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Yokoyama Takeshi
| Faculty of Fisheries Sciences Marine Life Science Marine Biotechnology and Microbiology | Associate Professor |
Researcher basic information
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Research activity information
■ Awards- Mar. 2018, RIKEN Center for Life Science Technologies, CLST Researcher Incentive Award
Structural analysis of various protein/ protein complexes by Cryo-EM - Mar. 2018, RIKEN, RIKEN Research Incentive Award
Structural analysis of various proteins/ protein complexes by Cryo-EM
- Cryo-EM elucidates the interaction mechanism of ozoralizumab, a humanized anti-TNFα NANOBODY® compound
Masashi Mima; Kyohei Sato; Takeshi Yokoyama; Chiemi Mishima-Tsumagari; Tatsuya Ohnuki; Yoshikazu Tanaka; Kunihiko Iwamoto
Biochemical and Biophysical Research Communications, 816, 153572, 153572, Elsevier BV, Jun. 2026, [Peer-reviewed]
Scientific journal - Glomerular routing of tumor-derived extracellular vesicles substantiates urinary biopsy.
Shota Kawaguchi; Taiga Ajiri; Rina Mitsuya; Reiko Tsuchiya; Koki Kunitake; Yoshikazu Tanaka; Takeshi Yokoyama; Kiichi Sato; Yusuke Sato; Zetao Zhu; Kunanon Chattrairat; Yasuko Kobayashi; Kimiko Inoue; Keisuke Imaeda; Kosei Ueno; Sou Ryuzaki; Akira Kato; Yasuyuki Kimura; Atsushi Natsume; Ryosuke Kojima; Takao Yasui
Science advances, 12, 8, eaeb0555, 20 Feb. 2026, [Peer-reviewed], [International Magazine]
English, Scientific journal, Urinary small extracellular vesicles (sEVs), which can reflect systemic conditions, hold great promise for noninvasive cancer diagnostics, yet the mechanism by which tumor-derived sEVs reach urine remains unclear. Here, we demonstrate that the glomerulus actively transcytoses circulating tumor-derived sEVs into urine. Using CRISPR guide RNA-tagged glioma sEVs and bioluminescent/fluorescent green-enhanced nano-lantern (GeNL)-tagged lung and pancreatic cancer sEVs, we tracked their journey from tumors to urine in multiple mouse models. In vivo and in vitro analyses revealed endocytic uptake and transcytotic release by glomerular cells, accompanied by changes in sEV size and surface composition. GeNL-tagged sEVs consistently showed higher signals in urine than plasma, indicating selective excretion. These findings redefine the glomerulus as a dynamic regulator of sEV processing and establish a mechanistic foundation for urinary liquid biopsy. - Synthesis and structure-activity relationship of azithromycin derivatives against non-tuberculous mycobacteria
Yuka Isozaki; Ali Ahsan Muzahid; Tatsuki Wakata; Maho Fujino; Yoshikazu Tanaka; Chigusa Hayashi; Yoshimasa Ishizaki; Tomokazu Ohishi; Ayumi Morita; Shunichi Ohba; Takeshi Yokoyama; Masayuki Igarashi; Kazunobu Toshima; Daisuke Takahashi
European Journal of Medicinal Chemistry, 304, 118520, 118520, Elsevier BV, Feb. 2026, [Peer-reviewed]
English, Scientific journal - Hypoxia-induced ribosomal RNA modifications in the peptidyl-transferase center contribute to anaerobic growth of bacteria
Kensuke Ishiguro; Karin Midorikawa; Naoki Shigi; Satoshi Kimura; Aivar Liiv; Takeshi Yokoyama; Takuhiro Ito; Mikako Shirouzu; Jaanus Remme; Kenjyo Miyauchi; Tsutomu Suzuki
Molecular Cell, Elsevier BV, Dec. 2025, [Peer-reviewed]
Scientific journal - A Structurally Robust Phospholipid Microtube Constructed by Membrane Phase Separation as a Scaffold for On-Tube Characterization of Membrane-Bound Proteins
Noriyuki Uchida; Ryu Ishizaka; Anju Kawakita; Hiroshi Ueno; Hiroyuki Noji; Rinshi S. Kasai; Takeshi Yokoyama; Saburo Kurihara; Tomoki Noguchi; Go Watanabe; Ayaka Iwasaki; Itsuki Ajioka; Kazuyoshi Muranishi; Ken Yoshizawa; Shingo Kanemura; Masaki Okumura; Takahiro Muraoka
Journal of the American Chemical Society, American Chemical Society (ACS), 23 Oct. 2025, [Peer-reviewed]
English, Scientific journal - Zinc finger domains bind low-complexity domain polymers
Naohiko Iguchi; Noriyoshi Isozumi; Yoshikazu Hattori; Tomohiro Imamura; Takeshi Yokoyama; Masatomo So; Hitoki Nanaura; Takao Kiriyama; Nobuyuki Eura; Minako Yamaoka; Naoki Iwasa; Tomo Shiota; Mari Nakanishi; Nanako Konishi; Haruka Ito; Akihito Takeuchi; Masashi Mori; Shinya Ohki; Hiroyuki Kumeta; Hironori Koga; Mai Watabe; Takuya Mabuchi; Shingo Kanemura; Masaki Okumura; Yoshikazu Tanaka; Ken Morishima; Masaaki Sugiyama; Fumika Ide; Hiroyoshi Matsumura; Takuya Yoshizawa; Ichiro Ota; Naoki Suzuki; Masashi Aoki; Yoshito Yamashiro; Tomohide Saio; Kazuma Sugie; Eiichiro Mori
Nature Communications, 16, 1, Springer Science and Business Media LLC, 16 Oct. 2025, [Peer-reviewed]
Scientific journal - Structure reveals a regulation mechanism of plant outward-rectifying K + channel GORK by structural rearrangements in the CNBD–Ankyrin bridge
Taro Yamanashi; Yuki Muraoka; Tadaomi Furuta; Tsukasa Kume; Natsuko Sekido; Shunya Saito; Shota Terashima; Takeshi Yokoyama; Yoshikazu Tanaka; Atsushi Miyamoto; Kanane Sato; Tomoyuki Ito; Hikaru Nakazawa; Mitsuo Umetsu; Ellen Tanudjaja; Masaru Tsujii; Ingo Dreyer; Julian I. Schroeder; Yasuhiro Ishimaru; Nobuyuki Uozumi
Proceedings of the National Academy of Sciences, 122, 30, Proceedings of the National Academy of Sciences, 23 Jul. 2025, [Peer-reviewed]
Scientific journal, Guard cells, which regulate stomatal apertures in plants, possess a sophisticated mechanism for regulating turgor pressure. The outward-rectifying “K + out ” channel GORK, expressed in guard cells of the plant Arabidopsis thaliana , is a central component that promotes stomatal closure by releasing K + to the extracellular space, thereby lowering turgor pressure. To date, the structural basis underlying the regulation of the K + transport activity of GORK is unclear. Using cryo-EM, we determined the structures of the GORK outward-rectifying K + channel with a resolution of 3.16 to 3.27 Å in five distinct conformations that differ significantly in their C-terminal cyclic nucleotide binding domain (CNBD) and ankyrin repeat (ANK) domain. The C-linker connects the transmembrane domains to the C-terminal domains, i.e., CNBD, CNBD–Ankyrin bridge, and ANK. The structural changes and interactions in the C-linker determine whether the closed state of GORK is closer to the preopen state or in a more removed state from the open state of the channel. In particular, interconversion in the short sequence within the CNBD–Ankyrin bridge plays a decisive role in this determination. This region forms an α-helix in the preopened state, while it adopts a nonhelical structure in further distant closed states. The dynamics of the cytosolic region strongly suggest that the K + channel activity of GORK is regulated by cytosolic signaling factors during stomatal closure. - Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement
Kyohei Sato; Shiro Uehara; Atsushi Tsugita; Mayuka Ishii; Shieru Ishiyama; Atsushi Maejima; Ishin Nakahara; Misae Nazuka; Takashi Matsui; Gatsogiannis Christos; Takeshi Yokoyama; Izumi Kumagai; Koki Makabe; Ryutaro Asano; Yoshikazu Tanaka
Cell Reports, 44, 7, 115965, 115965, Elsevier BV, Jul. 2025, [Peer-reviewed]
Scientific journal - Creation of a macrolide antibiotic against non-tuberculous Mycobacterium using late-stage boron-mediated aglycon delivery
Yuka Isozaki; Takumi Makikawa; Kosuke Kimura; Daiki Nishihara; Maho Fujino; Yoshikazu Tanaka; Chigusa Hayashi; Yoshimasa Ishizaki; Masayuki Igarashi; Takeshi Yokoyama; Kazunobu Toshima; Daisuke Takahashi
Science Advances, 11, 10, adt2352, Mar. 2025, [Peer-reviewed], [Corresponding author]
English, Scientific journal - Design of Cyborg Proteins by Loop Region Replacement with Oligo(ethylene glycol): Exploring Suitable Mutations for Cyborg Protein Construction Using Machine Learning
Wijak Yospanya; Akari Matsumura; Yukihiro Imasato; Tomoyuki Itou; Yusuke Aoki; Hikaru Nakazawa; Takashi Matsui; Takeshi Yokoyama; Mihoko Ui; Mitsuo Umetsu; Satoru Nagatoishi; Kouhei Tsumoto; Yoshikazu Tanaka; Kazushi Kinbara
Bulletin of the Chemical Society of Japan, Oxford University Press (OUP), 02 Sep. 2024, [Peer-reviewed]
Scientific journal, Abstract
We synthesized a “cyborg protein,” wherein a synthetic molecule partially substitutes the main peptide chain by linking two protein domains with a synthetic oligomer. Green fluorescent protein (GFP) served as the model for constructing the cyborg proteins. We prepared circularly permuted GFP (cpGFP) with new termini between β10 and β11, where the original N- and C-termini were linked by a cleavable peptide loop. The cyborg GFP was constructed from cpGFP by linking the β10 and β11 with oligo(ethylene glycol) using maleimide-cysteine couplings, followed by the enzymatic cleavage of the N- and C-termini linking loop by thrombin. With the help of machine learning, we were able to obtain the cpGFP mutants that significantly alter the fluorescence activity (53% increase) by thrombin treatment, which splits cpGFP into two fragments (fragmented-GFP), and by heat shock. When the cyborg GFP was constructed using this mutant, the fluorescence intensity increased by 13% after heat treatment, similar to cpGFP (33% increase), and the behavior was significantly different from that of the fragmented-GFP. This result suggests the possibility that the oligo(ethylene glycol) chain in the cyborg protein plays a similar role to the peptide in the main chain of the protein. - Inter-compatibility of eukaryotic and Asgard archaea ribosome-translocon machineries
Isaac Carilo; Yosuke Senju; Takeshi Yokoyama; Robert C. Robinson
Journal of Biological Chemistry, 107673, 107673, Elsevier BV, Aug. 2024, [Peer-reviewed]
Scientific journal - Characterization of a novel format scFv×VHH single‐chain biparatopic antibody against metal binding protein MtsA
Risa Asano; Miyu Takeuchi; Makoto Nakakido; Sho Ito; Chihiro Aikawa; Takeshi Yokoyama; Akinobu Senoo; Go Ueno; Satoru Nagatoishi; Yoshikazu Tanaka; Ichiro Nakagawa; Kouhei Tsumoto
Protein Science, 33, 6, Wiley, 15 May 2024, [Peer-reviewed]
English, Scientific journal, Abstract
Biparatopic antibodies (bpAbs) are engineered antibodies that bind to multiple different epitopes within the same antigens. bpAbs comprise diverse formats, including fragment‐based formats, and choosing the appropriate molecular format for a desired function against a target molecule is a challenging task. Moreover, optimizing the design of constructs requires selecting appropriate antibody modalities and adjusting linker length for individual bpAbs. Therefore, it is crucial to understand the characteristics of bpAbs at the molecular level. In this study, we first obtained single‐chain variable fragments and camelid heavy‐chain variable domains targeting distinct epitopes of the metal binding protein MtsA and then developed a novel format single‐chain bpAb connecting these fragment antibodies with various linkers. The physicochemical properties, binding activities, complex formation states with antigen, and functions of the bpAb were analyzed using multiple approaches. Notably, we found that the assembly state of the complexes was controlled by a linker and that longer linkers tended to form more compact complexes. These observations provide detailed molecular information that should be considered in the design of bpAbs. - "Rich arginine and strong positive charge" antimicrobial protein protamine: From its action on cell membranes to inhibition of bacterial vital functions.
