ロゴマーク
研究

研究

BDRでは、様々な分野の研究者が協力して、より高い目標に向かって研究を進めています。

セミナー・シンポジウム

セミナー・イベント

BDRでは、ライフサイエンス分野の国際的な研究者を招いて、年1回のシンポジウムや定期的なセミナーを開催しています。

働く・学ぶ

働く・学ぶ

BDRでは、様々なバックグラウンドを持つ人々を受け入れ、オープンで協力的な研究環境の構築に努めています。

つながる・楽しむ

つながる・楽しむ

BDRでは、様々なメディアや活動を通じて、研究の魅力や意義を社会に発信しています。

ニュース

ニュース

最新の研究、イベント、研究者のインタビューなど、理研BDRの最新情報をお届けします。

BDRについて

BDRについて

理研の強みを生かし学際的なアプローチで生命の根源を探求し、社会の課題に応えます。

白水美香子 | タンパク質機能・構造研究チーム

業績一覧

Kasahara K, Re S, Nawrocki G, et al.
Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution.
Nature Communications 12, 4099 (2021) doi: 10.1038/s41467-021-24349-5

Kukimoto-Niino M, Katsura K, Kaushik R, et al.
Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex.
Science Advances 7(30), eabg3147 (2021) doi: 10.1126/sciadv.abg3147

Bracun L, Yamagata A, Christianson BM, et al.
Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution.
Science Advances 7(25), eabf8864 (2021) doi: 10.1126/sciadv.abf8864

Terasawa, K., Kato, Y., Ikami, Y., Sakamoto, K., Ohtake, K., Kusano, S., Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M., Guan, J. L., Kobayashi, T., Iwata, T., Watabe, T., Yokoyama, S. and Hara-Yokoyama, M. "Direct homophilic interaction of LAMP2A with the two-domain architecture revealed by site-directed photo-crosslinks and steric hindrances in mammalian cells." Autophagy, 10.1080/15548627.2021.19110171-19 (2021).

Murayama, K., Kato-Murayama, M., Sato, T., Hosaka, T., Ishiguro, K., Mizuno, T., Kitao, K., Honma, T., Yokoyama, S., Tanaka, Y. and Shirouzu, M. "Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin." Phytochemistry, 186112727 (2021).

Makabe, K., Yokoyama, T., Uehara, S., Uchikubo-Kamo, T., Shirouzu, M., Kimura, K., Tsumoto, K., Asano, R., Tanaka, Y. and Kumagai, I. "Anti-EGFR antibody 528 binds to domain III of EGFR at a site shifted from the cetuximab epitope." Sci Rep, 11(1), 5790 (2021).

Sugizaki, A., Sato, K., Chiba, K., Saito, K., Kawagishi, M., Tomabechi, Y., Mehta, S. B., Ishii, H., Sakai, N., Shirouzu, M., Tani, T. and Terada, S. "POLArIS, a versatile probe for molecular orientation, revealed actin filaments associated with microtubule asters in early embryos." Proc Natl Acad Sci U S A, 118(11), e2019071118 (2021).

Mizuta, H., Okada, K., Araki, M., Adachi, J., Takemoto, A., Kutkowska, J., Maruyama, K., Yanagitani, N., Oh-Hara, T., Watanabe, K., Tamai, K., Friboulet, L., Katayama, K., Ma, B., Sasakura, Y., Sagae, Y., Kukimoto-Niino, M., Shirouzu, M., Takagi, S., Simizu, S., Nishio, M., Okuno, Y., Fujita, N. and Katayama, R. "Gilteritinib overcomes lorlatinib resistance in ALK-rearranged cancer." Nat Commun, 12(1), 1261 (2021).

Yamamoto, H., Sakai, N., Ohte, S., Sato, T., Sekimata, K., Matsumoto, T., Nakamura, K., Watanabe, H., Mishima-Tsumagari, C., Tanaka, A., Hashizume, Y., Honma, T., Katagiri, T., Miyazono, K., Tomoda, H., Shirouzu, M. and Koyama, H. "Novel bicyclic pyrazoles as potent ALK2 (R206H) inhibitors for the treatment of fibrodysplasia ossificans progressiva." Bioorg Med Chem Lett, 38127858 (2021).

