研究者詳細 - 内橋　貴之

論文 - 内橋　貴之

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Optimum Substrates for Imaging Biological Molecules with High-Speed Atomic Force Microscopy 査読有り

Takayuki Uchihashi, Hiroki Watanabe, Noriyuki Kodera

Methods in Molecular Biology 1814 巻頁： 159 - 179 2018年

エンドサイトーシス生物学の新展開ダイナミンによる膜切断過程の動態イメージング

竹田哲也, 小財稔矢, 楊恵然, 石黒大輝, 背山佳穂, 熊谷祐介, 阿部匡史, 山田浩司, 内橋貴之, 安藤敏夫, 竹居孝二

生命科学系学会合同年次大会 2017年度巻頁： [4AW17 - 2] 2017年12月

Two-step process for disassembly mechanism of proteasome α7 homo-tetradecamer by α6 revealed by high-speed atomic force microscopy 国際誌 Open Access

Kozai, T; Sekiguchi, T; Satoh, T; Yagi, H; Kato, K; Uchihashi, T

SCIENTIFIC REPORTS 7 巻 ( 1 ) 頁： 15373 - 15373 2017年11月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Scientific Reports

The 20S proteasome is a core particle of the eukaryotic proteasome responsible for proteolysis and is composed of layered α and β hetero-heptameric rings. The α7 subunit, which is one of components of the α ring, is known to self-assemble into a double-ringed homo-tetradecamer composed of two layers of the α7 heptameric ring. The α7 tetradecamer is known to disassemble upon the addition of α6 subunit, producing a 1:7 hetero-octameric α6-α7 complex. However, the detailed disassembly mechanism remains unclear. Here, we applied high-speed atomic force microscopy (HS-AFM) to dissect the disassembly process of the α7 double ring caused by interaction with the α6. HS-AFM movies clearly demonstrated two different modes of interaction in which the α6 monomer initially cracks at the interface between the stacked two α7 single rings and the subsequent intercalation of the α6 monomer in the open pore of the α7 single ring blocks the re-association of the single rings into the double ring. This result provides a mechanistic insight about the disassembly process of non-native homo-oligomers formed by proteasome components which is crucial for the initial process for assembly of 20S proteasome.

DOI： 10.1038/s41598-017-15708-8

Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy Open Access

Shibata, M; Nishimasu, H; Kodera, N; Hirano, S; Ando, T; Uchihashi, T; Nureki, O

NATURE COMMUNICATIONS 8 巻 ( 1 ) 頁： 1430 2017年11月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nature Communications

The CRISPR-Associated endonuclease Cas9 binds to a guide RNA and cleaves double-stranded DNA with a sequence complementary to the RNA guide. The Cas9-RNA system has been harnessed for numerous applications, such as genome editing. Here we use high-speed atomic force microscopy (HS-AFM) to visualize the real-space and real-Time dynamics of CRISPR-Cas9 in action. HS-AFM movies indicate that, whereas apo-Cas9 adopts unexpected flexible conformations, Cas9-RNA forms a stable bilobed structure and interrogates target sites on the DNA by three-dimensional diffusion. These movies also provide real-Time visualization of the Cas9-mediated DNA cleavage process. Notably, the Cas9 HNH nuclease domain fluctuates upon DNA binding, and subsequently adopts an active conformation, where the HNH active site is docked at the cleavage site in the target DNA. Collectively, our HS-AFM data extend our understanding of the action mechanism of CRISPR-Cas9.

DOI： 10.1038/s41467-017-01466-8

Na+-induced structural transition of MotPS for stator assembly of the Bacillus flagellar motor Open Access

Terahara, N; Kodera, N; Uchihashi, T; Ando, T; Namba, K; Minamino, T

SCIENCE ADVANCES 3 巻 ( 11 ) 頁： eaao4119 2017年11月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Science Advances

The bacterial flagellar motor consists of a rotor and a dozen stator units and regulates the number of active stator units around the rotor in response to changes in the environment. The MotPS complex is a Na+-type stator unit in the Bacillus subtilis flagellar motor and binds to the peptidoglycan layer through the peptidoglycan-binding (PGB) domain of MotS to act as the stator. The MotPS complex is activated in response to an increase in the Na+ concentration in the environment, but the mechanism of this activation has remained unknown. We report that activation occurs by a Na+-induced folding and dimer formation of the PGB domain of MotS, as revealed in real-time imaging by high-speed atomic force microscopy. The MotPS complex showed two distinct ellipsoid domains connected by a flexible linker. A smaller domain, corresponding to the PGB domain, became structured and unstructured in the presence and absence of 150 mM NaCl, respectively. When the amino-terminal portion of the PGB domain adopted a partially stretched conformation in the presence of NaCl, the center-to-center distance between these two domains increased by up to 5 nm, allowing the PGB domain to reach and bind to the peptidoglycan layer. We propose that assembly of the MotPS complex into a motor proceeds by means of Na+-induced structural transitions of its PGB domain.

