1
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Nowroz S, Nasrin SR, Kabir AMR, Yamashita T, Kusumoto T, Taira J, Tani M, Ichikawa M, Sada K, Kakugo A. Role of tubulin C-terminal tail on mechanical properties of microtubule. Biochem Biophys Res Commun 2024; 706:149761. [PMID: 38479245 DOI: 10.1016/j.bbrc.2024.149761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024]
Abstract
Tubulin C-terminal tail (CTT) is a disordered segment extended from each tubulin monomer of αβ tubulin heterodimers, the building blocks of microtubules. The tubulin CTT contributes to the cellular function of microtubules such as intracellular transportation by regulating their interaction with other proteins and cell shape regulation by controlling microtubule polymerization dynamics. Although the mechanical integrity of microtubules is crucial for their functions, the role of tubulin CTT on microtubule mechanical properties has remained elusive. In this work, we investigate the role of tubulin CTTs in regulating the mechanical properties of microtubules by estimating the persistence lengths and investigating the buckling behavior of microtubules with and without CTT. We find that microtubules with intact CTTs exhibit twice the rigidity of microtubules lacking tubulin CTTs. Our study will widen the scope of altering microtubule mechanical properties for its application in nano bio-devices and lead to novel therapeutic approaches for neurodegenerative diseases with altered microtubule properties.
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Affiliation(s)
- Senjuti Nowroz
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | - Syeda Rubaiya Nasrin
- Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | | | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan; Deaprtment of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, 142-8501, Japan
| | - Tomoichiro Kusumoto
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Junichi Taira
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Marie Tani
- Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Masatoshi Ichikawa
- Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan; Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akira Kakugo
- Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
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2
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Inoue D, Ohashi K, Takasuka TE, Kakugo A. In Vitro Synthesis and Design of Kinesin Biomolecular Motors by Cell-Free Protein Synthesis. ACS Synth Biol 2023; 12:1624-1631. [PMID: 37219894 DOI: 10.1021/acssynbio.3c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Kinesin is a biomolecular motor that generates force and motility along microtubule cytoskeletons in cells. Owing to their ability to manipulate cellular nanoscale components, microtubule/kinesin systems show great promise as actuators of nanodevices. However, classical in vivo protein production has some limitations for the design and production of kinesins. Designing and producing kinesins is laborious, and conventional protein production requires specific facilities to create and contain recombinant organisms. Here, we demonstrated the in vitro synthesis and editing of functional kinesins using a wheat germ cell-free protein synthesis system. The synthesized kinesins propelled microtubules on a kinesin-coated substrate and showed a higher binding affinity with microtubules than E. coli-produced kinesins. We also successfully incorporated affinity tags into the kinesins by extending the original sequence of the DNA template by PCR. Our method will accelerate the study of biomolecular motor systems and encourage their wider use in various nanotechnology applications.
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Affiliation(s)
- Daisuke Inoue
- Faculty of Design, Kyushu University, Room 605, Building 3, Shiobaru 4-9-1, Minami-Ku, Fukuoka 815-8540, Japan
| | - Keisuke Ohashi
- Graduate School of Global Food Resources, Hokkaido University, Sapporo 060-0810, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-0810, Japan
| | - Taichi E Takasuka
- Graduate School of Global Food Resources, Hokkaido University, Sapporo 060-0810, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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3
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Nishida K, Matsumura K, Tamura M, Nakamichi T, Shimamori K, Kuragano M, Kabir AMR, Kakugo A, Kotani S, Nishishita N, Tokuraku K. Effects of three microtubule-associated proteins (MAP2, MAP4, and Tau) on microtubules' physical properties and neurite morphology. Sci Rep 2023; 13:8870. [PMID: 37258650 DOI: 10.1038/s41598-023-36073-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/29/2023] [Indexed: 06/02/2023] Open
Abstract
The physical properties of cytoskeletal microtubules have a multifaceted effect on the expression of their cellular functions. A superfamily of microtubule-associated proteins, MAP2, MAP4, and tau, promote the polymerization of microtubules, stabilize the formed microtubules, and affect the physical properties of microtubules. Here, we show differences in the effects of these three MAPs on the physical properties of microtubules. When microtubule-binding domain fragments of MAP2, tau, and three MAP4 isoforms were added to microtubules in vitro and observed by fluorescence microscopy, tau-bound microtubules showed a straighter morphology than the microtubules bound by MAP2 and the three MAP4 isoforms. Flexural rigidity was evaluated by the shape of the teardrop pattern formed when microtubules were placed in a hydrodynamic flow, revealing that tau-bound microtubules were the least flexible. When full-length MAPs fused with EGFP were expressed in human neuroblastoma (SH-SY5Y) cells, the microtubules in apical regions of protrusions expressing tau were straighter than in cells expressing MAP2 and MAP4. On the other hand, the protrusions of tau-expressing cells had the fewest branches. These results suggest that the properties of microtubules, which are regulated by MAPs, contribute to the morphogenesis of neurites.
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Affiliation(s)
- Kohei Nishida
- Graduate School of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
| | - Kosuke Matsumura
- Graduate School of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
| | - Miki Tamura
- Graduate School of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
| | - Takuto Nakamichi
- Graduate School of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
| | - Keiya Shimamori
- Graduate School of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
| | - Masahiro Kuragano
- Graduate School of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan
| | | | - Akira Kakugo
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Susumu Kotani
- Faculty of Science, Kanagawa University, Kanagawa, 221-8686, Japan
| | - Naoki Nishishita
- Regenerative Medicine and Cell Therapy Laboratories, Kaneka Corporation, Kobe, 650-0047, Japan
| | - Kiyotaka Tokuraku
- Graduate School of Engineering, Muroran Institute of Technology, Muroran, 050-8585, Japan.
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4
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Inaba H, Sakaguchi M, Watari S, Ogawa S, Kabir AMR, Kakugo A, Sada K, Matsuura K. Reversible Photocontrol of Microtubule Stability by Spiropyran-Conjugated Tau-Derived Peptides. Chembiochem 2023; 24:e202200782. [PMID: 36935355 DOI: 10.1002/cbic.202200782] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 03/21/2023]
Abstract
Spatiotemporal modulation of microtubules by light has become an important aspect of the biological and nanotechnological applications of microtubules. We previously developed a Tau-derived peptide as a binding unit to the inside of microtubules. Here, we conjugated the Tau-derived peptide to spiropyran, which is reversibly converted to merocyanine by light, as a reversible photocontrol system to stabilize microtubules. Among the synthesized peptides with spiropyran/merocyanine at different positions, several peptides were bound to the inside of microtubules and stabilized the structures of microtubules. The peptide with spiropyran at the N-terminus induced polymerization and stabilization of microtubules, whereas the same peptide with the merocyanine form did not exert these effects. Reversible formation and dissociation of microtubules were achieved using the peptide with spiropyran conjugated at the N-terminus and irradiation with UV and visible light. Spiropyran-conjugated Tau-derived peptides would be useful for spatiotemporal modulation of microtubule stability through reversible photocontrol of binding.
