Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule

doi:10.1088/1674-1056/24/8/080701

中国物理B ›› 2015, Vol. 24 ›› Issue (8): 80701-080701.doi: 10.1088/1674-1056/24/8/080701

Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule

H. R. Saeidi^a, S. S. Setayandeh^a, A. Lohrasebi^{a b}

a Department of Physics, University of Isfahan, Isfahan, Iran;
b Computational Nano-Bioelectromagnetics Research Group, School of Nano-Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran

收稿日期:2014-09-24 修回日期:2015-03-14 出版日期:2015-08-05 发布日期:2015-08-05

Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule

H. R. Saeidi^a, S. S. Setayandeh^a, A. Lohrasebi^{a b}

a Department of Physics, University of Isfahan, Isfahan, Iran;
b Computational Nano-Bioelectromagnetics Research Group, School of Nano-Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran

Received:2014-09-24 Revised:2015-03-14 Online:2015-08-05 Published:2015-08-05
Contact: A. Lohrasebi E-mail:lohrasebi@nano.ipm.ac.ir

摘要/Abstract

摘要： Kinesin is a microtubule-associated motor protein which can respond to the external electric field due to its polarity. Using a molecular dynamics simulation method, the effect of such a field on the affinity of kinesin to the αβ-tubulin is investigated in this study. To consider kinesin affinity, the system is exposed to an electric field of 0.03 V/nm with frequency values of 1, 2,..., 9, and 10 GHz. It is found that the applied electric field can change kinesin affinity to the microtubule. These changes could perturb the normal operation of kinesin, such as the processive motility of kinesin on the microtubule.

关键词: kinesin affinity, oscillating electric field, molecular dynamic, αβ-tubulin dimer

Abstract: Kinesin is a microtubule-associated motor protein which can respond to the external electric field due to its polarity. Using a molecular dynamics simulation method, the effect of such a field on the affinity of kinesin to the αβ-tubulin is investigated in this study. To consider kinesin affinity, the system is exposed to an electric field of 0.03 V/nm with frequency values of 1, 2,..., 9, and 10 GHz. It is found that the applied electric field can change kinesin affinity to the microtubule. These changes could perturb the normal operation of kinesin, such as the processive motility of kinesin on the microtubule.

Key words: kinesin affinity, oscillating electric field, molecular dynamic, αβ-tubulin dimer

中图分类号: (Computer modeling and simulation)

07.05.Tp

76.60.-k (Nuclear magnetic resonance and relaxation) 87.15.R- (Reactions and kinetics) 87.10.Tf (Molecular dynamics simulation)

H. R. Saeidi, S. S. Setayandeh, A. Lohrasebi. Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule[J]. 中国物理B, 2015, 24(8): 80701-080701.

H. R. Saeidi, S. S. Setayandeh, A. Lohrasebi. Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule[J]. Chin. Phys. B, 2015, 24(8): 80701-080701.

参考文献 23

[1]	Dodding M P and Way M 2011 Embo Journal 30 3527
[2]	Schnitzer M J, Visscher K and Block S M 2000 Nature Cell Biology 2 718
[3]	Goulet A, Behnke-Parks W, Sindelar C, Major J, Rosenfeld S and Moores C 2012 Biol. Chem. 287 44654
[4]	Krukau A, Knecht V and Lipowsky R 2014 Phys. Chem. 16 6189
[5]	Geng Y Z, Zhang H, Ji Q and Yan S W 2014 Chin. Phys. Lett. 31 048702
[6]	Nitta R, Kikkawa M, Okada Y and Hirokawa N 2004 Science 305 678
[7]	Hirokawa N and Takemura R 2005 Nat. Rev. Neurosci. 6 201
[8]	Roostalu J, Hentrich C, Bieling P, Telley I A, Schiebel E and Surrey T 2011 Science 332 6025
[9]	Asbury C L, Fehr A N and Block S M 2003 Science 302 2130
[10]	Shao Q and Gao Y Q 2006 Proc. Natl. Acad. Sci. USA 103 8072
[11]	Xie P, Dou S X and Wang P Y 2005 Chin. Phys. 14 734
[12]	Jamali Y, Lohrasebi A and Rafii-Tabar H 2007 Physica A 381 239
[13]	Falzone N, Huyser C, Becker P, Leszczynski D and Franken D R 2011 Int. J. Andrology 34 20
[14]	Kesari K K, Kumar S, Nirala J, Siddiqui M H and Behari J 2013 Cell Biochem. Biophys. 65 285
[15]	Lin Y, Lin J and Chang C 2010 Biophys. 98 1009
[16]	Mailankot M, Kunnath A P, Jayalekshmi H, Koduru B and Valsalan R 2009 Clinics 64 561
[17]	Pall M L 2013 J. Cell. Mol. Med. 17 958
[18]	Rahbek U L, Tritsaris K and Dissing S 2005 Interactions 2 29
[19]	Saeidi H R, Lohrasebi A and Mahnam K 2014 J. Mol. Mod. 20 2395
[20]	Setayandeh S S and Lohrasebi A 2015 J. Mol. Mod. 21 85
[21]	Sajadi M, Lohrasebi A and Rafii-Tabar H 2013 Mol. Simul. 5 399
[22]	Singh A, Orsat V and Raghavan V 2013 Biomolecules 3 168
[23]	Hess B, Kutzner C, Van der Spoel D and Lindahl E 2008 J. Chem. Theor. Comput. 4 435

Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule

Molecular modeling of oscillating GHz electric field influence on the kinesin affinity to microtubule

RichHTML

PDF (PC)

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献 23

相关文章 15

Metrics

本文评价

推荐阅读 0

[1]	Tao-Wen Xiong(熊涛文), Xiao-Ping Chen(陈小平), Ye-Ping Lin(林也平), Xin-Fu He(贺新福), Wen Yang(杨文), Wang-Yu Hu(胡望宇), Fei Gao(高飞), and Hui-Qiu Deng(邓辉球). Molecular dynamics study of interactions between edge dislocation and irradiation-induced defects in Fe–10Ni–20Cr alloy[J]. 中国物理B, 2023, 32(2): 20206-020206.
[2]	Zilin Wang(王梓霖), Liang Yang(杨亮), Changsheng Liu(刘长生), and Shiwei Lin(林仕伟). Formation of nanobubbles generated by hydrate decomposition: A molecular dynamics study[J]. 中国物理B, 2023, 32(2): 23101-023101.
[3]	Long Zhou(周龙), Xu-Long Zhang(张旭龙), Yu-Ying Cao(曹玉莹), Fu Zheng(郑富), Hua Gao(高华), Hong-Fei Liu(刘红飞), and Zhi Ma(马治). Prediction of flexoelectricity in BaTiO₃ using molecular dynamics simulations[J]. 中国物理B, 2023, 32(1): 17701-017701.
[4]	Mengjiao Wu(吴梦娇), Huishu Ma(马慧姝), Haiping Fang(方海平), Li Yang(阳丽), and Xiaoling Lei(雷晓玲). Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions[J]. 中国物理B, 2023, 32(1): 18701-018701.
[5]	Tzu-Chia Chen, Mahyuddin KM Nasution, Abdullah Hasan Jabbar, Sarah Jawad Shoja, Waluyo Adi Siswanto, Sigiet Haryo Pranoto, Dmitry Bokov, Rustem Magizov, Yasser Fakri Mustafa, A. Surendar, Rustem Zalilov, Alexandr Sviderskiy, Alla Vorobeva, Dmitry Vorobyev, and Ahmed Alkhayyat. Effect of spatial heterogeneity on level of rejuvenation in Ni₈₀P₂₀ metallic glass[J]. 中国物理B, 2022, 31(9): 96401-096401.
[6]	Shiheng Cui(崔世恒), Huashan Liu(刘华山), and Hailong Peng(彭海龙). Spatial correlation of irreversible displacement in oscillatory-sheared metallic glasses[J]. 中国物理B, 2022, 31(8): 86108-086108.
[7]	Yongqin Zhang(张永钦), Hua Yang(杨华), Yaguang Sun(孙亚光),Xiangrui Zheng(郑香蕊), and Yafang Guo(郭雅芳). Molecular dynamics simulations of mechanical properties of epoxy-amine: Cross-linker type and degree of conversion effects[J]. 中国物理B, 2022, 31(6): 64209-064209.
[8]	Ning Wei(魏宁), Ai-Qiang Shi(史爱强), Zhi-Hui Li(李志辉), Bing-Xian Ou(区炳显), Si-Han Zhao(赵思涵), and Jun-Hua Zhao(赵军华). Effect of void size and Mg contents on plastic deformation behaviors of Al-Mg alloy with pre-existing void: Molecular dynamics study[J]. 中国物理B, 2022, 31(6): 66203-066203.
[9]	Yuanyuan Tian(田圆圆), Gangjie Luo(罗港杰), Qihong Fang(方棋洪), Jia Li(李甲), and Jing Peng(彭静). Strengthening and softening in gradient nanotwinned FCC metallic multilayers[J]. 中国物理B, 2022, 31(6): 66204-066204.
[10]	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.
[11]	Song Hu(胡松), C Y Zhao(赵长颖), and Xiaokun Gu(顾骁坤). Impact of thermostat on interfacial thermal conductance prediction from non-equilibrium molecular dynamics simulations[J]. 中国物理B, 2022, 31(5): 56301-056301.
[12]	Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强). Evaluation on performance of MM/PBSA in nucleic acid-protein systems[J]. 中国物理B, 2022, 31(4): 48701-048701.
[13]	Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日), and Wenjun Zong(宗文军). Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution[J]. 中国物理B, 2022, 31(4): 48702-048702.
[14]	Yutao Liu(刘玉涛), Tinghong Gao(高廷红), Yue Gao(高越), Lianxin Li(李连欣), Min Tan(谭敏), Quan Xie(谢泉), Qian Chen(陈茜), Zean Tian(田泽安), Yongchao Liang(梁永超), and Bei Wang(王蓓). Evolution of defects and deformation mechanisms in different tensile directions of solidified lamellar Ti-Al alloy[J]. 中国物理B, 2022, 31(4): 46105-046105.
[15]	Rangyue Zhang(张壤月), Guannan Shi(史冠男), Hanyu Tang(唐瀚宇), Yang Liu(刘阳), Yanhong Liu(刘艳红), and Feng Huang(黄峰). Effect of the number of defect particles on the structure and dispersion relation of a two-dimensional dust lattice system[J]. 中国物理B, 2022, 31(3): 35204-035204.