Momoka Ookubo; Yuka Tashiro; Kosuke Asano; Yoshiharu Kamei; Yoshikazu Tanaka; Takayuki Honda; Takeshi Yokoyama; Michiyo Honda
Biochimica et biophysica acta. Biomembranes, 1866, 5, 184323, 184323, 16 Apr. 2024, [Peer-reviewed], [International Magazine]
English, Scientific journal, Protamine, an antimicrobial protein derived from salmon sperm with a molecular weight of approximately 5 kDa, is composed of 60-70 % arginine and is a highly charged protein. Here, we investigated the mechanism of antimicrobial action of protamine against Cutibacterium acnes (C. acnes) focusing on its rich arginine content and strong positive charge. Especially, we focused on the attribution of dual mechanisms of antimicrobial protein, including membrane disruption or interaction with intracellular components. We first determined the dose-dependent antibacterial activity of protamine against C. acnes. In order to explore the interaction between bacterial membrane and protamine, we analyzed cell morphology, zeta potential, membrane permeability, and the composition of membrane fatty acid. In addition, the localization of protamine in bacteria was observed using fluorescent-labeled protamine. For investigation of the intracellular targets of protamine, bacterial translation was examined using a cell-free translation system. Based on our results, the mechanism of the antimicrobial action of protamine against C. acnes is as follows: 1) electrostatic interactions with the bacterial cell membrane; 2) self-internalization into the bacterial cell by changing the composition of the bacterial membrane; and 3) inhibition of bacterial growth by blocking translation inside the bacteria. However, owing to its strong electric charge, protamine can also interact with DNA, RNA, and other proteins inside the bacteria, and may inhibit various bacterial life processes beyond the translation process. - Discrimination of extracellular miRNA sources for the identification of tumor-related functions based on nanowire thermofluidics
Kunanon Chattrairat; Akira Yokoi; Min Zhang; Mikiko Iida; Kosuke Yoshida; Masami Kitagawa; Ayuka Niwa; Masatoshi Maeki; Takeshi Hasegawa; Takeshi Yokoyama; Yoshikazu Tanaka; Yusuke Miyazaki; Wataru Shinoda; Manabu Tokeshi; Kazuki Nagashima; Takeshi Yanagida; Hiroaki Kajiyama; Yoshinobu Baba; Takao Yasui
Device, 100363, 100363, Elsevier BV, Apr. 2024, [Peer-reviewed]
Scientific journal - Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine
Naho Akiyama; Kensuke Ishiguro; Takeshi Yokoyama; Kenjyo Miyauchi; Asuteka Nagao; Mikako Shirouzu; Tsutomu Suzuki
Nature Structural & Molecular Biology, 31, 5, 817, 825, Springer Science and Business Media LLC, 27 Mar. 2024, [Peer-reviewed]
English, Scientific journal - Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1
Mayuki Tanaka#; Takeshi Yokoyama#; Hironori Saito#; Madoka Nishimoto; Kengo Tsuda; Naoyuki Sotta; Hideki Shigematsu; Mikako Shirouzu; Shintaro Iwasaki; Takuhiro Ito; Toru Fujiwara
Nature Chemical Biology, 20, 5, 605, 614, Springer Science and Business Media LLC, 24 Jan. 2024, [Peer-reviewed], [Lead author]
Scientific journal - Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside
Junta Tomono; Kosuke Asano; Takuma Chiashi; Masato Suzuki; Masayuki Igarashi; Yoshiaki Takahashi; Yoshikazu Tanaka*; Takeshi Yokoyama*
The Journal of Biochemistry, 175, 6, 587, 598, Oxford University Press (OUP), 16 Jan. 2024, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal, Abstract
The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to visualize antibiotic actions on translating ribosomes in the cell-free system under macromolecular crowding conditions by cryo-electron microscopy, designated as the DARC method: the Direct visualization of Antibiotic binding on Ribosomes in the Cell-free translation system. This new method allows for acquiring a more comprehensive understanding of the mode of action of antibiotics on the translation inhibition without ribosome purification. Furthermore, with the direct link to biochemical analysis at the same condition as cryo-EM observation, we revealed the evolution of 2-DOS aminoglycosides from dibekacin (DBK) to arbekacin (ABK) by acquiring the synthetic tailored anchoring motif to lead to stronger binding affinity to ribosomes. Our cryo-EM structures of DBK and ABK bound ribosomes in the cell-free environment clearly depicted a synthetic tailored γ-amino-α-hydroxybutyryl (HABA) motif formed additional interactions with the ribosome enhancing antibiotic bindings. This new approach would be valuable for understanding the function of antibiotics for more efficient drug development. - Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth
Xuewei Zhao; Ding Ma; Kensuke Ishiguro; Hironori Saito; Shinichiro Akichika; Ikuya Matsuzawa; Mari Mito; Toru Irie; Kota Ishibashi; Kimi Wakabayashi; Yuriko Sakaguchi; Takeshi Yokoyama; Yuichiro Mishima; Mikako Shirouzu; Shintaro Iwasaki; Takeo Suzuki; Tsutomu Suzuki
Cell, 186, 25, 5517, 5535.e24, Elsevier BV, Dec. 2023, [Peer-reviewed]
English, Scientific journal - Synthesis of epitope-targeting nanobody based on native protein-protein interactions for FtsZ filamentation suppressor.
Hikaru Nakazawa; Taiji Katsuki; Takashi Matsui; Atsushi Tsugita; Takeshi Yokoyama; Tomoyuki Ito; Sakiya Kawada; Yoshikazu Tanaka; Mitsuo Umetsu
Biotechnology journal, e2300039, 17 Jul. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, Phage display and biopanning are powerful tools for generating binding molecules for a specific target. However, the selection process based only on binding affinity provides no assurance for the antibody's affinity to the target epitope. In this study, we propose a molecular-evolution approach guided by native protein-protein interactions to generate epitope-targeting antibodies. The binding-site sequence in a native protein was grafted into a complementarity-determining region (CDR) in the nanobody, and a nonrelated CDR loop (in the grafted nanobody) was randomized to create a phage display library. In this construction of nanobodies by integrating graft and evolution technology (CAnIGET method), suitable grafting of the functional sequence added functionality to the nanobody, and the molecular-evolution approach enhanced the binding function to inhibit the native protein-protein interactions. To apply for biological tool with growth screening, model nanobodies with an affinity for filamenting temperature-sensitive mutant Z (FtsZ) from Staphylococcus aureus were constructed and completely inhibited the polymerization of FtsZ as a function. Consequently, the expression of these nanobodies drastically decreased the cell division rate. We demonstrate the potential of the CAnIGET method with the use of native protein-protein interactions for steady epitope-specific evolutionary engineering. This article is protected by copyright. All rights reserved. - Simple Method for the Creation of a Bacteria-Sized Unilamellar Liposome with Different Proteins Localized to the Respective Sides of the Membrane.