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Affiliation(s)
- Hiroshi Inaba
- Tottori University: Tottori Daigaku, Department of Chemistry and Biotechnology, Graduate School of Engineering, Koyama-Minami 4-101, 680-8552, Tottori, JAPAN
| | - Minamo Sakaguchi
- Tottori University: Tottori Daigaku, Department of Chemistry and Biotechnology, Graduate School of Engineering, Koyama-Minami 4-101, 680-8552, Tottori, JAPAN
| | - Soei Watari
- Tottori University: Tottori Daigaku, Department of Chemistry and Biotechnology, Graduate School of Engineering, Koyama-Minami 4-101, 680-8552, Tottori, JAPAN
| | - Shigesaburo Ogawa
- Tottori University: Tottori Daigaku, Department of Chemistry and Biotechnology, Graduate School of Engineering, Koyama-Minami 4-101, 680-8552, Tottori, JAPAN
| | - Arif Md Rashedul Kabir
- Hokkaido University: Hokkaido Daigaku, Faculty of Science, Kita 10 Nishi 8, Kita-ku, 060-0810, Sapporo, JAPAN
| | - Akira Kakugo
- Kyoto University: Kyoto Daigaku, Department of Physics, Graduate School of Science, Oiwake-cho, Kitashirakawa, Sakyo-ku, 606-8502, Kyoto, JAPAN
| | - Kazuki Sada
- Hokkaido University: Hokkaido Daigaku, Faculty of Science, Kita 10 Nishi 8, Kita-ku, 060-0810, Sapporo, JAPAN
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5
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Rashid MR, Ganser C, Akter M, Nasrin SR, Kabir AMR, Sada K, Uchihashi T, Kakugo A. 3D structure of ring-shaped microtubule swarms revealed by high-speed atomic force microscopy. CHEM LETT 2023. [DOI: 10.1246/cl.220491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mst. Rubaya Rashid
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Christian Ganser
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | | | | | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takayuki Uchihashi
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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6
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Hiraiwa T, Akiyama R, Inoue D, Kabir AMR, Kakugo A. Collision-induced torque mediates the transition of chiral dynamic patterns formed by active particles. Phys Chem Chem Phys 2022; 24:28782-28787. [PMID: 36382471 DOI: 10.1039/d2cp03879j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Controlling the patterns formed by self-propelled particles through dynamic self-organization is a challenging task. Although varieties of patterns associated with chiral self-propelled particles have been reported, essential factors that determine the morphology of the patterns have remained unclear. Here, we explore theoretically how torque formed upon collision of the particles affects the dynamic self-organization of the particles and determine the patterns. Based on a particle-based model with collision-induced torque and torque associated with self-propulsion, we find that introducing collision-induced torque turns the homogeneous bi-directionally aligned particles into rotating mono-polar flocks, which helps resolve a discrepancy in the earlier observations in microfilament gliding assays.
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Affiliation(s)
- Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore. .,Universal Biology Institute, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
| | - Daisuke Inoue
- Faculty of Design, Kyushu University, Fukuoka 815-8540, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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7
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Inaba H, Sueki Y, Ichikawa M, Kabir AMR, Iwasaki T, Shigematsu H, Kakugo A, Sada K, Tsukazaki T, Matsuura K. Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside. Sci Adv 2022; 8:eabq3817. [PMID: 36070375 PMCID: PMC9451167 DOI: 10.1126/sciadv.abq3817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/22/2022] [Indexed: 05/24/2023]
Abstract
Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Yurina Sueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Muneyoshi Ichikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | | | - Takashi Iwasaki
- Department of Bioresources Science, Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomoya Tsukazaki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
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8
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Watari S, Inaba H, Tamura T, Kabir AMR, Kakugo A, Sada K, Hamachi I, Matsuura K. Light-induced stabilization of microtubules by photo-crosslinking of a Tau-derived peptide. Chem Commun (Camb) 2022; 58:9190-9193. [PMID: 35929838 DOI: 10.1039/d2cc01890j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For light-induced stabilization of microtubules (MTs) to manipulate cells, a photo-reactive diazirine group was conjugated to a Tau-derived peptide, a motif binding on the inside of MTs. Ultraviolet (UV) light irradiation induced significant stabilization of MTs via the formation of a covalent bond of the peptide and showed toxicity.
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Affiliation(s)
- Soei Watari
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan.
| | - Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan. .,Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, 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, Nishikyo-ku, Kyoto 615-8530, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan. .,Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
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9
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Kabir AMR, Munmun T, Sada K, Kakugo A. Fluctuation in the Sliding Movement of Kinesin-Driven Microtubules Is Regulated Using the Deep-Sea Osmolyte Trimethylamine N-Oxide. ACS Omega 2022; 7:18597-18604. [PMID: 35694499 PMCID: PMC9178762 DOI: 10.1021/acsomega.2c01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Nowadays, biomolecular motor-based miniaturized lab-on-a-chip devices have been attracting much attention for their wide range of nanotechnological applications. Most of the applications are dependent on the motor-driven active transportation of their associated filamentous proteins as shuttles. Fluctuation in the movement of the shuttles is a major contributor to the dispersion in motor-driven active transportation, which limits the efficiency of the miniaturized devices. In this work, by employing the biomolecular motor kinesin and its associated protein filament microtubule as a model active transport system, we demonstrate that the deep-sea osmolyte trimethylamine N-oxide (TMAO) is useful in regulating the fluctuation in the motility of microtubule shuttles. We show that the motional diffusion coefficient, a measure of the fluctuation in the movement of the kinesin-propelled microtubules, gradually decreases upon increasing the concentration of TMAO in the transportation system. We have been able to reduce the motional diffusion coefficient of microtubules more than 200 times by employing TMAO at a concentration of 2 M. We also show that upon elimination of TMAO, the motional diffusion coefficient of microtubules can be restored, which confirms that TMAO can be used as a tool to reversibly regulate the fluctuation in the sliding movement of kinesin-propelled microtubule shuttles. Such reversible regulation of the dynamic behavior of the shuttles does not require sacrificing the concentration of fuel used for transportation. Our results confirm the ability to manipulate the nanoscale motion of biomolecular motor-driven active transporters in an artificial environment. This work is expected to further enhance the tunability of biomolecular motor functions, which, in turn, will foster their nanotechnological applications based on active transportation.
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Affiliation(s)
| | - Tasrina Munmun
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty
of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Faculty
of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
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10
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Ishii S, Akter M, Keya JJ, Rashid MR, Afroze F, Nasrin SR, Kakugo A. Purification of Tubulin from Porcine Brain and its Fluorescence Dye Modification. Methods Mol Biol 2022; 2430:3-16. [PMID: 35476322 DOI: 10.1007/978-1-0716-1983-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Filamentous microtubules, polymers of the heterodimeric protein tubulins play one of the major roles in the emergent nano-biotechnological devices. To develop the feature of those devices, it is important to understand the function of microtubule in in vitro, hence, the availability of purified αβ-tubulin is required. Additionally, fluorescently labeled tubulin has become a powerful approach for extensively studying the dynamics of these components. In this chapter, the process of purifying the heterodimeric αβ-tubulin from porcine brain will be described, as well as the process of labeling of the purified tubulin with fluorescence dye.
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Affiliation(s)
- Satsuki Ishii
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Mst Rubaya Rashid
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Farhana Afroze
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | | | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan. .,Faculty of Science, Hokkaido University, Sapporo, Japan.
