Based on the crystal structure of a kinesin motor(1BG2)and tubulin(1TUB),the electric potential distribution on the surface of the motor head and the tubulin is obtained by electrostatic calculation,and the electrostatic interactions between the microtubule and the positive potential regions of kinesin are analyzed by comparing the crystal structures of them.Furthermore,through simulation by solving Poisson's equation,the electrostatic interactions of kinesin along the microtubule have been calculated,the results show that microtubule provides a periodic potential field for motor movement,and the period is consistent with that of the kinesin steps.Then combined with the calculated results, we present the electrostatic mechanism of kinesin movement.
HUANG Yanbin
,
GUO Haijun
,
LI Jie
,
LIU Xiuhong
,
JI Qing
. Effects of electrostatic interactions on the movement of kinesin[J]. Journal of Hebei University(Natural Science Edition), 2017
, 37(3)
: 237
-242
.
DOI: 10.3969/j.issn.1000-1565.2017.03.003
[1] HIROKAWA N,NODA Y,TANAKA Y,et al.Kinesin superfamily motor proteins and intracellular transport[J].Nature Reviews Molecular Cell Biology,2009,10(10):682-696.DOI:10.1038/nrm2774.
[2] MORFINI G,SCHMIDT N,WEISSMAN C,et al.Conventional kinesin:Biochemical heterogeneity and functional implications in health and disease[J].Brain Research Bulletin,2016,126:347-353.DOI:10.1016/j.brainresbull.2016.06.009.
[3] HIROKAWA N,TANAKA Y.Kinesin superfamily proteins(KIFs):Various functions and their relevance for important phenomena in life and diseases[J].Experimental Cell Research,2015,334(1):16-25.DOI:10.1016/j.yexcr.2015.02.016.
[4] MYERS S M,COLLINS I.Recent findings and future directions for interpolar mitotic kinesin inhibitors in cancer therapy[J].Future Medicinal Chemistry,2016,8(4):463-489.DOI:10.4155/fmc.16.5.
[5] ISOJIMA H,IINO R,NIITANI Y,et al.Direct observation of intermediate states during the stepping motion of kinesin-1[J].Nature Chemical Biology,2016,12(4):290-297.DOI:10.1038/nchembio.2028.
[6] KANADA R,KUWATA T,KENZAKI H,et al.Structure-based molecular simulations reveal the enhancement of biased brownian motions in single-headed kinesin[J].Plos Computational Biology,2013,9(2):e1002907.DOI:10.1371/journal.pcbi.1002907.
[7] MALEKI M,VASUDEV G,RUEDA L.The role of electrostatic energy in prediction of obligate protein-protein interactions[J].Proteome Science,2013,11(1):1-12.DOI:10.1186/1477-5956-11-S1-S11.
[8] DE JESUS M C,INGLE B L,BARAKAT K A,et al.The role of strong electrostatic interactions at the dimer interface of human glutathione synthetase.[J].The Protein Journal,2014,33(5):403-409.DOI:10.1007/s10930-014-9573-y.
[9] BENMAN H M,WESTBROOK J,FENG Z,et al.The protein data bank[J].Nucleic Acids Research,2000,28(1):235-242.DOI:10.1093/nar/28.1.235.
[10] KULL F J,SABLIN E P,LAU R,et al.Crystal structure of the kinesin motor domain reveals a structural similarity to myosin[J].Nature,1996,380(6574):550-555.DOI:10.1038/380550a0.
[11] NOGALES E,WOLF S G,DOWNING K H.Structure of the alpha beta tubulin dimer by electron crystallography[J].Nature,1998,391(6663):199-203.DOI:10.1038/34465.
[12] KIKKAWA M,HIROKAWA N.High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations[J].Embo Journal,2006,25(18):4187-4194.DOI:10.1038/sj.emboj.7601299.
[13] KIKKAWA M,SABLIN E P,OKADA Y,et al.Switch-based mechanism of kinesin motors[J].Nature,2001,411(6836):439-445.DOI:10.1038/35078000.
[14] BAKER N A,SEPT D,JOSEPH S,et al.Electrostatics of nanosystems:application to microtubules and the ribosome.[J].PNAS,2001,98(18):10037-10041.DOI:10.1073/pnas.181342398.
[15] YAN L.Electrostatic correlations:from plasma to biology[J].Reports on Progress in Physics,2002,65(11):1577-1632.DOI:http://dx.doi.org/10.1088/0034-4885/65/11/201.
[16] ZHANG L Q,BORTHAKUR S,BUCK M.Dissociation of a dynamic protein complex studied by all-atom molecular simulations.[J].Biophysical Journal,2016,110(4):877-886.DOI:10.1016/j.bpj.2015.12.036.
[17] MCCAMMON J A.Darwinian biophysics:Electrostatics and evolution in the kinetics of molecular binding[J].PNAS,2009,106(19):7683-7684.DOI:10.1073/pnas.0902767106.
[18] HIROKAWA N,NITTA R,OKADA Y.The mechanisms of kinesin motor motility:lessons from the monomeric motor KIF1A[J].Nature Reviews Molecular Cell Biology,2009,10(12):877-884.DOI:10.1038/nrm2807.
[19] ATHERTON J,FARABELLA I,YU I M,et al.Conserved mechanisms of microtubule-stimulated ADP release,ATP binding,and force generation in transport kinesins[J].Elife Sciences,2014,3(5):1209-1224.DOI:10.7554/eLife.03680.
[20] ZHENG W J,CHAKRABORTY S.Decrypting the structural,dynamic and energetic basis of kinesin interacting with tubulin dimer in three atpase states by all-atom molecular dynamics simulation[J].Biochemistry,2015,54(3):859-869.DOI:10.1021/bi501056h.
[21] ZHAO Y C,KULL F J,COCHRAN J C.Modulation of the kinesin ATPase cycle by neck linker docking and microtubule binding[J].Journal of Biological Chemistry,2010,285(33):25213-25220.DOI:10.1074/jbc.M110.123067.
[22] WANG L,SIU S W,GU W,et al.Downhill binding energy surface of the barnase-barstar complex [J].Biopolymers,2010,93(11):977-985.DOI:10.1002/bip.21507.