Directionality of dynein is controlled by the angle and length of its stalk

Can, Sinan; Lacey, Samuel; Gur, Mert; Carter, Andrew P.; Yildiz, Ahmet

doi:10.1038/s41586-019-0914-z

Title: Directionality of dynein is controlled by the angle and length of its stalk

Journal Article · Wed Feb 06 00:00:00 EST 2019 · Nature (London)

DOI:https://doi.org/10.1038/s41586-019-0914-z· OSTI ID:1571970

Can, Sinan ^[1]; Lacey, Samuel ^[2]; Gur, Mert ^[3]; Carter, Andrew P. ^[2]; Yildiz, Ahmet ^[4]

Univ. of California, Berkeley, CA (United States). Dept. of Physics
Medical Research Council, Lab. of Molecular Biology, Division of Structural Studies, Cambridge (United Kingdom)
Istanbul Technical Univ., Istanbul, Turkey). Dept. of Mechanical Engineering
Univ. of California, Berkeley, CA (United States). Dept. of Physics; Univ. of California, Berkeley, CA (United States). Dept. of Molecular and Cellular Biology

The ability of cytoskeletal motors to move unidirectionally along filamentous tracks is central to their role in cargo transport, motility and cell division. Kinesin and myosin motor families have a subclass that moves towards the opposite end of the microtubule or actin filament with respect to the rest of the motor family, whereas all dynein motors that have been studied so far exclusively move towards the minus end of the microtubule. Guided by cryo-electron microscopy and molecular dynamics simulations, we sought to understand the mechanism that underpins the directionality of dynein by engineering a Saccharomyces cerevisiae dynein that is directed towards the plus end of the microtubule. Here, using single-molecule assays, we show that elongation or shortening of the coiled-coil stalk that connects the motor to the microtubule controls the helical directionality of dynein around microtubules. By changing the length and angle of the stalk, we successfully reversed the motility towards the plus end of the microtubule. These modifications act by altering the direction in which the dynein linker swings relative to the microtubule, rather than by reversing the asymmetric unbinding of the motor from the microtubule. Lastly, because the length and angle of the dynein stalk are fully conserved among species, our findings provide an explanation for why all dyneins move towards the minus end of the microtubule.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1571970

Journal Information:: Nature (London), Vol. 566, Issue 7744; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 24 works

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References (35)