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11
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Akter M, Keya JJ, Kayano K, Kabir AMR, Inoue D, Hess H, Sada K, Kuzuya A, Asanuma H, Kakugo A. Cooperative cargo transportation by a swarm of molecular machines. Sci Robot 2022; 7:eabm0677. [PMID: 35442703 DOI: 10.1126/scirobotics.abm0677] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cooperation is a strategy that has been adopted by groups of organisms to execute complex tasks more efficiently than single entities. Cooperation increases the robustness and flexibility of the working groups and permits sharing of the workload among individuals. However, the utilization of this strategy in artificial systems at the molecular level, which could enable substantial advances in microrobotics and nanotechnology, remains highly challenging. Here, we demonstrate molecular transportation through the cooperative action of a large number of artificial molecular machines, photoresponsive DNA-conjugated microtubules driven by kinesin motor proteins. Mechanical communication via conjugated photoresponsive DNA enables these microtubules to organize into groups upon photoirradiation. The groups of transporters load and transport cargo, and cargo unloading is achieved by dissociating the groups into single microtubules. The group formation permits the loading and transport of cargoes with larger sizes and in larger numbers over long distances compared with single transporters. We also demonstrate that cargo can be collected at user-determined locations defined by ultraviolet light exposure. This work demonstrates cooperative task performance by molecular machines, which will help to construct molecular robots with advanced functionalities in the future.
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Affiliation(s)
- M Akter
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - J J Keya
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - K Kayano
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - A M R Kabir
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - D Inoue
- Faculty of Design, Kyushu University, Fukuoka 815-8540, Japan
| | - H Hess
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - K Sada
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - A Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University, Osaka 564-8680, Japan
| | - H Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - A Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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12
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Kabir AMR, Munmun T, Hayashi T, Yasuda S, Kimura AP, Kinoshita M, Murata T, Sada K, Kakugo A. Controlling the Rigidity of Kinesin-Propelled Microtubules in an In Vitro Gliding Assay Using the Deep-Sea Osmolyte Trimethylamine N-Oxide. ACS Omega 2022; 7:3796-3803. [PMID: 35128287 PMCID: PMC8811939 DOI: 10.1021/acsomega.1c06699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
The biomolecular motor protein kinesin and its associated filamentous protein microtubule have been finding important nanotechnological applications in the recent years. Rigidity of the microtubules, which are propelled by kinesin motors in an in vitro gliding assay, is an important metric that determines the success of utilization of microtubules and kinesins in various applications, such as transportation, sensing, sorting, molecular robotics, etc. Therefore, regulating the rigidity of kinesin-propelled microtubules has been critical. In this work, we report a simple strategy to regulate the rigidity of kinesin-propelled microtubules in an in vitro gliding assay. We demonstrate that rigidity of the microtubules, propelled by kinesins in an in vitro gliding assay, can be modulated simply by using the natural osmolyte trimethylamine N-oxide (TMAO). By varying the concentration of TMAO in the gliding assay, the rigidity of microtubules can be modulated over a wide range. Based on this strategy, we are able to reduce the persistence length of microtubules, a measure of microtubule rigidity, ∼8 fold by using TMAO at the concentration of 1.5 M. Furthermore, we found that the decreased rigidity of the kinesin-propelled microtubules can be restored upon elimination of TMAO from the in vitro gliding assay. Alteration in the rigidity of microtubules is accounted for by the non-uniformity of the force applied by kinesins along the microtubules in the presence of TMAO. This work offers a facile strategy to reversibly regulate the rigidity of kinesin-propelled microtubules in situ, which would widen the applications of the biomolecular motor kinesin and its associated protein microtubule in various fields.
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Affiliation(s)
| | - Tasrina Munmun
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomohiko Hayashi
- Institute
of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Satoshi Yasuda
- Graduate
School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Membrane
Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Atsushi P. Kimura
- Faculty
of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Masahiro Kinoshita
- Institute
of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate
School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Membrane
Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Takeshi Murata
- Graduate
School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Membrane
Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Kazuki Sada
- Faculty
of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Faculty
of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
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13
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Inaba H, Kabir AMR, Kakugo A, Sada K, Matsuura K. Structural Changes of Microtubules by Encapsulation of Gold Nanoparticles Using a Tau-Derived Peptide. CHEM LETT 2022. [DOI: 10.1246/cl.210761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552 Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552 Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, 060-0810 Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810 Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, 060-0810 Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810 Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552 Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552 Japan
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14
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Ishii S, Murayama K, Sada K, Asanuma H, Kakugo A. Unexpected Dissociation of Photoresponsive UV-ON DNA Carrying p-tert-Butyl Azobenzene under UV Light Irradiation. CHEM LETT 2022. [DOI: 10.1246/cl.210788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Satsuki Ishii
- Graduate School of Chemical Sciences & Engineering, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Aichi, 464-8603, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences & Engineering, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Aichi, 464-8603, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences & Engineering, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
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15
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Kawai K, Ikeda K, Sato A, Kabasawa A, Kojima M, Kokado K, Kakugo A, Sada K, Yoshino T, Matsunaga S. 1,2-Disubstituted 1,2-Dihydro-1,2,4,5-tetrazine-3,6-dione as a Dynamic Covalent Bonding Unit at Room Temperature. J Am Chem Soc 2022; 144:1370-1379. [PMID: 35040645 DOI: 10.1021/jacs.1c11665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dynamic covalent bonds are useful tools in a wide range of applications. Although various reversible chemical reactions have been studied for this purpose, the requirement for harsh conditions, such as high temperature and low or high pH, to activate generally stable covalent bonds limits their potential applications involving biomolecules or household utilization. Here, we report the design, synthesis, characterization, and dynamic covalent bonding properties of 1,2-disubstituted 1,2-dihydro-1,2,4,5-tetrazine-3,6-dione (TETRAD). Hetero-Diels-Alder reactions of TETRAD with furan derivatives and their retro-reactions proceeded rapidly at room temperature under neutral conditions, enabling a chemically induced sol-gel transition system.
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Affiliation(s)
- Kentaro Kawai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Ikeda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akane Sato
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akira Kabasawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Masahiro Kojima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kenta Kokado
- Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
| | - Akira Kakugo
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Tatsuhiko Yoshino
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Shigeki Matsunaga
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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16
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Keya JJ, Akter M, Kabir AMR, Ishii S, Kakugo A. Fabrication of Artificial Muscle from Microtubules, Kinesins, and DNA Origami Nanostructures. Methods Mol Biol 2022; 2430:231-240. [PMID: 35476336 DOI: 10.1007/978-1-0716-1983-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fabrication of molecular devices using biomolecules through biomimetic approaches has witnessed a surge in interest in recent years. DNA a versatile programmable material offers an opportunity to realize complicated operations through the designing of various nanostructures such as DNA origami. Here we describe the methods to use DNA origami for the self-assembly of the biomolecular motor system, microtubule (MT)-kinesin. A rodlike DNA origami motif facilitates the self-assembly of MTs into asters. A smooth muscle like molecular contraction system could be realized following the method where DNA mediated self-assembly of MTs permits dynamic contraction in the presence of kinesins through an energy dissipative process.
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Affiliation(s)
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Satsuki Ishii
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
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17
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Keya JJ, Kabir AMR, Akter M, Kakugo A. Dynamic Pattern Formation of Active Matters Triggered by Mechanical Stimuli. Methods Mol Biol 2022; 2430:193-203. [PMID: 35476333 DOI: 10.1007/978-1-0716-1983-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In vitro gliding assay of the filamentous protein microtubule (MT) on a kinesin motor protein coated surface has appeared as a classic platform for studying active matters. At high densities, the gliding MTs spontaneously align and self-organize into fascinating large-scale patterns. Application of mechanical stimuli e.g., stretching stimuli to the MTs gliding on a kinesin-coated surface can modulate their self-organization and patterns according to the boundary conditions. Depending on the mode of stretching, MT at high densities change their moving direction and exhibit various kinds of patterns such as stream, zigzag and vortex pattern. In this chapter, we discuss detail procedures on how to apply mechanical stimuli to the moving MTs on a kinesin coated substrate.
