TOHOKU UNIVERSITY Researchers

Details of the Researcher

Home

日本語 English

Tasuku Hamaguchi

Section

Institute of Multidisciplinary Research for Advanced Materials

Job title

Associate Professor

Degree

博士（理学）（大阪市立大学）
修士（理学）（大阪市立大学）

researchmap

https://researchmap.jp/read0153256

J-GLOBAL ID

201001003804108546

Research History 5

2022/04 - Present

Tohoku University　Institute of Multidisciplinary Research for Advanced Materials
2017/05 - 2022/03

RIKEN
2013/04 - 2017/03

Osaka City University
2012/04 - 2013/03

Osaka City University
2010/04 - 2012/03

Osaka City University

Education 4

Osaka City University　Graduate School of Science

2007/04 - 2010/03
Osaka City University　Graduate School of Science

2005/04 - 2007/03
Osaka City University　Faculty of Science

2001/04 - 2005/03
和歌山県立新宮高校

1998/04 - 2001/03

Professional Memberships 5

日本生物物理学会

2013 - Present
日本マイコプラズマ学会

2013/04 - 2017/03
日本細菌学会

2013/04 - 2017/03
日本農芸化学会

2005/04 - 2013/03
日本生化学会

2005/04 - 2013/03

Research Interests 8

Membrane protein
Single particle analysis
Cryo-TEM
Electron microscopy
AFM
Mycoplasma
Structural analysis
糖鎖遊離酵素

Research Areas 1

Life sciences / Morphology, anatomy /

Awards 2

FY2020 RIKEN Research Incentive Award

2021/03　High-resolution single particle analysis by cryo-EM
日本マイコプラズマ学術集会優秀発表賞

2015/05　日本マイコプラズマ学会

Papers 48

Versatile Nanoparticle Capsule Formation With Enhanced Encapsulation Efficiency via Solute‐Induced Liquid–Liquid Phase Separation International-journal Peer-reviewed

Takehiro Yachi, Honoka Watanabe, Rumi Niwa, Daisuke Unabara, Tasuku Hamaguchi, Yusuke Yonamine, Koji Yonekura, Kuniharu Ijiro, Hideyuki Mitomo

Small　2502573　2025/07
Publisher: Wiley-VCH GmbH
DOI： 10.1002/smll.202502573 　
Dimeric assembly of F1-like ATPase for the gliding motility of Mycoplasma

Takuma TOYONAGA, Takayuki KATO, Akihiro KAWAMOTO, Tomoko MIYATA, Keisuke KAWAKAMI, Junso FUJITA, Tasuku HAMAGUCHI, Keiichi NAMBA, Makoto MIYATA

Science Advances　11　(9)　2025/02/26
Publisher: American Association for the Advancement of Science's (AAAS)
DOI： 10.1126/sciadv.adr9319 　
Assembly Formation of P65, an Intrinsically Disordered Protein Involved in Gliding Machinery of Mycoplasma pneumoniae

Masaru Yabe, Takuma Toyonaga, Miki Kinoshita, Yukio Furukawa, Tasuku Hamaguchi, Yuhei O Tahara, Munehito Arai, Katsumi Imada, Makoto Miyata

Biomolecules　2025/02/17

DOI： 10.20944/preprints202502.1200.v1 　
Structure of endothelin ETB receptor–Gi complex in a conformation stabilized by unique NPxxL motif

Kazutoshi Tani, Saori Maki-Yonekura, Ryo Kanno, Tatsuki Negami, Tasuku Hamaguchi, Malgorzata Hall, Akira Mizoguchi, Bruno M. Humbel, Tohru Terada, Koji Yonekura, Tomoko Doi

Communications Biology　2024/10/16

DOI： 10.1038/s42003-024-06905-z 　
The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs

Koji Kato, Tasuku Hamaguchi, Minoru Kumazawa, Yoshiki Nakajima, Kentaro Ifuku, Shunsuke Hirooka, Yuu Hirose, Shin-ya Miyagishima, Takehiro Suzuki, Keisuke Kawakami, Naoshi Dohmae, Koji Yonekura, Jian-Ren Shen, Ryo Nagao

Proceedings of the National Academy of Sciences　121　(11)　2024/03/05
Publisher: Proceedings of the National Academy of Sciences
DOI： 10.1073/pnas.2319658121 　

ISSN： 0027-8424

eISSN： 1091-6490

More details Close

Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae , whereas no orthologous relationships were found between C. caldarium Lhcr1–3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.
クライオ電子顕微鏡による高分子の局所構造観察 Invited

浜口祐

高分子　72　(12)　595-598　2023/12
Publisher: 公益社団法人高分子学会
Formation of Polyion Complex Aggregate Formed from a Cationic Block Copolymer and Anionic Polysaccharide Peer-reviewed

Kazushi Ogata, Mineo Hashizume, Rintaro Takahashi, Tasuku Hamaguchi, Hiroshi Jinnai, Shin-ichi Yusa

Langmuir　39　(46)　16484-16493　2023/11/10
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.langmuir.3c02404 　

ISSN： 0743-7463

eISSN： 1520-5827
Structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs

Koji Kato, Tasuku Hamaguchi, Minoru Kumazawa, Yoshiki Nakajima, Kentaro Ifuku, Shunsuke Hirooka, Yuu Hirose, Shin-ya Miyagishima, Takehiro Suzuki, Keisuke Kawakami, Naoshi Dohmae, Koji Yonekura, Jian-Ren Shen, Ryo Nagao

BioRxiv　2023/10/27
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2023.10.25.563911 　

More details Close

Abstract Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and their structural variety in photosystem I-LHC (PSI-LHCI) supercomplexes has been shown. However, structural and evolutionary correlations of red-lineage LHCs are unknown. Here we determined a 1.92-Å resolution cryo-electron microscopic structure of a PSI-LHCI supercomplex isolated from the red algaCyanidium caldariumRK-1 (NIES-2137) which is an important taxon in the Cyanidiophyceae, and subsequently investigated these correlations through structural comparisons and phylogenetic analysis. The PSI-LHCI structure shows five LHCI subunits together with a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in red-lineage algae showed clear orthology of LHCs betweenC. caldariumandCyanidioschyzon merolae, whereas no orthologous relationships were found betweenC. caldariumLhcr1–3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.
Enantioselectivity of discretized helical supramolecule consisting of achiral cobalt phthalocyanines via chiral-induced spin selectivity effect Peer-reviewed

