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

doi:10.1088/1674-1056/acdfc1

中国物理B ›› 2023, Vol. 32 ›› Issue (10): 108701-108701.doi: 10.1088/1674-1056/acdfc1

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

Yi-Zhao Geng(耿轶钊)^1,2,†, Li-Ai Lu(鲁丽爱)^1,2, Ning Jia(贾宁)^1,2, Bing-Bing Zhang(张冰冰)^1,2, and Qing Ji(纪青)^1,2,‡

1 School of Science, Hebei University of Technology, Tianjin 300401, China;
2 Institute of Biophysics, Hebei University of Technology, Tianjin 300401, China

收稿日期:2023-04-02 修回日期:2023-05-14 接受日期:2023-06-20 出版日期:2023-09-21 发布日期:2023-10-09
通讯作者: Yi-Zhao Geng, Qing Ji E-mail:gengyz@hebut.edu.cn;jiqingch@hebut.edu.cn
基金资助:
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).

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

Yi-Zhao Geng(耿轶钊)^1,2,†, Li-Ai Lu(鲁丽爱)^1,2, Ning Jia(贾宁)^1,2, Bing-Bing Zhang(张冰冰)^1,2, and Qing Ji(纪青)^1,2,‡

1 School of Science, Hebei University of Technology, Tianjin 300401, China;
2 Institute of Biophysics, Hebei University of Technology, Tianjin 300401, China

Received:2023-04-02 Revised:2023-05-14 Accepted:2023-06-20 Online:2023-09-21 Published:2023-10-09
Contact: Yi-Zhao Geng, Qing Ji E-mail:gengyz@hebut.edu.cn;jiqingch@hebut.edu.cn
Supported by:
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).

1. 2023-108701-SI.pdf(1646KB)

摘要/Abstract

摘要： 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.

关键词: kinesin, tubulin, microtubule, molecular dynamics simulation

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.

Key words: kinesin, tubulin, microtubule, molecular dynamics simulation

中图分类号: (Motor proteins (myosin, kinesin dynein))

87.16.Nn

87.16.Ka (Filaments, microtubules, their networks, and supramolecular assemblies) 87.10.Tf (Molecular dynamics simulation)

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[J]. 中国物理B, 2023, 32(10): 108701-108701.

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

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

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