Kosaku Noba; Shogo Yoshimoto; Yoshikazu Tanaka; Takeshi Yokoyama; Tomoaki Matsuura; Katsutoshi Hori
ACS synthetic biology, 12, 5, 1437, 1446, 19 May 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, Artificial cells are membrane vesicles mimicking cellular functions. To date, giant unilamellar vesicles made from a single lipid membrane with a diameter of 10 μm or more have been used to create artificial cells. However, the creation of artificial cells that mimic the membrane structure and size of bacteria has been limited due to technical restrictions of conventional liposome preparation methods. Here, we created bacteria-sized large unilamellar vesicles (LUVs) with proteins localized asymmetrically to the lipid bilayer. Liposomes containing benzylguanine-modified phospholipids were prepared by combining the conventional water-in-oil emulsion method and the extruder method, and green fluorescent protein fused with SNAP-tag was localized to the inner leaflet of the lipid bilayer. Biotinylated lipid molecules were then inserted externally, and the outer leaflet was modified with streptavidin. The resulting liposomes had a size distribution in the range of 500-2000 nm with a peak at 841 nm (the coefficient of variation was 10.3%), which was similar to that of spherical bacterial cells. Fluorescence microscopy, quantitative evaluation using flow cytometry, and western blotting proved the intended localization of different proteins on the lipid membrane. Cryogenic electron microscopy and quantitative evaluation by α-hemolysin insertion revealed that most of the created liposomes were unilamellar. Our simple method for the preparation of bacteria-sized LUVs with asymmetrically localized proteins will contribute to the creation of artificial bacterial cells for investigating functions and the significance of their surface structure and size. - RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function
Chisa Shiraishi; Akinobu Matsumoto; Kazuya Ichihara; Taishi Yamamoto; Takeshi Yokoyama; Taisuke Mizoo; Atsushi Hatano; Masaki Matsumoto; Yoshikazu Tanaka; Eriko Matsuura-Suzuki; Shintaro Iwasaki; Shouji Matsushima; Hiroyuki Tsutsui; Keiichi I. Nakayama
Nature Communications, 14, 1, Springer Science and Business Media LLC, 20 Apr. 2023, [Peer-reviewed]
English, Scientific journal, Abstract
Although several ribosomal protein paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-containing ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-containing ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide further insight into the mechanisms and physiological relevance of tissue-specific translational regulation. - Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus
Yuko Murayama; Haruhiko Ehara; Mari Aoki; Mie Goto; Takeshi Yokoyama; Shun-ichi Sekine
Science Advances, 9, 6, eade7093, American Association for the Advancement of Science (AAAS), 10 Feb. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the adenosine triphosphate–dependent RNA translocase/helicase Rho, which causes RNA/DNA dissociation from the RNAP elongation complex (EC). However, the structural basis of the interplay between Rho and RNAP remains obscure. Here, we report the cryo–electron microscopy structure of the Thermus thermophilus RNAP EC engaged with Rho. The Rho hexamer binds RNAP through the carboxyl-terminal domains, which surround the RNA exit site of RNAP, directing the nascent RNA seamlessly from the RNA exit to its central channel. The β-flap tip at the RNA exit is critical for the Rho-dependent RNA release, and its deletion causes an alternative Rho-RNAP binding mode, which is irrelevant to termination. The Rho binding site overlaps with the binding sites of other macromolecules, such as ribosomes, providing a general basis of gene regulation. - A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation
Hiromi Watari; Hiromu Kageyama; Nami Masubuchi; Hiroya Nakajima; Kako Onodera; Pamela J. Focia; Takumi Oshiro; Takashi Matsui; Yoshio Kodera; Tomohisa Ogawa; Takeshi Yokoyama; Makoto Hirayama; Kanji Hori; Douglas M. Freymann; Misa Imai; Norio Komatsu; Marito Araki; Yoshikazu Tanaka; Ryuichi Sakai
Nature Communications, 13, 1, 7262, 7262, Springer Science and Business Media LLC, 25 Nov. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, Abstract
N-glycan-mediated activation of the thrombopoietin receptor (MPL) under pathological conditions has been implicated in myeloproliferative neoplasms induced by mutant calreticulin, which forms an endogenous receptor-agonist complex that traffics to the cell surface and constitutively activates the receptor. However, the molecular basis for this mechanism is elusive because oncogenic activation occurs only in the cell-intrinsic complex and is thus cannot be replicated with external agonists. Here, we describe the structure and function of a marine sponge-derived MPL agonist, thrombocorticin (ThC), a homodimerized lectin with calcium-dependent fucose-binding properties. In-depth characterization of lectin-induced activation showed that, similar to oncogenic activation, sugar chain-mediated activation persists due to limited receptor internalization. The strong synergy between ThC and thrombopoietin suggests that ThC catalyzes the formation of receptor dimers on the cell surface. Overall, the existence of sugar-mediated MPL activation, in which the mode of activation is different from the original ligand, suggests that receptor activation is unpredictably diverse in living organisms. - The carbohydrate tail of landomycin A is responsible for its interaction with the repressor protein LanK
Atsushi Tsugita; Shiro Uehara; Takashi Matsui; Takeshi Yokoyama; Iryna Ostash; Maksym Deneka; Subbarao Yalamanchili; Clay S. Bennett; Yoshikazu Tanaka; Bohdan Ostash
The FEBS Journal, Wiley, 16 Apr. 2022, [Peer-reviewed]
Scientific journal - Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system
Yoshiko Nakagawa; Howard C.-H. Shen; Yusuke Komi; Shinju Sugiyama; Takaaki Kurinomaru; Yuri Tomabechi; Elena Krayukhina; Kenji Okamoto; Takeshi Yokoyama; Mikako Shirouzu; Susumu Uchiyama; Megumi Inaba; Tatsuya Niwa; Yasushi Sako; Hideki Taguchi; Motomasa Tanaka
Nature Chemical Biology, 18, 3, 321, 331, Springer Science and Business Media LLC, 17 Feb. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, Disaggregation of amyloid fibrils is a fundamental biological process required for amyloid propagation. However, due to the lack of experimental systems, the molecular mechanism of how amyloid is disaggregated by cellular factors remains poorly understood. Here, we established a robust in vitro reconstituted system of yeast prion propagation and found that heat-shock protein 104 (Hsp104), Ssa1 and Sis1 chaperones are essential for efficient disaggregation of Sup35 amyloid. Real-time imaging of single-molecule fluorescence coupled with the reconstitution system revealed that amyloid disaggregation is achieved by ordered, timely binding of the chaperones to amyloid. Remarkably, we uncovered two distinct prion strain conformation-dependent modes of disaggregation, fragmentation and dissolution. We characterized distinct chaperone dynamics in each mode and found that transient, repeated binding of Hsp104 to the same site of amyloid results in fragmentation. These findings provide a physical foundation for otherwise puzzling in vivo observations and for therapeutic development for amyloid-associated neurodegenerative diseases. - Chimeric mutants of staphylococcal hemolysin, which act as both one‐component and two‐component hemolysin, created by grafting the stem domain
Nouran Ghanem; Natsuki Kanagami; Takashi Matsui; Kein Takeda; Jun Kaneko; Yasuyuki Shiraishi; Christian A. Choe; Tomomi Uchikubo‐Kamo; Mikako Shirouzu; Tsubasa Hashimoto; Tomohisa Ogawa; Tomoaki Matsuura; Po‐Ssu Huang; Takeshi Yokoyama; Yoshikazu Tanaka