Sakurai, T., Kukimoto-Niino, M., Kunimura, K., Yamane, N., Sakata, D., Aihara, R., Yasuda, T., Yokoyama, S., Shirouzu, M., Fukui, Y. and Uruno, T. "A conserved PI(4,5)P2-binding domain is critical for immune regulatory function of DOCK8." Life Sci Alliance, 4(4), (2021).

Ayukawa, R., Iwata, S., Imai, H., Kamimura, S., Hayashi, M., Ngo, K. X., Minoura, I., Uchimura, S., Makino, T., Shirouzu, M., Shigematsu, H., Sekimoto, K., Gigant, B. and Muto, E. "GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation." J Cell Biol, 220(4), (2021).

Nara, T., Nakagawa, Y., Tsuganezawa, K., Yuki, H., Sekimata, K., Koyama, H., Ogawa, N., Honma, T., Shirouzu, M., Fukami, T., Matsuo, Y., Inaoka, D. K., Kita, K. and Tanaka, A. "The ubiquinone synthesis pathway is a promising drug target for Chagas disease." PLoS One, 16(2), e0243855 (2021).

Dileep, K. V., Sakai, N., Ihara, K., Kato-Murayama, M., Nakata, A., Ito, A., Sivaraman, D. M., Shin, J. W., Yoshida, M., Shirouzu, M. and Zhang, K. Y. J. "Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors." Int J Biol Macromol, 170415-423 (2021).

Zyryanova, A. F., Kashiwagi, K., Rato, C., Harding, H. P., Crespillo-Casado, A., Perera, L. A., Sakamoto, A., Nishimoto, M., Yonemochi, M., Shirouzu, M., Ito, T. and Ron, D. "ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B." Mol Cell, 81(1), 88-103 e106 (2021).

Kobayashi, H., Hatakeyama, H., Nishimura, H., Yokota, M., Suzuki, S., Tomabechi, Y., Shirouzu, M., Osada, H., Mimaki, M., Goto, Y. I. and Yoshida, M. "Chemical reversal of abnormalities in cells carrying mitochondrial DNA mutations." Nat Chem Biol, 17(3), 335-343 (2021).

Ihara, K., Hato, M., Nakane, T., Yamashita, K., Kimura-Someya, T., Hosaka, T., Ishizuka-Katsura, Y., Tanaka, R., Tanaka, T., Sugahara, M., Hirata, K., Yamamoto, M., Nureki, O., Tono, K., Nango, E., Iwata, S. and Shirouzu, M. "Isoprenoid-chained lipid EROCOC17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography." Sci Rep, 10(1), 19305 (2020).

Murayama, K., Kato-Murayama, M., Itoh, Y., Miyazono, K., Miyazawa, K. and Shirouzu, M. "Structural basis for inhibitory effects of Smad7 on TGF-beta family signaling." J Struct Biol, 212(3), 107661 (2020).

Shimizu, Y., Shinoda, T., Shirasago, Y., Kondoh, M., Shinya, N., Hanada, K., Yagi, K., Suzuki, T., Wakita, T., Kimura-Someya, T., Shirouzu, M. and Fukasawa, M. "Occludin-binding single-chain variable fragment and antigen-binding fragment antibodies prevent hepatitis C virus infection." FEBS Lett, 595(2), 220-229 (2021).

Hasegawa, M., Hosaka, T., Kojima, K., Nishimura, Y., Nakajima, Y., Kimura-Someya, T., Shirouzu, M., Sudo, Y. and Yoshizawa, S. "A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage." Sci Rep, 10(1), 16752 (2020).

He, F., Endo, R., Kuwasako, K., Takahashi, M., Tsuda, K., Nagata, T., Watanabe, S., Tanaka, A., Kobayashi, N., Kigawa, T., Guntert, P., Shirouzu, M., Yokoyama, S. and Muto, Y. "(1)H, (13)C and (15)N resonance assignment of the YTH domain of YTHDC2." Biomol NMR Assign, Biomol NMR Assign, 15(1), 1-7 (2021).