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Affiliation(s)
| | | | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
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18
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Nasrin SR, Kabir AMR, Kakugo A. Cargo Transport by Microtubule-Associated Motor Protein Along Mechanically Deformed Microtubules. Methods Mol Biol 2022; 2430:291-302. [PMID: 35476340 DOI: 10.1007/978-1-0716-1983-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mechanical forces play pivotal roles in regulating various cellular functions. Biomolecular motor protein-driven intracellular transportation is one example which is affected by mechanical forces, although the mechanism at molecular level is unknown. In this chapter, we describe deformation of microtubules under compressive stress and we show that such deformation of microtubules affects the kinetics of dynein-driven cargo transportation along the microtubules. The extent of alteration in the kinetics of dynein-driven transportation is found strongly dependent on the extent of deformation of microtubules under compressive stress.
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Affiliation(s)
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan.
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19
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Nasrin SR, Afroze F, Kabir AMR, Kakugo A. Mechanical Deformation of Microtubules on a Two-Dimensional Elastic Medium. Methods Mol Biol 2022; 2430:303-314. [PMID: 35476341 DOI: 10.1007/978-1-0716-1983-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microtubule, the most rigid filamentous protein in cytoskeleton, plays significant roles in cellular mechano-transduction and mechano-regulation of cellular functions. In cells, the mechanical stress serves as a prevalent stimulus to frequently cause deformation of the microtubules participating in various cellular events. While the experimental and simulation-based approaches have confirmed the role of mechanical stress to tune mechanical properties of microtubule. Yet, the effect of mechanical force on the structural stability and the mechanism of microtubule deformation have remained obscure. Here, we describe the mechanical stress-induced deformation of microtubules using a custom-made mechanical device. We designed the device in a way which allows the microtubules to undergo deformation as response to the applied stress while attached on a two-dimensional elastic substrate through interaction with microtubule-associated motor protein, kinesin. We provide here the method to cause controlled bucking or fragmentation of microtubules by applying compressive or tensile stress on the microtubules, respectively. Such study is crucial to understand the mechanism of deformation in microtubules in cellular environment and their consequences in physiological activities.
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Affiliation(s)
| | - Farhana Afroze
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan.
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20
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Keya JJ, Akter M, Kabir AMR, Rashid MR, Kakugo A. Construction of Molecular Robots from Microtubules for Programmable Swarming. Methods Mol Biol 2022; 2430:219-230. [PMID: 35476335 DOI: 10.1007/978-1-0716-1983-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Swarm robotics has been attracting much attention in recent years in the field of robotics. This chapter describes a methodology for the construction of molecular swarm robots through precise control of active self-assembly of microtubules (MTs). Detailed protocols are presented for the construction of molecular robots through conjugation of DNA to MTs and demonstration of swarming of the MTs. The swarming is mediated by DNA-based interaction and photoirradiation which act as processors and sensors respectively for the robots. Furthermore, the required protocols to utilize the swarming of MTs for molecular computation is also described.
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Affiliation(s)
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Mst Rubaya Rashid
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
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21
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Araki S, Beppu K, Kabir AMR, Kakugo A, Maeda YT. Controlling Collective Motion of Kinesin-Driven Microtubules via Patterning of Topographic Landscapes. Nano Lett 2021; 21:10478-10485. [PMID: 34874725 DOI: 10.1021/acs.nanolett.1c03952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biomolecular motor proteins that generate forces by consuming chemical energy obtained from ATP hydrolysis play pivotal roles in organizing cytoskeletal structures in living cells. An ability to control cytoskeletal structures would benefit programmable protein patterning; however, our current knowledge is limited because of the underdevelopment of engineering approaches for controlling pattern formation. Here, we demonstrate the controlling of self-assembled patterns of microtubules (MTs) driven by kinesin motors by designing the boundary shape in fabricated microwells. By manipulating the collision angle of gliding MTs defined by the boundary shape, the self-assembly of MTs can be controlled to form protruding bundle and bridge patterns. Corroborated by the theory of self-propelled rods, we further show that the alignment of MTs determines the transition between the assembled patterns, providing a blueprint to reconstruct bridge structures in microchannels. Our findings introduce the tailoring of the self-organization of cytoskeletons and motor proteins for nanotechnological applications.
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Affiliation(s)
- Shunya Araki
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Kazusa Beppu
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Arif Md Rashedul Kabir
- Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Hokkaido Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Hokkaido Japan
| | - Yusuke T Maeda
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
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22
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Nasrin SR, Ganser C, Nishikawa S, Kabir AMR, Sada K, Yamashita T, Ikeguchi M, Uchihashi T, Hess H, Kakugo A. Deformation of microtubules regulates translocation dynamics of kinesin. Sci Adv 2021; 7:eabf2211. [PMID: 34644102 PMCID: PMC10763888 DOI: 10.1126/sciadv.abf2211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Microtubules, the most rigid components of the cytoskeleton, can be key transduction elements between external forces and the cellular environment. Mechanical forces induce microtubule deformation, which is presumed to be critical for the mechanoregulation of cellular events. However, concrete evidence is lacking. In this work, with high-speed atomic force microscopy, we unravel how microtubule deformation regulates the translocation of the microtubule-associated motor protein kinesin-1, responsible for intracellular transport. Our results show that the microtubule deformation by bending impedes the translocation dynamics of kinesins along them. Molecular dynamics simulation shows that the hindered translocation of kinesins can be attributed to an enhanced affinity of kinesins to the microtubule structural units in microtubules deformed by bending. This study advances our understanding of the role of cytoskeletal components in mechanotransduction.
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Affiliation(s)
| | - Christian Ganser
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Seiji Nishikawa
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | | | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takayuki Uchihashi
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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23
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Afroze F, Inoue D, Farhana TI, Hiraiwa T, Akiyama R, Kabir AMR, Sada K, Kakugo A. Monopolar flocking of microtubules in collective motion. Biochem Biophys Res Commun 2021; 563:73-78. [PMID: 34062389 DOI: 10.1016/j.bbrc.2021.05.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022]
Abstract
Flocking is a fascinating coordinated behavior of living organisms or self-propelled particles (SPPs). Particularly, monopolar flocking has been attractive due to its potential applications in various fields. However, the underlying mechanism behind flocking and emergence of monopolar motion in flocking of SPPs has remained obscured. Here, we demonstrate monopolar flocking of kinesin-driven microtubules, a self-propelled biomolecular motor system. Microtubules with an intrinsic structural chirality preferentially move towards counter-clockwise direction. At high density, the CCW motion of microtubules facilitates monopolar flocking and formation of a spiral pattern. The monopolar flocking of microtubules is accounted for by a torque generated when the motion of microtubules was obstructed due to collisions. Our results shed light on flocking and emergence of monopolar motion in flocking of chiral active matters. This work will help regulate the polarity in collective motion of SPPs which in turn will widen their applications in nanotechnology, materials science and engineering.
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Affiliation(s)
- Farhana Afroze
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan
| | - Daisuke Inoue
- Faculty of Design, Kyushu University, Fukuoka, 815-8540, Japan
| | - Tamanna Ishrat Farhana
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore; Universal Biology Institute, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka, 819-0395, Japan
| | | | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan; Faculty of Science, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan; Faculty of Science, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan.
