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Single-Molecule Fluorescent Particle Tracking

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Abstract

One of the most fascinating processes in biology is the directed movement of organisms, subcellular compartments, and single proteins. Tracking the cellular motion is of great interest to single-molecule biophysicists to understand the mechanism of wide variety of biological processes, from basic mechanism of molecular machines to protein--protein interactions. In the last two decades, random diffusion of proteins and lipids has been tracked under the fluorescence microscope to understand how they associate with their targeted molecules. However, cellular motility is not limited to diffusion of small particles. Many fundamental processes occur by discrete physical movements upon each enzymatic cycle. For example, motor proteins of cytoskeleton can transport intracellular cargoes by taking nanometer-sized steps along the linear tracks within the cell. Several high precision techniques have been developed to understand the working principles and kinetics of motors in a detailed manner. This chapter summarizes the recent advances in fluorescence microscopy techniques that allow high precision tracking of biological molecules.

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References

  1. Horio, T., and H. Hotani, Visualization of the dynamic instability of individual microtubules by dark-field microscopy. Nature, 1986;321(6070):605–7.

    Article  ADS  Google Scholar 

  2. Gelles, J., B. J. Schnapp, and M. P. Sheetz, Tracking kinesin-driven movements with nanometre-scale precision. Nature, 1988;331(6155):450–3.

    Article  ADS  Google Scholar 

  3. Svoboda, K., et al., Direct observation of kinesin stepping by optical trapping interferometry. Nature, 1993;365(6448):721–7.

    Article  ADS  Google Scholar 

  4. Funatsu, T., et al., Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous solution. Nature, 1995;374:555–9.

    Article  ADS  Google Scholar 

  5. Sakamoto, T., et al., Direct observation of the mechanochemical coupling in myosin Va during processive movement. Nature, 2008;455(7209):128–32.

    Article  ADS  Google Scholar 

  6. Hecht, E., Optics. 4th ed. San Francisco: Addison-Wesley, 2002.

    Google Scholar 

  7. Cheezum, M. K., W. F. Walker, and W. H. Guilford, Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys J, 2001;81(4):2378–88.

    Article  Google Scholar 

  8. Thompson, R. E., D. R. Larson, and W. W. Webb, Precise nanometer localization analysis for individual fluorescent probes. Biophys J, 2002;82(5):2775–83.

    Article  Google Scholar 

  9. Schmidt, T., et al., Imaging of single molecule diffusion. Proc Natl Acad Sci USA, 1996;93(7):2926–9.

    Article  ADS  Google Scholar 

  10. Kubitscheck, U., et al., Imaging and tracking of single GFP molecules in solution. Biophys J, 2000;78(4): 2170–9.

    Article  Google Scholar 

  11. Harada, Y., et al., Mechanochemical coupling in actomyosin energy transduction studied by in vitro movement assay. J Mol Biol, 1990;216(1):49–68.

    Article  ADS  Google Scholar 

  12. Lakowicz, J. R., Principles of Fluorescence. 2nd ed. New York: Kluwer Academic, 1999.

    Google Scholar 

  13. McKinney, S. A., et al., Structural dynamics of individual Holliday junctions. Nat Struct Biol, 2003;10(2):93–7.

    Article  Google Scholar 

  14. Yildiz, A., et al., Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. Science, 2003;300(5628):2061–5.

    Article  ADS  Google Scholar 

  15. Rasnik, I., S. A. McKinney, and T. Ha, Nonblinking and long-lasting single-molecule fluorescence imaging. Nat Methods, 2006;3(11):891–3.

    Article  Google Scholar 

  16. Adachi, K., et al., Stepping rotation of F1-ATPase visualized through angle-resolved single-fluorophore imaging. Proc Natl Acad Sci USA, 2000;97(13):7243–7.

    Article  ADS  Google Scholar 

  17. Sambongi, Y., et al., Mechanical rotation of the c subunit oligomer in ATP synthase (F0F1): direct observation. Science, 1999;286:1722–4.