The FEBS Journal, Wiley, 16 Feb. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, Staphylococcus aureus expresses several hemolytic pore-forming toxins (PFTs), which are all commonly composed of three domains: cap, rim and stem. PFTs are expressed as soluble monomers and assemble to form a transmembrane β-barrel pore in the erythrocyte cell membrane. The stem domain undergoes dramatic conformational changes to form a pore. Staphylococcal PFTs are classified into two groups: one-component α-hemolysin (α-HL) and two-component γ-hemolysin (γ-HL). The α-HL forms a homo-heptamer, whereas γ-HL is an octamer composed of F-component (LukF) and S-component (Hlg2). Because PFTs are used as materials for nanopore-based sensors, knowledge of the functional properties of PFTs is used to develop new, engineered PFTs. However, it remains challenging to design PFTs with a β-barrel pore because their formation as transmembrane protein assemblies requires large conformational changes. In the present study, aiming to investigate the design principles of the β-barrel formed as a consequence of the conformational change, chimeric mutants composed of the cap/rim domains of α-HL and the stem of LukF or Hlg2 were prepared. Biochemical characterization and electron microscopy showed that one of them assembles as a heptameric one-component PFT, whereas another participates as both a heptameric one- and heptameric/octameric two-component PFT. All chimeric mutants intrinsically assemble into SDS-resistant oligomers. Based on these observations, the role of the stem domain of these PFTs is discussed. These findings provide clues for the engineering of staphylococcal PFT β-barrels for use in further promising applications. - The landscape of translational stall sites in bacteria revealed by monosome and disome profiling
Tomoya Fujita; Takeshi Yokoyama; Mikako Shirouzu; Hideki Taguchi; Takuhiro Ito; Shintaro Iwasaki
RNA, 28, 3, rna.078188.120, rna.078188.120, Cold Spring Harbor Laboratory, 14 Dec. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; however, the landscape of ribosome pauses in bacteria remains ambiguous. Here, we harness monosome and disome (or collided ribosome) profiling strategies to survey ribosome pause sites in Escherichia coli. Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences: a low frequency of disomes at stop codons, collisions occurring immediately after 70S assembly on start codons, and shorter queues of ribosomes trailing upstream. The pause sites corresponded with the biochemical validation by integrated nascent chain profiling (iNP) to detect polypeptidyl-tRNA, an elongation intermediate. Moreover, the subset of those sites showed puromycin resistance, presenting slow peptidyl transfer. Among the identified sites, the ribosome pause at Asn586 of ycbZ was validated by biochemical reporter assay, tRNA sequencing (tRNA-Seq), and cryo-electron microscopy (cryo-EM) experiments. Our results provide a useful resource for ribosome stalling sites in bacteria - Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex
Mutsuko Kukimoto-Niino; Kazushige Katsura; Rahul Kaushik; Haruhiko Ehara; Takeshi Yokoyama; Tomomi Uchikubo-Kamo; Reiko Nakagawa; Chiemi Mishima-Tsumagari; Mayumi Yonemochi; Mariko Ikeda; Kazuharu Hanada; Kam Y. J. Zhang; Mikako Shirouzu
Science Advances, 7, 30, eabg3147, eabg3147, American Association for the Advancement of Science (AAAS), Jul. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, The dedicator of cytokinesis (DOCK) family of guanine nucleotide exchange factors (GEFs) promotes cell motility, phagocytosis, and cancer metastasis through activation of Rho guanosine triphosphatases. Engulfment and cell motility (ELMO) proteins are binding partners of DOCK and regulate Rac activation. Here, we report the cryo–electron microscopy structure of the active ELMO1-DOCK5 complex bound to Rac1 at 3.8-Å resolution. The C-terminal region of ELMO1, including the pleckstrin homology (PH) domain, aids in the binding of the catalytic DOCK homology region 2 (DHR-2) domain of DOCK5 to Rac1 in its nucleotide-free state. A complex α-helical scaffold between ELMO1 and DOCK5 stabilizes the binding of Rac1. Mutagenesis studies revealed that the PH domain of ELMO1 enhances the GEF activity of DOCK5 through specific interactions with Rac1. The structure provides insights into how ELMO modulates the biochemical activity of DOCK and how Rac selectivity is achieved by ELMO. - Anti-EGFR antibody 528 binds to domain III of EGFR at a site shifted from the cetuximab epitope
Koki Makabe; Takeshi Yokoyama; Shiro Uehara; Tomomi Uchikubo-Kamo; Mikako Shirouzu; Kouki Kimura; Kouhei Tsumoto; Ryutaro Asano; Yoshikazu Tanaka; Izumi Kumagai
Scientific Reports, 11, 1, 5790, 5790, Springer Science and Business Media LLC, Mar. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal,Abstract Antibodies have been widely used for cancer therapy owing to their ability to distinguish cancer cells by recognizing cancer-specific antigens. Epidermal growth factor receptor (EGFR) is a promising target for the cancer therapeutics, against which several antibody clones have been developed and brought into therapeutic use. Another antibody clone, 528, is an antagonistic anti-EGFR antibody, which has been the focus of our antibody engineering studies to develop cancer drugs. In this study, we explored the interaction of 528 with the extracellular region of EGFR (sEGFR) via binding analyses and structural studies. Dot blotting experiments with heat treated sEGFR and surface plasmon resonance binding experiments revealed that 528 recognizes the tertiary structure of sEGFR and exhibits competitive binding to sEGFR with EGF and cetuximab. Single particle analysis of the sEGFR–528 Fab complex via electron microscopy clearly showed the binding of 528 to domain III of sEGFR, the domain to which EGF and cetuximab bind, explaining its antagonistic activity. Comparison between the two-dimensional class average and the cetuximab/sEGFR crystal structure revealed that 528 binds to a site that is shifted from, rather than identical to, the cetuximab epitope, and may exclude known drug-resistant EGFR mutations. - Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation
Ryoki Nakamura; Tomohiro Numata; Go Kasuya; Takeshi Yokoyama; Tomohiro Nishizawa; Tsukasa Kusakizako; Takafumi Kato; Tatsuya Hagino; Naoshi Dohmae; Masato Inoue; Kengo Watanabe; Hidenori Ichijo; Masahide Kikkawa; Mikako Shirouzu; Thomas J. Jentsch; Ryuichiro Ishitani; Yasunobu Okada; Osamu Nureki
Communications Biology, 3, 1, Springer Science and Business Media LLC, Dec. 2020, [Peer-reviewed]
Scientific journal,Abstract Members of the leucine-rich repeat-containing 8 (LRRC8) protein family, composed of the five LRRC8A-E isoforms, are pore-forming components of the volume-regulated anion channel (VRAC). LRRC8A and at least one of the other LRRC8 isoforms assemble into heteromers to generate VRAC transport activities. Despite the availability of the LRRC8A structures, the structural basis of how LRRC8 isoforms other than LRRC8A contribute to the functional diversity of VRAC has remained elusive. Here, we present the structure of the human LRRC8D isoform, which enables the permeation of organic substrates through VRAC. The LRRC8D homo-hexamer structure displays a two-fold symmetric arrangement, and together with a structure-based electrophysiological analysis, revealed two key features. The pore constriction on the extracellular side is wider than that in the LRRC8A structures, which may explain the increased permeability of organic substrates. Furthermore, an N-terminal helix protrudes into the pore from the intracellular side and may be critical for gating. - Structural insights into tetraspanin CD9 function