DOI： 10.1126/sciadv.aao4119

Dedifferentiated liposarcoma in the maxillary gingiva: A clinical report and review of the literature

Enomoto Akifumi, Matsunaga Kazuhide, Shimoide Takeshi, Mukai Takao, Uchihashi Takayuki, Hamada Suguru

JOURNAL OF ORAL AND MAXILLOFACIAL SURGERY MEDICINE AND PATHOLOGY 29 巻 ( 6 ) 頁： 542 - 545 2017年11月

Fast Adsorption of Soft Hydrogel Microspheres on Solid Surfaces in Aqueous Solution Open Access

Matsui, S; Kureha, T; Hiroshige, S; Shibata, M; Uchihashi, T; Suzuki, D

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 56 巻 ( 40 ) 頁： 12146 - 12149 2017年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Angewandte Chemie - International Edition

The real-time adsorption behavior of polymeric colloidal microspheres onto solid surfaces in aqueous solution was visualized for the first time using high-speed atomic force microscopy (HS-AFM) to reveal how the softness of the microspheres affects their dynamic adsorption. Studies that focus on the deformability of microspheres upon dynamic adsorption have not yet been reported, most likely on account of a lack of techniques that appropriately depict the dynamic adsorption and deformation behavior of individual microspheres at the nanoscale in real time. In this study, the deformability of microspheres plays a crucial role on the adsorption kinetics, that is, soft hydrogel microspheres adsorb faster than harder elastomeric or rigid microspheres. These results should provide insight towards development of new colloidal nanomaterials that exhibit effective adsorption on specific sites in aqueous solution.

DOI： 10.1002/anie.201705808

Fast Adsorption of Soft Hydrogel Microspheres on Solid Surfaces in Aqueous Solution

Shusuke Matsui, Takuma Kureha, Seina Hiroshige, Mikihiro Shibata, Takayuki Uchihashi, Daisuke Suzuki

Angewandte Chemie 129 巻 ( 40 ) 頁： 12314 - 12317 2017年9月

Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT Open Access

Satoh, T; Song, C; Zhu, T; Toshimori, T; Murata, K; Hayashi, Y; Kamikubo, H; Uchihashi, T; Kato, K

SCIENTIFIC REPORTS 7 巻 ( 1 ) 頁： 12142 2017年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Scientific Reports

In the endoplasmic reticulum (ER), a protein quality control system facilitates the efficient folding of newly synthesised proteins. In this system, a series of N-linked glycan intermediates displayed on the protein surface serve as quality tags. The ER folding-sensor enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) acts as a gatekeeper in the ER quality control system by specifically catalysing monoglucosylation onto incompletely folded glycoproteins, thereby enabling them to interact with lectin-chaperone complexes. Here we characterise the dynamic structure of this enzyme. Our crystallographic data demonstrate that the sensor region is composed of four thioredoxin-like domains followed by a β-rich domain, which are arranged into a C-shaped structure with a large central cavity, while the C-terminal catalytic domain undergoes a ligand-dependent conformational alteration. Furthermore, small-angle X-ray scattering, cryo-electron microscopy and high-speed atomic force microscopy have demonstrated that UGGT has a flexible modular structure in which the smaller catalytic domain is tethered to the larger folding-sensor region with variable spatial arrangements. These findings provide structural insights into the working mechanism whereby UGGT operates as a folding-sensor against a variety of glycoprotein substrates through its flexible modular structure possessing extended hydrophobic surfaces for the recognition of unfolded substrates.

DOI： 10.1038/s41598-017-12283-w

Interdomain flip-flop motion visualized in flavocytochrome cellobiose dehydrogenase using high-speed atomic force microscopy during catalysis Open Access

Harada, H; Onoda, A; Uchihashi, T; Watanabe, H; Sunagawa, N; Samejima, M; Igarashi, K; Hayashi, T

CHEMICAL SCIENCE 8 巻 ( 9 ) 頁： 6561 - 6565 2017年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Chemical Science

Cellobiose dehydrogenase (CDH) is a dual domain flavocytochrome, which consists of a dehydrogenase (DH) domain containing a flavin adenine dinucleotide and a cytochrome (CYT) domain containing b-type heme. To directly visualize the dynamic domain motion of class-I CDH from Phanerochaete chrysosporium (PcCDH) during catalysis using high-speed atomic force microscopy, the apo-form of PcCDH was anchored to a heme-immobilized flat gold surface that can specifically fix the orientation of the CYT domain. The two domains of CDH are found to be immobile in the absence of cellobiose, whereas the addition of cellobiose triggers an interdomain flip-flop motion involving domain-domain association and dissociation. Our results indicate that dynamic motion of a dual domain enzyme during catalysis induces efficient electron transfer to an external electron acceptor.

