CoChat
Sign Up
Cited by 125Microtubule and mitosis dynamicsCancer Treatment and PharmacologyCellular Mechanics and Interactions

Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport

Open access
Shima, Tomohiro, Morikawa, Manatsu, Kaneshiro, Junichi, Kambara, Taketoshi, Kamimura, Shinji, Yagi, Toshiki, Iwamoto, Hiroyuki, Uemura, Sotaro +7 more·2018·Journal of Cell Biology
DOI 10.1083/jcb.201711178PMC PMC6279379
Open this paper in CoChat — free account

Abstract

Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly understood. Here, we report that kinesin-1 binding changes the microtubule lattice and promotes further kinesin-1 binding. This high-affinity state requires the binding of kinesin-1 in the nucleotide-free state. Microtubules return to the initial low-affinity state by washing out the binding kinesin-1 or by the binding of non-hydrolyzable ATP analogue AMPPNP to kinesin-1. X-ray fiber diffraction, fluorescence speckle microscopy, and second-harmonic generation microscopy, as well as cryo-EM, collectively demonstrated that the binding of nucleotide-free kinesin-1 to GDP microtubules changes the conformation of the GDP microtubule to a conformation resembling the GTP microtubule.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1083/jcb.201711178

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In vitro, at high concentrations in the no-nucleotide state, the kinesin-1 motor domain can extend microtubule lattice spacing, suggesting it prefers to bind to the expanded lattice conformation at lower concentrations.

    “Third, in vitro experiments have revealed that at high concentrations in the no-nucleotide state, the kinesin-1 motor domain can extend MT lattice spacing, suggesting that it prefers to bind to this expanded MT lattice conformation at lower concentrations (Peet et al., 2018; Shima et al., 2018).”

    From A live-cell marker to visualize the dynamics of stable microtubules throughout the cell cycle (2023) · cites this paper as Shima et al., 2018

  • Kinesin binding expands the microtubule lattice, suggesting that exclusive binding may arise from competition for an expanded versus compacted lattice.

    “Apart from steric clashes between tau and kinesin9,41, kinesin binding expands the microtubule lattice4,6 suggesting that exclusive binding may arise from competition for an expanded versus compacted lattice.”

    From Microtubule lattice spacing governs cohesive envelope formation of tau family proteins (2022) · cites this paper as [6]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

No references could be resolved yet.