Hiroki Aizawa, Takuro Sato, Saori Maki-Yonekura, Koji Yonekura, Kiyofumi Takaba, Tasuku Hamaguchi, Taketoshi Minato, Hiroshi M. Yamamoto

Nature Communications　14　(1)　2023/07/28
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41467-023-40133-z 　

eISSN： 2041-1723

More details Close

Abstract Enantioselectivity of helical aggregation is conventionally directed either by its homochiral ingredients or by introduction of chiral catalysis. The fundamental question, then, is whether helical aggregation that consists only of achiral components can obtain enantioselectivity in the absence of chiral catalysis. Here, by exploiting enantiospecific interaction due to chiral-induced spin selectivity (CISS) that has been known to work to enantio-separate a racemic mixture of chiral molecules, we demonstrate the enantioselectivity in the assembly of mesoscale helical supramolecules consisting of achiral cobalt phthalocyanines. The helical nature in our supramolecules is revealed to be mesoscopically incorporated by dislocation-induced discretized twists, unlike the case of chiral molecules whose chirality are determined microscopically by chemical bond. The relevance of CISS effect in the discretized helical supramolecules is further confirmed by the appearance of spin-polarized current through the system. These observations mean that the application of CISS-based enantioselectivity is no longer limited to systems with microscopic chirality but is expanded to the one with mesoscopic chirality.
Measurement of charges and chemical bonding in a cryo-EM structure Peer-reviewed

Saori Maki-Yonekura, Keisuke Kawakami, Kiyofumi Takaba, Tasuku Hamaguchi, Koji Yonekura

Communications Chemistry　6　(1)　98　2023/05/31
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s42004-023-00900-x 　

eISSN： 2399-3669

More details Close

Abstract Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, electron transfer, and ligand binding. These effects can potentially be measured in Coulomb potentials using cryogenic electron microscopy (cryo-EM). We here present charges and bond properties of hydrogen in a sub-1.2 Å resolution structure of a protein complex, apoferritin, by single-particle cryo-EM. A weighted difference map reveals positive densities for most hydrogen atoms in the core region of the complex, while negative densities around acidic amino-acid side chains are likely related to negative charges. The former positive densities identify the amino- and oxo-termini of asparagine and glutamine side chains. The latter observations were verified by spatial-resolution selection and a dose-dependent frame series. The average position of the hydrogen densities depends on the parent bonded-atom type, and this is validated by the estimated level of the standard uncertainties in the bond lengths.
Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography Peer-reviewed

Kiyofumi Takaba, Saori Maki-Yonekura, Ichiro Inoue, Kensuke Tono, Tasuku Hamaguchi, Keisuke Kawakami, Hisashi Naitow, Tetsuya Ishikawa, Makina Yabashi, Koji Yonekura

Nature Chemistry　2023/03/20
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41557-023-01162-9 　

ISSN： 1755-4330

eISSN： 1755-4349
Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins Peer-reviewed

Tomoki Himiyama, Tasuku Hamaguchi, Koji Yonekura, Tsutomu Nakamura

Bioconjugate Chemistry　2023/03/08
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.bioconjchem.3c00057 　

ISSN： 1043-1802

eISSN： 1520-4812
Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120. International-journal Peer-reviewed

Ryo Nagao, Koji Kato, Tasuku Hamaguchi, Yoshifumi Ueno, Naoki Tsuboshita, Shota Shimizu, Miyu Furutani, Shigeki Ehira, Yoshiki Nakajima, Keisuke Kawakami, Takehiro Suzuki, Naoshi Dohmae, Seiji Akimoto, Koji Yonekura, Jian-Ren Shen

Nature communications　14　(1)　920-920　2023/02/17

DOI： 10.1038/s41467-023-36504-1 　

More details Close

Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.
Structure and Function of Gli123 Involved in Mycoplasma mobile Gliding Peer-reviewed

Daiki Matsuike, Yuhei O. Tahara, Takahiro Nonaka, Heng Ning Wu, Tasuku Hamaguchi, Hisashi Kudo, Yuuki Hayashi, Munehito Arai, Makoto Miyata

Journal of Bacteriology　2023/02/07
Publisher: American Society for Microbiology
DOI： 10.1128/jb.00340-22 　

ISSN： 0021-9193

eISSN： 1098-5530

More details Close

Mycoplasmas are pathogenic bacteria that are widespread in animals. They are characterized by small cell and genome sizes but are equipped with unique abilities for infection, such as surface variation and gliding.
Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome Peer-reviewed

Keisuke Kawakami, Tasuku Hamaguchi, Yuu Hirose, Daisuke Kosumi, Makoto Miyata, Nobuo Kamiya, Koji Yonekura

Nature Communications　13　(1)　2022/06
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41467-022-30962-9 　

eISSN： 2041-1723

More details Close

Abstract Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer.
Theoretical Model of the Far-Red-Light-Adapted Photosystem I Reaction Center of Cyanobacterium Acaryochloris marina Using Chlorophyll d and the Effect of Chlorophyll Exchange Peer-reviewed

Akihiro Kimura, Hirotaka Kitoh-Nishioka, Toshimichi Aota, Tasuku Hamaguchi, Koji Yonekura, Keisuke Kawakami, Kyoko Shinzawa-Itoh, Natsuko Inoue-Kashino, Kentaro Ifuku, Eiki Yamashita, Yasuhiro Kashino, Shigeru Itoh

The Journal of Physical Chemistry B　2022/05/26
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.jpcb.2c00869 　

ISSN： 1520-6106

eISSN： 1520-5207
Structural basis for the absence of low-energy chlorophylls in a photosystem I trimer from Gloeobacter violaceus International-journal Peer-reviewed