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24
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Kabir AMR, Sada K, Kakugo A. Controlling the length of self-assembled microtubes through mechanical stress-induced scission. Chem Commun (Camb) 2021; 57:468-471. [PMID: 33367340 DOI: 10.1039/d0cc07327j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that mechanical stress-induced scission is an effective strategy to control the length of self-assembled microtubes. By applying mechanical stress with variable magnitude and mode, the length of microtubes can be tightly regulated. We have succeeded in reducing the average length of microtubes ∼twenty-fold through stretching and compression. The mechanical stress-induced scission of self-assembled, long microtubes into smaller fragments has no adverse effect on the functionality of the microtubes. This work will foster the applications of length-controlled, self-assembled microtubes in various fields.
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25
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Pramudwiatmoko A, Gutmann G, Ueno Y, Kakugo A, Yamamura M, Konagaya A. Tensegrity representation of microtubule objects using unified particle objects and springs. CBIJ 2020. [DOI: 10.1273/cbij.20.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Arif Pramudwiatmoko
- School of Computing, Department of Computer Science, Tokyo Institute of Technology
- Universitas Teknologi Yogyakarta
| | - Gregory Gutmann
- School of Computing, Department of Computer Science, Tokyo Institute of Technology
| | - Yutaka Ueno
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology
| | - Akira Kakugo
- Faculty of Science, Hokkaido University
- Graduate School of Chemical Sciences and Engineering, Hokkaido University
| | - Masayuki Yamamura
- School of Computing, Department of Computer Science, Tokyo Institute of Technology
| | - Akihiko Konagaya
- School of Computing, Department of Computer Science, Tokyo Institute of Technology
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Akter M, Keya JJ, Kabir AMR, Asanuma H, Murayama K, Sada K, Kakugo A. Photo-regulated trajectories of gliding microtubules conjugated with DNA. Chem Commun (Camb) 2020; 56:7953-7956. [PMID: 32537622 DOI: 10.1039/d0cc03124k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We regulate the persistency in motion of kinesin-driven microtubules (MTs) simply using a photoresponsive DNA (pDNA) and ultraviolet (UV)-visible light. The path persistence length of MTs, which is a measure of the persistency in their motion, increases and decreases upon illuminating the MTs with UV and visible light respectively. Moreover, pDNA is found to work as a shield for MTs against damage under UV irradiation.
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Affiliation(s)
- Mousumi Akter
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
| | | | | | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Osaka, 564-8680, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Osaka, 564-8680, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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Inaba H, Yamada M, Rashid MR, Kabir AMR, Kakugo A, Sada K, Matsuura K. Magnetic Force-Induced Alignment of Microtubules by Encapsulation of CoPt Nanoparticles Using a Tau-Derived Peptide. Nano Lett 2020; 20:5251-5258. [PMID: 32525681 DOI: 10.1021/acs.nanolett.0c01573] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Construction of magnetotactic materials is a significant challenge in nanotechnology applications such as nanodevices and nanotransportation. Artificial magnetotactic materials can be designed from magnetotactic bacteria because these bacteria use magnetic nanoparticles for aligning with and moving within magnetic fields. Microtubules are attractive scaffolds to construct magnetotactic materials because of their intrinsic motility. Nonetheless, it is challenging to magnetically control their orientation while retaining their motility by conjugating magnetic nanoparticles on their outer surface. Here we solve the issue by encapsulating magnetic cobalt-platinum nanoparticles inside microtubules using our developed Tau-derived peptide that binds to their internal pockets. The in situ growth of cobalt-platinum nanoparticles resulted in the formation of a linear-chain assembly of nanoparticles inside the microtubules. The magnetic microtubules significantly aligned with a high order parameter (0.71) along the weak magnetic field (0.37 T) and showed increased motility. This work provides a new concept for designing magnetotactic materials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Mayuki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Mst Rubaya Rashid
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Arif Md Rashedul Kabir
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
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Abstract
Recent advancements in molecular robotics have been greatly contributed by the progress in various fields of science and technology, particularly in supramolecular chemistry, bio- and nanotechnology, and informatics. Yet one of the biggest challenges in molecular robotics has been controlling a large number of robots at a time and employing the robots for any specific task as flocks in order to harness emergent functions. Swarming of molecular robots has emerged as a new paradigm with potentials to overcome this hurdle in molecular robotics. In this review article, we comprehensively discuss the latest developments in swarm molecular robotics, particularly emphasizing the effective utilization of bio- and nanotechnology in swarming of molecular robots. Importance of tuning the mutual interaction among the molecular robots in regulation of their swarming is introduced. Successful utilization of DNA, photoresponsive molecules, and natural molecular machines in swarming of molecular robots to provide them with processing, sensing, and actuating ability is highlighted. The potentials of molecular swarm robots for practical applications by means of their ability to participate in logical operations and molecular computations are also discussed. Prospects of the molecular swarm robots in utilizing the emergent functions through swarming are also emphasized together with their future perspectives.
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Affiliation(s)
| | - Daisuke Inoue
- Faculty of Design, Department of Human Science, Kyushu University, Fukuoka, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
- CONTACT Akira Kakugo Hokkaido University, Sapporo shi, Kita ku, Kita 10, Nishi 8, Science building-7, Room-215, Sapporo060-0810, Japan
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Keya JJ, Kudoh H, Kabir AMR, Inoue D, Miyamoto N, Tani T, Kakugo A, Shikinaka K. Radial alignment of microtubules through tubulin polymerization in an evaporating droplet. PLoS One 2020; 15:e0231352. [PMID: 32275729 PMCID: PMC7147791 DOI: 10.1371/journal.pone.0231352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/21/2020] [Indexed: 01/08/2023] Open
Abstract
We report the formation of spherulites from droplets of highly concentrated tubulin solution via nucleation and subsequent polymerization to microtubules (MTs) under water evaporation by heating. Radial alignment of MTs in the spherulites was confirmed by the optical properties of the spherulites observed using polarized optical microscopy and fluorescence microscopy. Temperature and concentration of tubulins were found as important parameters to control the spherulite pattern formation of MTs where evaporation plays a significant role. The alignment of MTs was regulated reversibly by temperature induced polymerization and depolymerization of tubulins. The formation of the MTs patterns was also confirmed at the molecular level from the small angle X-ray measurements. This work provides a simple method for obtaining radially aligned arrays of MTs.
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Affiliation(s)
| | - Hiroki Kudoh
- Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | | | - Daisuke Inoue
- Department of Human Science Faculty of Design, Kyushu University, Fukuoka, Japan
| | - Nobuyoshi Miyamoto
- Department of Life, Environment and Materials Science, Fukuoka Institute of Technology, Fukuoka, Japan
| | - Tomomi Tani
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail: (AK); (KS)
| | - Kazuhiro Shikinaka
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology, Sendai, Miyagi, Japan
- * E-mail: (AK); (KS)
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Abstract
Biomolecular motor systems are the smallest natural machines with an ability to convert chemical energy into mechanical work with remarkably high efficiency. Such attractive features enabled biomolecular motors to become classic tools in soft matter research over the past decade. For designing suitably engineered biomimetic systems, the biomolecular motors can potentially be used as molecular engines that can transform energy and ensure great advantages for the construction of bio-nanodevices and molecular robots. From the optimization of their prolonged lifetime to coordinate them into highly complex and ordered structures, enormous efforts have been devoted to make them useful in the synthetic environment. Synchronous operation of the biomolecular engines is one of the key criteria to coordinate them into certain different patterns, which depends on the local interaction of biomolecular motors. Utilizing chemical and physical stimuli, synchronization of biomolecular motor systems has become possible, which allows them to coordinate into different higher ordered patterns with different modes of functionality. Recently, programmed synchronous operation of the biomolecular engines has also been demonstrated, using a smart biomaterial to build up swarms reminiscent of nature. Here, we review the recent progress in the synchronized operation of biomolecular motors in engineered systems to explicitly program their interaction and further their applications. Such developments in the coordination of biomolecular motors have opened a broad way to explore the construction of future autonomous molecular machines and robots based on synchronization of biomolecular engines.
