Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms

Paschal, B. M., Shpetner, H. S. & Vallee, R. B. MAP 1C is a microtubule-activated ATPase which translocates microtubules in vitro. J. Cell Biol. 105, 1273–1282 (1987).Article 
CAS 
PubMed 

Google Scholar 
Khan, Y. A., White, K. I. & Brunger, A. T. The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines. Crit. Rev. Biochem. Mol. Biol. 57, 156–187 (2022).Article 
CAS 
PubMed 

Google Scholar 
Roberts, A. J., Kon, T., Knight, P. J., Sutoh, K. & Burgess, S. A. Functions and mechanics of dynein motor proteins. Nat. Rev. Mol. Cell Biol. 14, 713–726 (2013).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Huang, J., Roberts, A. J., Leschziner, A. E. & Reck-Peterson, S. L. Lis1 acts as a ‘clutch’ between the ATPase and microtubule-binding domains of the dynein motor. Cell 150, 975–986 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bhabha, G., Johnson, G. T., Schroeder, C. M. & Vale, R. D. How dynein moves along microtubules. Trends Biochem. Sci. 41, 94–105 (2016).Article 
CAS 
PubMed 

Google Scholar 
Cianfrocco, M. A., DeSantis, M. E., Leschziner, A. E. & Reck-Peterson, S. L. Mechanism and regulation of cytoplasmic dynein. Annu. Rev. Cell Dev. Biol. 31, 83–108 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Derr, N. D. et al. Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold. Science 338, 662–665 (2012).Article 
CAS 
PubMed 

Google Scholar 
Urnavicius, L. et al. Cryo-EM shows how dynactin recruits two dyneins for faster movement. Nature 554, 202–206 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Belyy, V. et al. The mammalian dynein–dynactin complex is a strong opponent to kinesin in a tug-of-war competition. Nat. Cell Biol. 18, 1018–1024 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Niekamp, S., Stuurman, N., Zhang, N. & Vale, R. D. Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility. Proc. Natl Acad. Sci. USA 118, e2101391118 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Millecamps, S. & Julien, J. P. Axonal transport deficits and neurodegenerative diseases. Nat. Rev. Neurosci. 14, 161–176 (2013).Article 
CAS 
PubMed 

Google Scholar 
Reck-Peterson, S. L. et al. Single-molecule analysis of dynein processivity and stepping behavior. Cell 126, 335–348 (2006).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sigal, Y. M., Zhou, R. & Zhuang, X. Visualizing and discovering cellular structures with super-resolution microscopy. Science 361, 880–887 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Rasnik, I., McKinney, S. A. & Ha, T. Nonblinking and long-lasting single-molecule fluorescence imaging. Nat. Methods 3, 891–893 (2006).Article 
CAS 
PubMed 

Google Scholar 
Altman, R. B. et al. Cyanine fluorophore derivatives with enhanced photostability. Nat. Methods 9, 68–71 (2012).Article 
CAS 

Google Scholar 
Tsunoyama, T. A. et al. Super-long single-molecule tracking reveals dynamic-anchorage-induced integrin function. Nat. Chem. Biol. 14, 497–506 (2018).Article 
CAS 
PubMed 

Google Scholar 
Tanenbaum, M. E., Gilbert, L. A., Qi, L. S., Weissman, J. S. & Vale, R. D. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159, 635–646 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, H. et al. Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling. Proc. Natl Acad. Sci. USA 115, 343–348 (2018).Article 
CAS 
PubMed 

Google Scholar 
Ghosh, R. P. et al. A fluorogenic array for temporally unlimited single-molecule tracking. Nat. Chem. Biol. 15, 401–409 (2019).Article 
CAS 
PubMed 

Google Scholar 
Chen, O. et al. Compact high-quality CdSe–CdS core–shell nanocrystals with narrow emission linewidths and suppressed blinking. Nat. Mater. 12, 445–451 (2013).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Shi, J. et al. All-optical fluorescence blinking control in quantum dots with ultrafast mid-infrared pulses. Nat. Nanotechnol. 16, 1355–1361 (2021).Article 
CAS 
PubMed 

Google Scholar 
Liu, Q. et al. Single upconversion nanoparticle imaging at sub-10 W cm2 irradiance. Nat. Photonics 12, 548–553 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Nam, S. H. et al. Long-term real-time tracking of lanthanide ion doped upconverting nanoparticles in living cells. Angew. Chem. Int. Ed. 50, 6093–6097 (2011).Article 
CAS 

Google Scholar 
Wang, F. et al. Microscopic inspection and tracking of single upconversion nanoparticles in living cells. Light Sci. Appl. 7, 18007 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wu, S. et al. Non-blinking and photostable upconverted luminescence from single lanthanide-doped nanocrystals. Proc. Natl Acad. Sci. USA 106, 10917–10921 (2009).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gargas, D. J. et al. Engineering bright sub-10-nm upconverting nanocrystals for single-molecule imaging. Nat. Nanotechnol. 9, 300–305 (2014).Article 
CAS 
PubMed 