Arakawa, S., Kamizaki, K., Kuwana, Y., Kataoka, N., Naoe, C., Takemoto, C., Yokogawa, T. and Hori, H. "Application of solid-phase DNA probe method with cleavage by deoxyribozyme for analysis of long non-coding RNAs." J Biochem., 168(3):273-283(2020).

Takaya, D., Niwa, H., Mikuni, J., Nakamura, K., Handa, N., Tanaka, A., Yokoyama, S. and Honma, T. "Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method." J Mol Graph Model., 99:107599(2020).

Tanabe, H., Fujii, Y., Okada-Iwabu, M., Iwabu, M., Kano, K., Kawana, H., Hato, M., Nakamura, Y., Terada, T., Kimura-Someya, T., Shirouzu, M., Kawano, Y., Yamamoto, M., Aoki, J., Yamauchi, T., Kadowaki, T. and Yokoyama, S. "Human adiponectin receptor AdipoR1 assumes closed and open structures." Commun Biol, 3(1), 446 (2020).

Takahashi, K., Akatsu, Y., Podyma-Inoue, K. A., Matsumoto, T., Takahashi, H., Yoshimatsu, Y., Koinuma, D., Shirouzu, M., Miyazono, K. and Watabe, T. "Targeting all transforming growth factor-beta isoforms with a Fc chimeric receptor impairs tumor growth and angiogenesis of oral squamous cell cancer." J Biol Chem, 295(36), 12559-12572 (2020).

Sato, T., Sekimata, K., Sakai, N., Watanabe, H., Mishima-Tsumagari, C., Taguri, T., Matsumoto, T., Fujii, Y., Handa, N., Tanaka, A., Shirouzu, M., Yokoyama, S., Hashizume, Y., Miyazono, K., Koyama, H. and Honma, T. "Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches." ACS Omega, 5(20), 11411-11423 (2020).

Nakamura, R., Numata, T., Kasuya, G., Yokoyama, T., Nishizawa, T., Kusakizako, T., Kato, T., Hagino, T., Dohmae, N., Inoue, M., Watanabe, K., Ichijo, H., Kikkawa, M., Shirouzu, M., Jentsch, T. J., Ishitani, R., Okada, Y. and Nureki, O. "Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation." Commun Biol, 3(1), 240 (2020).

Umeda, R., Satouh, Y., Takemoto, M., Nakada-Nakura, Y., Liu, K., Yokoyama, T., Shirouzu, M., Iwata, S., Nomura, N., Sato, K., Ikawa, M., Nishizawa, T. and Nureki, O. "Structural insights into tetraspanin CD9 function." Nat Commun, 11(1), 1606 (2020).

Yasukawa, M., Ando, Y., Yamashita, T., Matsuda, Y., Shoji, S., Morioka, M. S., Kawaji, H., Shiozawa, K., Machitani, M., Abe, T., Yamada, S., Kaneko, M. K., Kato, Y., Furuta, Y., Kondo, T., Shirouzu, M., Hayashizaki, Y., Kaneko, S. and Masutomi, K. "CDK1 dependent phosphorylation of hTERT contributes to cancer progression." Nat Commun, 11(1), 1557 (2020).

Shirai, F., Mizutani, A., Yashiroda, Y., Tsumura, T., Kano, Y., Muramatsu, Y., Chikada, T., Yuki, H., Niwa, H., Sato, S., Washizuka, K., Koda, Y., Mazaki, Y., Jang, M. K., Yoshida, H., Nagamori, A., Okue, M., Watanabe, T., Kitamura, K., Shitara, E., Honma, T., Umehara, T., Shirouzu, M., Fukami, T., Seimiya, H., Yoshida, M. and Koyama, H. "Design and Discovery of an Orally Efficacious Spiroindolinone-Based Tankyrase Inhibitor for the Treatment of Colon Cancer." J Med Chem, 63(8), 4183-4204 (2020).