Koji Kato, Tasuku Hamaguchi, Ryo Nagao, Keisuke Kawakami, Yoshifumi Ueno, Takehiro Suzuki, Hiroko Uchida, Akio Murakami, Yoshiki Nakajima, Makio Yokono, Seiji Akimoto, Naoshi Dohmae, Koji Yonekura, Jian-Ren Shen

eLife　11　2022/04/11
Publisher: eLife Sciences Publications, Ltd
DOI： 10.7554/elife.73990 　

eISSN： 2050-084X

More details Close

Photosystem I (PSI) is a multi-subunit pigment-protein complex that functions in light-harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO₂ fixation in photosynthetic organisms. PSI from different photosynthetic organisms has a variety of chlorophylls (Chls), some of which are at lower-energy levels than its reaction center P700, a special pair of Chls, and are called low-energy Chls. However, the sites of low-energy Chls are still under debate. Here, we solved a 2.04-Å resolution structure of a PSI trimer by cryo-electron microscopy from a primordial cyanobacterium Gloeobacter violaceus PCC 7421, which has no low-energy Chls. The structure shows the absence of some subunits commonly found in other cyanobacteria, confirming the primordial nature of this cyanobacterium. Comparison with the known structures of PSI from other cyanobacteria and eukaryotic organisms reveals that one dimeric and one trimeric Chls are lacking in the Gloeobacter PSI. The dimeric and trimeric Chls are named Low1 and Low2, respectively. Low2 is missing in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in Gloeobacter. These findings provide insights into not only the identity of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls in oxyphototrophs.
Hydrogen properties and charges in a sub-1.2 Å resolution cryo-EM structure revealed by a cold field emission beam

Saori Maki-Yonekura, Keisuke Kawakami, Tasuku Hamaguchi, Kiyofumi Takaba, Koji Yonekura

2021/12/22
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2021.12.21.473430 　

More details Close

Abstract The cold field emission (CFE) beam produces the less-attenuated contrast transfer function of electron microscopy, thereby enhancing high-resolution signals and this particularly benefits higher-resolution single particle cryogenic electron microscopy. Here, we present a sub-1.2 Å resolution structure of a standard protein sample, apoferritin. Image data were collected with the CFE beam in a high-throughput scheme while minimizing beam tilt deviations from the coma-free axis. A difference map reveals positive densities for most hydrogen atoms in the core region of the protein complex including those in water molecules, while negative densities around acidic amino-acid side chains likely represent negative charges. The position of the hydrogen densities depends on parent bonded-atom type, which is validated by an estimated level of coordinate errors.
Machine learning-based real-time object locator/evaluator for cryo-EM data collection International-journal Peer-reviewed

Koji Yonekura, Saori Maki-Yonekura, Hisashi Naitow, Tasuku Hamaguchi, Kiyofumi Takaba

Communications Biology　4　(1)　1044-1044　2021/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s42003-021-02577-1 　

eISSN： 2399-3642

More details Close

<title>Abstract</title>In cryo-electron microscopy (cryo-EM) data collection, locating a target object is error-prone. Here, we present a machine learning-based approach with a real-time object locator named yoneoLocr using YOLO, a well-known object detection system. Implementation shows its effectiveness in rapidly and precisely locating carbon holes in single particle cryo-EM and in locating crystals and evaluating electron diffraction (ED) patterns in automated cryo-electron crystallography (cryo-EX) data collection. The proposed approach will advance high-throughput and accurate data collection of images and diffraction patterns with minimal human operation.
Hydrogen properties in an organic molecule revealed by XFEL and electron crystallography

Kiyofumi Takaba, Saori Maki-Yonekura, Ichiro Inoue, Kensuke Tono, Tasuku Hamaguchi, Keisuke Kawakami, Hisahi Naitow, Tetsuya Ishikawa, Makina Yabashi, Koji Yonekura

2021/11/09
Publisher: American Chemical Society (ACS)
DOI： 10.26434/chemrxiv-2021-jvbfl 　

More details Close

Structure analysis of small crystals is important in synthetic organic chemistry, pharmaceutical and material sciences, and related areas, as the conformation of these molecules may differ in large and small crystals, thus affecting the interpretation of their functional properties and drug efficacy. From small crystals, X-ray and electron beams could furnish electron densities and Coulomb potentials of target molecules, respectively. The two beams provide distinctly different information, and this potential has not been fully explored. Here we present the detailed structure of an organic molecule, rhodamine-6g by X-ray free-electron laser (XFEL) and electron crystallography from the same sample batch of microcrystals. This is the first organic molecular structure determined using XFEL at subatomic resolution. Direct comparison between the electron-density and the Coulomb-potential maps together with theoretical models based on Poisson’s equation shows that the position of hydrogen atoms depends on bond type and charge distribution. The combined approach could lead to better insights into their chemical and/or binding properties for a broad range of organic molecules.
Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI

Koji Kato, Tasuku Hamaguchi, Ryo Nagao, Keisuke Kawakami, Yoshifumi Ueno, Takehiro Suzuki, Hiroko Uchida, Akio Murakami, Yoshiki Nakajima, Makio Yokono, Seiji Akimoto, Naoshi Dohmae, Koji Yonekura, Jian-Ren Shen

2021/10/01
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2021.09.29.462462 　

More details Close

<title>Abstract</title>Photosystem I (PSI) of photosynthetic organisms is a multi-subunit pigment-protein complex and functions in light harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO₂ fixation. PSI from different photosynthetic organisms has a variety of chlorophylls (Chls), some of which are at lower-energy levels than its reaction center P700, a special pair of Chls, and are called low-energy Chls. However, the site of low-energy Chls is still under debate. Here, we solved a 2.04-Å resolution structure of a PSI trimer by cryo-electron microscopy from a primitive cyanobacterium <italic>Gloeobacter violaceus</italic> PCC 7421, which has no low-energy Chls. The structure showed absence of some subunits commonly found in other cyanobacteria, confirming the primitive nature of this cyanobacterium. Comparison with the known structures of PSI from other cyanobacteria and eukaryotic organisms reveals that one dimeric and one trimeric Chls are lacking in the <italic>Gloeobacter</italic> PSI. The dimeric and trimeric Chls are named Low1 and Low2, respectively. Low2 does not exist in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in <italic>Gloeobacter</italic>. Since <italic>Gloeobacter</italic> is susceptible to light, this indicates that Low1 serves as a main photoprotection site in most oxyphototrophs, whereas Low2 is involved in either energy transfer or energy quenching in some of the oxyphototrophs. Thus, these findings provide insights into not only the functional significance of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls responsible for the photoprotection machinery from photosynthetic prokaryotes to eukaryotes.
Complementary use of high-resolution and high-precision cryo-ED and EM