Rie Umeda; Yuhkoh Satouh; Mizuki Takemoto; Yoshiko Nakada-Nakura; Kehong Liu; Takeshi Yokoyama; Mikako Shirouzu; So Iwata; Norimichi Nomura; Ken Sato; Masahito Ikawa; Tomohiro Nishizawa; Osamu Nureki
Nature Communications, 11, 1, 1606, 1606, Springer Science and Business Media LLC, Dec. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal, Tetraspanins play critical roles in various physiological processes, ranging from cell adhesion to virus infection. The members of the tetraspanin family have four membrane-spanning domains and short and large extracellular loops, and associate with a broad range of other functional proteins to exert cellular functions. Here we report the crystal structure of CD9 and the cryo-electron microscopic structure of CD9 in complex with its single membrane-spanning partner protein, EWI-2. The reversed cone-like molecular shape of CD9 generates membrane curvature in the crystalline lipid layers, which explains the CD9 localization in regions with high membrane curvature and its implications in membrane remodeling. The molecular interaction between CD9 and EWI-2 is mainly mediated through the small residues in the transmembrane region and protein/lipid interactions, whereas the fertilization assay revealed the critical involvement of the LEL region in the sperm-egg fusion, indicating the different dependency of each binding domain for other partner proteins. - HCV IRES Captures an Actively Translating 80S Ribosome
Takeshi Yokoyama; Kodai Machida; Wakana Iwasaki; Tomoaki Shigeta; Madoka Nishimoto; Mari Takahashi; Ayako Sakamoto; Mayumi Yonemochi; Yoshie Harada; Hideki Shigematsu; Mikako Shirouzu; Hisashi Tadakuma; Hiroaki Imataka; Takuhiro Ito
Molecular Cell, 74, 6, 1205, 1214.e8, Elsevier BV, Jun. 2019, [Peer-reviewed], [Lead author], [International Magazine]
English, Scientific journal, Translation initiation of hepatitis C virus (HCV) genomic RNA is induced by an internal ribosome entry site (IRES). Our cryoelectron microscopy (cryo-EM) analysis revealed that the HCV IRES binds to the solvent side of the 40S platform of the cap-dependently translating 80S ribosome. Furthermore, we obtained the cryo-EM structures of the HCV IRES capturing the 40S subunit of the IRES-dependently translating 80S ribosome. In the elucidated structures, the HCV IRES "body," consisting of domain III except for subdomain IIIb, binds to the 40S subunit, while the "long arm," consisting of domain II, remains flexible and does not impede the ongoing translation. Biochemical experiments revealed that the cap-dependently translating ribosome becomes a better substrate for the HCV IRES than the free ribosome. Therefore, the HCV IRES is likely to efficiently induce the translation initiation of its downstream mRNA with the captured translating ribosome as soon as the ongoing translation terminates. - Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc
Yongchan Lee; Pattama Wiriyasermkul; Chunhuan Jin; Lili Quan; Ryuichi Ohgaki; Suguru Okuda; Tsukasa Kusakizako; Tomohiro Nishizawa; Kazumasa Oda; Ryuichiro Ishitani; Takeshi Yokoyama; Takanori Nakane; Mikako Shirouzu; Hitoshi Endou; Shushi Nagamori; Yoshikatsu Kanai; Osamu Nureki
Nature Structural & Molecular Biology, 26, 6, 510, 517, Springer Science and Business Media LLC, Jun. 2019, [Peer-reviewed], [International Magazine]
English, Scientific journal, The L-type amino acid transporter 1 (LAT1 or SLC7A5) transports large neutral amino acids across the membrane and is crucial for brain drug delivery and tumor growth. LAT1 forms a disulfide-linked heterodimer with CD98 heavy chain (CD98hc, 4F2hc or SLC3A2), but the mechanism of assembly and amino acid transport are poorly understood. Here we report the cryo-EM structure of the human LAT1-CD98hc heterodimer at 3.3-Å resolution. LAT1 features a canonical Leu T-fold and exhibits an unusual loop structure on transmembrane helix 6, creating an extended cavity that might accommodate bulky amino acids and drugs. CD98hc engages with LAT1 through the extracellular, transmembrane and putative cholesterol-mediated interactions. We also show that two anti-CD98 antibodies recognize distinct, multiple epitopes on CD98hc but not its glycans, explaining their robust reactivities. These results reveal the principles of glycoprotein-solute carrier assembly and provide templates for improving preclinical drugs and antibodies targeting LAT1 or CD98hc. - Structural basis for eIF2B inhibition in integrated stress response
Kazuhiro Kashiwagi; Takeshi Yokoyama; Madoka Nishimoto; Mari Takahashi; Ayako Sakamoto; Mayumi Yonemochi; Mikako Shirouzu; Takuhiro Ito
Science, 364, 6439, 495, 499, American Association for the Advancement of Science (AAAS), 03 May 2019, [Peer-reviewed], [International Magazine]
English, Scientific journal, A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Normally, unphosphorylated eIF2 transfers the methionylated initiator tRNA to the ribosome in a guanosine 5′-triphosphate–dependent manner. By contrast, phosphorylated eIF2 inhibits its specific guanine nucleotide exchange factor, eIF2B. To elucidate how the eIF2 phosphorylation status regulates the eIF2B activity, we determined cryo–electron microscopic and crystallographic structures of eIF2B in complex with unphosphorylated or phosphorylated eIF2. The unphosphorylated and phosphorylated forms of eIF2 bind to eIF2B in completely different manners: the nucleotide exchange-active and -inactive modes, respectively. These structures explain how phosphorylated eIF2 dominantly inhibits the nucleotide exchange activity of eIF2B. - Cryo-EM structures of the human volume-regulated anion channel LRRC8
Go Kasuya#; Takanori Nakane#; Takeshi Yokoyama#; Yanyan Jia; Masato Inoue; Kengo Watanabe; Ryoki Nakamura; Tomohiro Nishizawa; Tsukasa Kusakizako; Akihisa Tsutsumi; Haruaki Yanagisawa; Naoshi Dohmae; Motoyuki Hattori; Hidenori Ichijo; Zhiqiang Yan; Masahide Kikkawa; Mikako Shirouzu; Ryuichiro Ishitani; Osamu Nureki
Nature Structural & Molecular Biology, 25, 9, 797, 804, Springer Science and Business Media LLC, Sep. 2018, [Peer-reviewed], [Lead author], [International Magazine]
English, Scientific journal, Maintenance of cell volume against osmotic change is crucial for proper cell functions. Leucine-rich repeat-containing 8 proteins are anion-selective channels that extrude anions to decrease the cell volume on cellular swelling. Here, we present the structure of human leucine-rich repeat-containing 8A, determined by single-particle cryo-electron microscopy. The structure shows a hexameric assembly, and the transmembrane region features a topology similar to gap junction channels. The LRR region, with 15 leucine-rich repeats, forms a long, twisted arc. The channel pore is located along the central axis and constricted on the extracellular side, where highly conserved polar and charged residues at the tip of the extracellular helix contribute to permeability to anions and other osmolytes. Two structural populations were identified, corresponding to compact and relaxed conformations. Comparing the two conformations suggests that the LRR region is flexible and mobile, with rigid-body motions, which might be implicated in structural transitions on pore opening. - Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1
Anna R. Chase; Ethan Laudermilch; Jimin Wang; Hideki Shigematsu; Takeshi Yokoyama; Christian Schlieker
Molecular Biology of the Cell, 28, 21, 2765, 2772, 15 Oct. 2017, [Peer-reviewed]
Scientific journal - Structure of the complete elongation complex of RNA polymerase II with basal factors