    Article  Google Scholar 

  18. Vale, R. D., The molecular motor toolbox for intracellular transport. Cell, 2003;112(4):467–80.

    Article  Google Scholar 

  19. Asbury, C. L., Kinesin: world’s tiniest biped. Curr Opin Cell Biol, 2005;17(1):89–97.

    Article  Google Scholar 

  20. Spudich, J. A., The myosin swinging cross-bridge model. Nat Rev Mol Cell Biol, 2001;2(5):387–92.

    Article  Google Scholar 

  21. Hua, W., J. Chung, and J. Gelles, Distinguishing inchworm and hand-over-hand processive kinesin movement by neck rotation measurements. Science, 2002;295(5556):844–8.

    Article  ADS  Google Scholar 

  22. Mehta, A. D., et al., Myosin-V is a processive actin-based motor. Nature, 1999;400(6744):590–3.

    Article  ADS  Google Scholar 

  23. Okten, Z., et al., Myosin VI walks hand-over-hand along actin. Nat Struct Mol Biol, 2004;11(9):884–7.

    Article  Google Scholar 

  24. Yildiz, A., et al., Myosin VI steps via a hand-over-hand mechanism with its lever arm undergoing fluctuations when attached to actin. J Biol Chem, 2004;279(36):37223–6.

    Article  Google Scholar 

  25. Kaseda, K., H. Higuchi, and K. Hirose, Alternate fast and slow stepping of a heterodimeric kinesin molecule. Nat Cell Biol, 2003;5(12):1079–82.

    Article  Google Scholar 

  26. Asbury, C. L., A. N. Fehr, and S. M. Block, Kinesin moves by an asymmetric hand-over-hand mechanism. Science, 2003;302(5653):2130–4.

    Article  ADS  Google Scholar 

  27. Yildiz, A., et al., Kinesin walks hand-over-hand. Science, 2004;303:676–8.

    Article  ADS  Google Scholar 

  28. Reck-Peterson, S. L., et al., Single-molecule analysis of dynein processivity and stepping behavior. Cell, 2006;126(2):335–48.

    Article  Google Scholar 

  29. Xiao, M., et al., Rapid DNA mapping by fluorescent single molecule detection. Nucl Acids Res, 2007;35(3):e16.

    Article  Google Scholar 

  30. Ha, T., et al., Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci, 1996;93(13):6264–8.

    Article  ADS  Google Scholar 

  31. Gordon, M. P., T. Ha, and P. R. Selvin, Single-molecule high-resolution imaging with photobleaching. Proc Natl Acad Sci USA, 2004;101(17):6462–5.

    Article  ADS  Google Scholar 

  32. Qu, X., et al., Nanometer-localized multiple single-molecule fluorescence microscopy. Proc Natl Acad Sci USA, 2004;101(31):11298–303.

    Article  ADS  Google Scholar 

  33. Lacoste, T. D., et al., Ultrahigh-resolution multicolor colocalization of single fluorescent probes. Proc Natl Acad Sci USA, 2000;97(17):9461–6.

    Article  ADS  Google Scholar 

  34. Churchman, L. S., et al., Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proc Natl Acad Sci USA, 2005;102(5):1419–23.

    Article  ADS  Google Scholar 

  35. Warshaw, D. M., et al., Differential labeling of myosin V heads with quantum dots allows direct visualization of hand-over-hand processivity. Biophys J, 2005. 88(5):L30–2.

    Article  Google Scholar 

  36. Iino, R., I. Koyama, and A. Kusumi, Single molecule imaging of green fluorescent proteins in living cells: E-cadherin forms oligomers on the free cell surface. Biophys J, 2001;80(6):2667–77.

    Article  Google Scholar 

  37. Harms, G. S., et al., Single-molecule imaging of l-type Ca(2+) channels in live cells. Biophys J, 2001;81(5):2639–46.

    Article  Google Scholar 

  38. Murakoshi, H., et al., Single-molecule imaging analysis of Ras activation in living cells. Proc Natl Acad Sci USA, 2004;101(19):7317–22.