Koji Yonekura, Saori Maki-Yonekura, Kiyofumi Takaba, Tasuku Hamaguchi, Hisashi Naitow, Keisuke Kawakami

Microscopy and Microanalysis　27　(S1)　204-206　2021/08
Publisher: Cambridge University Press (CUP)
DOI： 10.1017/s143192762100132x 　

ISSN： 1431-9276

eISSN： 1435-8115
Chained Structure of Dimeric F1-like ATPase in Mycoplasma mobile Gliding Machinery International-journal Peer-reviewed

Takuma Toyonaga, Takayuki Kato, Akihiro Kawamoto, Noriyuki Kodera, Tasuku Hamaguchi, Yuhei O. Tahara, Toshio Ando, Keiichi Namba, Makoto Miyata

mBio　e0141421　2021/07/20
Publisher: American Society for Microbiology
DOI： 10.1128/mbio.01414-21 　

eISSN： 2150-7511

More details Close

F ₁ F _o -ATPase, a rotary ATPase, is widespread in the membranes of mitochondria, chloroplasts, and bacteria and converts ATP energy with a proton motive force across the membrane by its physical rotation. Homologous protein complexes play roles in ion and protein transport. <named-content content-type="genus-species">Mycoplasma mobile</named-content> , a pathogenic bacterium, was recently suggested to have a special motility system evolutionarily derived from F ₁ -ATPase.
Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer International-journal Peer-reviewed

Huaxin Yu, Tasuku Hamaguchi, Yoshiki Nakajima, Koji Kato, Keisuke Kawakami, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

Biochimica et Biophysica Acta (BBA) - Bioenergetics　1862　(10)　148471-148471　2021/07
Publisher: Elsevier BV
DOI： 10.1016/j.bbabio.2021.148471 　

ISSN： 0005-2728

More details Close

Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.
Structural implications for a phycobilisome complex from the thermophilic cyanobacterium Thermosynechococcus vulcanus Peer-reviewed

Keisuke Kawakami, Ryo Nagao, Yuhei O. Tahara, Tasuku Hamaguchi, Takehiro Suzuki, Naoshi Dohmae, Daisuke Kosumi, Jian-Ren Shen, Makoto Miyata, Koji Yonekura, Nobuo Kamiya

Biochimica et Biophysica Acta (BBA) - Bioenergetics　1862　(9)　148458-148458　2021/05
Publisher: Elsevier BV
DOI： 10.1016/j.bbabio.2021.148458 　

ISSN： 0005-2728
Structural insights into the targeting specificity of ubiquitin ligase for S.cerevisiae isocitrate lyase but not C.albicans isocitrate lyase Peer-reviewed

Keito Hiragi, Kazuya Nishio, Shu Moriyama, Tasuku Hamaguchi, Akira Mizoguchi, Koji Yonekura, Kazutoshi Tani, Tsunehiro Mizushima

Journal of Structural Biology　107748-107748　2021/05
Publisher: Elsevier BV
DOI： 10.1016/j.jsb.2021.107748 　

ISSN： 1047-8477
Real-time object locator for cryo-EM data collection --- You only navigate EM once ---

Koji Yonekura, Saori Maki-Yonekura, Hisashi Naitow, Tasuku Hamaguchi, Kiyofumi Takaba

2021/04/09

DOI： 10.1101/2021.04.07.438905 　
Structure of the far-red light utilizing photosystem I of Acaryochloris marina International-journal Peer-reviewed

Tasuku Hamaguchi, Keisuke Kawakami, Kyoko Shinzawa-Itoh, Natsuko Inoue-Kashino, Shigeru Itoh, Kentaro Ifuku, Eiki Yamashita, Kou Maeda, Koji Yonekura, Yasuhiro Kashino

Nature Communications　12　(1)　2333-2333　2021/04
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41467-021-22502-8 　

eISSN： 2041-1723

More details Close

<title>Abstract</title><italic>Acaryochloris marina</italic> is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of <italic>A. marina</italic> photosystem I (PSI) reaction center, determined by cryo-electron microscopy at 2.58 Å resolution. The structure reveals an arrangement of electron carriers and light-harvesting pigments distinct from other type I reaction centers. The paired chlorophyll, or special pair (also referred to as P740 in this case), is a dimer of chlorophyll <italic>d</italic> and its epimer chlorophyll <italic>d</italic>′. The primary electron acceptor is pheophytin <italic>a</italic>, a metal-less chlorin. We show the architecture of this PSI reaction center is composed of 11 subunits and we identify key components that help explain how the low energy yield from far-red light is efficiently utilized for driving oxygenic photosynthesis.
Advances in cryo-EM and ED with a cold-field emission beam and energy filtration —Refinements of the CRYO ARM 300 system in RIKEN SPring-8 center— International-journal Peer-reviewed

Saori Maki-Yonekura, Tasuku Hamaguchi, Hisashi Naitow, Kiyofumi Takaba, Koji Yonekura

Microscopy　70　(2)　232-240　2021/03/24
Publisher: Oxford University Press (OUP)
DOI： 10.1093/jmicro/dfaa052 　

ISSN： 2050-5698

eISSN： 2050-5701

More details Close

<title>Abstract</title> We have designed and evaluated a cryo-electron microscopy (cryo-EM) system for higher-resolution single particle analysis and high-precision electron 3D crystallography. The system comprises a JEOL CRYO ARM 300 electron microscope—the first machine of this model—and a direct detection device camera, a scintillator-coupled camera, GPU clusters connected with a camera control computer and software for automated-data collection and efficient and accurate operation. The microscope provides parallel illumination of a highly coherent 300-kV electron beam to a sample from a cold-field emission gun and filters out energy-loss electrons through the sample with an in-column energy filter. The gun and filter are highly effective in improving imaging and diffraction, respectively, and have provided high quality data since July 2018. We here report on the characteristics of the cryo-EM system, updates, our progress and future plan for running such cryo-EM machines in RIKEN SPring-8 Center.
High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams International-journal Peer-reviewed

Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

Communications Biology　4　(1)　382-382　2021/03
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s42003-021-01919-3 　

eISSN： 2399-3642

More details Close

<title>Abstract</title>Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.
Cryo-EM and ED with a Cold-Field Emission Beam and Energy Filtration Peer-reviewed