Haruhiko Ehara; Takeshi Yokoyama; Hideki Shigematsu; Shigeyuki Yokoyama; Mikako Shirouzu; Shun-ichi Sekine
Science, 357, 6354, 921, 924, 01 Sep. 2017, [Peer-reviewed], [International Magazine]
English, Scientific journal - Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G
Nobuhiro Iwakura; Takeshi Yokoyama; Fabio Quaglia; Kaoru Mitsuoka; Kazuhiro Mio; Hideki Shigematsu; Mikako Shirouzu; Akira Kaji; Hideko Kaji
PLOS ONE, 12, 5, e0177972, e0177972, 24 May 2017, [Peer-reviewed], [International Magazine]
English, Scientific journal - Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility
Masahiko Yamagishi; Hideki Shigematsu; Takeshi Yokoyama; Masahide Kikkawa; Mitsuhiro Sugawa; Mari Aoki; Mikako Shirouzu; Junichiro Yajima; Ryo Nitta
Structure, 24, 8, 1322, 1334, Aug. 2016, [Peer-reviewed]
Scientific journal - Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC
Hyeongseop Jeong; Jin-Sik Kim; Saemee Song; Hideki Shigematsu; Takeshi Yokoyama; Jaekyung Hyun; Nam-Chul Ha
Structure, 24, 2, 272, 276, Feb. 2016, [Peer-reviewed]
Scientific journal - Structural insights into initial and intermediate steps of the ribosome-recycling process
Takeshi Yokoyama; Tanvir R Shaikh; Nobuhiro Iwakura; Hideko Kaji; Akira Kaji; Rajendra K Agrawal
The EMBO Journal, 31, 7, 1836, 1846, 04 Apr. 2012, [Peer-reviewed], [Lead author]
Scientific journal - Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments
Takeshi Yokoyama; Tsutomu Suzuki
Nucleic Acids Research, 36, 11, 3539, 3551, Jun. 2008, [Peer-reviewed], [Lead author]
Scientific journal - Ligand-induced translation by the allosteric ribosome bearing an aptamer-fused rRNA
T. Yokoyama; T. Suzuki
Nucleic Acids Symposium Series, 51, 1, 383, 384, Oxford University Press (OUP), 01 Nov. 2007, [Lead author]
Scientific journal
- 実験医学 42(9)「ホウ素による翻訳制御の新しいしくみ―80SリボソームがmRNA上を滑って移動する」
田中真幸; 横山武司; 藤原 徹
羊土社, 20 May 2024 - 高分子 72(8)「クライオ電子顕微鏡で生体高分子を観る」
横山武司
Aug. 2023, Japanese, [Peer-reviewed], [Single work] - 「クライオ電子顕微鏡ハンドブック」第４章１４節 クライオ電子顕微鏡で見る、リボソームの「かたち」と「動き」
伴野 詢太; 田中 良和; 横山 武司, クライオ電子顕微鏡で見る、リボソームの「かたち」と「動き」
NTS, Jan. 2023 - Single particle cryo-EM of ribosomal complexes: visualization of how ribosome works in translation
Takeshi Yokoyama
Jan. 2022, Japanese, [Peer-reviewed], [Single work] - 月刊「細胞」 53(14)「タンパク質合成装置リボソームを題材としたクライオ電子顕微鏡単粒子解析の概説」
横山 武司
Dec. 2021, Japanese, [Single work] - Actual Situation of Cryo-Electron Microscopy Single Particle Analysis; From Sample Preparation to Image Analysis
Tsubasa HASHIMOTO; Takeshi YOKOYAMA; Yoshikazu TANAKA
The Crystallographic Society of Japan, 31 May 2021, [Single work] - 医学のあゆみ 262(5)「クライオ電子顕微鏡によって明らかにされたタンパク質合成工場の仕組み」
横山 武司; 白水 美香子
2017, Japanese - 実験医学 36(8)「クライオ電顕でリボソームの構造と動きを解き明かす」
横山 武司
羊土社, 2017, [Single work]
- クライオ電子顕微鏡入門編
第４回東北大学クライオ電子顕微鏡コース（INGEM）, 14 Jan. 2026, Japanese
14 Jan. 2026 - 16 Jan. 2026 - 抗菌薬でリボソームは 「どのように」停止するのか？ クライオ電顕で迫る、 リボソーム標的抗菌薬の作用機構
横山武司
名古屋大学大学院生命農学研究科、GTRセミナー, 08 Jan. 2026, Japanese, Invited oral presentation
08 Jan. 2026 - 08 Jan. 2026, [Invited] - High-resolution cryo-EM analysis of ribosome in diverse translational state
相澤雄太; 田中良和; 横山武司
2025年度 生理研研究会 Frontiers of cryo-electron microscopy and tomography, 28 Oct. 2025, Japanese, Invited oral presentation
28 Oct. 2025 - 29 Oct. 2025, [Invited] - クライオ電子顕微鏡法
横山武司
第35回（2025年度）電子顕微鏡大学, 21 Oct. 2025, Japanese, Invited oral presentation
20 Oct. 2025 - 21 Oct. 2025, [Invited] - クライオ電子顕微鏡で蛋白質合成工場リボソームを見る
横山武司
日本植物学会第89回大会, 18 Sep. 2025, Japanese, Invited oral presentation
18 Sep. 2025 - 20 Sep. 2025, [Invited] - Direct visualization of ribosomes under molecular crowding environments by cryo-electron microscopy
Takeshi Yokoyama
Korea-Japan International Symposium on Protein Science Korean Society for Protein Science (KSPS) 2025 Institute for Protein Research (IPR) Seminar NEXUS-BINDS Symposium, 21 Jun. 2025, English, Invited oral presentation
20 Jun. 2025 - 22 Jun. 2025, [Invited] - The DARC method、無細胞翻訳系の直接観察による分子夾雑環境下のリボソームの可視化
横山武司
第3回岡山大学J-PEAKS事業シナジーセッション「クライオ電顕・トモグラフィワークショップ～アカデミア・インダストリーネットワーク形成に向けて～」, 21 Mar. 2025, Japanese, Invited oral presentation
21 Mar. 2025 - 21 Mar. 2025, [Invited] - The DARC method: クライオ電顕により分子夾雑環境のタンパク質合成の現場を可視化する
横山武司
2025農芸化学会、シンポジウム：タンパク質発現系の最適化のポイントと応用研究の最前線, 06 Mar. 2025, Japanese, Invited oral presentation
05 Mar. 2025 - 08 Mar. 2025, [Invited] - Sample Preparation
Takeshi Yokoyama
Cryo-electron Microscopy Course at OIST, 27 Jan. 2025, English, Invited oral presentation
27 Jan. 2025 - 31 Jan. 2025, [Invited] - クライオ電子顕微鏡入門編
横山武司
第３回 東北大学INGEMクライオ電顕コース, 20 Jan. 2025, Japanese
20 Jan. 2025 - 22 Jan. 2025 - Direct visualization of antibiotic action on translating ribosomes in the molecular crowding cell-free environments
Takeshi Yokoyama
NEXUS Thailand-Japan Bilateral Research Exchange Symposium, 17 Jan. 2025, English
16 Jan. 2025 - 17 Jan. 2025 - The DARC method: クライオ電子顕微鏡で分子夾雑環境下のリボソームの動態を直接可視化する
横山武司
大阪大学蛋白質研究所セミナー、リボソーム・翻訳システムをハックする, 13 Dec. 2024, Japanese, Invited oral presentation
13 Dec. 2024 - 13 Dec. 2024, [Invited] - Direct visualization of antibiotic action on the ribosome in a molecular crowding cell-free translation system
Takeshi Yokoyama
Ribosome Meeting 2024 in Japan, 04 Dec. 2024, English, Invited oral presentation
02 Dec. 2024 - 04 Dec. 2024, [Invited] - クライオ電子顕微鏡の創薬研究への応用：抗菌薬の進化を可視化する
横山武司
東北大学 Research Showcase Vol. 6, 28 Nov. 2024, Japanese, Invited oral presentation
28 Nov. 2024 - 28 Nov. 2024, [Invited] - クライオ電子顕微鏡法
横山武司
第34回（2024年度）電子顕微鏡大学, 22 Nov. 2024, Japanese
21 Nov. 2024 - 22 Nov. 2024, [Invited] - クライオ電子顕微鏡で解き明かす生命のタンパク質合成の仕組み
横山武司
山形大学理工学研究科、バイオ化学工学専攻、集中講義, 07 Oct. 2024, Japanese, Public discourse
07 Oct. 2024 - 07 Oct. 2024, [Invited] - 抗菌薬はどのように作用するか？クライオ電子顕微で 分子夾雑環境のリボソームの動態を解き明かす
横山武司
第７回形態解析ワークショップ、日本橋ライフサイエンスHUB, 05 Oct. 2024, Japanese, Invited oral presentation
05 Oct. 2024 - 05 Oct. 2024, [Invited] - クライオ電子顕微鏡を用いた 無細胞翻訳系の直接観察による抗菌薬作用機構の解明
横山武司
理化学研究所放射光科学研究センターセミナー, 02 Oct. 2024, Japanese, Invited oral presentation
02 Oct. 2024 - 02 Oct. 2024, [Invited] - Direct visualization of ribosomes in molecular crowding environments by cryo-electron microscopy
Takeshi Yokoyama
日本顕微鏡学会第80回学術講演会, 03 Jun. 2024, English, Invited oral presentation
02 Jun. 2024 - 05 Jun. 2024, [Invited] - Sample preparation
Takeshi Yokoyama
Cryo-Electron Microscopy Course at OIST, 05 Feb. 2024, English
05 Feb. 2024 - 05 Feb. 2024, [Invited] - Cryo-electron microscopy visualizes gene expression mechanisms by ribosomes
Takeshi Yokoyama
Mahidol University Seminar, 21 Nov. 2023, English, Others
21 Nov. 2023 - 21 Nov. 2023, [Invited] - INGEMクライオ電子顕微鏡施設を駆使した、リボソーム複合体のクライオ電子顕微鏡構造解析
横山武司
INGEM&ToMMoセミナーシリーズ第28回〜未来型医療の実現に向けた課題〜, 03 Oct. 2023, Japanese, Invited oral presentation
03 Oct. 2023 - 03 Oct. 2023 - リボソームを無細胞翻訳系内で「観察」し、抗菌薬の進化を解明する
横山武司
第23回日本蛋白質科学会年会、ワークショップ「高次構造体のはたらきを観る！」, 07 Jul. 2023, English, Invited oral presentation
05 Jul. 2023 - 07 Jul. 2023, [Invited] - Cryo-electron microscopy of ribosomal complexes to understand their roles in infectious diseases
Takeshi Yokoyama
Seminar at Munster University, 25 May 2023, English, Public discourse
25 May 2023 - 25 May 2023, [Invited] - クライオ電子顕微鏡を用いて、 蛋白質合成装置リボソームの動きを可視化する
横山武司
第２回生命科学系３研究科合同セミナー、めざせ！近未来のPI、東北大学大学院生命科学研究科、大阪大学大学院生命機能研究科、京都大学大学院生命科学研究科, 10 Mar. 2023, Japanese, Invited oral presentation
10 Mar. 2023 - 10 Mar. 2023 - クライオ電子顕微鏡を駆使した翻訳システム動態の可視化
横山武司
第４回生体内超分子システム研究会、神奈川県立産業技術総合研究所, 27 Feb. 2023, Japanese, Invited oral presentation
27 Feb. 2023 - 27 Feb. 2023, [Invited] - Sample preparation
横山武司
Cryo-Electron Microscopy Course at OIST, 06 Feb. 2023, English
06 Feb. 2023 - 10 Feb. 2023, [Invited] - Revealing how small structural differences on antibiotics increase the activity on its target
Takeshi Yokoyama