Google Scholar 
Liu, Y. et al. Amplified stimulated emission in upconversion nanoparticles for super-resolution nanoscopy. Nature 543, 229–233 (2017).Article 
CAS 
PubMed 

Google Scholar 
Tian, B. et al. Low irradiance multiphoton imaging with alloyed lanthanide nanocrystals. Nat. Commun. 9, 3082 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Zhao, J. et al. Single-nanocrystal sensitivity achieved by enhanced upconversion luminescence. Nat. Nanotechnol. 8, 729–734 (2013).Article 
CAS 
PubMed 

Google Scholar 
Wang, F. et al. Tuning upconversion through energy migration in core-shell nanoparticles. Nat. Mater. 10, 968–973 (2011).Article 
CAS 
PubMed 

Google Scholar 
Zhang, Y. et al. Multicolor barcoding in a single upconversion crystal. J. Am. Chem. Soc. 136, 4893–4896 (2014).Article 
CAS 
PubMed 

Google Scholar 
Zhou, L. et al. Single-band upconversion nanoprobes for multiplexed simultaneous in situ molecular mapping of cancer biomarkers. Nat. Commun. 6, 6938 (2015).Article 
CAS 
PubMed 

Google Scholar 
Xu, G. et al. New generation cadmium-free quantum dots for biophotonics and nanomedicine. Chem. Rev. 116, 12234–12327 (2016).Article 
CAS 
PubMed 

Google Scholar 
Chen, G. et al. (α-NaYbF4:Tm3+)/CaF2 core/shell nanoparticles with efficient near-infrared to near-infrared upconversion for high-contrast deep tissue bioimaging. ACS Nano 6, 8280–8287 (2012).Han, H. S. et al. Spatial charge configuration regulates nanoparticle transport and binding behavior in vivo. Angew. Chem. Int. Ed. 52, 1414–1419 (2013).Article 
CAS 

Google Scholar 
Abdul Jalil, R. & Zhang, Y. Biocompatibility of silica coated NaYF4 upconversion fluorescent nanocrystals. Biomaterials 29, 4122–4128 (2008).Article 
CAS 
PubMed 

Google Scholar 
Chen, S. et al. Near-infrared deep brain stimulation via upconversion nanoparticle-mediated optogenetics. Science 359, 679–684 (2018).Article 
CAS 
PubMed 

Google Scholar 
Cui, B. et al. One at a time, live tracking of NGF axonal transport using quantum dots. Proc. Natl Acad. Sci. USA 104, 13666–13671 (2007).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kaplan, L., Ierokomos, A., Chowdary, P., Bryant, Z. & Cui, B. Rotation of endosomes demonstrates coordination of molecular motors during axonal transport. Sci. Adv. 4, e1602170 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Monnier, N. et al. Inferring transient particle transport dynamics in live cells. Nat. Methods 12, 838–840 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gu, Y. et al. Rotational dynamics of cargos at pauses during axonal transport. Nat. Commun. 3, 1030 (2012).Article 
PubMed 

Google Scholar 
Yogev, S., Cooper, R., Fetter, R., Horowitz, M. & Shen, K. Microtubule organization determines axonal transport dynamics. Neuron 92, 449–460 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bray, D. & Bunge, M. B. Serial analysis of microtubules in cultured rat sensory axons. J. Neurocytol. 10, 589–605 (1981).Article 
CAS 
PubMed 

Google Scholar 
Encalada, S. E., Szpankowski, L., Xia, C. H. & Goldstein, L. S. Stable kinesin and dynein assemblies drive the axonal transport of mammalian prion protein vesicles. Cell 144, 551–565 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hendricks, A. G. et al. Motor coordination via a tug-of-war mechanism drives bidirectional vesicle transport. Curr. Biol. 20, 697–702 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Reck-Peterson, S. L., Redwine, W. B., Vale, R. D. & Carter, A. P. The cytoplasmic dynein transport machinery and its many cargoes. Nat. Rev. Mol. Cell Biol. 19, 382–398 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Huang, Y. A., Zhou, B., Wernig, M. & Sudhof, T. C. ApoE2, ApoE3, and ApoE4 differentially stimulate APP transcription and Aβ secretion. Cell 168, 427–441.e21 (2017).Miller, R. H. & Lasek, R. J. Cross-bridges mediate anterograde and retrograde vesicle transport along microtubules in squid axoplasm. J. Cell Biol. 101, 2181–2193 (1985).Article 
CAS 
PubMed 

Google Scholar 
Sims, P. A. & Xie, X. S. Probing dynein and kinesin stepping with mechanical manipulation in a living cell. Chemphyschem 10, 1511–1516 (2009).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Shubeita, G. T. et al. Consequences of motor copy number on the intracellular transport of kinesin-1-driven lipid droplets. Cell 135, 1098–1107 (2008).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Rai, A. K., Rai, A., Ramaiya, A. J., Jha, R. & Mallik, R. Molecular adaptations allow dynein to generate large collective forces inside cells. Cell 152, 172–182 (2013).Article 
CAS 
PubMed 

