Table 1.
Structural properties of actin filaments investigated by molecular dynamics.
| Filament Model | Bound Nucleotide | DNase-I Loop1 | Crossover Length2 (Å) | Filament RMSD3 (Å) |
|---|---|---|---|---|
| Oda | ATP | unfolded | 362(±4) | 5.7(±0.5) |
| ATP | folded | 354(±5) | 6.9(±0.3) | |
| ADP | unfolded | 357(±4) | 5.6(±0.4) | |
| ADP | folded | 357(±3) | 6.4(±0.6) | |
| Holmes | ATP | unfolded | 364(±2) | 8.3(±1.0) |
| ATP | folded | 363(±6) | 10.5(±0.4) | |
| ADP | unfolded | 373(±2) | 7.1(±0.4) | |
| ADP | folded | 366(±5) | 8.2(±0.4) | |
| Oda + phalloidin | ATP | unfolded | 362(±1) | 5.0(±0.2) |
1
Refers to the initial conformation of the DNase-I binding loop. Further details are provided in the methods section.
2
The crossover length is calculated by averaging the unit cell length over the last 20 ns of each simulation. Simulations were performed of one filament crossover distance (13 actin subunits) with periodicity along the longitudinal axis of the filament.
3
The RMSD (of 4875 Cα atoms) is calculated with respect to the initial structure and using the last 20 ns of each data set as described in the methods section.