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A. Nakayama, M. Watanabe, R. Yamashiro, H. Kuroyanagi, H. Matsuyama, A. Oshima, I. Mori, S. Nakano (2024) A hyperpolarizing neuron recruits undocked innexin hemichannels to transmit neural information in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A. 121(21)e2406565121. doi: 10.1073/pnas.2406565121
P. Artigas, D. J. Meyer, V. C. Young, K. Spontarelli, J. Eastman, E. Strandquist, H. Rui, B. Roux, M. A. Birk, H. Nakanishi, K. Abe, C. Gatto (2023) A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities. Proc. Natl. Acad. Sci. U.S.A. 120(52)e2313999120. doi: 10.1073/pnas.2313999120
H. V. Madapally, K. Abe, V. Dubey, H. Khandelia (2023) Specific protonation of acidic residues confers K+ selectivity to the gastric proton pump. J. Biol. Chem. 8:105542. doi: 10.1016/j.jbc.2023.105542
S. Suzuki, K. Tanaka, K. Nishikawa, H. Suzuki, A. Oshima, Y. Fujiyoshi (2023) Structural basis of hydroxycarboxylic acid receptor signaling mechanisms through ligand binding. Nat. Commun. 14:5899. doi: 10.1038/s41467-023-41650-7
K. Abe, M. Ozako, M. Inukai, Y. Matsuyuki, S. Kitayama, C. Kanai, C. Nagai, C. C. Gopalasingam, C. Gerle, H. Shigematsu, N. Umekubo, S. Yokoshima, A. Yoshimori (2023) Deep learning driven de novo drug design based on gastric proton pump structures. Commun. Biol. 6:956. doi: 10.1038/s42003-023-05334-8
K. Irie, Y. Oda, T. Sumikama, A. Oshima, Y. Fujiyoshi (2023) The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel. Nat. Commun. 14(1):4236. doi: 10.1038/s41467-023-39987-0
K. Abe, T. Nishizawa, P. Artigas (2023) An unusual conformation from Na+-sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na+-binding. Biochim. Biophys. Acta, Mol. Cell Res. doi: 10.1016/j.bbamcr.2023.119543
C. Gerle, Y. Misumi, A. Kawamoto, H. Tanaka, H. Kawai-Kubota, R. Tokutsu, E. Kim, D. Chorev, K. Abe, C.V. Robinson, K. Mitsuoka, J. Minagawa, G. Kurisu (2023) Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin. Biochim. Biophys. Acta, Bioenerg. 1864(4):148986. doi: 10.1016/j.bbabio.2023.148986
D. Kozai, N. Numoto, K. Nishikawa, A. Kamegawa, S. Kawasaki, Y. Hiroaki, K. Irie, A. Oshima, H. Hanzawa, K. Shimada, Y. Kitano, Y. Fujiyoshi (2023) Recognition mechanism of a novel gabapentinoid drug, mirogabalin, for recombinant human α2δ1, a voltage-gated calcium channel subunit. J. Mol. Biol. 435(10):168049. doi: 10.1016/j.jmb.2023.168049
Y. Kanematsu, A. Narita, T. Oda, R. Koike, M. Ota, Y. Takano, K. Moritsugu, I. Fujiwara, K. Tanaka, H. Komatsu, T. Nagae, N. Watanabe, M. Iwasa, Y. Maeda, S. Takeda (2022) Structures and mechanisms of actin ATP hydrolysis. Proc. Natl. Acad. Sci. U.S.A. 119 (43) e2122641119. doi: 10.1073/pnas.2122641119
V. C. Young, H. Nakanishi, D. J. Meyer, T. Nishizawa, A. Oshima, P. Artigas, K. Abe (2022) Structure and function of H+/K+ pump mutants reveal Na+/K+ pump mechanisms. Nat. Commun. 13:5270. doi: 10.1038/s41467-022-32793-0
S. Suzuki, M. Iida, Y. Hiroaki, K. Tanaka, A. Kawamoto, T. Kato, A. Oshima (2022) Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM. Commun. Biol. 5, 707. doi: 10.1038/s42003-022-03668-3
K. Kataoka, S. Suzuki, T. Tenno, N. Goda, E. Hibino, A. Oshima, H. Hiroaki (2022) A cryptic phosphate-binding pocket on the SPFH domain of human stomatin that regulates a novel fibril-like self-assembly. Curr. Res. Struct. Biol. 4:158-166. doi: 10.1016/j.crstbi.2022.05.002