    Article  ADS  Google Scholar 

  39. Douglass, A. D., and R. D. Vale, Single-molecule microscopy reveals plasma membrane microdomains created by protein-protein networks that exclude or trap signaling molecules in T cells. Cell, 2005;121(6):937–50.

    Article  Google Scholar 

  40. Kohout, S. C., et al., Subunit organization and functional transitions in Ci-VSP. Nat Struct Mol Biol, 2008;15(1):106–8.

    Article  Google Scholar 

  41. Tombola, F., M. H. Ulbrich, and E. Y. Isacoff, The voltage-gated proton channel Hv1 has two pores, each controlled by one voltage sensor. Neuron, 2008;58(4):546–56.

    Article  Google Scholar 

  42. Sako, Y., S. Minoghchi, and T. Yanagida, Single-molecule imaging of EGFR signalling on the surface of living cells. Nat Cell Biol, 2000;2(3):168–72.

    Article  Google Scholar 

  43. Dahan, M., et al., Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking. Science, 2003;302(5644):442–5.

    Article  ADS  Google Scholar 

  44. Lakadamyali, M., et al., Visualizing infection of individual influenza viruses. Proc Natl Acad Sci USA, 2003;100(16):9280–5.

    Article  ADS  Google Scholar 

  45. Lakadamyali, M., M. J. Rust, and X. Zhuang, Ligands for clathrin-mediated endocytosis are differentially sorted into distinct populations of early endosomes. Cell, 2006;124(5):997–1009.

    Article  Google Scholar 

  46. Bertrand, E., et al., Localization of ASH1 mRNA particles in living yeast. Mol Cell, 1998;2(4):437–45.

    Article  MathSciNet  Google Scholar 

  47. Golding, I., et al., Real-time kinetics of gene activity in individual bacteria. Cell, 2005;123(6):1025–36.

    Article  Google Scholar 

  48. Yu, J., et al., Probing gene expression in live cells, one protein molecule at a time. Science, 2006; 311(5767):1600–3.

    Article  ADS  Google Scholar 

  49. Kural, C., et al., Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated movement? Science, 2005;308(5727):1469–72.

    Article  ADS  Google Scholar 

  50. Kural, C., et al., Tracking melanosomes inside a cell to study molecular motors and their interaction. Proc Natl Acad Sci USA, 2007;104(13):5378–82.

    Article  ADS  Google Scholar 

  51. Gennerich, A., and D. Schild, Sizing-up finite fluorescent particles with nanometer-scale precision by convolution and correlation image analysis. Eur Biophys J, 2005;34(3):181–99.

    Article  Google Scholar 

  52. Nan, X., et al., Observation of individual microtubule motor steps in living cells with endocytosed quantum dots. J Phys Chem B, 2005;109(51):24220–4.

    Article  Google Scholar 

  53. Watanabe, T. M., and H. Higuchi, Stepwise movements in vesicle transport of HER2 by motor proteins in living cells. Biophys J, 2007;92(11):4109–20.

    Article  Google Scholar 

  54. Nan, X., P. A. Sims, and X. S. Xie, Organelle tracking in a living cell with microsecond time resolution and nanometer spatial precision. Chemphyschem, 2008;9(5):707–12.

    Article  Google Scholar 

  55. Enderlein, J., E. Toprak, and P. R. Selvin, Polarization effect on position accuracy of fluorophore localization. Opt Express, 2006;14(18):8111–20.

    Article  ADS  Google Scholar 

  56. Yasuda, R., et al., Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase. Nature, 2001;410(6831):898–904.

    Article  ADS  Google Scholar 

  57. Xie, X. S., and R. C. Dunn, Probing single molecule dynamics. Science, 1994;265(5170):361–4.

    Article  ADS  Google Scholar 

  58. Ha, T., et al., Single molecule dynamics studied by polarization modulation. Phys Rev Lett, 1996;77: 3979–82.

    Article  ADS  Google Scholar 

  59. Sase, I., et al., Axial rotation of sliding actin filaments revealed by single-fluorophore imaging. Proc Natl Acad Sci USA, 1997;94(11):5646–50.