Direction determination in the minus-end-directed kinesin motor ncd Sablin, Elena P.; Case, Ryan B.; Dai, Shirleko C. Nature, Vol. 395, Issue 6704 https://doi.org/10.1038/27463	journal	October 1998
Targeted molecular dynamics: A new approach for searching pathways of conformational transitions Schlitter, J.; Engels, M.; Krüger, P. Journal of Molecular Graphics, Vol. 12, Issue 2 https://doi.org/10.1016/0263-7855(94)80072-3	journal	June 1994
Structure and Functional Role of Dynein's Microtubule-Binding Domain Carter, A. P.; Garbarino, J. E.; Wilson-Kubalek, E. M. Science, Vol. 322, Issue 5908 https://doi.org/10.1126/science.1164424	journal	December 2008
The 2.8 Å crystal structure of the dynein motor domain Kon, Takahide; Oyama, Takuji; Shimo-Kon, Rieko Nature, Vol. 484, Issue 7394 https://doi.org/10.1038/nature10955	journal	March 2012
Helix sliding in the stalk coiled coil of dynein couples ATPase and microtubule binding Kon, Takahide; Imamula, Kenji; Roberts, Anthony J. Nature Structural & Molecular Biology, Vol. 16, Issue 3 https://doi.org/10.1038/nsmb.1555	journal	February 2009
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
Structure of human cytoplasmic dynein-2 primed for its power stroke Schmidt, Helgo; Zalyte, Ruta; Urnavicius, Linas Nature, Vol. 518, Issue 7539 https://doi.org/10.1038/nature14023	journal	December 2014
Dynein achieves processive motion using both stochastic and coordinated stepping Qiu, Weihong; Derr, Nathan D.; Goodman, Brian S. Nature Structural & Molecular Biology, Vol. 19, Issue 2 https://doi.org/10.1038/nsmb.2205	journal	January 2012
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ ₁ and χ ₂ Dihedral Angles Best, Robert B.; Zhu, Xiao; Shim, Jihyun Journal of Chemical Theory and Computation, Vol. 8, Issue 9 https://doi.org/10.1021/ct300400x	journal	August 2012
An extended microtubule-binding structure within the dynein motor domain Gee, Melissa A.; Heuser, John E.; Vallee, Richard B. Nature, Vol. 390, Issue 6660 https://doi.org/10.1038/37663	journal	December 1997
Cytoplasmic dynein transports cargos via load-sharing between the heads Belyy, Vladislav; Hendel, Nathan L.; Chien, Alexander Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6544	journal	November 2014
The power stroke of myosin VI and the basis of reverse directionality Bryant, Zev; Altman, David; Spudich, James A. Proceedings of the National Academy of Sciences, Vol. 104, Issue 3 https://doi.org/10.1073/pnas.0610144104	journal	December 2006
Structural mechanism of the dynein power stroke Lin, Jianfeng; Okada, Kyoko; Raytchev, Milen Nature Cell Biology, Vol. 16, Issue 5 https://doi.org/10.1038/ncb2939	journal	April 2014
High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis Alushin, Gregory M.; Lander, Gabriel C.; Kellogg, Elizabeth H. Cell, Vol. 157, Issue 5 https://doi.org/10.1016/j.cell.2014.03.053	journal	May 2014
Functions and mechanics of dynein motor proteins Roberts, Anthony J.; Kon, Takahide; Knight, Peter J. Nature Reviews Molecular Cell Biology, Vol. 14, Issue 11 https://doi.org/10.1038/nrm3667	journal	September 2013
Creating biomolecular motors based on dynein and actin-binding proteins Furuta, Akane; Amino, Misako; Yoshio, Maki Nature Nanotechnology, Vol. 12, Issue 3 https://doi.org/10.1038/nnano.2016.238	journal	November 2016
Single-Molecule Analysis of Dynein Processivity and Stepping Behavior Reck-Peterson, Samara L.; Yildiz, Ahmet; Carter, Andrew P. Cell, Vol. 126, Issue 2 https://doi.org/10.1016/j.cell.2006.05.046	journal	July 2006
Optical trapping Neuman, Keir C.; Block, Steven M. Review of Scientific Instruments, Vol. 75, Issue 9 https://doi.org/10.1063/1.1785844	journal	September 2004
Force-Induced Bidirectional Stepping of Cytoplasmic Dynein Gennerich, Arne; Carter, Andrew P.; Reck-Peterson, Samara L. Cell, Vol. 131, Issue 5 https://doi.org/10.1016/j.cell.2007.10.016	journal	November 2007
Insights into dynein motor domain function from a 3.3-Å crystal structure Schmidt, Helgo; Gleave, Emma S.; Carter, Andrew P. Nature Structural & Molecular Biology, Vol. 19, Issue 5 https://doi.org/10.1038/nsmb.2272	journal	March 2012
Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules Imai, Hiroshi; Shima, Tomohiro; Sutoh, Kazuo Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9179	journal	September 2015
Kinesin’s Front Head Is Gated by the Backward Orientation of Its Neck Linker Dogan, Merve Yusra; Can, Sinan; Cleary, Frank B. Cell Reports, Vol. 10, Issue 12 https://doi.org/10.1016/j.celrep.2015.02.061	journal	March 2015
Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization Yildiz, A. Science, Vol. 300, Issue 5628 https://doi.org/10.1126/science.1084398	journal	June 2003
Cytoplasmic dynein regulates its attachment to microtubules via nucleotide state-switched mechanosensing at multiple AAA domains Nicholas, Matthew P.; Berger, Florian; Rao, Lu Proceedings of the National Academy of Sciences, Vol. 112, Issue 20 https://doi.org/10.1073/pnas.1417422112	journal	May 2015
Angular measurements of the dynein ring reveal a stepping mechanism dependent on a flexible stalk Lippert, Lisa G.; Dadosh, Tali; Hadden, Jodi A. Proceedings of the National Academy of Sciences, Vol. 114, Issue 23 https://doi.org/10.1073/pnas.1620149114	journal	May 2017
Cytoplasmic Dynein Moves Through Uncoordinated Stepping of the AAA+ Ring Domains DeWitt, M. A.; Chang, A. Y.; Combs, P. A. Science, Vol. 335, Issue 6065 https://doi.org/10.1126/science.1215804	journal	December 2011
AAA+ Ring and Linker Swing Mechanism in the Dynein Motor Roberts, Anthony J.; Numata, Naoki; Walker, Matt L. Cell, Vol. 136, Issue 3 https://doi.org/10.1016/j.cell.2008.11.049	journal	February 2009
Structural Basis for Microtubule Binding and Release by Dynein Redwine, W. B.; Hernandez-Lopez, R.; Zou, S. Science, Vol. 337, Issue 6101 https://doi.org/10.1126/science.1224151	journal	September 2012
Tension on the linker gates the ATP-dependent release of dynein from microtubules Cleary, Frank B.; Dewitt, Mark A.; Bilyard, Thomas Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5587	journal	August 2014
Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures Kellogg, Elizabeth H.; Hejab, Nisreen M. A.; Howes, Stuart Journal of Molecular Biology, Vol. 429, Issue 5 https://doi.org/10.1016/j.jmb.2017.01.001	journal	March 2017
Bidirectional Helical Motility of Cytoplasmic Dynein around Microtubules Can, Sinan; DeWitt, Mark; Yildiz, Ahmet Biophysical Journal, Vol. 108, Issue 2 https://doi.org/10.1016/j.bpj.2014.11.145	journal	January 2015
Kinesin's Front Head is Gated by the Backward Orientation of its Neck Linker Can, Sinan; Yusra Dogan, Merve; Cleary, Frank Biophysical Journal, Vol. 110, Issue 3 https://doi.org/10.1016/j.bpj.2015.11.2456	journal	February 2016
Determination of microtubule polarity by cryo-electron microscopy Chrétien, Denis; Kenney, John M.; Fuller, Stephen D. Structure, Vol. 4, Issue 9 https://doi.org/10.1016/s0969-2126(96)00110-4	journal	September 1996
The Affinity of the Dynein Microtubule-binding Domain Is Modulated by the Conformation of Its Coiled-coil Stalk Gibbons, I. R.; Garbarino, Joan E.; Tan, Carol E. Journal of Biological Chemistry, Vol. 280, Issue 25 https://doi.org/10.1074/jbc.m501636200	journal	April 2005
Bidirectional helical motility of cytoplasmic dynein around microtubules Can, Sinan; Dewitt, Mark A.; Yildiz, Ahmet eLife, Vol. 3 https://doi.org/10.7554/elife.03205	journal	July 2014