Shoji, S., Hanada, K., Takahashi, M., Watanabe, K., Yonemochi, M., Tomabechi, Y. and Shirouzu, M. "The NF-kappaB regulator IkappaBbeta exhibits different molecular interactivity and phosphorylation status from IkappaBalpha in an IKK2-catalysed reaction." FEBS Lett, 594(10), 1532-1549 (2020).

Nasako, H., Akizuki, R., Takashina, Y., Ishikawa, Y., Shinoda, T., Shirouzu, M., Asai, T., Matsunaga, T., Endo, S. and Ikari, A. "Claudin-2 binding peptides, VPDSM and DSMKF, down-regulate claudin-2 expression and anticancer resistance in human lung adenocarcinoma A549 cells." Biochim Biophys Acta Mol Cell Res, 1867(4), 118642 (2020).

Tsuganezawa, K., Sekimata, K., Nakagawa, Y., Utata, R., Nakamura, K., Ogawa, N., Koyama, H., Shirouzu, M., Fukami, T., Kita, K. and Tanaka, A. "Identification of small molecule inhibitors of human COQ7." Bioorg Med Chem, 28(1), 115182 (2020).

Shimizu, H., Saito, A., Mikuni, J., Nakayama, E. E., Koyama, H., Honma, T., Shirouzu, M., Sekine, S. I. and Shioda, T. "Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase." PLoS Negl. Trop. Dis., 13(11), e0007894 (2019).

Needham, D. M., Yoshizawa, S., Hosaka, T., Poirier, C., Choi, C. J., Hehenberger, E., Irwin, N. A. T., Wilken, S., Yung, C. M., Bachy, C., Kurihara, R., Nakajima, Y., Kojima, K., Kimura-Someya, T., Leonard, G., Malmstrom, R. R., Mende, D. R., Olson, D. K., Sudo, Y., Sudek, S., Richards, T. A., DeLong, E. F., Keeling, P. J., Santoro, A. E., Shirouzu, M., Iwasaki, W. and Worden, A. Z. "A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators." Proc. Natl. Acad. Sci. U S A, 116(41), 20574-20583 (2019).

Shimizu, K., Yamasaki, S., Sakurai, M., Yumoto, N., Ikeda, M., Mishima-Tsumagari, C., Kukimoto-Niino, M., Watanabe, T., Kawamura, M., Shirouzu, M. and Fujii, S. I. "Granzyme A Stimulates pDCs to Promote Adaptive Immunity via Induction of Type I IFN." Front. Immunol., 10, 1450 (2019).

Lee, Y., Wiriyasermkul, P., Jin, C., Quan, L., Ohgaki, R., Okuda, S., Kusakizako, T., Nishizawa, T., Oda, K., Ishitani, R., Yokoyama, T., Nakane, T., Shirouzu, M., Endou, H., Nagamori, S., Kanai, Y. and Nureki, O. "Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc.", Nat. Struct. Mol. Biol. 26(6), 510-517. (2019).

Yokoyama, T., Machida, K., Iwasaki, W., Shigeta, T., Nishimoto, M., Takahashi, M., Sakamoto, A., Yonemochi, M., Harada, Y., Shigematsu, H., Shirouzu, M., Tadakuma, H., Imataka, H. and Ito, T. "HCV IRES Captures an Actively Translating 80S Ribosome.", Mol. Cell, 74(6), 1205-1214 e1208 (2019).

Kashiwagi, K., Yokoyama, T., Nishimoto, M., Takahashi, M., Sakamoto, A., Yonemochi, M., Shirouzu, M. and Ito, T. "Structural basis for eIF2B inhibition in integrated stress response.", Science, 364(6439), 495-499 (2019).

Segawa, K., Watanabe-Matsui, M., Tsuda, K., Matsui, T., Shirouzu, M., Igarashi, K. and Murayama, K. "Biophysical characterization of heme binding to the intrinsically disordered region of Bach1.", Eur Biophys J., 48(4), 361–369 (2019).

Shiba, T., Inaoka, DK., Takahashi, G., Tsuge, C., Kido, Y., Young, L., Ueda, S., Balogun, EO., Nara, T., Honma, T., Tanaka, A., Inoue, M., Saimoto, H., Harada, S., Moore, AL. and Kita K. "Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase.", Biophys. Biochem. Acta, Bioenergetics, 1860(5), 375-382 (2019).

