Abstract

Simultaneous nanometric tracking of multiple motor proteins was achieved by combining multicolor fluorescent labeling of target proteins and imaging spectroscopy, revealing dynamic behaviors of multiple motor proteins at the sub-diffraction-limit scale. Using quantum dot probes of distinct colors, we experimentally verified the localization precision to be a few nanometers at temporal resolution of 30 ms or faster. One-dimensional processive movement of two heads of a single myosin molecule and multiple myosin molecules was successfully traced. Furthermore, the system was modified for two-dimensional measurement and applied to tracking of multiple myosin molecules. Our approach is useful for investigating cooperative movement of proteins in supramolecular nanomachinery.

© 2016 Optical Society of America

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2016 (1)

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
[Crossref] [PubMed]

2015 (4)

X. Shi, M. Li, W. Zhao, A. Liang, X. Liu, and H. Gai, “Spectral imaging superlocalization microscopy for quantum dots,” Sens. Actuators B Chem. 207, 308–312 (2015).
[Crossref]

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
[Crossref] [PubMed]

F. Kohler and A. Rohrbach, “Synchronization of elastically coupled processive molecular motors and regulation of cargo transport,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 91(1), 012701 (2015).
[Crossref] [PubMed]

T. McLaughlin, M. R. Diehl, and A. Kolomeisky, “Collective dynamics of cytoskeletal motor proteins,” Soft Matter 12, 14–21 (2015).
[Crossref] [PubMed]

2014 (1)

D. J. Rowland and J. S. Biteen, “Top-hat and asymmetric Gaussian-based fitting functions for quantifying directional single-molecule motion,” ChemPhysChem 15(4), 712–720 (2014).
[Crossref] [PubMed]

2013 (5)

F. Berger, C. Keller, R. Lipowsky, and S. Klumpp, “Elastic coupling effects in cooperative transport by a pair of molecular motors,” Cell. Mol. Bioeng. 6(1), 48–64 (2013).
[Crossref]

P. J. Cutler, M. D. Malik, S. Liu, J. M. Byars, D. S. Lidke, and K. A. Lidke, “Multi-color quantum dot tracking using a high-speed hyperspectral line-scanning microscope,” PLoS One 8(5), e64320 (2013).
[Crossref] [PubMed]

L. Hilbert, S. Cumarasamy, N. B. Zitouni, M. C. Mackey, and A.-M. Lauzon, “The kinetics of mechanically coupled myosins exhibit group size-dependent regimes,” Biophys. J. 105(6), 1466–1474 (2013).
[Crossref] [PubMed]

M. Kaya and H. Higuchi, “Stiffness, working stroke, and force of single-myosin molecules in skeletal muscle: elucidation of these mechanical properties via nonlinear elasticity evaluation,” Cell. Mol. Life Sci. 70(22), 4275–4292 (2013).
[Crossref] [PubMed]

T. M. Watanabe, F. Fujii, T. Jin, E. Umemoto, M. Miyasaka, H. Fujita, and T. Yanagida, “Four-dimensional spatial nanometry of single particles in living cells using polarized quantum rods,” Biophys. J. 105(3), 555–564 (2013).
[Crossref] [PubMed]

2012 (6)

K. Ikezaki, T. Komori, M. Sugawa, Y. Arai, S. Nishikawa, A. H. Iwane, and T. Yanagida, “Simultaneous observation of the lever arm and head explains myosin VI dual function,” Small 8(19), 3035–3040 (2012).
[Crossref] [PubMed]

K. Fujita, M. Iwaki, A. H. Iwane, L. Marcucci, and T. Yanagida, “Switching of myosin-V motion between the lever-arm swing and brownian search-and-catch,” Nat. Commun. 3, 956 (2012).
[Crossref] [PubMed]

X. Shi, Z. Xie, Y. Song, Y. Tan, E. S. Yeung, and H. Gai, “Superlocalization spectral imaging microscopy of a multicolor quantum dot complex,” Anal. Chem. 84(3), 1504–1509 (2012).
[Crossref] [PubMed]

M. A. DeWitt, A. Y. Chang, P. A. Combs, and A. Yildiz, “Cytoplasmic dynein moves through uncoordinated stepping of the AAA+ ring domains,” Science 335(6065), 221–225 (2012).
[Crossref] [PubMed]

S. Walcott, D. M. Warshaw, and E. P. Debold, “Mechanical coupling between myosin molecules causes differences between ensemble and single-molecule measurements,” Biophys. J. 103(3), 501–510 (2012).
[Crossref] [PubMed]