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Pac1/LIS1 stabilizes an uninhibited conformation of dynein to coordinate its localization and activity Marzo, Matthew G.; Griswold, Jacqueline M.; Markus, Steven M. Nature Cell Biology, Vol. 22, Issue 5 https://doi.org/10.1038/s41556-020-0492-1	journal	April 2020
Lis1 activates dynein motility by modulating its pairing with dynactin Elshenawy, Mohamed M.; Kusakci, Emre; Volz, Sara Nature Cell Biology, Vol. 22, Issue 5 https://doi.org/10.1038/s41556-020-0501-4	journal	April 2020
Dynein harnesses active fluctuations of microtubules for faster movement Ezber, Yasin; Belyy, Vladislav; Can, Sinan Nature Physics, Vol. 16, Issue 3 https://doi.org/10.1038/s41567-019-0757-4	journal	January 2020
Cargo adaptors regulate stepping and force generation of mammalian dynein–dynactin Elshenawy, Mohamed M.; Canty, John T.; Oster, Liya Nature Chemical Biology, Vol. 15, Issue 11 https://doi.org/10.1038/s41589-019-0352-0	journal	September 2019
Structural basis for two-way communication between dynein and microtubules Nishida, Noritaka; Komori, Yuta; Takarada, Osamu Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14842-8	journal	February 2020
Coupling of ATPase activity, microtubule binding, and mechanics in the dynein motor domain Niekamp, Stefan; Coudray, Nicolas; Zhang, Nan The EMBO Journal, Vol. 38, Issue 13 https://doi.org/10.15252/embj.2018101414	journal	May 2019
Small stepping motion of processive dynein revealed by load-free high-speed single-particle tracking Ando, Jun; Shima, Tomohiro; Kanazawa, Riko Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-58070-y	journal	January 2020
Processivity of molecular motors under vectorial loads Khataee, Hamid; Mahamdeh, Mohammed; Neufeld, Zoltan Physical Review E, Vol. 102, Issue 2 https://doi.org/10.1103/physreve.102.022406	journal	August 2020

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