S. Tanaka, M. Morita, T. Yamagishi, H. Madapally, K. Hayashida, H. Khandelia, C. Gerle, H. Shigematsu, A. Oshima, K. Abe (2022) Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump. J. Med. Chem. 65, 11, 7843?7853. doi: 10.1021/acs.jmedchem.2c00338
C. Ak?l, S. Ali, L. T. Tran, J. Gaillard, W. Li, K. Hayashida, M. Hirose, T. Kato, A. Oshima, K. Fujishima, L. Blanchoin, A. Narita, R. C. Robinson (2022) Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution. Sci. Adv. 8(12), eabm2225. doi: 10.1126/sciadv.abm2225
M. Kuzuya, H. Hirano, K. Hayashida, M. Watanabe, K. Kobayashi, T. Terada, M. I. Mahmood, F. Tama, K. Tani, Y. Fujiyoshi, A. Oshima (2022) Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N-terminus and phospholipids. Sci. Signal. 15, eabg6941. doi: 10.1126/scisignal.abg6941
H. Nakanishi, K. Hayashida, T. Nishizawa, A. Oshima, K. Abe (2022) Cryo-EM of the ATP11C flippase reconstituted in Nanodiscs shows a distended phospholipid bilayer inner membrane around transmembrane helix 2. J. Biol. Chem. 298, 101498. doi: 10.1016/j.jbc.2021.101498
K. Abe, K. Yamamoto, K. Irie, T. Nishizawa, A. Oshima (2021) Gastric proton pump with two occluded K+ engineered with sodium pump-mimetic mutations. Nat. Commun.12, 5709. doi: 10.1038/s41467-021-26024-1
S. Endo, H. Oguri, J. Segawa, M. Kawai, D. Hu, S. Xia, T. Okada, K. Irie, S. Fujii, H. Gouda, K. Iguchi, T. Matsukawa, N. Fujimoto, T. Nakayama, N. Toyooka, T. Matsunaga, A. Ikari (2020) Development of Novel AKR1C3 Inhibitors as New Potential Treatment for Castration-Resistant Prostate Cancer. J Med Chem. 63:10396-10411. doi: 10.1021/acs.jmedchem.0c00939
H. Nakanishi, T. Nishizawa, K. Segawa, O. Nureki, Y. Fujiyoshi, S. Nagata, K. Abe (2020) Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM. Cell Rep. 32:108208. doi: 10.1016/j.celrep.2020.108208.
K. Ikeda, S. Suzuki, Y. Shigemitsu, T. Tenno, N. Goda, A. Oshima, H. Hiroaki (2020) Presence of intrinsically disordered proteins can inhibit the nucleation phase of amyloid fibril formation of Aβ(1?42) in amino acid sequence independent manner. Sci Rep. 10:12334
H. Nakanishi, K. Irie, K. Segawa, K. Hasegawa, Y. Fujiyoshi, S. Nagata, K. Abe (2020) Crystal structure of a human plasma membrane phospholipid flippase. J. Biol. Chem. 295:10180-10194
S. Miller, Y. Son, Y. Aikawa, E. Makino, Y. Nagai, A. Srivastava, T. Oshima, A. Sugiyama, A. Hara, K. Abe, K. Hirata, S. Oishi, S. Hagihara, A. Sato, F. Tama, K. Itami, S. Kay, M. Hatori, T. Hirota, (2020) Isoform-selective Regulation of Mammalian Cryptochromes. Nat Chem Biol. 16, 676?685
A. Oshima (2020) Structural insights into gap junction channels boosted by cryo-EM. Curr. Opin. Struct. Biol. 63, 42-48
T. Shimomura, Y. Yonekawa, H. Nagura, M. Tateyama, Y. Fujiyoshi, K. Irie (2020) A native prokaryotic voltage-dependent calcium channel with a novel selectivity filter sequence. eLife 9, e52828.
B. Burendei, R. Shinozaki, M. Watanabe, T. Terada, K. Tani, Y. Fujiyoshi, A. Oshima (2020) Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids. Sci. Adv. 6, eaax3157
A. Urbani, V. Giorgio, A. Carrer, C. Franchin, G. Arrigoni, C. Jiko, K. Abe, S. Maeda, K. Shinzawa-Itoh, J. F. M. Bogers, D. G. G. McMillan, C. Gerle, I. Szabo, P. Bernardi (2019) Purified F-ATP synthase forms a Ca2+-dependent high-conductance channel matching the mitochondrial permeability transition pore. Nat. Commun.10, 4341
K. Yamamoto, V. Dubey, K. Irie, H. Nakanishi, H. Khandelia, Y. Fujiyoshi, K. Abe (2019) A single K+-binding site in the crystal structure of the gastric proton pump. eLife 8, e47701.
