Table 2.
Geometric parameters that characterize the nucleotide-binding pocket in actin subunits from MD simulations.
| Filament Model | Bound Nucleotide | DNase-I Loop1 | B12 (Å) | B22 (Å) | B32 (Å) | B42 (Å) |
|---|---|---|---|---|---|---|
| Oda | ATP | unfolded | 4.6(±0.2) | 5.7(±0.4) | 4.5(±0.4) | 4.0(±0.5) |
| ADP | unfolded | 3.6(±0.5) | ||||
| ADP | folded | 5.8(±1.5) | ||||
| Holmes | ATP | unfolded | 5.8(±0.3) | 4.9(±0.3) | 3.8(±0.4) | 3.3(±0.8) |
| ADP | unfolded | 2.6(±0.6) | ||||
| ADP | folded | 3.3(±0.8) | ||||
| G-actin | ATP | unfolded | 6.1(±.4) | 3.4(±.1) | 5.2(±.2) | 3.0(±1.0) |
| Oda3 (initial structure) | ADP | unfolded | 5.1 | 4.3 | ||
| Monomeric actin3 (initial structure) | ATP | unfolded | 7.1 | 3.9 | ||
| Oda | ATP phalloidin | unfolded | 4.7(±0.2) | 4.2(±0.7) | 5.7(± 0.4) | 4.0(±0.8) |
Refers to the initial conformation of the DNase-I binding loop. Further details are provided in the methods section.
Definition of geometrical parameters: B1: distance between Q137 Cδ side chain atom and Pγ atom of bound ATP, B2: Distance between Pγ atom of bound ATP and O atom of closest coordinating water molecule, B3: Distance between Pγ atom of bound ATP and Cα atom of G156, B4: Distance between O atom in Q137 side chain and H atom of closest coordinating water molecule.
The initial Oda structure properties were taken from PDB entry 2ZWH. The initial G-actin structure was taken from PDB entry 1NWK and prepared as described in the text.