Takayuki Uchihashi

Graduate School of Science, Nagoya University
Professor
A02
Research AreasProbe Microscopy, Biophysics
Participating Group (2020-2021)

High-Speed AFM Visualization of Structural Dynamics of Porous Coordination Polymers Induced External Stimuli

Keywords
High-Speed Atomic Force Microscopy, Metal-Organic Framework, Metal–Macrocycle Framework, Structural Dynamics, External Stimulus
Co-Researcher
Co-Researcher: Nobuhiko Hosono (Graduate School of Frontier Sciences, University of Tokyo, Lecturer)
Co-Researcher: Shohei Tashiro (Graduate School of Science, University of Tokyo, Associate Professor)

Research Outline

Porous Coordination Polymer (PCP), which is expected to have many industrial applications, possess the typical characteristics of soft crystals because its crystal structure flexibly changes in response to external stimuli such as guest molecule adsorption, pressure, and electric field. Changes in the crystal structure in response to external stimuli are brought by local changes in intramolecular structure and triggered global changes in the crystal. Understanding the local structural and physical changes, and their propagation dynamics at the crystal surface should be quite important for the functional design and performance improvement of porous crystals. In this study, the nanoscale dynamics of PCP surfaces in response to external stimuli are directly visualized by high-speed atomic force microscopy (AFM). The research subjects are visualizations of I): adsorption of guest molecules onto porous crystals such as MMFs and MOFs and surface propagation of lattice distortion, II): growth process of gold nanoparticles on MMF surface, and III) lattice distortion induction and selective control of guest molecule adsorption by local mechanical stimuli. These studies will enable us to gain fundamental knowledge for functional design and performance improvement of PCPs.

Crystal Distortion of PCP Induced by External Stimuli
Visualization of MOF Surface with High-Speed AFM
Participating Group (2018-2019)

Development of Evaluation Techniques for Structure and Physical Properties and Dynamics of Soft Crystals Based on High-Speed Atomic Force Microscopy

Keywords
High-Speed Atomic Force Microscopy, Single-Molecule Visualization, Dynamics　Measurement, Structure Imaging, Mechanical Property, Soft Crystal

Research Outline

Soft crystals change their optical and mechanical properties in response to the external environment and weak mechanical stimuli. Changes in the physical properties in response to the stimuli are resulted from changes in the molecular structure and the associated assembled structure. Microscopy techniques which enable probing dynamics of structure and physical properties on the crystal surface with high spatiotemporal resolution should provide deep insight into function expression mechanisms of soft crystals. This researcher has been developing high-speed atomic force microscopy (HS-AFM) and succeeded in visualizing the structural dynamics of biomolecules at work. Recently, the application of HS-AFM is extended to visualizing artificial molecular systems and therefore should be a powerful tool for evaluating dynamic properties of soft crystals. The aim of this research is to establish techniques to visualize the dynamics of the structure and physical properties on soft crystals in response to external stimulus such as photo irradiation and mechanical force based on HS-AFM technique, and to reveal nanoscale mechanisms of the emergent functions of soft crystals.

Concept figure of measurement of soft crystal with HS-AFM
Examples of HS-AFM imaging. (upper panels) Diffusion of single defects on protein 2D crystal. (lower panels) Dynamics of coordination polymer

