Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations
Fig 5
Analysis of the recovery-stroke process.
(A) A representative trajectory for the AAA6↓ simulation. (B) Local structural change at the interface between AAA6/C-terminal module and the AAA1 in the standard setup simulation. The post-power-stroke structure (left) and an intermediate snapshot structure (right) are depicted. For the latter, the atomic structure was reconstituted from a coarse-grained snapshot. E4297 in the AAA6/C-terminal module and R2084 in the AAA1 module interact in the post-power-stroke structure, whereas they are apart in the intermediate structure. Atomistic model was reconstructed by the protocol given in Method. (C) Local structural change at the interface between the AAA6/C-terminal module (red for the post-power-stroke structure), salmon pink (100 x 104 MD step), and white (103 x 104 MD step)) and the AAA5 module (orange for the post-power-stroke structure), light orange (100 x 104 MD step), and white (103 x 104 MD step) in the standard setup simulation. Arrows labeled with 1 and 2 represent the sequential movement. (D) Three examples of the conformational change in MTBD/Stalk along scaled time. (E) Averaged conformational change in the MTBD/Stalk along scaled time for the forward (red) and recovery (blue) strokes. The time in each trajectory is scaled to be zero at the time of the AAA4 (AAA5) transitions and one at the time of the AAA5 (AAA4) transitions for the forward (recovery) strokes.