Shirai, F., Tsumura, T., Yashiroda, Y., Yuki, H., Niwa, H., Sato, S., Chikada, T., Koda, Y., Washizuka, K., Yoshimoto, N., Abe, M., Onuki, T., Mazaki, Y., Hirama, C., Fukami, T., Watanabe, H., Honma, T., Umehara, T., Shirouzu, M., Okue, M., Kano, Y., Watanabe, T., Kitamura, K., Shitara, E., Muramatsu, Y., Yoshida, H., Mizutani, A., Seimiya, H., Yoshida, M. and Koyama, H. "Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.", J Med Chem., 62(7), 3407-3427 (2019).

Kukimoto-Niino, M., Tsuda, K., Ihara, K., Mishima-Tsumagari, C., Honda, K., Ohsawa, N. and Shirouzu, M. "Structural basis for the dual substrate specificity of DOCK7 guanine nucleotide exchange factor.", Structure, 27(5), 741-748.e3 (2019).

Sekimata, K., Sato, T., Sakai, N., Watanabe, H., Mishima-Tsumagari, C., Taguri, T., Matsumoto, T., Fujii, Y., Handa, N., Honma, T., Tanaka, A., Shirouzu, M., Yokoyama, S., Miyazono, K., Hashizume, Y. and Koyama, H. "Bis-Heteroaryl Pyrazoles: Identification of Orally Bioavailable Inhibitors of Activin Receptor-Like Kinase-2 (R206H)." Chem. Pharm. Bull., 67(3), 224-235 (2019).

Maruyama, S., Suzuki, K., Imamura, M., Sasaki, H., Matsunami, H., Mizutani, K., Saito, Y., Imai, FL., Ishizuka-Katsura, Y., Kimura-Someya, T., Shirouzu, M., Uchihashi, T., Ando, T., Yamato, I. and Murata, T. "Metastable asymmetrical structure of a shaftless V1 motor.", Science Advances, 5(1), eaau8149 (2019).

Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka H. and Sekine, SI. "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.", Science, 363(6428), 744-747 (2019).

Adachi, J., Katsura, K., Seki, E., Takemoto, C., Shirouzu, M., Terada, T., Mukai, T., K. and Yokoyama S. "Cell-free protein synthesis using S30 extracts from Escherichia coli RFzero strains for efficient incorporation of non-natural amino acids into proteins.", International Journal of Molecular Sciences, 20(3), 492 (2019).

Tanaka, M., Ishige, A., Yaguchi, M., Matsumoto, T., Shirouzu, M., Yokoyama, S., Ishikawa, F., Kitabayashi, I., Takemori, T. and Harada, M. "Development of a simple new flow cytometric antibody-dependent cellular cytotoxicity (ADCC) assay with excellent sensitivity", Journal of Immunol Methods, 464, 74-86 (2019)

Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M. and Sekine, SI. "Structural basis of the nucleosome transition during RNA polymerase II passage", Science, 362(6414), 595-598 (2018)

Shigematsu, H., Imasaki, T., Doki, C., Sumi, T., Aoki, M., Uchikubo-Kamo, T., Sakamoto, A., Tokuraku, K., Shirouzu, M. and Nitta, R. "Structural insight into microtubule stabilization and kinesin inhibition by Tau-family MAPs.", J. Cell Biol., 217(12), 4155-4163 (2018)

Shima, T., Morikawa, M., Kaneshiro, J., Kambara. T., Kamimura, S., Yagi, T., Iwamoto, H., Uemura, S., Shigematsu, H., Shirouzu, M., Ichimura, T., Watanabe, T. M., Nitta, R., Okada, Y. and Hirokawa, N.  "Kinesin-binding–triggered conformation switching of microtubules contributes to polarized transport", J. Cell Biol., 217(12), 4164-4183 (2018)

Ohbayashi, N., Murayama, K., Kato-Murayama, M., Kukimoto-Niino, M., Uejima, T., Matsuda, T., Ohsawa, N., Yokoyama, S., Nojima ,H. and Shirouzu, M. "Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib", ChemistryOpen, 7(9), 721-727 (2018)