H. Lu, A. K. Efremov, C. S. Bookwalter, E. B. Krementsova, J. W. Driver, K. M. Trybus, and M. R. Diehl, “Collective dynamics of elastically coupled myosin V motors,” J. Biol. Chem. 287(33), 27753–27761 (2012).
[Crossref] [PubMed]

2010 (2)

S. Nishikawa, I. Arimoto, K. Ikezaki, M. Sugawa, H. Ueno, T. Komori, A. H. Iwane, and T. Yanagida, “Switch between large hand-over-hand and small inchworm-like steps in myosin VI,” Cell 142(6), 879–888 (2010).
[Crossref] [PubMed]

D. K. Jamison, J. W. Driver, A. R. Rogers, P. E. Constantinou, and M. R. Diehl, “Two kinesins transport cargo primarily via the action of one motor: implications for intracellular transport,” Biophys. J. 99(9), 2967–2977 (2010).
[Crossref] [PubMed]

2009 (1)

2008 (4)

M. J. I. Müller, S. Klumpp, and R. Lipowsky, “Tug-of-war as a cooperative mechanism for bidirectional cargo transport by molecular motors,” Proc. Natl. Acad. Sci. U.S.A. 105(12), 4609–4614 (2008).
[Crossref] [PubMed]

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B 93(1), 1–12 (2008).
[Crossref]

J. Yajima, K. Mizutani, and T. Nishizaka, “A torque component present in mitotic kinesin Eg5 revealed by three-dimensional tracking,” Nat. Struct. Mol. Biol. 15(10), 1119–1121 (2008).
[Crossref] [PubMed]

Y. Sowa and R. M. Berry, “Bacterial flagellar motor,” Q. Rev. Biophys. 41(2), 103–132 (2008).
[Crossref] [PubMed]

2007 (1)

T. Mori, R. D. Vale, and M. Tomishige, “How kinesin waits between steps,” Nature 450(7170), 750–754 (2007).
[Crossref] [PubMed]

2006 (4)

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

S. Toba, T. M. Watanabe, L. Yamaguchi-Okimoto, Y. Y. Toyoshima, and H. Higuchi, “Overlapping hand-over-hand mechanism of single molecular motility of cytoplasmic dynein,” Proc. Natl. Acad. Sci. U.S.A. 103(15), 5741–5745 (2006).
[Crossref] [PubMed]

2005 (3)

A. Kusumi, C. Nakada, K. Ritchie, K. Murase, K. Suzuki, H. Murakoshi, R. S. Kasai, J. Kondo, and T. Fujiwara, “Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed single-molecule tracking of membrane molecules,” Annu. Rev. Biophys. Biomol. Struct. 34(1), 351–378 (2005).
[Crossref] [PubMed]

L. S. Churchman, Z. Okten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. U.S.A. 102(5), 1419–1423 (2005).
[Crossref] [PubMed]

D. M. Warshaw, G. G. Kennedy, S. S. Work, E. B. Krementsova, S. Beck, and K. M. Trybus, “Differential labeling of myosin V heads with quantum dots allows direct visualization of hand-over-hand processivity,” Biophys. J. 88(5), L30–L32 (2005).
[Crossref] [PubMed]

2004 (1)

Z. Okten, L. S. Churchman, R. S. Rock, and J. A. Spudich, “Myosin VI walks hand-over-hand along actin,” Nat. Struct. Mol. Biol. 11(9), 884–887 (2004).
[Crossref] [PubMed]

2003 (3)

C. Veigel, J. E. Molloy, S. Schmitz, and J. Kendrick-Jones, “Load-dependent kinetics of force production by smooth muscle myosin measured with optical tweezers,” Nat. Cell Biol. 5(11), 980–986 (2003).
[Crossref] [PubMed]

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

H. C. Berg, “The rotary motor of bacterial flagella,” Annu. Rev. Biochem. 72(1), 19–54 (2003).
[Crossref] [PubMed]

2002 (2)

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

M. Futamata, T. Takenouchi, and K. Katakura, “Highly efficient and aberration-corrected spectrometer for advanced Raman spectroscopy,” Appl. Opt. 41(22), 4655–4665 (2002).
[Crossref] [PubMed]

2001 (2)

M. Nishiyama, E. Muto, Y. Inoue, T. Yanagida, and H. Higuchi, “Substeps within the 8-nm step of the ATPase cycle of single kinesin molecules,” Nat. Cell Biol. 3(4), 425–428 (2001).
[Crossref] [PubMed]

W. van Sark, P. Frederix, D. J. Van den Heuvel, H. C. Gerritsen, A. A. Bol, J. N. J. van Lingen, C. D. Donega, and A. Meijerink, “Photooxidation and photobleaching of single CdSe/ZnS quantum dots probed by room-temperature time-resolved spectroscopy,” J. Phys. Chem. B 105(35), 8281–8284 (2001).
[Crossref]