Google Scholar 
Chowdary, P. D. et al. Nanoparticle-assisted optical tethering of endosomes reveals the cooperative function of dyneins in retrograde axonal transport. Sci. Rep. 5, 18059 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hayashi, K., Tsuchizawa, Y., Iwaki, M. & Okada, Y. Application of the fluctuation theorem for noninvasive force measurement in living neuronal axons. Mol. Biol. Cell 29, 3017–3025 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Elshenawy, M. M. et al. Cargo adaptors regulate stepping and force generation of mammalian dynein-dynactin. Nat. Chem. Biol. 15, 1093–1101 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
DeWitt, M. A., Chang, A. Y., Combs, P. A. & Yildiz, A. Cytoplasmic dynein moves through uncoordinated stepping of the AAA+ ring domains. Science 335, 221–225 (2012).Article 
CAS 
PubMed 

Google Scholar 
Schnitzer, M. J. & Block, S. M. Statistical kinetics of processive enzymes. Cold Spring Harb. Symp. Quant. Biol. 60, 793–802 (1995).Article 
CAS 
PubMed 

Google Scholar 
Moffitt, J. R. & Bustamante, C. Extracting signal from noise: kinetic mechanisms from a Michaelis–Menten-like expression for enzymatic fluctuations. FEBS J. 281, 498–517 (2014).Article 
CAS 
PubMed 

Google Scholar 
Cho, C., Reck-Peterson, S. L. & Vale, R. D. Regulatory ATPase sites of cytoplasmic dynein affect processivity and force generation. J. Biol. Chem. 283, 25839–25845 (2008).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, X., Rao, L. & Gennerich, A. The regulatory function of the AAA4 ATPase domain of cytoplasmic dynein. Nat. Commun. 11, 5952 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bhabha, G. et al. Allosteric communication in the dynein motor domain. Cell 159, 857–868 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Holzbaur, E. L. F. & Johnson, K. A. Microtubules accelerate ADP release by dynein. Biochemistry 28, 7010–7016 (1989).Article 
CAS 
PubMed 

Google Scholar 
Kinoshita, Y., Kambara, T., Nishikawa, K., Kaya, M. & Higuchi, H. Step sizes and rate constants of single-headed cytoplasmic dynein measured with optical tweezers. Sci. Rep. 8, 16333 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Trevisiol, A. et al. Monitoring ATP dynamics in electrically active white matter tracts. eLife 6, e24241 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Strack, S. & Usachev, Y. M. (eds). Techniques to Investigate Mitochondrial Function in Neurons (Springer, 2017).Pathak, D. et al. The role of mitochondrially derived ATP in synaptic vesicle recycling. J. Biol. Chem. 290, 22325–22336 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Nicholas, M. P. et al. Cytoplasmic dynein regulates its attachment to microtubules via nucleotide state-switched mechanosensing at multiple AAA domains. Proc. Natl Acad. Sci. USA 112, 6371–6376 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Astumian, R. D., Mukherjee, S. & Warshel, A. The physics and physical chemistry of molecular machines. Chemphyschem 17, 1719–1741 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hwang, W. & Karplus, M. Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins. Proc. Natl Acad. Sci. USA 116, 19777–19785 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Carter, A. P. et al. Structure and functional role of dynein’s microtubule-binding domain. Science 322, 1691–1695 (2008).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
DeWitt, M. A., Cypranowska, C. A., Cleary, F. B., Belyy, V. & Yildiz, A. The AAA3 domain of cytoplasmic dynein acts as a switch to facilitate microtubule release. Nat. Struct. Mol. Biol. 22, 73–80 (2015).Article 
CAS 
PubMed 

Google Scholar 
Moffitt, J. R. et al. Intersubunit coordination in a homomeric ring ATPase. Nature 457, 446–450 (2009).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, Y. et al. Rapid single-step induction of functional neurons from human pluripotent stem cells. Neuron 78, 785–798 (2013).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Loring, J. F. & Rao, M. S. Establishing standards for the characterization of human embryonic stem cell lines. Stem Cells 24, 145–150 (2006).Article 
PubMed 

Google Scholar 
French, A. et al. Enabling consistency in pluripotent stem cell-derived products for research and development and clinical applications through material standards. Stem Cells Transl. Med. 4, 217–223 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, Q., Feng, W., Yang, T., Yi, T. & Li, F. Upconversion luminescence imaging of cells and small animals. Nat. Protoc. 8, 2033–2044 (2013).Article 
CAS 
PubMed 

Google Scholar 
Kyoung, M., Zhang, Y., Diao, J., Chu, S. & Brunger, A. T. Studying calcium-triggered vesicle fusion in a single vesicle-vesicle content and lipid-mixing system. Nat. Protoc. 8, 1–16 (2013).Article 
CAS 
PubMed 

Google Scholar 
Serge, A., Bertaux, N., Rigneault, H. & Marguet, D. Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes. Nat. Methods 5, 687–694 (2008).Article 
CAS 
PubMed 

Google Scholar 
Chen, J. et al. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell 156, 1274–1285 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kerssemakers, J. W. et al. Assembly dynamics of microtubules at molecular resolution. Nature 442, 709–712 (2006).Article 
CAS 
PubMed 

Google Scholar