Koji Yonekura, Saori Maki-Yonekura, Tasuku Hamaguchi, Hisashi Naitow, Kiyofumi Takaba, Keisuke Kawakami

Applications of Microscopy in Materials and Life Sciences　233-241　2021
Publisher: Springer Singapore
DOI： 10.1007/978-981-16-2982-2_23 　

ISSN： 2662-3161

eISSN： 2662-317X
High-resolution cryo-EM structure of photosystem II: Effects of electron beam damage

Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

2020/10/19
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2020.10.18.344648 　

More details Close

<jats:title>Abstract</jats:title><jats:p>Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state, and its final state structure has not been solved because of the low efficiencies of the S-state transitions in the crystals. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, which was reduced by reducing the electron dose. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.</jats:p>
Erratum to "A new cryo-EM system for single particle analysis" [J. Struct. Biol. 207 (1) (2019) 40-48]. International-journal

Tasuku Hamaguchi, Saori Maki-Yonekura, Hisashi Naitow, Yoshinori Matsuura, Tetsuya Ishikawa, Koji Yonekura

Journal of structural biology　211　(3)　107558-107558　2020/09/01

DOI： 10.1016/j.jsb.2020.107558 　
Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release Peer-reviewed

Hisashi Naitow, Tasuku Hamaguchi, Saori Maki-Yonekura, Masamichi Isogai, Nobuyuki Yoshikawa, Koji Yonekura

Communications Biology　3　(1)　2020/09
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s42003-020-01217-4 　

eISSN： 2399-3642
ATP合成酵素とPGKから進化したMycoplasma mobile滑走モーターの構造

豊永拓真, 加藤貴之, 川本晃大, 浜口祐, 古寺哲幸, 安藤敏夫, 難波啓一, 宮田真人

日本マイコプラズマ学会雑誌　(46)　44-46　2020/03
Publisher: 日本マイコプラズマ学会
ISSN： 1340-2382
Tidy up cryo-EM sample grids with 3D printed tools International-journal Peer-reviewed

Tasuku Hamaguchi, Koji Yonekura

Journal of Structural Biology　209　(1)　107414-107414　2020/01
Publisher: Elsevier BV
DOI： 10.1016/j.jsb.2019.107414 　

ISSN： 1047-8477

More details Close

Cryo-EM technology has developed to the point of high-throughput structure determination of biological macromolecules embedded in vitreous ice. Nonetheless, challenging targets need extensive sample screening, often of many cryo-EM sample grids prepared under various conditions. We have designed and made tools for manipulating sample grids in storage cases. These tools are made of a plastic fiber using a wide-use 3D printer, a fused deposition modeling type, and polished under acetone gas. A grid case stacker organizes many frozen-hydrated cryo-EM grids and the stackers can be piled up inside a standard 50 mL centrifuge tube. We have also introduced tools that facilitate handling of grid cases under liquid nitrogen and a stocker of the grid retainers contained in a CRYO ARM electron microscope. Blueprints of the tools named CryoGridTools are available from a GitHub site.
A new cryo-EM system for single particle analysis International-journal Peer-reviewed

Tasuku Hamaguchi, Saori Maki-Yonekura, Hisashi Naitow, Yoshinori Matsuura, Tetsuya Ishikawa, Koji Yonekura

Journal of Structural Biology　207　(1)　40-48　2019/07
Publisher: Elsevier BV
DOI： 10.1016/j.jsb.2019.04.011 　

ISSN： 1047-8477

More details Close

A new cryo-EM system has been investigated for single particle analysis of protein structures. The system provides parallel illumination of a highly-coherent 300 kV electron beam from a cold-field emission gun, and boosts image contrast with an in-column energy filter and a hole-free phase plate. It includes motorized cryo-sample loading and automated liquid-nitrogen filling for cooling multiple samples. In this study, we describe gun and electron beam characteristics, and demonstrate the suitability of this system for single particle reconstructions. The performance of the system is tested on two examples, a spherical virus and apoferritin. GUI programs have also been developed to control and monitor the system for correct illumination, imaging with less ellipticity and steady magnification, and timing of flashing and liquid-nitrogen filling. These programs are especially useful for efficient application of the system to single particle cryo-EM.
Identification of novel protein domain for sialyloligosaccharide binding essential to Mycoplasma mobile gliding. International-journal Peer-reviewed

Hamaguchi T, Kawakami M, Furukawa H, Miyata M

FEMS Microbiology Letters　366　(3)　fnz016　2019/01/21

DOI： 10.1093/femsle/fnz016 　

More details Close

Sialic acids, terminal structures of sialylated glycoconjugates, are widely distributed in animal tissues and are often involved in intercellular recognitions, including some bacteria and viruses. Mycoplasma mobile, a fish pathogenic bacterium, binds to sialyloligosaccharide (SO) through adhesin Gli349 and glides on host cell surfaces. The amino acid sequence of Gli349 shows no similarity to known SO-binding proteins. In the present study, we predicted the binding part of Gli349, produced it in Escherichia coli and proved its binding activity to SOs of fetuin using atomic force microscopy. Binding was detected with a frequency of 10.3% under retraction speed of 400 nm/s and was shown to be specific for SO, as binding events were competitively inhibited by the addition of free 3'-sialyllactose. The histogram of the unbinding forces showed 24 pN and additional peaks. These results suggested that the distal end of Gli349 constitutes a novel sialoadhesin domain and is directly involved in the gliding mechanism of M. mobile.
Integrated Information and Prospects for Gliding Mechanism of the Pathogenic Bacterium Mycoplasma pneumoniae Peer-reviewed

Makoto Miyata, Tasuku Hamaguchi

FRONTIERS IN MICROBIOLOGY　7　960　2016/06

DOI： 10.3389/fmicb.2016.00960 　

ISSN： 1664-302X
Prospects for the gliding mechanism of Mycoplasma mobile Peer-reviewed

Makoto Miyata, Tasuku Hamaguchi

CURRENT OPINION IN MICROBIOLOGY　29　15-21　2016/02

DOI： 10.1016/j.mib.2015.08.010 　

ISSN： 1369-5274

eISSN： 1879-0364
C3-P-08Structure and function of P1 adhesin ofMycoplasma pneumoniae

