Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

doi:10.1088/1674-1056/ac598b

中国物理B ›› 2022, Vol. 31 ›› Issue (5): 58702-058702.doi: 10.1088/1674-1056/ac598b

Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

Jian-Gang Wang(王建港)^1,2, Xiao-Xuan Shi(史晓璇)^1,2, Yu-Ru Liu(刘玉如)², Peng-Ye Wang(王鹏业)², Hong Chen(陈洪)^1,†, and Ping Xie(谢平)^2,‡

1 School of Material Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China;
2 Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China

收稿日期:2022-01-07 修回日期:2022-02-20 发布日期:2022-04-29
通讯作者: Hong Chen,E-mail:hchen2017@163.com;Ping Xie,E-mail:pxie@aphy.iphy.ac.cn E-mail:hchen2017@163.com;pxie@aphy.iphy.ac.cn

Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

Jian-Gang Wang(王建港)^1,2, Xiao-Xuan Shi(史晓璇)^1,2, Yu-Ru Liu(刘玉如)², Peng-Ye Wang(王鹏业)², Hong Chen(陈洪)^1,†, and Ping Xie(谢平)^2,‡

1 School of Material Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China;
2 Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China

Received:2022-01-07 Revised:2022-02-20 Published:2022-04-29
Contact: Hong Chen,E-mail:hchen2017@163.com;Ping Xie,E-mail:pxie@aphy.iphy.ac.cn E-mail:hchen2017@163.com;pxie@aphy.iphy.ac.cn
About author:2022-3-2

1. 2022-058702-SI.pdf(5590KB)

摘要/Abstract

摘要： Kinesin is a molecular motor that can step processively on microtubules via the hydrolysis of ATP molecules. An important factor characterizing the processivity of the kinesin motor is its dissociation from the microtubule. Here, using all-atom molecular dynamics simulations, we studied the dissociation process of the kinesin head in weak-microtubule-binding or ADP state from tubulin on the basis of the available high-resolution structural data for the head and tubulin. By analyzing the simulated snapshots of the structure of the head-tubulin complex we provided detailed structural and dynamic information for the dissociation process. We found that the dissociation of the head along different directions relative to the tubulin exhibits very different dynamic behaviors. Moreover, the potential forms or energy landscapes of the interaction between the head and tubulin along different directions were determined. The studies have important implications for the detailed molecular mechanism of the dissociation of the kinesin motor and thus are critical to the mechanism of its processivity.

关键词: kinesin, dissociation, energy landscape, molecular dynamics simulation

Abstract: Kinesin is a molecular motor that can step processively on microtubules via the hydrolysis of ATP molecules. An important factor characterizing the processivity of the kinesin motor is its dissociation from the microtubule. Here, using all-atom molecular dynamics simulations, we studied the dissociation process of the kinesin head in weak-microtubule-binding or ADP state from tubulin on the basis of the available high-resolution structural data for the head and tubulin. By analyzing the simulated snapshots of the structure of the head-tubulin complex we provided detailed structural and dynamic information for the dissociation process. We found that the dissociation of the head along different directions relative to the tubulin exhibits very different dynamic behaviors. Moreover, the potential forms or energy landscapes of the interaction between the head and tubulin along different directions were determined. The studies have important implications for the detailed molecular mechanism of the dissociation of the kinesin motor and thus are critical to the mechanism of its processivity.

Key words: kinesin, dissociation, energy landscape, molecular dynamics simulation

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

87.16.Nn

87.15.rs (Dissociation) 87.10.Tf (Molecular dynamics simulation)

Jian-Gang Wang(王建港), Xiao-Xuan Shi(史晓璇), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业),Hong Chen(陈洪), and Ping Xie(谢平). Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations[J]. 中国物理B, 2022, 31(5): 58702-058702.

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Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

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