Coarse-grained modeling of the structural states and transition underlying the powerstroke of dynein motor domain
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Results of NMA and structural alignment for dynein motor domain: Panels (a)–(c) show the dynamic domain partition for modes 1–3, respectively; domains 1–3 are colored red, green, and blue, respectively; the axis of the rotation of domain 1 (2) relative to domain 3 is represented by an arrow with blue stem and red (green) tip. Panel (d) shows the structural alignment in helices between two X-ray structures of dynein motor domain (PDB codes: 3qmz and 3ay1, shown as opaque and transparent, respectively); AAA1–AAA6 are colored blue, cyan, green, yellow, orange, and red; linker domain is colored purple; two arrows show the rotation of linker and further closing of AAA1–AAA2 interface from 3qmz to 3ay1. Panel (e) shows a cartoon for both pre- and post-powerstroke conformations of dynein motor domain; the large/small domain of each AAA+ module is represented by a large/small circle; key parts of dynein are labeled; the same color scheme as panel (d) is used for AAA1–AAA6 and linker; also shown are the MTBD (colored gray) and MT (colored light gray, with plus and minus ends marked).
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Structural modeling of pre-powerstroke conformation of dynein motor domain: Panel (a) shows the model of pre-powerstroke conformation aligned with the post-powerstroke conformation (PDB code: 3qmz); the post-powerstroke conformation is opaque, while the pre-powerstroke conformation is transparent (except for the linker and stalk which are shown as thick opaque tubes); three red arrows show stalk tilting, linker rotation, and displacement of linker tip. Panel (b) shows an enlarged view of AAA1–AAA2 interface, where the Arginine finger of AAA2 is shown as a yellow bead and the Walker A motif of AAA1 is colored red. The same color scheme as Fig. 1(d) is used for AAA1–AAA6 and linker.
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Modeling of the transition from the pre-powerstroke to the post-powerstroke conformation of dynein motor domain: Panel (a) shows an intermediate conformation of the predicted transition pathway aligned with the pre-powerstroke and post-powerstroke conformations; the intermediate conformation is colored gray, the post-powerstroke conformation is opaque, and the pre-powerstroke conformation is transparent; the linker domain is removed for clarity; one can see that the intermediate conformation and pre-powerstroke conformation are similar in AAA1, AAA2, AAA5, and AAA6, while the intermediate conformation and post-powerstroke conformation are similar in stalk and buttress. Panel (b) shows the linker domain in the intermediate conformation (gray), post-powerstroke conformation (opaque), and pre-powerstroke conformation (transparent). Panel (c) shows the AAA1–AAA2 interface in the intermediate conformation (gray), post-powerstroke conformation (opaque), and pre-powerstroke conformation (transparent). The same color scheme as Fig. 1(d) is used for AAA1–AAA6 and linker.
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