e-ASIA joint symposium on marine biodiversity as a source of new chemotypes, 08 Dec. 2022, English, Invited oral presentation
08 Dec. 2022 - 08 Dec. 2022, [Invited] - Observing ribosomes in ice
Takeshi Yokoyama
Mahidol University Seminar, 07 Dec. 2022, English, Invited oral presentation
07 Dec. 2022 - 07 Dec. 2022, [Invited] - How small structural differences on antibiotics increase the activity on the ribosome
Takeshi Yokoyama
The 33th Tokyo RNA Club, Ribosome dynamics and regulation, 05 Dec. 2022, English, Invited oral presentation
05 Dec. 2022 - 05 Dec. 2022, [Invited] - クライオ電子顕微鏡を用いた、生体高分子複合体の構造と動態の可視化
横山武司
2022年度 産総研OPERANDO-OIL・ COMS・量子ビーム計測クラブ合同研究会, 30 Nov. 2022, Japanese, Invited oral presentation
30 Nov. 2022 - 30 Nov. 2022, [Invited] - 遺伝暗号解読装置リボソームを停止撹乱する、抗菌薬の作用機構の解明
横山武司
第11回分子モーター討論会, 15 Nov. 2022, Japanese, Invited oral presentation
14 Nov. 2022 - 15 Nov. 2022, [Invited] - How small structural differences on antibiotics increase the activity on the ribosome
Takeshi Yokoyama
The 30th Tokyo RNA Club, Translational machinery and regulation, 29 Sep. 2022, English, Invited oral presentation
29 Sep. 2022 - 29 Sep. 2022, [Invited] - クライオ電子顕微鏡を用いてリボソームのかたちと動きを解き明かす
横山武司
第48回徳島大学先端酵素学研究所セミナー, 15 Sep. 2022, Japanese, Public discourse
15 Sep. 2022 - 15 Sep. 2022, [Invited] - 多様な試料の構造解析への対応に向けた、クライオ電子顕微鏡構造解析の実際
横山武司
第22回日本蛋白質科学会年会、ワークショップ「手法にこだわって、クライオ電子顕微鏡を使いこなす！」, 09 Jun. 2022, Japanese, Invited oral presentation
07 Jun. 2022 - 09 Jun. 2022, [Invited] - クライオ電子顕微鏡を用いた単粒子解析の基礎と実際
横山武司
東京大学大学院、新領域創成科学研究科、基礎講義Ⅱ:細胞の生化学、遺伝情報発現, 19 May 2022, Japanese, Invited oral presentation
19 May 2022 - 19 May 2022, [Invited] - クライオ電子顕微鏡単粒子解析によるリボソーム構造解析の実際とMg結合の可視化
横山 武司
第2回レドックスR&D戦略委員会 春のシンポジウム ―最先端技術が切り拓くレドックスバイオロジー, 04 Mar. 2022, Japanese, Invited oral presentation
04 Mar. 2022 - 04 Mar. 2022, [Invited] - 薬剤耐性菌対策に向けたクライオ電子顕微鏡を駆使したリボソームを標的とする抗菌薬の開発
横山武司
東北大学大学院薬学研究科、第五回医薬品開発研究センターシンポジウム、創薬への革新的アプローチ, 22 Feb. 2022, Japanese, Invited oral presentation
22 Feb. 2022 - 22 Feb. 2022, [Invited] - クライオ電子顕微鏡単粒子解析による、タンパク質合成を阻害する新規抗菌薬の可視化
横山武司
第44回日本分子生物学会年会タンパク質会合の新展開, 01 Dec. 2021, Japanese, Nominated symposium
01 Dec. 2021 - 03 Dec. 2021, [Invited] - クライオ電子顕微鏡を用いた単粒子解析の基礎と実際
横山武司
日本顕微鏡学会、若手研究部会、2021年度シンポジウム, 17 Nov. 2021, Japanese, Invited oral presentation
17 Nov. 2021 - 17 Nov. 2021, [Invited] - クライオ電子顕微鏡を用いて、生体高分子複合体のかたちを解き明かす
横山武司
FRIS/TI-FRIS Life Science Seminar Vol. 2, 05 Nov. 2021, Japanese, Public discourse
05 Nov. 2021 - 05 Nov. 2021, [Invited] - Toward better understanding and measures for infectious diseases by single particle cryo-electron microscopy of ribosome complexes
Takeshi Yokoyama
Ukraine-Thaiand-Japan joint bilateral research program symposium, 26 Jul. 2021, English, Nominated symposium
26 Jul. 2021 - 26 Jul. 2021 - 感染症の理解と対策に向けたリボソームのクライオ電子顕微鏡構造解析
横山 武司
第58回日本生化学会北海道支部例会 日本生化学会北海道支部・東北支部/日本生物物理学会北海道支部 合同シンポジウム, 10 Jul. 2021, Japanese, Invited oral presentation
10 Jul. 2021 - 10 Jul. 2021, [Invited] - RNAヘリックス挿入リボソームを用いた、クライオ電顕構造多型解析の検討
横山武司
第21回日本蛋白質科学会年会、ワークショプ「処理を工夫してクライオ電顕で構造決定が難しいタンパク質に取り組む！」, 18 Jun. 2021, Japanese, Invited oral presentation
16 Jun. 2021 - 18 Jun. 2021, [Invited] - 多剤耐性菌対策に向けた、クライオ電顕によるリボソームを標的とした抗菌薬の可視化
横山武司
日本顕微鏡学会、第77回学術講演会「最先端顕微鏡技術により明らかになった微生物の仕組み、多様性」, 15 Jun. 2021, Japanese, Invited oral presentation
14 Jun. 2021 - 16 Jun. 2021, 32106159, [Invited] - 多剤耐性菌対策に向けた、クライオ電顕構造解析によるリボソームへの新規抗菌薬結合の可視化
横山武司
第94回日本細菌学会総会、シンポジウム「抗菌薬標的蛋白質の生化学」, 25 Mar. 2021
[Invited] - 黄色ブドウ球菌膜孔形成毒素ステムドメインの改変による膜孔形成能の考察
横山 武司、ガネム ノーラン、金上 奈津希、松井 崇、橋本 翼、小川 智久、田中 良和
第94回日本細菌学会総会、シンポジウム「生命金属の新潮流」, 23 Mar. 2021
[Invited] - Toward better understanding and measures for infectious diseases by single particle cryo-electron microscopy of ribosome complexes
Takeshi Yokoyama
e-ASIA/J-RAPID joint symposium, 16 Mar. 2021, English
[Invited] - クライオ電子顕微鏡法を用いて、タンパク質複合体の 「かたち」と「動き」を解き明かす。
横山武司
INGEM & ToMMoセミナーシリーズ第９回, 04 Mar. 2021, Public discourse
[Invited] - Sample preparation
横山武司
Cryo-Electron Microscopy Course at OIST, 15 Feb. 2021, English, Invited oral presentation
[Invited] - クライオ電子顕微鏡法を用いて、タンパク質複合体の 「かたち」と「動き」を解き明かす。
横山武司
新潟大学・理学部・理学科・集中講義, 16 Dec. 2020, Public discourse
[Invited] - クライオ電子顕微鏡法を用いて、タンパク質複合体の 「かたち」と「動き」を解き明かす。
横山武司
北里大学・理学部・物理学科・特別講義, 10 Dec. 2020, Public discourse
10 Dec. 2020 - 10 Dec. 2020, [Invited] - クライオ電顕・単粒子解析におけるtips
安達成彦; 横山武司
第三回クライオ電顕ネットワーク・ユーザーグループミーティング, 04 Dec. 2020, Invited oral presentation
[Invited] - クライオ電子顕微鏡法を用いて、タンパク質複合体の 「かたち」と「動き」を解き明かす。
Takeshi Yokoyama
東京理科大学大学院・基礎工学研究科・生物工学専攻・集中講義, 11 Nov. 2020, Japanese, Public discourse
[Invited] - HCV IRES captures a translating 80S ribosome to hijack host translational machinery
Takeshi Yokoyama
Cryo-Electron Microscopy Course at OIST, 03 Feb. 2020, English, Public discourse
[Invited] - Cryo-electron microscopy provides insights into structure-function relationships of ribosome
Takeshi Yokoyama
東京農工大学・生命工学専攻セミナー, 29 Jan. 2020, Japanese, Public discourse
[Invited] - 感染症の理解と対策に向けた、リボソームのクライオ電顕単粒子解析
Takeshi Yokoyama
生理研研究会「クライオ電子顕微鏡によるタンパク質の高分解能単粒子解析」, 26 Nov. 2019, Japanese, Invited oral presentation
[Invited] - HCV IRES Captures an Actively Translating 80S Ribosome
Takeshi Yokoyama
ISNAC2019, 31 Oct. 2019, English, Oral presentation - クライオ電子顕微鏡を用いた生体高分子の構造解析の現状と今後
Takeshi Yokoyama
東北大学大学院・生命科学研究科セミナー, 22 Jul. 2019, Japanese, Public discourse
[Invited] - クライオ電子顕微鏡法を用いて、タンパク質複合体の 「かたち」と「動き」を解き明かす。
Takeshi Yokoyama
横浜市立大学・集中講義「分子解析科学概説III」, 19 Jul. 2019, Japanese, Public discourse
[Invited] - cryo-electron microscopy provides insights into structure-function relationships of ribosome
Takeshi Yokoyama
筑波大学・生存ダイナミクス研究センター・TARA Seminar, 02 Jul. 2019, Japanese, Invited oral presentation
[Invited] - クライオ電子顕微鏡: 気になっていること・困っていること
Takeshi Yokoyama
日本顕微鏡学会・第75回学術講演会, 17 Jun. 2019, Japanese, Invited oral presentation
[Invited] - Cryo-electron microscopy of ribosomal complexes
Takeshi Yokoyama
Cryo-Electron Microscopy Course at OIST, 19 Feb. 2019, English, Public discourse
[Invited] - Sample preparation
Takeshi Yokoyama
Cryo-Electron Microscopy Course at OIST, 19 Feb. 2019, English, Public discourse
[Invited] - HCV IRES captures a translating 80S ribosome to hijack host translational machinery
Takeshi Yokoyama
第20回日本RNA学会年会, 09 Jul. 2018, English, Oral presentation - Studies on Data Acquisition Conditions for Near-atomic Resolution Cryo-EM Single Particle Analysis
Takeshi Yokoyama
生理研研究会「クライオ電子顕微鏡によるタンパク質の高分解能単粒子解析」, 28 Nov. 2017, Japanese, Invited oral presentation
[Invited] - Studies on Data Acquisition Conditions for Near-atomic Resolution Cryo-EM Single Particle Analysis
Takeshi Yokoyama
第55回日本生物物理学会年会・ワークショップ 「構造生物学研究ツールの進展～どう 使い分けるか？」, 21 Sep. 2017, English, Invited oral presentation
[Invited] - ガラス状の氷の膜に試料を閉じ込め電子顕微鏡で直接観察する技術、クライオ電子顕微鏡法を用いて、リボソームの「かたち」と「動き」を解き明かす。
Takeshi Yokoyama
東京大学大学院・新領域創成科学研究科・集中講義・翻訳研究の最前線（２）, 17 May 2017, Japanese, Public discourse
[Invited] - 原子分解能での構造解析へと向けた リボソームのクライオ電子顕微鏡単粒子解析
Takeshi Yokoyama
第39回日本分子生物学会年会・シンポジウム：次世代構造生物学へ向けて, 30 Nov. 2016, Japanese, Oral presentation - 原子分解能での構造解析へと向けたリボソームのクライオ電子顕微鏡単粒子解析
横山 武司
第16回日本蛋白質科学会年会・ワークショップ「蛋白質科学の視点から迫る新生鎖生物学」, 09 Jun. 2016, Japanese, Invited oral presentation
[Invited] - Towards near atomic resolution structural analysis of ribosomes in electron cryomicroscopy
Takeshi Yokoyama
国際蛋白研セミナー Introduction and overview of cryo-electron microscopy, 19 Feb. 2016, English, Invited oral presentation
[Invited]
■ Research Themes
- 感染性細菌リボソームを舞台とした抗菌薬誘導耐性メカニズムの分子基盤
科学研究費助成事業
Apr. 2025 - Mar. 2028
横山武司(代表), 星野仁彦
日本学術振興会, 基盤研究(B), Principal investigator - 抗菌薬の動的作用点を探索する、革新的リボソーム創薬基盤の確立
新興・再興感染症研究基盤創生事業 多分野融合研究領域
Sep. 2025 - Mar. 2027
横山武司(代表); 五十嵐雅之; 鈴木仁人; 星野仁彦; 長尾翌手可
日本医療研究開発機構（AMED）, Principal investigator - 新規作用機序によりリボソームの翻訳課程を阻害する抗グラム陰性菌薬リードの創製
基礎基盤研究助成金
Jan. 2024 - Dec. 2026
渡辺匠; 五十嵐雅之; 横山武司(分担)