2000 (1)

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A. 97(17), 9461–9466 (2000).
[Crossref] [PubMed]

1999 (3)

S. A. Empedocles, R. Neuhauser, K. Shimizu, and M. G. Bawendi, “Photoluminescence from single semiconductor nanostructures,” Adv. Mater. 11(15), 1243–1256 (1999).
[Crossref]

A. D. Mehta, R. S. Rock, M. Rief, J. A. Spudich, M. S. Mooseker, and R. E. Cheney, “Myosin-V is a processive actin-based motor,” Nature 400(6744), 590–593 (1999).
[Crossref] [PubMed]

A. L. Wells, A. W. Lin, L. Q. Chen, D. Safer, S. M. Cain, T. Hasson, B. O. Carragher, R. A. Milligan, and H. L. Sweeney, “Myosin VI is an actin-based motor that moves backwards,” Nature 401(6752), 505–508 (1999).
[Crossref] [PubMed]

1996 (1)

R. D. Vale, T. Funatsu, D. W. Pierce, L. Romberg, Y. Harada, and T. Yanagida, “Direct observation of single kinesin molecules moving along microtubules,” Nature 380(6573), 451–453 (1996).
[Crossref] [PubMed]

1995 (3)

H. Miyata, H. Yoshikawa, H. Hakozaki, N. Suzuki, T. Furuno, A. Ikegami, K. Kinosita, T. Nishizaka, and S. Ishiwata, “Mechanical measurements of single actomyosin motor force,” Biophys. J. 68(4Suppl), 286S–289S (1995).
[PubMed]

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S. Walcott, D. M. Warshaw, and E. P. Debold, “Mechanical coupling between myosin molecules causes differences between ensemble and single-molecule measurements,” Biophys. J. 103(3), 501–510 (2012).
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Cell (1)

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W. van Sark, P. Frederix, D. J. Van den Heuvel, H. C. Gerritsen, A. A. Bol, J. N. J. van Lingen, C. D. Donega, and A. Meijerink, “Photooxidation and photobleaching of single CdSe/ZnS quantum dots probed by room-temperature time-resolved spectroscopy,” J. Phys. Chem. B 105(35), 8281–8284 (2001).
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C. Veigel, J. E. Molloy, S. Schmitz, and J. Kendrick-Jones, “Load-dependent kinetics of force production by smooth muscle myosin measured with optical tweezers,” Nat. Cell Biol. 5(11), 980–986 (2003).
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M. Nishiyama, E. Muto, Y. Inoue, T. Yanagida, and H. Higuchi, “Substeps within the 8-nm step of the ATPase cycle of single kinesin molecules,” Nat. Cell Biol. 3(4), 425–428 (2001).
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K. Fujita, M. Iwaki, A. H. Iwane, L. Marcucci, and T. Yanagida, “Switching of myosin-V motion between the lever-arm swing and brownian search-and-catch,” Nat. Commun. 3, 956 (2012).
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M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
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Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
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A. D. Mehta, R. S. Rock, M. Rief, J. A. Spudich, M. S. Mooseker, and R. E. Cheney, “Myosin-V is a processive actin-based motor,” Nature 400(6744), 590–593 (1999).
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Figures (8)

Fig. 1
Fig. 1

Schematic of spectral discrimination of multiple motor proteins walking along a filament. NA: Numerical aperture.

Fig. 2
Fig. 2

(a) Diagram of our optical setup for 1D-SRTM, which consists of a total internal reflection illumination fluorescence microscope and an imaging polychromator. (b,c) Experimental demonstration of spectral discrimination of QDs. Four QDs in nanoscale proximity on the zeroth diffraction image (b) are discriminated by emission wavelength on first diffraction image (c). Both images are summations of 10 successive images acquired with a temporal resolution of 30 ms.

Fig. 3
Fig. 3

(a) Fluctuation and differences in spectral shape of QD525, QD565, and QD605. For each type of QD, two individual QDs were selected to show individual differences in the emission wavelength. For each individual QD, five spectra with characteristic shapes out of 500 serial spectra were selected to show spectral variation. These spectra were obtained with a grating of 150 grooves/mm for higher spectral resolution and more wavelength divisions than the other measurements. The exposure time for one spectrum was 100 ms. (b) Representative time traces of fluorescence intensity of QD525, QD565, and QD605, which was obtained with 30 ms exposure time. (c) Representative raw image of a fluorescence spot of a QD (QD565). The image is an accumulation of the first 10 frames obtained with a 100 ms temporal resolution. (d,e) Temporal fluctuation of the centroid position of the fluorescence spot in (c) estimated with an elliptical Gaussian function: trajectory of the position on the xy plane (d) and separately plotted x and y coordinates relative to the mean positions as a function of time (e). The right axis of (e) represents the wavelength variation from the mean wavelength, which was calibrated from the xd coordinate.

