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Anchor Effect of Interactions Between Kinesin’s Nucleotide-Binding Pocket and Microtubule

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Abstract

Microtubule not only provides the track for kinesin but also modulates kinesin’s mechanochemical cycle. Microtubule binding greatly increases the rates of two chemical steps occurring inside the nucleotide-binding pocket (NBP) of kinesin, i.e., ATP hydrolysis and ADP release. Kinesin neck linker docking (the key force-generation step) is initiated by the motor head rotation induced by ATP binding which needs an anchor provided by microtubule. These functions of microtubule can only be accomplished through interactions with kinesin. Based on the newly obtained crystal structures of kinesin-microtubule complexes, we investigate the interactions between kinesin’s NBP and microtubule using molecular dynamics simulations. We find that the N-3 motif of NBP has direct interactions with a group of negatively charged residues on α-tubulin through Ser235 and Lys237. These specific long-range interactions induce binding of NBP to microtubule at the right position and assist the formation of the indirect interaction between NBP and microtubule. These interactions between N-3 and microtubule have an important anchor effect for kinesin’s motor domain during its rotation with Ser235 as the rotation center, and also play a crucial role in stabilizing the ATP-hydrolysis environment.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China under Grant Nos. 11545014, 11605038 and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Science, China (Grant No. Y5KF211CJ1).

Conflict of Interest

Yumei Jin, Yizhao Geng, Lina Lü, Yilong Ma, Gang Lü, Hui Zhang, and Qing Ji declare that they have no conflicts of interest.

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No human studies were carried out by the authors for this article. No animal studies were carried out by the authors for this article.

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Authors and Affiliations

  1. Institute of Biophysics, Hebei University of Technology, Tianjin, 300401, China

    Yumei Jin, Yizhao Geng, Lina Lü, Yilong Ma & Qing Ji

  2. School of Science, Hebei University of Technology, Tianjin, 300401, China

    Yumei Jin, Yizhao Geng, Lina Lü, Yilong Ma, Hui Zhang & Qing Ji

  3. Mathematical and Physical Science School, North China Electric Power University, Baoding, 071003, China

    Gang Lü

  4. State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, 100190, China

    Qing Ji

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  1. Yumei Jin
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Correspondence to Yizhao Geng or Qing Ji.

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Associate Editor Mian Long oversaw the review of this article.

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Jin, Y., Geng, Y., Lü, L. et al. Anchor Effect of Interactions Between Kinesin’s Nucleotide-Binding Pocket and Microtubule. Cel. Mol. Bioeng. 10, 162–173 (2017). https://doi.org/10.1007/s12195-017-0477-8

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