A. Oshima (2019) Potential of cryo-EM for high-resolution structural analysis of gap junction channels. Curr. Opin. Struct. Biol. 54:78-85
S. Nakamura, K. Irie, H. Tanaka, K. Nishikawa, H. Suzuki, A. Tamura, S. Tsukita, Y. Fujiyoshi (2019) Morphologic determinant of tight junctions revealed by claudin-3 structures. Nat. Commun.10,816
S. Nakamura, Y. Fujiyoshi, K. Irie (2018)Enhancement of the thermostability of mouse claudin-3 on complex formation with the carboxyl-terminal region of Clostridium perfringens enterotoxin improves crystal quality. Acta Crystallogr. F Struct. Biol. Commun. 74(Pt 3):150-155.
K. Abe, K. Irie, H. Nakanishi, H. Suzuki, Y. Fujiyoshi (2018) Crystal structures of the gastric proton pump. Nature 556:214-218
K. Irie, Y. Haga, T. Shimomura, Y. Fujiyoshi (2018) Optimized expression and purification of NavAb provide the structural insight into the voltage dependence. FEBS Lett. 592:274-283
A. Oshima (2017) Structure of an innexin gap junction channel and cryo-EM sample preparation. Microscopy 66:371-379
W. Shihoya, T. Nishizawa, K. Yamashita, A. Inoue, K. Hirata, F.M.N. Kadji, A. Okuta, K. Tani, J. Aoki, Y. Fujiyoshi, T. Doi, O. Nureki (2017) X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog. Nat. Struct. Mol. Biol. 24:758-764
K. Abe, J. Shimokawa, M. Naito, K. Munson, O. Vagin, G. Sachs, H. Suzuki, K. Tani, Y. Fujiyoshi (2017) The cryo-EM structure of gastric H+,K+-ATPase with bound BYK99, a high-affinity member of K+-competitive, imidazo[1,2-a]pyridine inhibitors. Sci. Rep. 7:6632
H. Suzuki, K. Tani, Y. Fujiyoshi (2017) Crystal structures of claudins: insights into their intermolecular interactions. Ann. N. Y. Acad. Sci. 1397:25-34
A. Oshima, K. Tani, Y. Fujiyoshi (2016) Atomic structure of the innexin-6 gap junction channel determined by cryo-EM. Nat. Commun. 7:13681
W. Shihoya, T. Nishizawa, A. Okuta, K. Tani, N. Dohmae, Y. Fujiyoshi, O. Nureki, T. Doi (2016) Activation mechanism of endothelin ETB receptor by endothelin-1. Nature 537:363-368
T. Shimomura, K. Irie, Y. Fujiyoshi (2016) Molecular determinants of prokaryotic voltage-gated sodium channels for recognition of local anesthetics. FEBS J. 283:2881-2895.
K. Abe, Y. Fujiyoshi (2016) Cryo-electron microscopy for structure analyses of membrane proteins in the lipid bilayer. Curr. Opin. Struct. Biol. 39:71-78
A. Okuta, K. Tani, S. Nishimura, Y. Fujiyoshi, T. Doi (2016) Thermostabilization of the human endothelin type-B receptor. J. Mol. Biol. 428:2265-2274.
A. Oshima, T. Matsuzawa, K. Murata, K. Tani, Y. Fujiyoshi (2016) Hexadecameric structure of an invertebrate gap junction channel. J. Mol. Biol. 428:1227-1236.
H. Tanaka, Y. Yamamoto, H. Kashihara, Y. Yamazaki, K. Tani, Y. Fujiyoshi, K. Mineta, K. Takeuchi, A. Tamura, S. Tsukita (2016) Claudin-21 has a paracellular channel role at tight junctions. Mol. Cell Biol. 36:954-964.
H. Nagura, T. Doi, Y. Fujiyoshi (2016) Characterization of physiologic phenotypes of dentate gyrus synapses of PDZ1/2 domain-deficient PSD-95 knockin mice. Eur. J. Neurosci. 43:618-625.
A. Kamegawa, Y. Hiroaki, K. Tani, Y. Fujiyoshi (2016) Two-dimensional crystal structure of aquaporin-4 bound to the inhibitor acetazolamide. Microscopy (Oxf) 65:177-184.
Y. Bando, K. Irie, T. Shimomura, H. Umeshima, Y. Kushida, M. Kengaku, Y. Fujiyoshi, T. Hirano, Y. Tagawa (2016) Control of Spontaneous Ca2+ Transients Is Critical for Neuronal Maturation in the Developing Neocortex. Cereb. Cortex. 26:106-117.
Y. Fujiyoshi (2015) Development of the field of structural physiology. Proc. Jpn. Acad. Ser. B. Phys. Biol. Sci. 91:447-468.
F. Hauer, C. Gerle, N. Fischer, A. Oshima, K. Shinzawa Itoh, S. Shimada, K. Yokoyama, Y. Fujiyoshi, H. Stark (2015) GraDeR: Membrane Protein Complex Preparation for Single-Particle Cryo-EM. Structure 23:1769-1775.
