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Protein Eng Des Sel. 2016 Aug;29(8):317-325. doi: 10.1093/protein/gzw022. Epub 2016 Jun 21.

Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations.

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Advanced Institute for Computational Science, RIKEN, QBiC Building B, 6-2-4, Furuedai, Suita, Osaka 565-0874, Japan.
Technology Research Association for Next Generation Natural Products Chemistry (N2PC), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.
IMSBIO Co. Ltd, Owl Tower, 4-21-1, Higashi-Ikebukuro, Toshima-ku, Tokyo 170-0013, Japan.
Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1, Ozuka-Higashi, Asa-Minami-ku, Hiroshima 731-3194, Japan.
Department of Biological Sciences, Graduate School of Science, and Faculty of Science, Osaka University, 1-1, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan.


Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA(+) ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named 'the ADP model' and 'the ATP model', where ADP and ATP are bound to AAA1 in the AAA(+) ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results.


ADP and ATP; dynein; elastic properties; molecular dynamics simulation

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