DOI： 10.1039/c7sc01672g

Scanning Probe Microscopy FOREWORD Open Access

Takahashi, T; Fukui, K; Kageshima, M; Komeda, T; Nakajima, K; Nakayama, T; Sumitomo, K; Uchihashi, T

JAPANESE JOURNAL OF APPLIED PHYSICS 56 巻 ( 8 ) 2017年8月

High-Resolution Imaging of a Single Gliding Protofilament of Tubulins by HS-AFM Open Access

Keya, JJ; Inoue, D; Suzuki, Y; Kozai, T; Ishikuro, D; Kodera, N; Uchihashi, T; Kabir, AMR; Endo, M; Sada, K; Kakugo, A

SCIENTIFIC REPORTS 7 巻 ( 1 ) 頁： 6166 2017年7月

High-Speed Atomic Force Microscopy Reveals Loss of Nuclear Pore Resilience as a Dying Code in Colorectal Cancer Cells

Mohamed, MS; Kobayashi, A; Taoka, A; Watanabe-Nakayama, T; Kikuchi, Y; Hazawa, M; Minamoto, T; Fukumori, Y; Kodera, N; Uchihashi, T; Ando, T; Wong, RW

ACS NANO 11 巻 ( 6 ) 頁： 5567 - 5578 2017年6月

High-speed AFM revealed single-molecule blocking dynamics of a scorpion toxin on the KcsA potassium channel 査読有り

Ayumi Sumino, Takayuki Uchihashi, Takashi Sumikama, Shigetoshi Oiki

JOURNAL OF PHYSIOLOGICAL SCIENCES 67 巻頁： S117 2017年3月

Oriented Reconstitution of the Full-Length KcsA Potassium Channel in a Lipid Bilayer for AFM Imaging 査読有り Open Access

Sumino, A; Uchihashi, T; Oiki, S

JOURNAL OF PHYSICAL CHEMISTRY LETTERS 8 巻 ( 4 ) 頁： 785 - 793 2017年2月

Nuclear Pore Selective Barrier Dynamics as Revealed by High-Speed Atomic Force Microscopy in Colorectal Cancer Cells.

Mohamed, MS; Kobayashi, A; Taoka, A; Watanabe-Nakayama, T; Kikuchi, Y; Hazawa, M; Minamoto, T; Fukumori, Y; Kodera, N; Uchihashi, T; Ando, T; Wong, R

MOLECULAR BIOLOGY OF THE CELL 28 巻 2017年

High-speed atomic force microscopy imaging of live mammalian cells. Open Access

Shibata M, Watanabe H, Uchihashi T, Ando T, Yasuda R

Biophysics and physicobiology 14 巻 ( 0 ) 頁： 127-135 - 135 2017年

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：一般社団法人日本生物物理学会

Direct imaging of morphological dynamics of live mammalian cells with nanometer resolution under physiological conditions is highly expected, but yet challenging. High-speed atomic force microscopy (HS-AFM) is a unique technique for capturing biomolecules at work under near physiological conditions. However, application of HS-AFM for imaging of live mammalian cells was hard to be accomplished because of collision between a huge mammalian cell and a cantilever during AFM scanning. Here, we review our recent improvements of HS-AFM for imaging of activities of live mammalian cells without significant damage to the cell. The improvement of an extremely long (~3 μm) AFM tip attached to a cantilever enables us to reduce severe damage to soft mammalian cells. In addition, a combination of HS-AFM with simple fluorescence microscopy allows us to quickly locate the cell in the AFM scanning area. After these improvements, we demonstrate that developed HS-AFM for live mammalian cells is possible to image morphogenesis of filopodia, membrane ruffles, pits open-close formations, and endocytosis in COS-7, HeLa cells as well as hippocampal neurons.

DOI： 10.2142/biophysico.14.0_127

"Clusterase" model of dynamin-mediated membrane fission.

Takeda, T; Kozai, T; Yang, H; Kaho, S; Yusuke, K; Tadashi, A; Hiroshi, Y; Uchihashi, T; Ando, T; Takei, K

MOLECULAR BIOLOGY OF THE CELL 28 巻頁： . 2017年

"Clusterase" model of dynamin-mediated membrane fission.

Takeda T, Kozai T, Yang H, Kaho S, Yusuke K, Tadashi A, Hiroshi Y, Uchihashi T, Ando T, Takei K

MOLECULAR BIOLOGY OF THE CELL 28 巻頁： . 2017年

高速原子間力顕微鏡で可視化する生体・人工高分子の動態

内橋貴之

表面科学学術講演会要旨集 37 巻 ( 0 ) 頁： 254 2017年

記述言語：日本語出版者・発行元：公益社団法人日本表面真空学会

高速原子間力顕微鏡(HS-AFM)は1frame/s以上のフレームレートで溶液環境にある分子の様々なダイナミクスをリアルタイムで可視化でき、これまで多くのタンパク質の機能動態観察に成功している。本講演では、HS-AFMの要素技術について概説するとともに、最近の生体分子および人工超分子に応用した例について紹介する。

DOI： 10.14886/sssj2008.37.0_254

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