U Matsumoto, Yoshito Kawakita, Tsuyoshi Kenri, Shigetaro Mori, Tasuku Hamaguchi, Miki Kinoshita, Akihiro Kawamoto, Takayuki Kato, Keiichi Namba, Makoto Miyata

Microscopy　64　(suppl 1)　i130.1-i130　2015/11
Publisher: Oxford University Press ({OUP})
DOI： 10.1093/jmicro/dfv311 　

ISSN： 2050-5698
C3-P-09Structural analyses of Gli123 protein, essential forMycoplasma mobilegliding

Daiki Matsuike, Yuhei O Tahara, Tasuku Hamaguchi, Makoto Miyata

Microscopy　64　(suppl 1)　i130.2-i130　2015/11
Publisher: Oxford University Press ({OUP})
DOI： 10.1093/jmicro/dfv312 　

ISSN： 2050-5698
Gliding Motility of Mycoplasma mobile on Uniform Oligosaccharides Peer-reviewed

Taishi Kasai, Tasuku Hamaguchi, Makoto Miyata

JOURNAL OF BACTERIOLOGY　197　(18)　2952-2957　2015/09

DOI： 10.1128/JB.00335-15 　

ISSN： 0021-9193

eISSN： 1098-5530
Reprint of “Prospects for the gliding mechanism of Mycoplasma mobile”

Miyata, M., Hamaguchi, T.

Current Opinion in Microbiology　28　2015

DOI： 10.1016/j.mib.2015.12.002 　

ISSN： 1879-0364 1369-5274
Reprint of “Prospects for the gliding mechanism of Mycoplasma mobile”

Makoto Miyata, Tasuku Hamaguchi

Current Opinion in Microbiology　28　122-128　2015
Publisher: Elsevier {BV}
DOI： 10.1016/j.mib.2015.12.002 　

ISSN： 1369-5274
Purification, characterization and molecular cloning of a novel endo-beta-N-acetylglucosaminidase from the basidiomycete, Flammulina velutipes Peer-reviewed

Tasuku Hamaguchi, Tsukasa Ito, Yukako Inoue, Tipaporn Limpaseni, Piamsook Pongsawasdi, Kazuo Ito

GLYCOBIOLOGY　20　(4)　420-432　2010/04

DOI： 10.1093/glycob/cwp188 　

ISSN： 0959-6658

eISSN： 1460-2423
Transglycosylation of Asparagine-linked Complex-type Oligosaccharides from Glycoproteins by Endo-.BETA.-N-acetylglucosaminidase HS Peer-reviewed

Kimiko Miyagawa, Mutsumi Matsumoto, Shigeki Yabuno, Naoko Kawakami, Tasuku Hamaguchi, Masaru Iizuka, Noshi Minamiura, Kazuo Ito

Journal of Applied Glycoscience　54　(2)　139-146　2007
Publisher: The Japanese Society of Applied Glycoscience
DOI： 10.5458/jag.54.139 　

ISSN： 1344-7882

eISSN： 1880-7291

More details Close

Endo-β-N-acetylglucosaminidases hydrolyze N,N´-diacetylchitobiose linkages of asparagine-linked oligosaccharides. They can also cleave the linkage with suitable agents having hydroxyl groups and transfer the released oligosaccharides to the agents. Thus endo-β-N-acetylglucosaminidases are very useful for synthesis of neoglycoconjugates having asparagine-linked oligosaccharides. On the other hand, the structures of asparagine-linked oligosaccharides are divided into three groups, high-mannose type, hybrid type and complex type. We discovered a novel endo-β-N-acetylglucosaminidase (Endo), named Endo HS. Endo HS can specifically hydrolyze bi-, tri- and tetraantennary complex-type oligosaccharides from glycoproteins. We have investigated the transglycosylation reaction by Endo HS. Endo HS transferred the biantennary complex type oligosaccharide from human transferrin to p-nitrophenyl (PNP)-β-D-Glc and PNP-β-D-Gal. Endo HS was strictly distinct from other enzymes in transferring oligosaccharide to the Gal moiety. The amount of the transglycosylation product increased depending on the concentration of the acceptors. Endo HS also transferred the oligosaccharide to PNP-α-D-Glc, PNP-α-D-Gal, PNP-β-D-Man, PNP-β-D-Xyl, PNP-β-D-GlcNAc and PNP-glycerol. The amount of the transglycosylation product successively increased and became constant and then barely decreased. No apparent difference in the K_m value for human transferrin as an oligosaccharide donor was observed using different acceptors such as PNP-β-D-Glc and PNP-glycerol. Endo HS also transferred the triantennary complex-type oligosaccharide from calf fetuin and the bi-, tri- and tetraantennary complex-type oligosaccharides from human α₁-acid glycoprotein to PNP-β-D-Glc. In addition to glycoproteins, Endo HS transferred biantennary complex-type oligosaccharide from glycopeptides. Furthermore, Endo HS transferred bi- and triantennary complex-type oligosaccharides from glycoasparagines to various monosaccharides, oligosaccharides, sugar alcohols and glycosides. The addition of polar organic solvents was also effective for the transglycosylation efficiency. The results demonstrate that Endo HS is a useful tool for synthesis of neoglycoconjugates having a wide variety of complex-type asparagine-linked oligosaccharides from glycoproteins.
Evidence for the transglycosylation of complex type oligosaccharides of glycoproteins by endo-beta-N-acetylglucosaminidase HS Peer-reviewed

Kazuo Ito, Kimiko Miyagawa, Mutsumi Matsumoto, Shigeki Yabuno, Naoko Kawakami, Tasuku Hamaguchi, Masaru Iizuka, Noshi Minamiura

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS　454　(1)　89-99　2006/10

DOI： 10.1016/j.abb.2006.06.004 　

ISSN： 0003-9861

Show all ︎Show first 5

Misc. 2

Theoretical analysis of optical properties and light harvesting mechanisms in far-red adapted A. marina photosystem I.