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Affiliation(s)
- Jakia Jannat Keya
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
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Kabir AMR, Sada K, Kakugo A. Breaking of buckled microtubules is mediated by kinesins. Biochem Biophys Res Commun 2020; 524:249-254. [PMID: 31983434 DOI: 10.1016/j.bbrc.2020.01.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/14/2020] [Indexed: 11/28/2022]
Abstract
Microtubule is the most rigid component of eukaryotic cytoskeleton that plays pivotal roles in many important cellular events. Microtubules are known to undergo bending or buckling in cells which often results in breaking of this cytoskeletal protein filament. Various cellular events such as cell migration, chromosome segregation, etc. are dependent on the buckling induced breaking of microtubules. However, the reason behind the breaking of buckled microtubules in cell has remained obscure yet. In this work, we have demonstrated breaking of microtubules on a 2D elastic medium by applying compressive stress. The applied compressive stress caused buckling of the microtubules which ultimately resulted in their breaking. We show that breaking of the buckled microtubules cannot be accounted for by considering the changes in curvature of the microtubules due to mechanical deformation. Our results confirm that, it is the interaction of kinesin, a microtubule-associated motor protein, with microtubules which plays the key role in breaking of the buckled microtubules on the 2D elastic medium. The breaking of buckled microtubules is ascribed to decrease in rigidity of microtubules upon interaction with kinesins. This work for the first time confirms the involvement of a microtubule-associated motor protein in breaking of microtubules under compressive stress, which will help further clarify the mechanism of breaking of buckled microtubules in cells and its significance in the cellular events.
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Affiliation(s)
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
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Nasrin SR, Afrin T, Kabir AMR, Inoue D, Torisawa T, Oiwa K, Sada K, Kakugo A. Regulation of Biomolecular-Motor-Driven Cargo Transport by Microtubules under Mechanical Stress. ACS Appl Bio Mater 2020; 3:1875-1883. [DOI: 10.1021/acsabm.9b01010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Syeda Rubaiya Nasrin
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | - Tanjina Afrin
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | | | - Daisuke Inoue
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | - Takayuki Torisawa
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima 411-8540, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima 411-8540, Japan
| | - Kazuhiro Oiwa
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Hyogo, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
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Munmun T, Kabir AMR, Katsumoto Y, Sada K, Kakugo A. Controlling the kinetics of interaction between microtubules and kinesins over a wide temperature range using the deep-sea osmolyte trimethylamine N-oxide. Chem Commun (Camb) 2020; 56:1187-1190. [PMID: 31922177 DOI: 10.1039/c9cc09324a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trimethylamine N-oxide is found to be effective in regulating the interaction between microtubules and kinesins over a wide temperature range. The lifetime of the motility of microtubules on kinesins at high temperatures is prolonged using trimethylamine N-oxide. The activation energy of microtubule motility is increased by trimethylamine N-oxide. Prolonged operation at high temperatures decreased the activation energy of MT motility despite the increase in concentration of trimethylamine N-oxide.
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Affiliation(s)
- Tasrina Munmun
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan.
| | | | - Yukiteru Katsumoto
- Department of Chemistry, Faculty of Science, Fukuoka University, Nanakuma 8-19-1, Jonan-ku, Fukuoka 814-0180, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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36
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Inoue D, Gutmann G, Nitta T, Kabir AMR, Konagaya A, Tokuraku K, Sada K, Hess H, Kakugo A. Adaptation of Patterns of Motile Filaments under Dynamic Boundary Conditions. ACS Nano 2019; 13:12452-12460. [PMID: 31585030 DOI: 10.1021/acsnano.9b01450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Boundary conditions are important for pattern formation in active matter. However, it is still not well-understood how alterations in the boundary conditions (dynamic boundary conditions) impact pattern formation. To elucidate the effect of dynamic boundary conditions on the pattern formation by active matter, we investigate an in vitro gliding assay of microtubules on a deformable soft substrate. The dynamic boundary conditions were realized by applying mechanical stress through stretching and compression of the substrate during the gliding assay. A single cycle of stretch-and-compression (relaxation) of the substrate induces perpendicular alignment of microtubules relative to the stretch axis, whereas repeated cycles resulted in zigzag patterns of microtubules. Our model shows that the orientation angles of microtubules correspond to the direction to attain smooth movement without buckling, which is further amplified by the collective migration of the microtubules. Our results provide an insight into understanding the rich dynamics in self-organization arising in active matter subjected to time-dependent boundary conditions.
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Affiliation(s)
- Daisuke Inoue
- Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan
| | - Greg Gutmann
- Department of Computer Science , Tokyo Institute of Technology , Yokohama 226-8502 , Japan
| | - Takahiro Nitta
- Applied Physics Course, Faculty of Engineering , Gifu University , Gifu 501-1193 , Japan
| | | | - Akihiko Konagaya
- Department of Computer Science , Tokyo Institute of Technology , Yokohama 226-8502 , Japan
| | - Kiyotaka Tokuraku
- Department of Applied Sciences , Muroran Institute of Technology , Muroran 050-8585 , Japan
| | - Kazuki Sada
- Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan
- Graduate School of Chemical Sciences and Engineering , Hokkaido University , Sapporo 060-0810 , Japan
| | - Henry Hess
- Department of Biomedical Engineering , Columbia University , New York , New York 10027 , United States
| | - Akira Kakugo
- Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan
- Graduate School of Chemical Sciences and Engineering , Hokkaido University , Sapporo 060-0810 , Japan
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Nasrin SR, Rashedul Kabir AM, Konagaya A, Ishihara T, Sada K, Kakugo A. Stabilization of microtubules by cevipabulin. Biochem Biophys Res Commun 2019; 516:760-764. [DOI: 10.1016/j.bbrc.2019.06.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/20/2022]
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Inaba H, Yamamoto T, Iwasaki T, Kabir AMR, Kakugo A, Sada K, Matsuura K. Fluorescent Tau-derived Peptide for Monitoring Microtubules in Living Cells. ACS Omega 2019; 4:11245-11250. [PMID: 31460226 PMCID: PMC6648849 DOI: 10.1021/acsomega.9b01089] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/18/2019] [Indexed: 06/04/2023]
Abstract
Microtubules (MTs) are key cytoskeletal components that modulate various cellular activities with their dynamic structural changes, including polymerization and depolymerization. To monitor the dynamics of MTs in living cells, many drug-based fluorescent probes have been developed; however, these also potentially disturb the polymerization/depolymerization of MTs. Here, we report nondrug, peptide-based fluorescent probes to monitor MTs in living cells. We employed a Tau-derived peptide (TP) that has been shown to bind MTs without inhibiting polymerization/depolymerization in vitro. We show that a tetramethylrhodamine (TMR)-labeled TP (TP-TMR) is internalized into HepG2 cells and binds to intracellular MTs, enabling visualization of MTs as clear, fibrous structures. The binding of TP-TMR shows no apparent effects on polymerization/depolymerization of MTs induced by MT-targeted drugs and temperature change. The main uptake mechanism of TP-TMR was elucidated as endocytosis, and partial endosomal escape resulted in the binding of TP-TMR to MTs. TP-TMR exhibited no cytotoxicity compared with MT-targeted drug scaffolds. These results indicate that TP scaffolds can be exploited as useful MT-targeted tools in living cells, such as in long-term imaging of MTs.