Ueda, H., Matsunaga, H., Matsushita, Y., Maeda, S., Iwamoto, R., Yokoyama, S. and Shirouzu M. "Ecto-F0/F1 ATPase as a novel candidate of prothymosin α receptor", Expert Opinion on Biological Therapy, 18(1), 89-94 (2018)

Sakurai, T., Uruno, T., Sugiura, Y., Tatsuguchi, T., Yamamura, K., Ushijima, M., Hattori, Y., Kukimoto-Niino, M., Mishima-Tsumagari, C., Watanabe, M., Suematsu, M., Fukui, Y., "Cholesterol sulfate is a DOCK2 inhibitor that mediates tissue-specific immune evasion in the eye", Sci. Signal., 11(541), eaao4874 (2018)

Kasuya, G., Nakane, T., Yokoyama, T., Jia, Y., Inoue, M., Watanabe, K., Nakamura, R., Nishizawa, T., Kusakizako, T., Tsutsumi, A., Yanagisawa, H., Dohmae, N., Hattori, M., Ichijo, H., Yan, Z., Kikkawa, M., Shirouzu, M., Ishitani, R. and Nureki, O. "Cryo-EM structures of the human volume-regulated anion channel LRRC8" Nat. Struct. Mol. Biol., 25 (9), 797-804 (2018)

Katsura, K., Tomabechi, Y., Matsuda, T., Yonemochi, M., Mikunia, J., Ohsawa, N., Terada, T., Yokoyama, S., Kukimoto-Niino, M., Takemoto, C. and Shirouzu, M. "Phosphorylated and non-phosphorylated HCK kinase domains produced by cell-free protein expression", Protein Expr. Purif., 150 92-99 (2018).

Inouye, S., Tomabechi, Y., Hosoya, T., Sekine, SI. and Shirouzu, M. "Slow luminescence kinetics of semi-synthetic aequorin: Expression, purification and structure determination of cf3-aequorin", J.Biochem., 164(3), 247-255 (2018).

Yamagata, A., Miyazaki, Y., Yokoi, N., Shigematsu, H., Sato, Y., Goto-Ito, S., Maeda, A., Goto, T., Sanbo, M., Hirabayashi, M., Shirouzu, M., Fukata, Y., Fukata, M. and Fukai, S. "Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22", Nat Commun., 9(1), 1546, (2018).

Tamogami, J., Kikukawa, T., Ohkawa, K., Ohsawa, N., Nara, T., Demura, M., Miyauchi, S., Kimura-Someya, T., Shirouzu, M., Yokoyama, S., Shimono, K. and Kamo, N. "Interhelical interactions between D92 and C218 in the cytoplasmic domain regulate proton uptake upon N-decay in the proton transport of Acetabularia rhodopsin II", J Photochem Photobiol B. 183, 35-45, (2018).

Nishio, K., Belle, R., Katoh, T., Kawamura, A., Sengoku, T., Hanada, K., Ohsawa, N., Shirouzu, M., Yokoyama, S. and Suga, H. "Thioether Macrocyclic Peptides Selected against TET1 Compact Catalytic Domain Inhibit TET1 Catalytic Activity", Chembiochem. 19(9), 979-985, (2018).

Sumi, T., Imasaki, T., Aoki, M., Sakai, N., Nitta, E., Shirouzu, M. and Nitta R.  "Structural Insights into the Altering Function of CRMP2 by Phosphorylation", Cell Struct Funct., 43(1),15-23(2018).

Matsuda, T., Ito, T., Takemoto, C., Katsura, K., Ikeda, M., Wakiyama, M., Kukimoto-Niino, M., Yokoyama, S., Kurosawa, Y. and Shirouzu, M. "Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction", PLoS One,13(2) e0193158(2018).

Hori, T., Okuno, T., Hirata, K., Yamashita, K., Kawano, Y., Yamamoto, M., Hato, M., Nakamura, M., Shimizu, T., Yokomizo, T., Miyano, M. and Yokoyama, S. "Na+-mimicking ligands stabilize the inactive state of leukotriene B4 receptor BLT1", Nat Chem Biol., 14, 262-269 (2018).