    Article  ADS  Google Scholar 

  60. Sosa, H., et al., ADP-induced rocking of the kinesin motor domain revealed by single-molecule fluorescence polarization microscopy. Nat Struct Biol, 2001;8(6):540–4.

    Article  Google Scholar 

  61. Asenjo, A. B., N. Krohn, and H. Sosa, Configuration of the two kinesin motor domains during ATP hydrolysis. Nat Struct Biol, 2003;10(10):836–42.

    Article  Google Scholar 

  62. Asenjo, A. B., Y. Weinberg, and H. Sosa, Nucleotide binding and hydrolysis induces a disorder–order transition in the kinesin neck-linker region. Nat Struct Mol Biol, 2006;13(7):648–54.

    Article  Google Scholar 

  63. Forkey, J. N., et al., Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization. Nature, 2003;422(6930):399–404.

    Article  ADS  Google Scholar 

  64. Syed, S., et al., Adaptability of myosin V studied by simultaneous detection of position and orientation. EMBO J, 2006;25(9):1795–803.

    Article  Google Scholar 

  65. Bartko, A. P., K. Xu, and R. M. Dickson, Three-dimensional single molecule rotational diffusion in glassy state polymer films. Phys Rev Lett, 2002;89(2):026101/1–4.

    Article  ADS  Google Scholar 

  66. Patra, D., I. Gregor, and J. Enderlein, Image analysis of defocused single-molecule images for three-dimensional molecule orientation studies. J Phys Chem A, 2004;108(33):6836–41.

    Article  Google Scholar 

  67. Toprak, E., et al., Defocused orientation and position imaging (DOPI) of myosin V. Proc Natl Acad Sci USA, 2006;103(17):6495–9.

    Article  ADS  Google Scholar 

  68. Shaner, N. C., et al., Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol, 2004;22(12):1567–72.

    Article  Google Scholar 

  69. Cinelli, R. A., et al., The enhanced green fluorescent protein as a tool for the analysis of protein dynamics and localization: local fluorescence study at the single-molecule level. Photochem Photobiol, 2000;71(6):771–6.

    Article  Google Scholar 

  70. Howarth, M., et al., Monovalent, reduced-size quantum dots for imaging receptors on living cells. Nat Methods, 2008;5(5):397–9.

    Article  Google Scholar 

  71. Smith, A. M., and S. Nie, Minimizing the hydrodynamic size of quantum dots with multifunctional multidentate polymer ligands. J Am Chem Soc, 2008;130(34):11278–9.

    Article  Google Scholar 

  72. Dunn, A. R., and J. A. Spudich, Dynamics of the unbound head during myosin V processive translocation. Nat Struct Mol Biol, 2007;14(3):246–8.

    Article  Google Scholar 

  73. Egner, A., S. Jakobs, and S. W. Hell, Fast 100-nm resolution three-dimensional microscope reveals structural plasticity of mitochondria in live yeast. Proc Natl Acad Sci USA, 2002;99(6):3370–5.

    Article  ADS  Google Scholar 

  74. Klar, T. A., et al., Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proc Natl Acad Sci USA, 2000;97(15):8206–10.

    Article  ADS  Google Scholar 

  75. Schermelleh, L., et al., Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science, 2008;320(5881):1332–6.

    Article  ADS  Google Scholar 

  76. Rust, M. J., M. Bates, and X. Zhuang, Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods, 2006;3(10):793–5.

    Article  Google Scholar 

  77. Betzig, E., et al., Imaging intracellular fluorescent proteins at nanometer resolution. Science, 2006;313(5793):1642–5.

    Article  ADS  Google Scholar 

  78. Rosenberg, S. A., et al., Rotational motions of macro-molecules by single-molecule fluorescence microscopy. Acc Chem Res, 2005;38(7):583–93.

    Article  Google Scholar 

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Yildiz, A. (2009). Single-Molecule Fluorescent Particle Tracking. In: Hinterdorfer, P., Oijen, A. (eds) Handbook of Single-Molecule Biophysics. Springer, New York, NY. https://doi.org/10.1007/978-0-387-76497-9_1

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