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Affiliation(s)
- Hiroshi Inaba
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Takahisa Yamamoto
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Takashi Iwasaki
- Department
of Bioresources Science, Graduate School of Agricultural Sciences, Tottori University, Koyama-Minami 4-101, Tottori 680-8553, Japan
| | - Arif Md. Rashedul Kabir
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazunori Matsuura
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
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Matsuda K, Kabir AMR, Akamatsu N, Saito A, Ishikawa S, Matsuyama T, Ditzer O, Islam MS, Ohya Y, Sada K, Konagaya A, Kuzuya A, Kakugo A. Artificial Smooth Muscle Model Composed of Hierarchically Ordered Microtubule Asters Mediated by DNA Origami Nanostructures. Nano Lett 2019; 19:3933-3938. [PMID: 31037942 DOI: 10.1021/acs.nanolett.9b01201] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA has been well-known for its applications in programmable self-assembly of materials. Nonetheless, utility of DNA origami, which offers more opportunity to realize complicated operations, has been very limited. Here we report self-assembly of a biomolecular motor system, microtubule-kinesin mediated by DNA origami nanostructures. We demonstrate that a rodlike DNA origami motif facilitates self-assembly of microtubules into asters. A smooth-muscle like molecular contraction system has also been realized using the DNA origami in which self-assembled microtubules exhibited fast and dynamic contraction in the presence of kinesins through an energy dissipative process. This work provides potential nanotechnological applications of DNA and biomolecular motor proteins.
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Affiliation(s)
| | | | - Naohide Akamatsu
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
| | | | - Shumpei Ishikawa
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
| | - Tsuyoshi Matsuyama
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
| | - Oliver Ditzer
- Faculty of Chemistry and Food Chemistry , Technische Universität Dresden , Prüfungsamt, 01062 Dresden , Germany
| | - Md Sirajul Islam
- Organization for Research and Development of Innovative Science and Technology , Kansai University , Osaka 564-8680 , Japan
| | - Yuichi Ohya
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
- Organization for Research and Development of Innovative Science and Technology , Kansai University , Osaka 564-8680 , Japan
| | | | - Akihiko Konagaya
- Department of Computational Intelligence and Systems Science , Tokyo Institute of Technology , Kanagawa 226-8502 , Japan
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
- Organization for Research and Development of Innovative Science and Technology , Kansai University , Osaka 564-8680 , Japan
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Islam MJ, Matsuo K, Menezes HM, Takahashi M, Nakagawa H, Kakugo A, Sada K, Tamaoki N. Substrate selectivity and its mechanistic insight of the photo-responsive non-nucleoside triphosphate for myosin and kinesin. Org Biomol Chem 2019; 17:53-65. [PMID: 30534753 DOI: 10.1039/c8ob02714e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Linear motor proteins including kinesin and myosin are promising biomaterials for developing nano-devices. Photoswitchable substrates of these biomotors can be used to optically regulate the motility of their associated cytoskeletal filaments in in vitro systems. Here, we describe the discovery of the myosin selective azobenzene-tethered triphosphate. It enables the specific photocontrol over myosin in a reversible mode with the composite motility assay composed of both kinesin and myosin. The mechanistic insight into this myosin selectivity is also explained with the docking simulation study.
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Affiliation(s)
- Md Jahirul Islam
- Research Institute for Electronic Science, Hokkaido University, Kita 20, Nishi 10, Kita-Ku, Sapporo, Japan.
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Inaba H, Yamamoto T, Iwasaki T, Kabir AMR, Kakugo A, Sada K, Matsuura K. Stabilization of microtubules by encapsulation of the GFP using a Tau-derived peptide. Chem Commun (Camb) 2019; 55:9072-9075. [DOI: 10.1039/c9cc04345d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Encapsulation of the GFP inside microtubules by using a Tau-derived peptide increased the stability, rigidity, and velocity of microtubules.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology
- Graduate School of Engineering, Tottori University
- Tottori 680-8552
- Japan
- Centre for Research on Green Sustainable Chemistry
| | - Takahisa Yamamoto
- Department of Chemistry and Biotechnology
- Graduate School of Engineering, Tottori University
- Tottori 680-8552
- Japan
| | - Takashi Iwasaki
- Department of Bioresources Science, Graduate School of Agricultural Sciences
- Tottori University
- Tottori 680-8553
- Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University
- Sapporo 060-0810
- Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University
- Sapporo 060-0810
| | - Kazuki Sada
- Faculty of Science, Hokkaido University
- Sapporo 060-0810
- Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University
- Sapporo 060-0810
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology
- Graduate School of Engineering, Tottori University
- Tottori 680-8552
- Japan
- Centre for Research on Green Sustainable Chemistry
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Kato R, Kakugo A, Shikinaka K, Ohsedo Y, Kabir AMR, Miyamoto N. Liquid Crystalline Colloidal Mixture of Nanosheets and Rods with Dynamically Variable Length. ACS Omega 2018; 3:14869-14874. [PMID: 30555995 PMCID: PMC6289543 DOI: 10.1021/acsomega.8b01050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/10/2018] [Indexed: 05/22/2023]
Abstract
Here, we demonstrate the novel double-component liquid crystalline colloids composed of mesogenic inorganic nanosheets and the rods with dynamically variable length controlled by temperature. As the length-controllable rod, stiff biopolymer microtubule is used, which was successfully polymerized/depolymerized from tubulin proteins through a biochemical process even in the presence of the nanosheets. The mesoscopic structure of the liquid crystal phase was reversibly modifiable as caused by the change of the rod length.
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Affiliation(s)
- Riki Kato
- Department
of Material Science and Production Engineering, Graduate School of Fukuoka Institute of Technology, 3-30-1 Wajiro-Higashi, Higashi-ku, Fukuoka 811-0295, Japan
| | - Akira Kakugo
- Faculty
of Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- E-mail: (A.K.)
| | - Kazuhiro Shikinaka
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology, Nigatake, 4-2-1, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Yutaka Ohsedo
- Center
for Liberal Arts and Sciences, Ashikaga
University, 286-1 Omae-cho, Ashikaga-shi, Tochigi 326-8558, Japan
| | - Arif Md. Rashedul Kabir
- Faculty
of Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Nobuyoshi Miyamoto
- Department
of Material Science and Production Engineering, Graduate School of Fukuoka Institute of Technology, 3-30-1 Wajiro-Higashi, Higashi-ku, Fukuoka 811-0295, Japan
- Department
of Life, Environment and Materials Chemistry, Fukuoka Institute of Technology, 3-30-1 Wajiro-Higashi, Higashi-ku, Fukuoka 811-0295, Japan
- Laboratoire
de Physique des Solides, UMR CNRS 8502, Bâtiment 510, Université
Paris-Sud, 91405 Orsay, France
- E-mail: (N.M.)