Publications

Academic papers/reviewed

A02-15

  1. "Nanostructure and thermoresponsiveness of poly(N-isopropyl methacrylamide)-based hydrogel microspheres prepared via aqueous free radical precipitation polymerization", Y. Nishizawa, H. Minato, T. Inui, I. Saito, T. Kureha, M. Shibayama, *T. Uchihashi, *D. Suzuki, RSC Advances 11, 13130-13137(2021).
    DOI: 10.1039/D1RA01650D
  2. "Protein Needles Designed to Self-Assemble through Needle Tip Engineering", K. Kikuchi, T. Fukuyama, T. Uchihashi, T. Furuta, Y. T. Maeda, *T. Ueno, Small., 18(10)2106401.
    DOI: 10.1002/smll.202106401
  3. "Quantitative Visualization of the Interaction between Complement Component C1 and Immunoglobulin G: The Effect of CH1 Domain Deletion", S. Yanaka, S. Nishiguchi, R. Yogo, H. Watanabe, J. Shen, H. Yagi, *T. Uchihashi, *K. Kato, International Journal of Molecular Sciences, 23, 2090(2022).
    DOI: 10.3390/ijms23042090
  4. "Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images", B. Dasgupta, O. Miyashita, T. Uchihashi, *F. Tama*, Frontiers in in Molecular Biosciences: Biological Modeling and Simulation 8, 704274 (2021).
    DOI: 10.3389/fmolb.2021.704274
  5. "Shape-selective one-step synthesis of branched gold nanoparticles on the crystal surface of redox-active PdII-macrocycles", Y. Yamashita, *S. Tashiro, Y. Ishii, T. Uchihashi, N. Matsushita, R.Kubota, *M. Shionoya, Dalton Transactions, 51, 1318-1324 (2022). (領域内共同研究 A02公募 田代)
    DOI: 10.1039/D1DT03973C
  6. "A Thermoresponsive Micellar Assembly Constructed from a Hexameric Hemoprotein Modified with Poly(N-isopropylacrylamide) toward an Artificial Light-harvesting System" S. Hirayama, *K. Oohora, *T. Uchihashi, *T. Hayashi, J. Am. Chem. Soc., 142, 182-1831 (2020).
    DOI: 10.1021/jacs.9b10080
  7. "Construction of a Hexameric Hemoprotein Sheet and Direct Observation of Dynamic Process of its Formation" *K. Oohora, S. Hirayama, *T. Uchihashi, T. Hayashi*, Chem. Lett., 49, 186-190 (2020).
    DOI: 10.1246/cl.190855
  8. "Convergent evolution of processivity in bacterial and fungal cellulases" T. Uchiyama, T. Uchihashi, A. Nakamura, H. Watanabe" S. Kaneko, M.Samejima, *K. Igarashi, Proc. Natl. Acad. Sci. USA, 117, 19896-19903 (2020). (#: equal contribution)
    DOI: 10.1073/pnas.2011366117
  9. "Dynamics of oligomer and amyloid fibril formation by yeast prion Sup35 observed by high-speed atomic force microscopy" H. Konno, T. Watanabe-Nakayama, T. Uchihashi, M. Okuda, L. Zhu, N. Kodera, Y. Kikuchi, T. Ando , *H. Taguchi, Proc. Natl. Acad. Sci. USA, 117, 7831-7836 (2020).
    DOI: 10.1073/pnas.1916452117
  10. "Nanostructures, Thermoresponsiveness, and Assembly Mechanism of Hydrogel Microspheres during Aqueous Free-Radical Precipitation Polymerization" Y. Nishizawa, H. Minato, T. Inui, *T. Uchihashi, *D. Suzuki, Langmuir, 37, 151-159 (2020).
    DOI: 10.1021/acs.langmuir.0c02654
  11. "On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q" S. Yanaka, R. Yogo, H. Watanab, Y. Taniguchi, T.Satoh, N. Komura, H. Ando, H. Yagi, N. Yuki, *T. Uchihashi, *K. Kato, Int. J. Mol. Sci., 21, 147 (2020).
    DOI: 10.3390/ijms21010147
  12. "Rad50 zinc hook functions as a constitutive dimerization module interchangeable with SMC hinge" H. Tatebe, C. T. Lim, H. Konno, K. Shiozaki, A. Shinohara, *T. Uchihashi, *A. Furukohri, Nat. Commun., 11, article number: 370 (2020).
    DOI: 10.1038/s41467-019-14025-0
  13. "Schizorhodopsins: A novel family of rhodopsins from Asgard archaea that function as light-driven inward H+ pumps" *K. Inoue, S. P. Tsunoda, M. Singh, S. Tomida, S. Hososhima, M. Konno, R. Nakamura, H. Watanabe, P.-A. Bulzu, H. L. Banciu, A.-Ş. Andrei, T. Uchihashi, R. Ghai, O.Béjà, H. Kandori, Sci. Adv., 6, eaaz 2441 (2020).
    DOI: 10.1126/sciadv.aaz2441
  14. "Structural Dynamics of a Protein Domain Relevant to the Water-Oxidizing Complex in Photosystem II as Visualized by High-Speed Atomic Force Microscopy" T. Tokano, Y. Kato, S. Sugiyama, *T. Uchihashi, *T. Noguchi, J . Phys. Chem. B, 124, 5847-5857 (2020).
    DOI: 10.1021/acs.jpcb.0c03892