Research works printed but not linked: 61

  1. Alushin G.M., Lander G.C., Kellogg E.H., Zhang R., Baker D., and Nogales E. 2014 High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell. 157: 1117– 1129. 10.1016/j.cell.2014.03.053 24855948 PMC4054694 · DOI · Paper page
  2. Bradke F., and Dotti C.G. 1997 Neuronal polarity: vectorial cytoplasmic flow precedes axon formation. Neuron. 19: 1175– 1186. 10.1016/S0896-6273(00)80410-9 9427242 · DOI
  3. Cao L., Wang W., Jiang Q., Wang C., Knossow M., and Gigant B. 2014 The structure of apo-kinesin bound to tubulin links the nucleotide cycle to movement. Nat. Commun. 5: 5364 10.1038/ncomms6364 25395082 · DOI
  4. Castoldi M., and Popov A.V. 2003 Purification of brain tubulin through two cycles of polymerization-depolymerization in a high-molarity buffer. Protein Expr. Purif. 32: 83– 88. 10.1016/S1046-5928(03)00218-3 14680943 · DOI
  5. Chang Q., Nitta R., Inoue S., and Hirokawa N. 2013 Structural basis for the ATP-induced isomerization of kinesin. J. Mol. Biol. 425: 1869– 1880. 10.1016/j.jmb.2013.03.004 23500491 · DOI
  6. Deng C.-Y., Lei W.-L., Xu X.-H., Ju X.-C., Liu Y., and Luo Z.-G. 2014 JIP1 mediates anterograde transport of Rab10 cargos during neuronal polarization. J. Neurosci. 34: 1710– 1723. 10.1523/JNEUROSCI.4496-13.2014 24478353 PMC8186508 · DOI
  7. Desai A., and Mitchison T.J. 1998 Preparation and characterization of caged fluorescein tubulin. Methods Enzymol. 298: 125– 132. 10.1016/S0076-6879(98)98014-4 9751877 · DOI
  8. Desai A., Murray A., Mitchison T.J., and Walczak C.E. 1999 The use of Xenopus egg extracts to study mitotic spindle assembly and function in vitro. Methods Cell Biol. 61: 385– 412. 10.1016/S0091-679X(08)61991-3 9891325 · DOI
  9. Dimitrov A., Quesnoit M., Moutel S., Cantaloube I., Poüs C., and Perez F. 2008 Detection of GTP-tubulin conformation in vivo reveals a role for GTP remnants in microtubule rescues. Science. 322: 1353– 1356. 10.1126/science.1165401 18927356 · DOI
  10. Edelstein A., Amodaj N., Hoover K., Vale R., and Stuurman N. 2010 Computer control of microscopes using µManager. Curr. Protoc. Mol. Biol. 14: 14– 14. 10.1002/0471142727.mb1420s92 PMC3065365 20890901 · DOI
  11. Eipper B.A. 1975 Purification of rat brain tubulin. Ann. N. Y. Acad. Sci. 253(1 The Biology o): 239– 246. 10.1111/j.1749-6632.1975.tb19203.x 1056743 · DOI
  12. Field C.M., Nguyen P.A., Ishihara K., Groen A.C., and Mitchison T.J. 2014 Xenopus Egg Cytoplasm with Intact Actin. Methods Enzymol. 540: 399– 415. 10.1016/B978-0-12-397924-7.00022-4 24630119 · DOI
  13. Fujisawa T., Inoue K., Oka T., Iwamoto H., Uruga T., Kumasaka T., Inoko Y., Yagi N., Yamamoto M., and Ueki T. 2000 Small-angle x-ray scattering station at the SPring-8 RIKEN beamline. J. Appl. Cryst. 33: 797– 800. 10.1107/S002188980000131X · DOI
  14. Furuta K., and Toyoshima Y.Y. 2008 Minus-end-directed motor Ncd exhibits processive movement that is enhanced by microtubule bundling in vitro. Curr. Biol. 18: 152– 157. 10.1016/j.cub.2007.12.056 18207739 · DOI · Paper page
  15. Gard D.L., and Kirschner M.W. 1987 Microtubule assembly in cytoplasmic extracts of Xenopus oocytes and eggs. J. Cell Biol. 105: 2191– 2201. 10.1083/jcb.105.5.2191 3680377 PMC2114874 · DOI
  16. Gigant B., Wang W., Dreier B., Jiang Q., Pecqueur L., Plückthun A., Wang C., and Knossow M. 2013 Structure of a kinesin-tubulin complex and implications for kinesin motility. Nat. Struct. Mol. Biol. 20: 1001– 1007. 10.1038/nsmb.2624 23872990 · DOI
  17. Grigorieff N. 2007 FREALIGN: high-resolution refinement of single particle structures. J. Struct. Biol. 157: 117– 125. 10.1016/j.jsb.2006.05.004 16828314 · DOI
  18. Grigorieff N. 2016 Frealign: An Exploratory Tool for Single-Particle Cryo-EM. Methods Enzymol. 579: 191– 226. 10.1016/bs.mie.2016.04.013 27572728 PMC6760665 · DOI
  19. Hackney D.D. 1995 Implications of diffusion-controlled limit for processivity of dimeric kinesin head domains. Biophys. J. 68: 267S– 269S. 7787088 PMC1281942
  20. Hirokawa N., Niwa S., and Tanaka Y. 2010 Molecular motors in neurons: transport mechanisms and roles in brain function, development, and disease. Neuron. 68: 610– 638. 10.1016/j.neuron.2010.09.039 21092854 · DOI · Paper page
  21. Hyman A.A., Salser S., Drechsel D.N., Unwin N., and Mitchison T.J. 1992 Role of GTP hydrolysis in microtubule dynamics: information from a slowly hydrolyzable analogue, GMPCPP. Mol. Biol. Cell. 3: 1155– 1167. 10.1091/mbc.3.10.1155 1421572 PMC275679 · DOI