K. Minatohara, Y. Murata, Y. Fujiyoshi, T. Doi (2015) An Intracellular Domain with a Novel Sequence Regulates Cell Surface Expression and Synaptic Clustering of Leucine-Rich Repeat Transmembrane Proteins in Hippocampal Neurons. J Neurochem. 134:618-628.
C. Jiko, K.M. Davies, K. Shinzawa-Itoh, K. Tani, S. Maeda, D.J. Mills, T. Tsukihara, Y. Fujiyoshi, W. Kuhlbrandt, C. Gerle (2015) Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystals. Elife. 4:e06119.
Y. Saitoh, H. Suzuki, K. Tani, K. Nishikawa, K. Irie, Y. Ogura, A. Tamura, S. Tsukita, Y. Fujiyoshi (2015) Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin. Science 347:775-778
H. Suzuki, K. Tani, A. Tamura, S. Tsukita, Y. Fujiyoshi (2015) Model for the architecture of claudin-based paracellular ion channels through tight junctions. J. Mol. Biol. 427:291-297
K. Abe, K. Tani, Y. Fujiyoshi (2014) Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating. J. Biol. Chem. 289:30590-30601
H. Suzuki, T. Nishizawa, K. Tani, Y. Yamazaki, A. Tamura, R. Ishitani, N. Dohmae, S. Tsukita, O. Nureki, Y. Fujiyoshi (2014) Crystal Structure of a Claudin Provides Insight into the Architecture of Tight Junctions. Science 344:304-307
D. Morito, K. Nishikawa, J. Hoseki, A. Kitamura, Y. Kotani, K. Kiso, M. Kinjo, Y. Fujiyoshi, K. Nagata (2014) Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA+ ATPase, which dynamically changes its oligomeric state. Sci. Rep. 4:4442
K. Tani, Y. Fujiyoshi (2014) Water channel structures analysed by electron crystallography. Biochim. Biophys. Acta. 1840:1605-1613
F. Yang, K. Abe, K. Tani, Y. Fujiyoshi (2013) Carbon sandwich preparation preserves quality of two-dimensional crystals for cryo-electron microscopy. Microscopy (Oxf) 62:597-606
C.J. Tsai, K. Tani, K. Irie, Y. Hiroaki, T. Shimomura, D.G. McMillan, G.M. Cook, G.F.X. Schertler, Y. Fujiyoshi, X.D. Li (2013) Two alternative conformations of a voltage-gated sodium channel. J. Mol. Biol. 425:4074-4088.
H. Suzuki, Y. Ito, Y. Yamazaki, K. Mineta, M. Uji, K. Abe, K. Tani, Y. Fujiyoshi, S. Tsukita (2013) The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat. Nat. Commun. 4:1766.
K. Tani, C. P. Arthur, M. Tamakoshi, K. Yokoyama, K. Mitsuoka, Y. Fujiyoshi, C. Gerle (2013) Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus thermophilus. Microscopy (Oxf) 62:467-474
M. Goda, Y. Fujiyoshi, M. Sugimoto, R. Fujii (2013) Novel Dichromatic Chromatophores in the Integument of the Mandarin Fish Synchiropus splendidus. Biol. Bull. 224:14-17.
A. Oshima, T. Matsuzawa, K. Nishikawa, Y. Fujiyoshi (2013) Oligomeric structure and functional characterization of C. elegans innexin-6 gap junction channels. J. Biol. Chem. 288:10513-10521.
K. Minatohara, S. H. Ichikawa, T. Seki, Y. Fujiyoshi, T. Doi (2013) Ligand binding of PDZ domains has various roles in the synaptic clustering of SAP102 and PSD-95. Neurosci. Lett. 533:44-49.
H. Nagura, Y. Ishikawa, K. Kobayashi, K. Takao, T. Tanaka, K. Nishikawa, H. Tamura, S. Shiosaka, H. Suzuki, T. Miyakawa, Y. Fujiyoshi, T. Doi (2012) Impaired synaptic clustering of postsynaptic density proteins and altered signal transmission in hippocampal neurons, and disrupted learning behavior in PDZ1 and PDZ2 ligand binding-deficient PSD-95 knockin mice. Mol Brain 5:43.
K. Abe, K. Tani, T. Friedrich, Y. Fujiyoshi (2012) Cryo-EM structure of gastric H+,K+-ATPase with a single occupied cation-binding site. Proc. Natl. Acad. Sci. U.S.A. 109:18401-18406
N. Unwin, Y. Fujiyoshi (2012) Gating movement of acetylcholine receptor caught by plunge-freezing. J. Mol. Biol. 422:617-634.
K. Irie, T. Shimomura, Y. Fujiyoshi (2012) The C-terminal helical bundle of the tetrameric prokaryotic sodium channel accelerates the inactivation rate. Nat. Commun. 3:793.