  15. "Structural insights into the mechanism of rhodopsin phosphodiesterase" T. Ikuta, W. Shihoya, M. Sugiura, K. Yoshida, M. Watari, T. Tokano, K. Yamashita, K. Katayama, S. P. Tsunoda, T. Uchihashi, *H. Kandori, *O Nureki, Nat. Commu., 11, 5605 (2020).
    DOI: 10.1038/s41467-020-19376-7
  16. "Supramolecular tholos-like architecture constituted by archaeal proteins without functional annotation" M. Yagi-Utsumi1, A. Sikudar, C. Song, J. Park, R. Inoue, H. Watanabe, R. N. Burton-Smith, T. Kozai, T. Suzuki, A. Kodama, K. Ishii1, H. Yagi, T. Satoh, S. Uchiyama, T. Uchihashi, K. Joo, J. Lee, M. Sugiyama, K. Murata, K. Kato, Sci. Rep., 10, 1540 (2020).
    DOI: 10.1038/s41598-020-58371-2
  17. "Thermoresponsive structural changes of single poly(N-isopropyl acrylamide) hydrogel microspheres under densely packed conditions on a solid substrate" H. Minato, Y. Nishizawa, *T. Uchihashi, *D. Suzuki, Polym. J., 52, 1137-1141 (2020).
    DOI: 10.1038/s41428-020-0372-3
  18. "Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins" T. Miyamoto, Y. Hayashi, K. Yoshida, H. Watanabe, T. Uchihashi, K. Yonezawa, N. Shimizu, H. Kamikubo, S. Hirota, ACS Synth. Biol., 2019, 85, 1112-1120.
    DOI: 10.1021/acssynbio.9b00019
  19. "Crystal structure of heliorhodopsin" W. Shihoya, K. Inoue, M. Singh, M. Konno, S. Hososhima, K. Yamashita, K. Ikeda, A. Higuchi, T. Izume, S. Okazaki, M. Hashimoto, R. Mizutori, S. Tomida, Y. Yamauchi, R. Abe-Yoshizumi, K. Katayama, S. P. Tsunoda, M. Shibata, Y. Furutani, A. Pushkarev, O. Béjà, T. Uchihashi, *H. Kandori, *O. Nureki, Nature, 574, 132-136 (2019).
    DOI: 10.1038/s41586-019-1604-6
  20. "Hydrogel Microellipsoids that Form Robust String‐Like Assemblies at the Air/Water Interface" K. Honda, Y. Sazuka, K. Iizuka, S. Matsui, T. Uchihashi, T. Kureha, M. Shibayama, T. Watanabe and  D. Suzuki, Angewandte Chemie International Edition, 2019, 58, 7294-7298.
    DOI: 10.1002/anie.201901611
  21. "Mutational and combinatorial control of self-assembling and disassembling of human proteasome α-subunits" T. Sekiguchi, T. Satoh, E. Kurimoto, C. Son, T. Kozai, H. Watanabe, K. Ishii, H. Yagi, S. Yanaka, S. Uchiyama, T. Uchihashi, K. Murata, *K. Kato, Int. J. Mol. Sci., 20, 2608 (2019).
    DOI: 10.3390/ijms20092308
  22. "Non-Thermoresponsive Decanano-sized Domains in Thermoresponsive Hydrogel Microspheres Revealed by Temperature-Controlled High-Speed Atomic Force Microscopy" Y. Nishizawa, S. Matsui, K. Urayama, T. Kureha, M. Shibayama, T. Uchihashi and D. Suzuki, Angewandte Chemie International Edition, 2019, 58, 8809-8813.
    DOI: 10.1002/anie.201903483
  23. "Protein Uptake into Individual Hydrogel Microspheres Visualized by High-Speed Atomic Force Microscopy" S. Matsui, K. Hosho, H. Minato, T. Uchihashi and  D. Suzuki, Chemical Communications, 2019, 55, 10064-10067.
    DOI: 10.1039/C9CC05116C
  24. "A ring-shaped hemoprotein trimer thermodynamically controlled by the supramolecular heme–heme pocket interaction" K. Oohora, R. Kajihara, N. Fujimaki, T. Uchihashi, T. Hayashi, Chem. Commun., 2019, 55, 1544-1547.
    DOI: 10.1039/C8CC09314H
  25. "Direct Observation and Manipulation of Supramolecular Polymerization by High-Speed Atomic Force Microscopy" T. Fukui, T. Uchihashi, N. Sasaki, M. Takeuchi, K. Sugiyasu, Angew. Chem. Int. Ed., 2018, 57, 15465-15470.
    DOI: 10.1002/anie.201809165
  26. "Microtubule Self-Healing and Defect Creation Investigated by In-Line Force Measurements During High-Speed Atomic Force Microscopy Imaging" C. Ganser and T. Uchihashi, Nanoscale, 2019, 11, 125-135.
    DOI: 10.1039/C8NR07392A
  27. "Monitoring Thermo-responsive Morphological Changes in Individual Hydrogel Microspheres" S. Matsui, Y. Nishizawa, T. Uchihashi, D. Suzuki, ACS Omega, 2018, 3, 10836-10842.
    DOI: 10.1021/acsomega.8b01770
  28. "Supramolecular Hemoprotein Assembly with a Periodic Structure Showing Heme–Heme Exciton Coupling" K. Oohora, N. Fujimaki, R. Kajihata, H. Watanabe, T. Uchihashi, T. Hayashi, J. Am. Chem. Soc., 2018, 140, 10145-10148.
    DOI: 10.1021/jacs.8b06690
Related Website(s)
Contact
uchihast@d.phys.nagoya-u.ac.jp