  22. Hyman A.A., Chrétien D., Arnal I., and Wade R.H. 1995 Structural changes accompanying GTP hydrolysis in microtubules: information from a slowly hydrolyzable analogue guanylyl-(alpha,beta)-methylene-diphosphonate. J. Cell Biol. 128: 117– 125. 10.1083/jcb.128.1.117 7822409 PMC2120325 · DOI · Paper page
  23. Ihaka R., and Gentleman R. 1996 R: A Language for Data Analysis and Graphics. J. Comput. Graph. Stat. 5: 299– 314. 10.1080/10618600.1996.10474713 · DOI
  24. Jacobson C., Schnapp B., and Banker G.A. 2006 A change in the selective translocation of the Kinesin-1 motor domain marks the initial specification of the axon. Neuron. 49: 797– 804. 10.1016/j.neuron.2006.02.005 16543128 · DOI
  25. Kamimura S., Fujita Y., Wada Y., Yagi T., and Iwamoto H. 2016 X-ray fiber diffraction analysis shows dynamic changes in axial tubulin repeats in native microtubules depending on paclitaxel content, temperature and GTP-hydrolysis. Cytoskeleton (Hoboken). 73: 131– 144. 10.1002/cm.21283 26873786 · DOI
  26. Kaneshiro J., Okada Y., Shima T., Tsujii M., Imada K., Ichimura T., and Watanabe T.M. 2018 Second harmonic generation polarization microscopy as a tool for protein structure analysis. bioRxiv (Preprint posted June 4, 2018). 10.1101/338137 PMC6812877 31660282 · DOI
  27. Kaul N., Soppina V., and Verhey K.J. 2014 Effects of α-tubulin K40 acetylation and detyrosination on kinesin-1 motility in a purified system. Biophys. J. 106: 2636– 2643. 10.1016/j.bpj.2014.05.008 24940781 PMC4070028 · DOI
  28. Kremer J.R., Mastronarde D.N., and McIntosh J.R. 1996 Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116: 71– 76. 10.1006/jsbi.1996.0013 8742726 · DOI
  29. Kucukelbir A., Sigworth F.J., and Tagare H.D. 2014 Quantifying the local resolution of cryo-EM density maps. Nat. Methods. 11: 63– 65. 10.1038/nmeth.2727 24213166 PMC3903095 · DOI
  30. Kuznetsov S.A., and Gelfand V.I. 2001 Purification of kinesin from the brain. Methods Mol. Biol. 164: 1– 7. 10.1385/1-59259-069-1:1 11217600 · DOI
  31. Li X., Mooney P., Zheng S., Booth C.R., Braunfeld M.B., Gubbens S., Agard D.A., and Cheng Y. 2013 Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods. 10: 584– 590. 10.1038/nmeth.2472 23644547 PMC3684049 · DOI
  32. Marceiller J., Drechou A., Durand G., Perez F., and Poüs C. 2005 Kinesin is involved in protecting nascent microtubules from disassembly after recovery from nocodazole treatment. Exp. Cell Res. 304: 483– 492. 10.1016/j.yexcr.2004.12.007 15748893 · DOI
  33. Mastronarde D.N. 2005 Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152: 36– 51. 10.1016/j.jsb.2005.07.007 16182563 · DOI
  34. Metlagel Z., Kikkawa Y.S., and Kikkawa M. 2007 Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language. J. Struct. Biol. 157: 95– 105. 10.1016/j.jsb.2006.07.015 16996276 · DOI
  35. Mindell J.A., and Grigorieff N. 2003 Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142: 334– 347. 10.1016/S1047-8477(03)00069-8 12781660 · DOI
  36. Mitchison T., and Kirschner M. 1984 Dynamic instability of microtubule growth. Nature. 312: 237– 242. 10.1038/312237a0 6504138 · DOI · Paper page
  37. Morikawa M., Yajima H., Nitta R., Inoue S., Ogura T., Sato C., and Hirokawa N. 2015 X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding. EMBO J. 34: 1270– 1286. 10.15252/embj.201490588 25777528 PMC4426485 · DOI
  38. Muto E., Sakai H., and Kaseda K. 2005 Long-range cooperative binding of kinesin to a microtubule in the presence of ATP. J. Cell Biol. 168: 691– 696. 10.1083/jcb.200409035 15738263 PMC2171822 · DOI
  39. Nakata T., and Hirokawa N. 2003 Microtubules provide directional cues for polarized axonal transport through interaction with kinesin motor head. J. Cell Biol. 162: 1045– 1055. 10.1083/jcb.200302175 12975348 PMC2172855 · DOI
  40. Nakata T., Niwa S., Okada Y., Perez F., and Hirokawa N. 2011 Preferential binding of a kinesin-1 motor to GTP-tubulin-rich microtubules underlies polarized vesicle transport. J. Cell Biol. 194: 245– 255. 10.1083/jcb.201104034 21768290 PMC3144414 · DOI · Paper page
  41. Ngo K.X., Kodera N., Katayama E., Ando T., and Uyeda T.Q. 2015 Cofilin-induced unidirectional cooperative conformational changes in actin filaments revealed by high-speed atomic force microscopy. eLife. 4: e04806 10.7554/eLife.04806 PMC4337605 25642645 · DOI