Koda, Y., Kikuzato, K., Mikuni, J., Tanaka, A., Yuki, H., Honma, T., Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M., Shirai, F. and Koyama, H. "Identification of pyrrolo[2,3-d]pyrimidines as potent HCK and FLT3-ITD dual inhibitors", Bioorg. Med. Chem. Lett., 27 (22), 4994-4998 (2017).

Hasegawa, K., Someya, Y., Shigematsu, H., Kimura-Someya, T., Nuemket, N. and Kumasaka, T. "Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain", Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 73 (10), 568-573 (2017).

Shoji, S., Hanada, K., Ohsawa, N. and Shirouzu, M. "Central catalytic domain of BRAP (RNF52) recognizes the types of ubiquitin chains and utilizes oligo-ubiquitin for ubiquitylation", Biochem. J., 474 (18), 3207-3226 (2017).

Niwa, S., Nakamura, F., Tomabechi, Y., Aoki, M., Shigematsu, H., Matsumoto, T., Yamagata, A., Fukai, S., Hirokawa, N., Goshima, Y., Shirouzu, M. and Nitta, R. "Structural basis for CRMP2-induced axonal microtubule formation", Sci Rep, 7 (1), 10681 (2017).

Chase, A. R., Laudermilch, E., Wang, J., Shigematsu, H., Yokoyama, T. and Schlieker, C. "Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1", Mol. Biol. Cell, 28 (21), 2765-2772 (2017).

Iwaoka, R., Nagata, T., Tsuda, K., Imai, T., Okano, H., Kobayashi, N. and Katahira, M. "Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA", Biomol NMR Assign, 11 (2), 265-268 (2017).

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Iwaoka, R., Nagata, T., Tsuda, K., Imai, T., Okano, H., Kobayashi, N. and Katahira, M. "Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA", Molecules, 22 (7), 1207 (2017).

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Yuki, H., Kikuzato, K., Koda, Y., Mikuni, J., Tomabechi, Y., Kukimoto-Niino, M., Tanaka, A., Shirai, F., Shirouzu, M., Koyama, H. and Honma, T. "Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen", Bioorg. Med. Chem., 25 (16), 4259-4264 (2017).

Katsura, K., Matsuda, T., Tomabechi, Y., Yonemochi, M., Hanada, K., Ohsawa, N., Sakamoto, K., Takemoto, C. and Shirouzu, M. "A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis", J. Biochem., 162 (5), 357-369 (2017).

Iwakura, N., Yokoyama, T., Quaglia, F., Mitsuoka, K., Mio, K., Shigematsu, H., Shirouzu, M., Kaji, A. and Kaji, H. "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", PLoS ONE., 12(5), e0177972 (2017).

Nagano-Shoji, M., Hamamoto, Y., Mizuno, Y., Yamada, A., Kikuchi, M., Shirouzu, M., Umehara, T., Yoshida, M., Nishiyama, M. and Kosono, S. "Characterization of lysine acetylation of a phosphoenolpyruvate carboxylase involved in glutamate overproduction in Corynebacterium glutamicum", Mol. Microbiol., 104 (4), 677-689 (2017).

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Tamogami, J., Kikukawa, T., Nara, T., Demura, M., Kimura-Someya, T., Shirouzu, M., Yokoyama, S., Miyauchi, S., Shimono, K. and Kamo, N. "Existence of two O-like intermediates in the photocycle of Acetabularia rhodopsin II, a light-driven proton pump from a marine alga", Biophys Physicobiol, 14, 49-55 (2017).

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Sotokawauchi, A., Kato-Murayama, M., Murayama, K., Hosaka, T., Maeda, I., Onjo, M., Ohsawa, N., Kato, DI., Arima, K. and Shirouzu, M. "Structural Basis of Cucumisin Protease Activity Regulation by Its Propeptide", J. Biochem., 161 (1), 45-53 (2017).

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Muramatsu, T., Takemoto, C., Kim, YT., Wang, H., Nishii, W., Terada, T., Shirouzu, M. and Yokoyama, S. "SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity", Proc. Natl. Acad. Sci. U.S.A., 113 (46), 12997-13002 (2016).