シオノギ感染症研究振興財団, Coinvestigator - 分泌経路におけるメゾスケール構造体プロファイリングの開拓
科学研究費助成事業
Sep. 2023 - Mar. 2026
奥村 正樹; 横山 武司(分担); 村岡 貴博; 松崎 元紀
日本学術振興会, 国際共同研究加速基金(海外連携研究), 東北大学, Coinvestigator, 23KK0105 - 革新的配糖化技術を基盤とした肺非結核性抗酸菌（NTM）症に対する新規抗菌物質の創製
創薬研究助成金
Jan. 2024 - Dec. 2025
高橋大介; 五十嵐雅之; 横山武司(分担)
シオノギ感染症研究振興財団, Coinvestigator - マグネシウム結合によるリボソーム活性制御の構造基盤
科学研究費助成事業 新学術領域研究(研究領域提案型)
Apr. 2022 - Mar. 2024
横山武司 (代表)
日本学術振興会, Principal investigator - 細菌の細胞分裂におけるFtsZ繊維化機構の解明
科学研究費助成事業
Apr. 2021 - Mar. 2024
松井 崇; 横山 武司(分担); 渡辺 豪
本研究では、真正細菌の細胞分裂制御に関わるタンパク質であるFtsZを対象とする。そのなかでも、FtsZが有する重合・乖離機構や重合構造の湾曲化などの繊維化機構を分子動力学計算、X線結晶構造解析やクライオ電子顕微鏡によるフィラメント構造の構造解析により、解明するものである。
本研究を達成するために、本年度は申請者らが過去に行ったFtsZ変異体の発現・調製・結晶構造解析に倣って2状態（T構造およびR構造）それぞれの構造状態への安定化に寄与すると思われる残基の点変異体の結晶構造解析を行った。その結果、複数の変異体の結晶構造を得ることに成功したが、これらの点変異部位ではもう一方の構造状態へ遷移するような構造変化が生じないことが明らかとなった。この結果をもとに、現在、異なる領域に存在する残基に対する変異体の構造解析に向けて、変異体試料を調製中である。これらに並行して、クライオ電子顕微鏡用試料調製にも着手し、いくつかのFtsZにおいて安定的な重合状態を再現性良く調製できる状況を確立した。
分子動力学計算においては、FtsZの構造状態の違いでの安定性を評価することに成功し、現在、重合構造状態での分子動力学計算に向けて計算条件等を検討している。
さらに、構造解析が計画通り進まない場合に備え、重合状態の結合界面を正確に捉えることを目標に、ナノフローHPLCを接続した質量分析計 (nanoLC-MS/MS) を用いた相互作用残基の同定解析法の確立を目指し、研究を進めている。種々の実験条件を検討したところ、タンパク質の構造状態を反映した情報をMSにより捉らえる手法を確立できたため、これらの手法も駆使してFtsZの繊維化機構の解明を目指してく。
日本学術振興会, 基盤研究(C), 北里大学, Coinvestigator, 21K06036 - クライオ電子顕微鏡解析によるデングウイルスの蛋白質合成機構の解明
二国間交流事業、タイとの共同研究（NRCT）
Apr. 2021 - Mar. 2024
横山武司 (代表)
日本学術振興会, 東北大学, Principal investigator - リボソームの動的分子構造と細胞内分布の統合的理解
戦略的創造研究推進事業、さきがけ、細胞の高次構造体
Dec. 2020 - Mar. 2024
横山 武司 (代表)
科学技術振興機構, さきがけ, Principal investigator - 翻訳システムの合理的改変による人工制御
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Apr. 2021 - Mar. 2023
横山 武司 (代表)
核酸にコードされた遺伝情報をアミノ酸の配列へと変換する「翻訳システム」は、巨大なRNA-タンパク質複合体であるリボソームを「発動分子」とし、GTPの加水分解をエネルギーとして利用する翻訳因子が協調的に働くことで成り立っている。本研究課題では、タンパク合成を司る分子機械であるリボソームや相互作用するリボスイッチなどのRNA分子に着目し、クライオ電顕で「形を見ながら」「合理的設計」し、翻訳マシナリーを自在に制御し高度化することを目的とする。申請者が専門とするクライオ電子顕微鏡法は、生体試料を「そのまま」急速凍結することでガラス状の氷に閉じ込め、透過型電子顕微鏡を用いて観察する手法である。取得された生体高分子複合体の粒子像は、画像処理によって、構造の違いにより分類し、高分解能で3次元立体構造を得ることが出来る。本研究課題では、まず無細胞翻訳系を用いて、既存のRNAスイッチによる翻訳制御を機能解析する。さらに、試料溶液をそのまま凍結することで、発動分子が機能する様子を察し、翻訳制御の様子をさまざまな関連因子が共存する環境下で可視化する。本年度は、大腸菌内で変異リボソームの活性を測定するための直交翻訳系の確立、変異リボソームの構造解析をクライオ電子顕微鏡でおこなった。
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Tohoku University, Principal investigator, 21H00380 - 最先端タンパク質構造解析を駆使した生物学的相分離の理解
学際科学フロンティア研究所、領域創成研究プログラム
Apr. 2020 - Mar. 2022
横山 武司(代表)、池田 真教、天貝 佑太、奥村 正樹
東北大学・学際科学フロンティア研究所, 学際科学フロンティア研究所、領域創成研究プログラム, Principal investigator - 抗生物質の再評価と既承認薬の再配置による新規抗菌薬の創製
新興・再興感染症に対する革新的医薬品等開発推進研究事業
Apr. 2020 - Mar. 2022
鈴木仁人 (代表) 横山武司 (分担)
日本医療研究開発機構（AMED）, 新興・再興感染症に対する革新的医薬品等開発推進研究事業, Coinvestigator - 病原菌の鉄獲得プロセスの最上流で機能する膜孔形成毒素の分子機構の活写
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Apr. 2020 - Mar. 2022
横山 武司 (代表)
黄色ブドウ球菌は６種類もの多様な膜孔形成毒素タンパク質を有している。一成分で７量体を形成し、ウサギ赤血球選択性を強く示すαヘモリジンと、二成分で８量体を形成し、ウサギ及びヒトの赤血球に選択性を示すγヘモリジンが存在する。膜孔形成の際、Cap及びRimと呼ばれる領域がお互いに会合することで多量体化する。本研究課題では、このCap/Rim領域とStem領域をαヘモリジン及びγヘモリジンとのコンビネーションで組み合わせた変異体を作成し、溶血作用を有する多量体を形成出来るかどうか検証した。興味深いことに、Cap/Rim領域がαヘモリジン、Stem領域がγヘモリジンを形成するLukF由来の配列を有するAF3変異体において、溶血作用を有することが確認された。さらに、Stem領域をLukFのカウンターパートであるHlg2由来の配列に置き換えた変異体AG2においては溶血作用が見られなかった。その結果、本来LukFとHlg2由来のStemが交互に会合することで８量体を形成しているγヘモリジン由来の配列を持つキメラタンパク質においても膜孔を形成出来ることが示唆された。実際の複合体がどのように複合体を形成しているのか確認するため、AF3（機能的変異体）AG2（不活化変異体）それぞれを精製し、透過型電子顕微鏡を用いて負染色像を観察し、単粒子解析を駆使することで、これらの変異体の立体構造解析を行った。構造解析の結果、Cap/Rim領域は７量体を形成するαヘモリジン由来、またStem領域はγヘモリジン由来の配列を有する変異体AF3及びAG2は両方ともCap/Rim領域の性質を有する７量体構造を形成することが明らかになった。これらの結果から、ヘモリジンの膜孔形成機構の一旦を明らかにすることができた。この研究の結果はGhanem et al., FEBS Journal, 2022として論文発表を行った。
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Tohoku University, Principal investigator, 20H05492 - Structural insights into the transcription-translation complex revealed by cryo-EM
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
Apr. 2019 - Mar. 2022
yokoyama takeshi
In central dogma, transcription that copies genetic information encoded on DNA to RNA having the corresponding sequence, and translation that subsequently converts the nucleic acid sequence into the amino acids sequence that forms proteins, those are important processes playing fundamental roles in gene expression. In prokaryotes, both of these processes take place in the cytoplasm, so the machineries involved in transcription and translation are spatially close to each other and work in a coordinated manner. In this research project, the structure-function relationship between RNA polymerase, which controls transcription, and ribosome, which controls translation, was investigated by using single particle cryo-EM analyses. mRNA exposed from RNA polymerase was visualized at high resolution as it was incorporated into ribosomes.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Tohoku University, Principal investigator, 19K06518 - クライオ電顕による細胞内ネイティブ複合体構造解析
創薬等先端技術支援基盤プラットフォーム（BINDS）
Apr. 2017 - Mar. 2021
日本医療研究開発機構（AMED）, 創薬等先端技術支援基盤プラットフォーム（BINDS）, Coinvestigator
Industrial Property Rights
- 日本顕微鏡学会第82回学術講演会、微生物セッション（オーガナイザー）
25 Jun. 2026
Planning etc, Panel chair etc
Academic society etc
横山武司、高橋知里 - 日本顕微鏡学会第82回学術講演会、最先端顕微鏡法に関する国際若手シンポジウム（セッションチェア）
24 May 2026
Panel chair etc - 第４回東北大学クライオ電子顕微鏡コース（INGEM）（講師・運営）
14 Jan. 2026 - 16 Jan. 2026
Planning etc - 2025 SPring-8 生体高分子クライオ電子顕微鏡体験会（講師）
20 Aug. 2025 - 22 Aug. 2025
Planning etc - Workshop on Structural Analysis Using cryo-EM at Mahidol University（オーガナイザー・講師・運営）
21 Apr. 2025 - 23 Apr. 2025
Planning etc, Panel chair etc, Supervision
Takeshi Yokoyama, Sarin Chimnaronk - 第３回東北大学クライオ電子顕微鏡コース（INGEM）（講師・運営）
20 Jan. 2025 - 22 Jan. 2025
Planning etc - 第３回クライオ電顕施設技術交流会（クライオ電顕ネットワーク）
17 Dec. 2024 - 18 Dec. 2024
Planning etc
Academic society etc
千田俊哉、吉川雅英、東北大学：横山武司、濱口祐 - 日本顕微鏡学会第80回学術講演会、クライオ電子顕微鏡により解明された微生物分子構造と分子マシナリー（オーガナイザー）
04 Jun. 2024 - 04 Jun. 2024
Planning etc, Panel chair etc
横山武司、宮崎直幸 - 日本顕微鏡学会第80回学術講演会、最先端電子顕微鏡法に関する国際若手シンポジウム（セッションチェア）
02 Jun. 2024 - 02 Jun. 2024
Panel chair etc
麻生亮太郎、柏木有太郎 - 第２回東北大学クライオ電子顕微鏡コース（INGEM）（講師・運営）
04 Oct. 2023 - 06 Oct. 2023
Planning etc
Academic society etc - 第23回日本蛋白質科学会年会、ワークショップ：高次構造体のはたらきを観る！（オーガナイザー）
07 Jul. 2023 - 07 Jul. 2023
Planning etc, Panel chair etc
Academic society etc
小杉貴洋、横山武司 - 第23回日本蛋白質科学会年会、ワークショップ：クライオ電子顕微鏡の手法にこだわったら、こんなすごいことがわかってしまいました！（オーガナイザー）
05 Jul. 2023 - 05 Jul. 2023
Planning etc, Panel chair etc
Academic society etc
守屋俊夫、横山武司 - 日本顕微鏡学会第79回学術講演会、最先端電子顕微鏡法に関する国際若手シンポジウム（セッションチェア）
25 Jun. 2023 - 25 Jun. 2023
Panel chair etc
Academic society etc
麻生亮太郎、柏木有太郎 - 日本顕微鏡学会第47回関東支部講演会
07 Mar. 2023 - 07 Mar. 2023
Planning etc, Panel chair etc
Academic society etc
吉川 純、原野幸治、横山武司、葦原雅道、佐藤庸平、森川大輔 - 第１回東北大学クライオ電子顕微鏡コース（INGEM）（講師・運営）
26 Oct. 2022 - 28 Oct. 2022
Planning etc
Academic society etc - 第22回日本蛋白質科学会年会、ワークショップ：手法にこだわって、クライオ電子顕微鏡を使いこなす！（オーガナイザー）
09 Jun. 2022 - 09 Jun. 2022
Planning etc, Panel chair etc
Competition etc
守屋俊夫、横山武司 - 日本顕微鏡学会第78回学術講演会、感染症を観る！（オーガナイザー）
13 May 2022 - 13 May 2022
Planning etc, Panel chair etc
Competition etc
横山武司、宮崎直幸 - 日本顕微鏡学会第78回学術講演会、最先端電子顕微鏡法に関する国際若手シンポジウム（オーガナイザー）
10 May 2022 - 10 May 2022
Planning etc, Panel chair etc
Competition etc
石川亮、横山武司 - 第21回日本蛋白質科学会年会、ワークショップ：画像処理を工夫してクライオ電顕で構造決定が難しいタンパク質に取り組む！(オーガナイザー)
18 Jun. 2021 - 18 Jun. 2021
Planning etc, Panel chair etc
Competition etc
守屋俊夫、横山武司 - 第21回日本蛋白質科学会年会、ワークショップ：生命金属科学の最前線：生命における金属のはたらき（オーガナイザー）
16 Jun. 2021 - 16 Jun. 2021
Planning etc, Panel chair etc
Competition etc
天貝佑太、横山武司
- 第16回HOPEミーティング（モデレーター）
10 Mar. 2025 - 13 Mar. 2025
Presenter, Others
日本学術振興会 第16回HOPEミーティング
パシフィコ横浜
Graduate students, Researchers - 第11回HOPEミーティング（モデレーター）
04 Mar. 2019 - 08 Mar. 2019
Presenter, Others
日本学術振興会
第11回HOPEミーティング
沖縄科学技術大学院大学（OIST）
Graduate students, Researchers - 第10回HOPEミーティング（モデレーター）
12 Mar. 2018 - 15 Mar. 2018
Presenter, Others
日本学術振興会
第10回HOPEミーティング
横浜ベイホテル東急
Graduate students, Researchers