  42. Ngo K.X., Umeki N., Kijima S.T., Kodera N., Ueno H., Furutani-Umezu N., Nakajima J., Noguchi T.Q.P., Nagasaki A., Tokuraku K., and Uyeda T.Q.P. 2016 Allosteric regulation by cooperative conformational changes of actin filaments drives mutually exclusive binding with cofilin and myosin. Sci. Rep. 6: 35449 10.1038/srep35449 27762277 PMC5071871 · DOI
  43. Nitta R., Kikkawa M., Okada Y., and Hirokawa N. 2004 KIF1A alternately uses two loops to bind microtubules. Science. 305: 678– 683. 10.1126/science.1096621 15286375 · DOI
  44. Okada Y., and Hirokawa N. 1999 A processive single-headed motor: kinesin superfamily protein KIF1A. Science. 283: 1152– 1157. 10.1126/science.283.5405.1152 10024239 · DOI · Paper page
  45. Okada Y., Yamazaki H., Sekine-Aizawa Y., and Hirokawa N. 1995 The neuron-specific kinesin superfamily protein KIF1A is a unique monomeric motor for anterograde axonal transport of synaptic vesicle precursors. Cell. 81: 769– 780. 10.1016/0092-8674(95)90538-3 7539720 · DOI
  46. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. 2004 UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem. 25: 1605– 1612. 10.1002/jcc.20084 15264254 · DOI
  47. Plotnikov S.V., Millard A.C., Campagnola P.J., and Mohler W.A. 2006 Characterization of the myosin-based source for second-harmonic generation from muscle sarcomeres. Biophys. J. 90: 693– 703. 10.1529/biophysj.105.071555 16258040 PMC1367074 · DOI
  48. Psilodimitrakopoulos S., Petegnief V., de Vera N., Hernandez O., Artigas D., Planas A.M., and Loza-Alvarez P. 2013 Quantitative imaging of microtubule alteration as an early marker of axonal degeneration after ischemia in neurons. Biophys. J. 104: 968– 975. 10.1016/j.bpj.2013.01.020 23473479 PMC3870801 · DOI
  49. Reed N.A., Cai D., Blasius T.L., Jih G.T., Meyhofer E., Gaertig J., and Verhey K.J. 2006 Microtubule acetylation promotes kinesin-1 binding and transport. Curr. Biol. 16: 2166– 2172. 10.1016/j.cub.2006.09.014 17084703 · DOI · Paper page
  50. Scheres S.H.W. 2012 RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180: 519– 530. 10.1016/j.jsb.2012.09.006 23000701 PMC3690530 · DOI · Paper page
  51. Schneider G., Chicken E., and Becvarik R. 2018 NSM3: Functions and Datasets to Accompany Hollander, Wolfe, and Chicken. Nonparametric Statistical Methods, Third edition, R package version 1.12. https://CRAN.R-roject.org/package=NSM3 (accessed May 7, 2018).
  52. Scrucca L., Fop M., Murphy T.B., and Raftery A.E. 2016 mclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models. R J. 8: 289– 317. 27818791 PMC5096736
  53. Tahirovic S., and Bradke F. 2009 Neuronal polarity. Cold Spring Harb. Perspect. Biol. 1: a001644 10.1101/cshperspect.a001644 20066106 PMC2773638 · DOI
  54. Uchida M., Mouriño-Pérez R.R., Freitag M., Bartnicki-García S., and Roberson R.W. 2008 Microtubule dynamics and the role of molecular motors in Neurospora crassa. Fungal Genet. Biol. 45: 683– 692. 10.1016/j.fgb.2007.10.013 18069024 · DOI
  55. Umeki N., Hirose K., and Uyeda T.Q.P. 2016 Cofilin-induced cooperative conformational changes of actin subunits revealed using cofilin-actin fusion protein. Sci. Rep. 6: 20406 10.1038/srep20406 26842224 PMC4740740 · DOI
  56. Van Heel M. 1987 Similarity measures Between Images. Ultramicroscopy. 21: 95– 100. 10.1016/0304-3991(87)90010-6 · DOI
  57. Vilfan A., Frey E., Schwabl F., Thormählen M., Song Y.H., and Mandelkow E. 2001 Dynamics and cooperativity of microtubule decoration by the motor protein kinesin. J. Mol. Biol. 312: 1011– 1026. 10.1006/jmbi.2001.5020 11580246 · DOI
  58. Yajima H., Ogura T., Nitta R., Okada Y., Sato C., and Hirokawa N. 2012 Conformational changes in tubulin in GMPCPP and GDP-taxol microtubules observed by cryoelectron microscopy. J. Cell Biol. 198: 315– 322. 10.1083/jcb.201201161 22851320 PMC3413364 · DOI
  59. Yokota H., Han Y.-W., Allemand J.-F., Xi X.G., Bensimon D., Croquette V., Ito Y., and Harada Y. 2009 Single-molecule Visualization of Binding Modes of Helicase to DNA on PEGylated Surfaces. Chem. Lett. 38: 308– 309. 10.1246/cl.2009.308 · DOI
  60. Zhang R., and Nogales E. 2015 A new protocol to accurately determine microtubule lattice seam location. J. Struct. Biol. 192: 245– 254. 10.1016/j.jsb.2015.09.015 26424086 PMC4634897 · DOI
  61. Zhang R., Alushin G.M., Brown A., and Nogales E. 2015 Mechanistic origin of microtubule dynamic instability and its modulation by EB proteins. Cell. 162: 849– 859. 10.1016/j.cell.2015.07.012 26234155 PMC4537847 · DOI · Paper page

