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Kubota R, Tanaka W, Hamachi I. Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies. Chem Rev 2021; 121:14281-14347. [DOI: 10.1021/acs.chemrev.0c01334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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Kubota R, Makuta M, Suzuki R, Ichikawa M, Tanaka M, Hamachi I. Force generation by a propagating wave of supramolecular nanofibers. Nat Commun 2020; 11:3541. [PMID: 32669562 PMCID: PMC7363860 DOI: 10.1038/s41467-020-17394-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/17/2020] [Indexed: 01/07/2023] Open
Abstract
Dynamic spatiotemporal patterns that arise from out-of-equilibrium biochemical reactions generate forces in living cells. Despite considerable recent efforts, rational design of spatiotemporal patterns in artificial molecular systems remains at an early stage of development. Here, we describe force generation by a propagating wave of supramolecular nanofibers. Inspired by actin dynamics, a reaction network is designed to control the formation and degradation of nanofibers by two chemically orthogonal stimuli. Real-time fluorescent imaging successfully visualizes the propagating wave based on spatiotemporally coupled generation and collapse of nanofibers. Numerical simulation indicates that the concentration gradient of degradation stimulus and the smaller diffusion coefficient of the nanofiber are critical for wave emergence. Moreover, the force (0.005 pN) generated by chemophoresis and/or depletion force of this propagating wave can move nanobeads along the wave direction.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Masahiro Makuta
- Department of Physics, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ryo Suzuki
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masatoshi Ichikawa
- Department of Physics, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Motomu Tanaka
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.,Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, 69120, Heidelberg, Germany
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan. .,JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8530, Japan.
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Georgiades P, Allan VJ, Wright GD, Woodman PG, Udommai P, Chung MA, Waigh TA. The flexibility and dynamics of the tubules in the endoplasmic reticulum. Sci Rep 2017; 7:16474. [PMID: 29184084 PMCID: PMC5705721 DOI: 10.1038/s41598-017-16570-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
The endoplasmic reticulum (ER) is a single organelle in eukaryotic cells that extends throughout the cell and is involved in a large number of cellular functions. Using a combination of fixed and live cells (human MRC5 lung cells) in diffraction limited and super-resolved fluorescence microscopy (STORM) experiments, we determined that the average persistence length of the ER tubules was 3.03 ± 0.24 μm. Removing the branched network junctions from the analysis caused a slight increase in the average persistence length to 4.71 ± 0.14 μm, and provides the tubule's persistence length with a moderate length scale dependence. The average radius of the tubules was 44.1 ± 3.2 nm. The bending rigidity of the ER tubule membranes was found to be 10.9 ± 1.2 kT (17.0 ± 1.3 kT without branch points). We investigated the dynamic behaviour of ER tubules in live cells, and found that the ER tubules behaved like semi-flexible fibres under tension. The majority of the ER tubules experienced equilibrium transverse fluctuations under tension, whereas a minority number of them had active super-diffusive motions driven by motor proteins. Cells thus actively modulate the dynamics of the ER in a well-defined manner, which is expected in turn to impact on its many functions.
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Affiliation(s)
- Pantelis Georgiades
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK
| | - Victoria J Allan
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK.
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK.
| | - Graham D Wright
- IMB Microscopy Unit, Institute of Medical Biology, A*STAR, 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Republic of Singapore
| | - Philip G Woodman
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
| | - Parinya Udommai
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Manloeng A Chung
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Thomas A Waigh
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK.
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK.
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Barooji YF, Rørvig-Lund A, Semsey S, Reihani SNS, Bendix PM. Dynamics of membrane nanotubes coated with I-BAR. Sci Rep 2016; 6:30054. [PMID: 27444356 PMCID: PMC4956757 DOI: 10.1038/srep30054] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/29/2016] [Indexed: 12/16/2022] Open
Abstract
Membrane deformation is a necessary step in a number of cellular processes such as filopodia and invadopodia formation and has been shown to involve membrane shaping proteins containing membrane binding domains from the IRSp53-MIM protein family. In reconstituted membranes the membrane shaping domains can efficiently deform negatively charged membranes into tubules without any other proteins present. Here, we show that the IM domain (also called I-BAR domain) from the protein ABBA, forms semi-flexible nanotubes protruding into Giant Unilamellar lipid Vesicles (GUVs). By simultaneous quantification of tube intensity and tubular shape we find both the diameter and stiffness of the nanotubes. I-BAR decorated tubes were quantified to have a diameter of ~50 nm and exhibit no stiffening relative to protein free tubes of the same diameter. At high protein density the tubes are immobile whereas at lower density the tubes diffuse freely on the surface of the GUV. Bleaching experiments of the fluorescently tagged I-BAR confirmed that the mobility of the tubes correlates with the mobility of the I-BAR on the GUV membrane. Finally, at low density of I-BAR the protein upconcentrates within tubes protruding into the GUVs. This implies that I-BAR exhibits strong preference for negatively curved membranes.
