 335 | 356 | 349 | 335 | 347 | 890 | 883 |
| Water ‡ | 75,938 | 28,123 | 29,000 | 75,501 | 28,200 | 28,372 | 28,299 | 115,170 | 118,774 | 76,076 | 76,549 |
| Total atoms or particles | 106,364 | 41,871 | 41,392 | 106,352 | 41,120 | 41,603 | 41,524 | 476,183 | 476,473 | 106,012 | 105,248 |
| System size (nm) |
26.5×26.5×18.7 | 16.9×16.9×17.9 | 16.3×16.3×19.1 | 26.3×26.3×19.0 | 16.9×16.9×17.9 | 16.9×16.9×17.9 | 16.9×16.9×17.9 | 15.9×15.9×19.9 | 15.4×15.4×21.1 | 26.5×26.5×18.7 | 26.5×26.5×18.7 |
| Time (μs) | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 10 | 8 | 80 | 20 |
POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; WT: wild type; DMPC:1–2-dimyristoleoyl-sn-glycero-3-phosphocholine; POPG:1–2-palmitoyl-2-oleoylglycero-3-phosphoglycerol.
*
MARTINI 2.2 forcefield.
†
CHARMM36m forcefield.
‡
One CG water particle is equivalent to four AA water molecules.
§
Five additional 10 μs simulations were carried out for this system under applied lateral tensions of 0, 0.5. 2.5, 5.0, and 10 mN/m.