Cited by

Sorted by citations

Authors
Shima, T., Morikawa, M., Kaneshiro, J., Kambara, T., Kamimura, S., Yagi, T., Iwamoto, H., Uemura, S., Shigematsu, H., Shirouzu, M., Ichimura, T., Watanabe, T. M., Nitta, R., Okada, Y., & Hirokawa, N.
Affiliations
  • RIKEN Center for Biosystems Dynamics Research (JP)
  • The University of Tokyo (JP)
  • Chuo University (JP)
  • Prefectural University of Hiroshima (JP)
  • Japan Synchrotron Radiation Research Institute (JP)
  • King Abdulaziz University (SA)
Corresponding author
Okada, Yasushi
ORCID
Venue
Journal of Cell Biology
Publisher
Rockefeller University Press
Published
2018-10-08
Volume
217
Issue
12
Pages
4164-4183
ISSN
  • 0021-9525 (ISSN-L)
  • 1540-8140
DOI
10.1083/jcb.201711178
PMC
PMC6279379
OpenAlex
W2899644340
Cited by
125
References
0
Citations by year
2026: 15 · 2025: 17 · 2024: 15 · 2023: 16 · 2022: 18 · 2021: 18 · 2020: 14 · 2019: 11 · 2018: 1
FWCI
6.10
Type
journal article
Language
en
Open access
Licence
Locations
  • The Journal of Cell Biology (publishedVersion, cc-by-nc-sa)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
  • PubMed Central (publishedVersion, cc-by-nc-sa)
  • PubMed (publishedVersion)
Funders
  • Ministry of Education, Culture, Sports, Science and Technology (23000013, 16H06372, 16H05119, 15H01334, 26115721, 26650069, 25293046, 15H01656, 17H05897, 15K08168)
  • Uehara Memorial Foundation
  • Takeda Science Foundation
  • Mochida Memorial Foundation for Medical and Pharmaceutical Research
  • RIKEN
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
  • Health Sciences › Medicine › Oncology › Cancer Treatment and Pharmacology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular Mechanics and Interactions
Keywords
kinesin-1, polarized transport, microtubule lattice, AMP-PNP, neuronal transport
MeSH terms
Adenylyl Imidodiphosphate, Animals, Biological Transport, Active, Chlorocebus aethiops, Dogs, Guanosine Diphosphate, Guanosine Triphosphate, HeLa Cells, Humans, Microtubules, Vero Cells, Kinesins, Madin Darby Canine Kidney Cells

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review