Fig. 4
Fig. 4

Experimental examination of localization precision achieved by the proposed technique. (a) Size of fluorescence spot on first diffraction images (sx and sy) and normal images (s) estimated by elliptical Gaussian fitting. (b) Localization precision against number of detected photons measured under three distinct conditions: diffraction image with a pixel size of 93.4 nm (blue circles), diffraction image with a pixel size of 37.0 nm (red squares), and reflection image (zeroth diffraction) with a pixel size of 37.0 nm (green triangles). Solid curves were obtained by curve fitting of Eq. (3b). (c) Summary of localization precision estimated for six types of QD at temporal resolutions of 10 and 30 ms. The pixel size was 37.0 nm. (d) Number of detected photons of different types of QD at temporal resolutions of 10 and 30 ms.

Fig. 5
Fig. 5

Simultaneous nanometry of two heads of an M5 molecule by 1D-SRTM. (a) A fluorescence image of a TMR-labeled actin filament oriented parallel to the slit direction, which was obtained by zeroth order imaging. (b) Spatiotemporal variation of two fluorescence spots originating from two QDs (QD525 and QD585) attached to two heads of M5, composed of the first diffraction images at 0 and 7 s and two kymographs at the peak wavelengths of the two QDs. The image set was acquired with a temporal resolution of 30 ms. (c) Trajectories of the movement of the two spots. (d) Temporal profile of the displacement of the two QDs in the y direction. (e,f) Demonstration of tracking of four QD-M6 at sub-diffraction-limit scale. (e) Representative first diffraction image of the four fluorescence spots originating from four different QDs (QD525, QD585, QD605, and QD655). (f) Trajectories of the four spots in (e). (g) Temporal profile of the displacement of the four QDs in the y direction, made by the same data set as (f). Raw traces are shown with thin lines, whereas smoothed traces (binomial, n = 3) are shown with thick lines.

Fig. 6
Fig. 6

2D-SRTM. (a) Configuration of the relay optics of the detection path for two-dimensional tracking. Path I lets an image pass without rotation, whereas path II rotates the image by 90°. (b) Left: normal fluorescence image obtained as zeroth diffraction (specular reflection of the grating). Areas inside of the red dashed squares are the same sample areas with different orientations. We defined the direction of the xd and yd axes of the upper view to be identical to those of the xs and ys axes on the sample plane, which yields the relationship between the xd and yd axes seen in the lower view and the xs and ys axes, as shown on the right.

Fig. 7
Fig. 7

Demonstration of estimation of two-dimensional coordinates of stationary QDs by 2D-SRTM. Representative raw images of (a) zeroth diffraction and (b) first diffraction of many QDs. Three QDs in an aggregate indicated by the dashed squares in (a) are separately recognized in the first diffraction image (b). The three QDs labeled A, B, and C represent QD525, QD585, and QD655, respectively. Both images are summations of 100 successive images acquired with a temporal resolution of 30 ms. The y and x coordinates are estimated from the upper and lower views of the first diffraction image, respectively. (c) Trajectories of the estimated two-dimensional coordinates of the three QDs plotted on a close-up of the zeroth diffraction image of the aggregate.

Fig. 8
Fig. 8

(a) Representative first diffraction image containing four fluorescence spots in both the upper and lower views, which is one frame in a movie obtained with a temporal resolution of 100 ms. (b) Temporal fluctuation of intensity of two fluorescence spots labeled 1 and 2 observed in both views. (c) Pearson’s correlation coefficients of temporal profile of intensity for all 16 possible pairs of four fluorescence spots in both upper and lower halves of (a). (d) Reconstructed two-dimensional trajectory of the four QDs on the sample coordinates (xs, ys), where we found that they are moving along a single actin filament.

Equations (4)

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I( x d , y d | x s , y s )= U( x d x s x disp ( λ ), y d y s ,λ ) g( λ )dλ
F( x d , y d )= C 0 + C 1 exp{ ( x d x 0 ) 2 s x 2 2 ( y d y 0 ) 2 s y 2 2 }
(Δx) 2 = s x 2 N + a 2 /12 N + 8π b 2 s x 3 s y a 2 N 2
(Δy) 2 = s y 2 N + a 2 /12 N + 8π b 2 s x s y 3 a 2 N 2

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