木村明洋, 鬼頭宏任, 青田俊道, 浜口祐, 米倉功治, 川上恵典, 新沢(伊藤)恭子, 井上(菓子野)名津子, 伊福健太郎, 菓子野康浩, 山下栄樹, 伊藤繁

日本物理学会講演概要集(CD-ROM)　77　(1)　2022

ISSN： 2189-079X
Luminescent Model by Wide-use 3D Printer Peer-reviewed

HAMAGUCHI Tasuku, KAWAKAMI Masaru, MIYATA Makoto

The Biophysical Society of Japan General Incorporated Association, Seibutsu Butsuri　57　(4)　216-218　2017
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.57.216

Presentations 39

低GC生物マイコプラズマ由来新規Cas9の探索

上野莉香子, 池内健, 豊永拓真, 濵口祐, 米倉功治

公益社団法人日本顕微鏡学会第81回学術講演会　2025/06/11
クライオEELS/EF-TEMによる凍結溶媒内バイオマテリアルの多元素マッピング観察

海原大輔, 佐藤庸平, 濵口祐, 米倉功治

公益社団法人日本顕微鏡学会第81回学術講演会　2025/06/10
CryoEMによって可視化したマイコプラズマ滑走型Rotary ATPaseの回転

豊永拓真, 海原大輔, 濵口祐, 米倉功治

公益社団法人日本顕微鏡学会第81回学術講演会　2025/06/09
Cryo-EM Analysis of Chained G1-ATPase, Motor for Mycoplasma Gliding International-presentation

Takuma Toyonaga, Daisuke Unabara, Tasuku Hamaguchi, Makoto Miyata, Koji Yonekura

Sixth Japan-Canada Microscopy Societies Joint Symposium 2025　2025/06/10
Cryo-EM Structure of PSI-LHCI from a Red alga Cyanidium caldarium International-presentation

Koji Kato, Tasuku Hamaguchi, Minoru Kumazawa, Yoshiki Nakajima, Kentaro Ifuku, Yuu Hirose, Keisuke Kawakami, Koji Yonekura, Ryo Nagao, Jian-Ren Shen

The 13th Asia Pacific Microscopy Congress 2025 (APMC13)　2025/02/04
東北大・多元研の取り組み

濵口祐

第3回クライオ電子顕微鏡施設技術交流会　2024/12/18
マイコプラズマ滑走運動を駆動する新奇回転分子モーターのCryoEM構造

豊永拓真, 濵口祐, 宮田真人, 米倉功治

第24回東北大学多元物質科学研究所研究発表会　2024/12/12
クライオFIB-SEMおよびクライオTEMを利用した納豆芽胞の可視化

丹羽瑠美, 濵口祐, 米倉功治

第24回東北大学多元物質科学研究所研究発表会　2024/12/12
クライオEELS/EF-TEMによる凍結溶媒内ソフトマテリアルの元素マッピング観察

海原大輔, 佐藤庸平, 濵口祐, 米倉功治

第24回東北大学多元物質科学研究所研究発表会　2024/12/12
Structure of the far-red light utilizing photosystem I of Acaryochloris marina International-presentation

Keisuke Kawakami, Tasuku Hamaguchi, Kyoko Shinzawa-Itoh, Natsuko Inoue-Kashino, Shigeru Itoh, Kentaro Ifuku, Eiki Yamashita, Kou Maeda, Koji Yonekura, Yasuhiro, Kashino

2nd Asia-Oceania International Congress on Photosynthesis (AOICP)　2024/09/18
Cryo-EM structure of PSI-LHCI from a red alga Cyanidium caldarium International-presentation

Koji Kato, Tasuku Hamaguchi, Minoru Kumazawa, Yoshiki Nakajima, Kentaro Ifuku, Yuu Hirose, Keisuke Kawakami, Koji Yonekura, Ryo Nagao, Jian-Ren Shen

2nd Asia-Oceania International Congress on Photosynthesis (AOICP)　2024/09/18
Cryo-EM Observations and Analyses in Life/material Science Invited

Tasuku Hamaguchi

2024/09/14
クライオ電子顕微鏡によるソフトマテリアル局所構造の可視化に向けたアプローチとその成果 Invited

濵口祐

日本顕微鏡学会ソフトマテリアル分科会 2024 年度第 1 回講演会～ソフトマテリアル向けの最新局所構造解析　2024/07/25
CryoEM structure of dimeric F1-like ATPase in Mycoplasma mobile suggests a rotary catalytic mechanism for the gliding motility International-presentation

Takuma TOYONAGA, Takayuki KATO, Akihiro KAWAMOTO, Tomoko MIYATA, Keisuke KAWAKAMI, Junso FUJITA, Tasuku HAMAGUCHI, Keiichi NAMBA, Makoto MIYATA

21st IUPAB Congress 2024　2024/06/28
クライオEELS/EF-TEMによる凍結溶媒内ソフトマテリアルの元素マッピング観察

海原大輔, 佐藤庸平, 濵口祐, 米倉功治

日本顕微鏡学会第80回学術講演会　2024/06/04
溶液中の粒子配向を改善した高精度単粒子解析

岡圭吾, 濵口祐, 海原大輔, 米倉功治

日本顕微鏡学会第80回学術講演会　2024/06/03
クライオ電子顕微鏡によるオイルワックスゲルの新たな評価手法の検討

太田裕基, 山下美香, 鈴木留佳, 畑毅, 濵口祐, 陣内浩司

日本顕微鏡学会第80回学術講演会　2024/06/03
クライオ電子顕微鏡によるソフトマテリアル可視化に向けた取り組み Invited

濵口祐

クライオ電子顕微鏡・技術説明会　2024/02/14
Investigation and application of solvent effects in high-resolution single-particle cryogenic-electron microscopy International-presentation

Keigo Oka, Tasuku Hamaguchi, Daisuke Unabara, Koji Yonekura

2023 Joint Symposium　2023/12/11
Cryo-EM observation of wide range of soft-materials International-presentation Invited

Tasuku Hamaguchi, Keisuke Kawakami, Daisuke Unabara, Koji Yonekura

2023/11/14
多様な液体材料観察を可能とするクライオEM試料作製法の検討とトモグラフィー解析

海原大輔, 浜口祐, 米倉功治

日本顕微鏡学会第66回シンポジウム　2023/11/12
アキラルCo(Ⅱ)フタロシアニンで構成された螺旋超分子のMC-AFMによる電流測定

相澤洋紀, 佐藤拓朗, 米倉功治, 米倉‐眞木沙織, 濱口祐, 高場圭章, 湊丈俊, 山本浩史

第17回分子科学討論会2023大阪　2023/09/13
Cryo-EM observation of γ-polyglutamic acid hydrogels from Bacillus subtilis of Firmicutes International-presentation