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Affiliation(s)
- Younes F Barooji
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Andreas Rørvig-Lund
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Szabolcs Semsey
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - S Nader S Reihani
- Department of Physics, Sharif University of Technology, Teheran 11365-9161, Iran
| | - Poul M Bendix
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
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Yamamoto A, Abuillan W, Burk AS, Körner A, Ries A, Werz DB, Demé B, Tanaka M. Influence of length and conformation of saccharide head groups on the mechanics of glycolipid membranes: Unraveled by off-specular neutron scattering. J Chem Phys 2016; 142:154907. [PMID: 25903910 DOI: 10.1063/1.4918585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The mechanical properties of multilayer stacks of Gb3 glycolipid that play key roles in metabolic disorders (Fabry disease) were determined quantitatively by using specular and off-specular neutron scattering. Because of the geometry of membrane stacks deposited on planar substrates, the scattered intensity profile was analyzed in a 2D reciprocal space map as a function of in-plane and out-of-plane scattering vector components. The two principal mechanical parameters of the membranes, namely, bending rigidity and compression modulus, can be quantified by full calculation of scattering functions with the aid of an effective cut-off radius that takes the finite sample size into consideration. The bulkier "bent" Gb3 trisaccharide group makes the membrane mechanics distinctly different from cylindrical disaccharide (lactose) head groups and shorter "bent" disaccharide (gentiobiose) head groups. The mechanical characterization of membranes enriched with complex glycolipids has high importance in understanding the mechanisms of diseases such as sphingolipidoses caused by the accumulation of non-degenerated glycosphingolipids in lysosomes or inhibition of protein synthesis triggered by the specific binding of Shiga toxin to Gb3.
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Affiliation(s)
- Akihisa Yamamoto
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120 Heidelberg, Germany
| | - Wasim Abuillan
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120 Heidelberg, Germany
| | - Alexandra S Burk
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120 Heidelberg, Germany
| | - Alexander Körner
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120 Heidelberg, Germany
| | - Annika Ries
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, 37077 Göttingen, Germany
| | - Daniel B Werz
- Institute of Organic Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Bruno Demé
- Institut Laue-Langevin, 38042 Grenoble Cedex 9, Grenoble, France
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, 69120 Heidelberg, Germany
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Noguchi H, Sakashita A, Imai M. Shape transformations of toroidal vesicles. SOFT MATTER 2015; 11:193-201. [PMID: 25380516 DOI: 10.1039/c4sm01890g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Morphologies of genus-1 and 2 toroidal vesicles are studied numerically by dynamically triangulated membrane models and experimentally by confocal laser microscopy. Our simulation results reproduce shape transformations observed in our experiments well. At large reduced volumes of the genus-1 vesicles, obtained vesicle shapes agree with the previous theoretical prediction, in which axisymmetric shapes are assumed: double-necked stomatocyte, discoidal toroid, and circular toroid. However, for small reduced volumes, it is revealed that a non-axisymmetric discoidal toroid and handled discocyte exist in thermal equilibrium in the parameter range, in which the previous theory predicts axisymmetric discoidal shapes. Polygonal toroidal vesicles and subsequent budding transitions are also found. The entropy caused by shape fluctuations slightly modifies the stability of the vesicle shapes.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
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Fluorescent quantification of size and lamellarity of membrane nanotubes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:595-602. [PMID: 25256431 DOI: 10.1007/s00249-014-0989-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/28/2014] [Accepted: 09/08/2014] [Indexed: 12/31/2022]
Abstract
Membrane nanotubes, ubiquitous in cellular systems, adopt a spectrum of curvatures and shapes that are dictated by their intrinsic physical characteristics as well as their interactions with the local cellular environment. A high bending flexibility is needed in the crowded cytoplasm where tubes often need to bend significantly in the axial direction at sub-micron length scales. We find the stiffness of spontaneously formed membrane nanotubes by measuring the persistence length of reconstituted membrane nanotubes freely suspended in solution and imaged by fluorescence microscopy. By quantifying the tube diameter we demonstrate for the first time that the persistence length scales linearly with radius. Although most tubes are uni-lamellar, the predicted linear scaling between tube radius and persistence length allows us to identify tubes that spontaneously form as multilamellar structures upon hydration. We provide the first experimental evidence that illumination of lipid fluorophores can have a profound effect on the lipid bilayer which we sensitively detect as a continuous change in the tube persistence length with time. The novel assay and methodology here presented has potential for quantification of the structural reinforcement of membrane tubes by scaffolding proteins.
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