Kinesin-microtubule interaction reveals the mechanism of kinesin-1 for discriminating the binding site on microtubule

doi:10.1088/1674-1056/acdfc1

Abstract Microtubule catalyzes the mechanochemical cycle of kinesin, a kind of molecular motor, through its crucial roles in kinesin's gating, ATPase and force-generation process. These functions of microtubule are realized through the kinesin-microtubule interaction. The binding site of kinesin on the microtubule surface is fixed. For most of the kinesin-family members, the binding site on microtubule is in the groove between $\alpha $-tubulin and $\beta $-tubulin in a protofilament. The mechanism of kinesin searching for the appropriate binding site on microtubule is still unclear. Using the molecular dynamics simulation method, we investigate the interactions between kinesin-1 and the different binding positions on microtubule. The key non-bonded interactions between the motor domain and tubulins in kinesin's different nucleotide-binding states are listed. The differences of the amino-acid sequences between $\alpha$- and $\beta$-tubulins make kinesin-1 binding to the $\alpha$-$\beta$ groove much more favorable than to the $\beta$-$\alpha$ groove. From these results, a two-step mechanism of kinesin-1 to discriminate the correct binding site on microtubule is proposed. Most of the kinesin-family members have the conserved motor domain and bind to the same site on microtubule, the mechanism may also be shared by other family members of kinesin.

Keywords: kinesin tubulin microtubule molecular dynamics simulation

Received: 02 April 2023
Revised: 14 May 2023
Accepted manuscript online: 20 June 2023

PACS:	87.16.Nn	(Motor proteins (myosin, kinesin dynein))
	87.16.Ka	(Filaments, microtubules, their networks, and supramolecular assemblies)
	87.10.Tf	(Molecular dynamics simulation)

Fund: This work was supported by the Natural Science Foundation of Hebei Province of China (Grant No. A2020202007) and the National Natural Science Foundation of China (Grant No. 11605038).

Corresponding Authors: Yi-Zhao Geng, Qing Ji
E-mail: gengyz@hebut.edu.cn;jiqingch@hebut.edu.cn

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Yi-Zhao Geng(耿轶钊), Li-Ai Lu(鲁丽爱), Ning Jia(贾宁), Bing-Bing Zhang(张冰冰), and Qing Ji(纪青) Kinesin-microtubule interaction reveals the mechanism of kinesin-1 for discriminating the binding site on microtubule 2023 Chin. Phys. B 32 108701

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Kinesin-microtubule interaction reveals the mechanism of kinesin-1 for discriminating the binding site on microtubule

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