Tasuku Hamaguchi, Daisuke Unabara, Koji Yonekura

24th Biennial Congress of the International Organization for Mycoplasmology (IOM)　2023/07/17
Cryo-EM observations for proteins and soft-materials Invited

Tasuku Hamaguchi, Keisuke Kawakami, Daisuke Unabara, Koji Yonekura

2023/06/25
多元物質科学研究所におけるクライオ電子顕微鏡を用いた取り組み（利用方法から観察事例まで） Invited

浜口祐

2022年度東北大学多元物質科学研究所イノベーションエクスチェンジ　2023/01/18
CRYO ARMオーナーズMTG Invited

浜口祐

第一回CRYO ARMオーナーズMTG　2022/12/26
Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome

Keisuke Kawakami, Tasuku Hamaguchi, Yuu Hirose, Daisuke Kosumi, Makoto Miyata, Nobuo Kamiya, Koji Yonekura

AsBIC10 2022　2022/11/30
Analysis of Japanese sake using synchrotron light and cryo-TEM Invited

Switzerland-Japan Workshop for Synchrotron Light and Wine/Sake, 2022　2022/11/25
理研・東北大の施設報告

浜口祐

AMED/BINDS第1回クライオ電子顕微鏡施設技術交流会　2022/11/21
高精度クライオEMによる構造解析 Invited

浜口祐

生理研研究会「新世代のクライオ電子顕微鏡」　2022/11/01
Cryo-EM single particle analyses for co-factors extremely sensitive to radiation Invited

2022/11/01
CYPを対象としたCryo-EM Invited

米倉功治, 浜口祐, 高場圭章, 川上恵典, 眞木さおり

CBI学会2022年大会　2022/10/25
High-precision structural analysis by cryo-electron microscopy

Tasuku Hamaguchi, Keisuke Kawakami, Saori Maki-Yonekura, Koji Yonekura

2022/09/30
ソフトマテリアル研究拠点：創薬

浜口祐

ソフトマテリアル研究拠点会議　2022/08/10
High-resolution and high-precision cryo-ED and EM Invited

Yonekura K, Maki-Yonekura S, Takaba K, Hamaguchi T, Naitow H, Kawakami K

Biological Structural Dynamics by Ultrafast X-ray and 4D Electron Microscopy, Pacifichem 2021　2021/12/16
The development of 3D ED on studying structure and charge state of protein microcrystals International-presentation Invited

Yonekura K, Maki-Yonekura S, Takaba K, Hamaguchi T, Naitow H, Kawakami K

25th IUCr Congress Satellite School on Electron Crystallography　2021/08/11
Complementary use of high-resolution and high-precision cryo-ED and EM Invited

Yonekura K, Maki-Yonekura S, Takaba K, Hamaguchi T, Naitow H, Kawakami K

Microscopy and Microanalysis (M&M) 2021　2021/08/02
Cryo-ED and EM for higher-resolution and higher-precision structure analysis Invited

Yonekura, K, Maki-Yonekura, S. Hamaguchi, T, Naitow, H, Kiyofumi, T

Japan-Canada Joint Symposium 2020, Development and applications of the methods combining interference/phase measurement techniques and analytic techniques, Japanese Society of Microscopy　2020/05/26
Cryo-ED and EM for Higher-Resolution and Higher-Precision Structures Invited

Yonekura K, Maki-Yonekura S, Hamaguchi T, Naitow H, Takaba K

12th Asia-Pacific Microscopy Conference (APMC2020) Hyderabad International Convention Center, Hyderabad, India　2020/02/04

Show all Show first 5

Industrial Property Rights 1

立体模型の製造方法、及び立体模型

浜口祐, 宮田真人

Property Type: Patent

Research Projects 4

安全かつ効率的なCas3ゲノム編集ツール開発に資する機能構造相関研究

竹下浩平, 浜口祐, 清水伸隆, 吉見一人

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 基盤研究(B)

Institution: 国立研究開発法人理化学研究所

2024/04/01 - 2025/03/31
Integrative Structural Biology Studies on the development for safe and efficient Cas3 genome editing tools

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Institute of Physical and Chemical Research

2022/04/01 - 2025/03/31
エクソソーム局在性膜タンパク質EAAC1およびCD63の構造解析

浜口祐

Offer Organization: 日本学術振興会

System: 科学研究費助成事業基盤研究(C)

Category: 基盤研究(C)

Institution: 国立研究開発法人理化学研究所

2020/04 - 2023/03

More details Close

マウス由来グルタミン酸トランスポーター（EAAC1）について，Expi293F株を用いた高発現系の確立と，精製法の最適化を行った．EAAC1はグルタミン酸だけでなく，システインの輸送にも関わることが提唱されており，その輸送機構の解明を目指し，システイン存在下での精製を行った．また同時にクライオ電子顕微鏡撮影において妨げとなる塩，界面活性剤，安定化剤などの低濃度条件下において，EAAC1をmg/mlオーダーにて精製することに成功した．また，界面活性剤とともに共存する脂質量を調製することで，濃縮効率と安定性が改善された．得られたEAAC1を用いて，ネガティブ染色電子顕微鏡観察法により粒子の可視化を試みたところ，均一性が評価でき，得られた粒子のサイズ分布はEAAC1が３量体で存在する際に想定される粒子径とおおむね同じであった．このことから，EAAC1が本来の機能を維持した状態で精製できたものと考えられた．このように調製したEAAC1についてクライオ電子顕微鏡構造解析に向けて様々なグリッド作成条件を検討を行ったところグルタミン酸輸送体と思われる像の撮影に成功した．また，粒子には界面活性剤に由来すると考えられるミセルバンド像も見られた．しかし，界面活性剤存在下でのグリッド作成時に頻出する粒子の低分布・低密度化が生じており，さらなる高濃度化が必要であると考えられた．現在までにサンプルの培養，可溶化，精製を繰り返し，構造解析を実現可能な量の試料調製を行った．また，テトラスパニンについては細胞中での高発現が確認できており，様々な可溶化，製紙恵方を試みたが，現在までに均一なタンパク質粒子としては得られていない．
機能性人工核酸のロジカル設計・創出技術の実現と未来型医療の開拓

Offer Organization: 理研-産総研「チャレンジ研究」

2021/04 - 2022/03