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Inaba H, Yamamoto T, Kabir AMR, Kakugo A, Sada K, Matsuura K. Cover Feature: Molecular Encapsulation Inside Microtubules Based on Tau-Derived Peptides (Chem. Eur. J. 56/2018). Chemistry 2018. [DOI: 10.1002/chem.201804321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology; Graduate School of Engineering; Tottori University; Koyama-Minami 4-101 Tottori 680-8552 Japan
- Centre for Research on Green Sustainable Chemistry; Tottori University; Koyama-Minami 4-101 Tottori 680-8552 Japan
| | - Takahisa Yamamoto
- Department of Chemistry and Biotechnology; Graduate School of Engineering; Tottori University; Koyama-Minami 4-101 Tottori 680-8552 Japan
| | - Arif Md. Rashedul Kabir
- Faculty of Science; Hokkaido University; Kita 10 Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Akira Kakugo
- Faculty of Science; Hokkaido University; Kita 10 Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; Hokkaido 060-0810 Japan
| | - Kazuki Sada
- Faculty of Science; Hokkaido University; Kita 10 Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; Hokkaido 060-0810 Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology; Graduate School of Engineering; Tottori University; Koyama-Minami 4-101 Tottori 680-8552 Japan
- Centre for Research on Green Sustainable Chemistry; Tottori University; Koyama-Minami 4-101 Tottori 680-8552 Japan
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Inaba H, Yamamoto T, Kabir AMR, Kakugo A, Sada K, Matsuura K. Molecular Encapsulation Inside Microtubules Based on Tau-Derived Peptides. Chemistry 2018; 24:14958-14967. [PMID: 30088680 PMCID: PMC6220817 DOI: 10.1002/chem.201802617] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Indexed: 11/20/2022]
Abstract
Microtubules are cytoskeletal filaments that serve as attractive scaffolds for developing nanomaterials and nanodevices because of their unique structural properties. The functionalization of the outer surface of microtubules has been established for this purpose. However, no attempts have been made to encapsulate molecules inside microtubules with 15 nm inner diameter. The encapsulation of various molecular cargos inside microtubules constitutes a new concept for nanodevice and nanocarrier applications of microtubules. Here, we developed peptide motifs for binding to the inner surface of microtubules, based on a repeat domain of the microtubule‐associated protein Tau. One of the four Tau‐derived peptides, 2N, binds to a taxol binding pocket of β‐tubulin located inside microtubules by preincubation with tubulin dimer and subsequent polymerization of the peptide‐tubulin complex. By conjugation of 2N to gold nanoparticles, encapsulation of gold nanoparticles inside microtubules was achieved. The methodology for molecular encapsulation inside microtubules by the Tau‐derived peptide is expected to advance the development of microtubule‐based nanomaterials and nanodevices.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
| | - Takahisa Yamamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
| | - Arif Md Rashedul Kabir
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Hokkaido, 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, Hokkaido, 060-0810, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
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Miyatake Y, Kuribayashi-Shigetomi K, Ohta Y, Ikeshita S, Subagyo A, Sueoka K, Kakugo A, Amano M, Takahashi T, Okajima T, Kasahara M. Visualising the dynamics of live pancreatic microtumours self-organised through cell-in-cell invasion. Sci Rep 2018; 8:14054. [PMID: 30232338 PMCID: PMC6145923 DOI: 10.1038/s41598-018-32122-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/03/2018] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) reportedly progresses very rapidly through the initial carcinogenesis stages including DNA damage and disordered cell death. However, such oncogenic mechanisms are largely studied through observational diagnostic methods, partly because of a lack of live in vitro tumour imaging techniques. Here we demonstrate a simple live-tumour in vitro imaging technique using micro-patterned plates (micro/nanoplates) that allows dynamic visualisation of PDAC microtumours. When PDAC cells were cultured on a micro/nanoplate overnight, the cells self-organised into non-spheroidal microtumours that were anchored to the micro/nanoplate through cell-in-cell invasion. This self-organisation was only efficiently induced in small-diameter rough microislands. Using a time-lapse imaging system, we found that PDAC microtumours actively stretched to catch dead cell debris via filo/lamellipoedia and suction, suggesting that they have a sophisticated survival strategy (analogous to that of starving animals), which implies a context for the development of possible therapies for PDACs. The simple tumour imaging system visualises a potential of PDAC cells, in which the aggressive tumour dynamics reminds us of the need to review traditional PDAC pathogenesis.
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Affiliation(s)
- Yukiko Miyatake
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Kaori Kuribayashi-Shigetomi
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo, Japan. .,Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan.
| | - Yusuke Ohta
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Shunji Ikeshita
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Agus Subagyo
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan.,Creative Research Institution Sousei, Hokkaido University, Sapporo, Japan
| | - Kazuhisa Sueoka
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Maho Amano
- Research Development Section, Hokkaido University, Sapporo, Japan
| | | | - Takaharu Okajima
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
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48
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Abstract
Recently we demonstrated swarming of a self-propelled biomolecular motor system microtubule (MT)-kinesin where interactions among thousands of motile MTs were regulated in a highly programmable fashion by using DNA as a processor. However, precise control of this potential system is yet to be achieved to optimize the swarm behavior. In this work, we systematically controlled swarming of MTs on kinesin adhered surface by different physicochemical parameters of MT-kinesin and DNA. Tuning the length of DNA sequences swarming was precisely controlled with thermodynamic and kinetic feasibility. In addition, swarming was regulated using different concentration of DNA crosslinkers. Reversibility of swarming was further controlled by changing the concentration of strand displacement DNA signal allowing dissociation of swarm. The control over the swarm was accompanied by variable stiffness of MTs successfully, providing translational and circular motion. Moreover, the morphology of swarm was also found to be changed not only depending on the stiffness but also body length of MTs. Such detail study of precise control of swarming would provide new insights in developing a promising molecular swarm robotic system with desired functions.
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Affiliation(s)
- Jakia Jannat Keya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | | | - Daisuke Inoue
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave., New York, NY, 10027, USA
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University, Osaka, 564-8680, Japan.
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave., New York, NY, 10027, USA.
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Sasaki R, Kabir AMR, Inoue D, Anan S, Kimura AP, Konagaya A, Sada K, Kakugo A. Construction of artificial cilia from microtubules and kinesins through a well-designed bottom-up approach. Nanoscale 2018; 10:6323-6332. [PMID: 29557448 DOI: 10.1039/c7nr05099b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Self-organized structures of biomolecular motor systems, such as cilia and flagella, play key roles in the dynamic processes of living organisms, like locomotion or the transportation of materials. Although fabrication of such self-organized structures from reconstructed biomolecular motor systems has attracted much attention in recent years, a systematic construction methodology is still lacking. In this work, through a bottom-up approach, we fabricated artificial cilia from a reconstructed biomolecular motor system, microtubule/kinesin. The artificial cilia exhibited a beating motion upon the consumption, by the kinesins, of the chemical energy obtained from the hydrolysis of adenosine triphosphate (ATP). Several design parameters, such as the length of the microtubules, the density of the kinesins along the microtubules, the depletion force among the microtubules, etc., have been identified, which permit tuning of the beating frequency of the artificial cilia. The beating frequency of the artificial cilia increases upon increasing the length of the microtubules, but declines for the much longer microtubules. A high density of the kinesins along the microtubules is favorable for the beating motion of the cilia. The depletion force induced bundling of the microtubules accelerated the beating motion of the artificial cilia and increased the beating frequency. This work helps understand the role of self-assembled structures of the biomolecular motor systems in the dynamics of living organisms and is expected to expedite the development of artificial nanomachines, in which the biomolecular motors may serve as actuators.
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Affiliation(s)
- Ren Sasaki
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
| | | | - Daisuke Inoue
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Shizuka Anan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akihiko Konagaya
- Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. and Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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50
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Satou K, Takeuchi D, Fujii S, Orihara H, Kayano K, Rashedul Kabir AM, Kunita I, Kakugo A. Microrheology of Microtubule Aqueous Solution. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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