Suzuki, K., Mizutani, K., Maruyama, S., Shimono, K., Imai, FL., Muneyuki, E., Kakinuma, Y., Ishizuka-Katsura, Y., Shirouzu, M., Yokoyama, S., Yamato, I. and Murata, T. "Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor", Nat Commun., 7, 13235 (2016).

Wang, D., Nitta, R., Morikawa, M., Yajima, H., Inoue, S., Shigematsu, H., Kikkawa, M. and Hirokawa, N. "Motility and microtubule depolymerization mechanisms of the Kinesin-8 motor, KIF19A", ELife, 5, e18101 (2016).

Shinoda, T., Shinya, N., Ito, K., Ohsawa, N., Terada, T., Hirata, K., Kawano, Y., Yamamoto, M., Kimura-Someya, T., Yokoyama, S. and Shirouzu, M. "Structural basis for disruption of claudin assembly in tight junctions by an enterotoxin", Sci Rep, 6, 33632 (2016).

Terasawa, K., Tomabechi, Y., Ikeda, M., Ehara, H., Kukimoto-Niino, M., Wakiyama, M., Podyma-Inoue, K. A., Rajapakshe, A. R., Watabe, T., Shirouzu, M. and Hara-Yokoyama, M. "Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes", Biochem. Biophys. Res. Commun., 479 (3), 489-495 (2016).

Masuda, M., Uno, Y., Ohbayashi, N., Ohata, H., Mimata, A., Kukimoto-Niino, M., Moriyama, H., Kashimoto, S., Inoue, T., Goto, N., Okamoto, K., Shirouzu, M., Sawa, M. and Yamada, T. "TNIK inhibition abrogates colorectal cancer stemness", Nat Commun., 7, 12586 (2016).

Shinoda, T., Shinya, N., Ito, K., Ishizuka-Katsura, Y., Ohsawa, N., Terada, T., Hirata, K., Kawano, Y., Yamamoto, M., Tomita, T., Ishibashi, Y., Hirabayashi, Y., Kimura-Someya, T., Shirouzu, M. and Yokoyama, S. "Cell-free methods to produce structurally intact mammalian membrane proteins", Sci Rep, 6, 30442 (2016).

Yamagishi, M., Shigematsu, H., Yokoyama, T., Kikkawa, M., Sugawa, M., Aoki, M., Shirouzu, M., Yajima, J. and Nitta, R. "Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility", Structure, 24 (8), 1322-1334 (2016).

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Verba, K. A., Wang, R. Y., Arakawa, A., Liu, Y., Shirouzu, M., Yokoyama, S. and Agard, D. A. "Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase", Science, 352 (6293), 1542-1547 (2016).

Yip, W. S., Shigematsu, H., Taylor, D. W. and Baserga, S. J. "Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs", Nucleic Acids Res., 44 (18), 8976-8989 (2016).

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Suenaga, T., Watanabe-Matsui, M., Uejima, T., Shima, H., Matsui, T., Ikeda-Saito, M., Shirouzu, M., Igarashi, K. and Murayama, K. "Charge-state-distribution analysis of Bach2 intrinsically disordered heme binding region", J. Biochem., 160 (5), 291-298 (2016).

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Jeong, H., Kim, JS., Song, S., Shigematsu, H., Yokoyama, T., Hyun, J., and Ha, NC. "Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC", Structure, 24 (2), 272–276 (2016).

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Tomabechi, Y., Hosoya, T., Ehara, H., Sekine, S., Shirouzu, M., and Inouye, S. "Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine", Biochem. Biophys. Res. Commun., 470 (1), 88–93 (2016).

Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Umehara, T., and Yokoyama, S. "Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation", Sci Rep, 5, 17204 (2015).

Nagano, S., Seki, E., Lin, TY., Shirouzu, M., Yokoyama, S., and Heddle, J. G. "Investigating the Roles of the C-Terminal Domain of Plasmodium falciparum GyrA", PLoS ONE, 10 (11), e0142313 (2015).

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Tokmakov, A. A., Kurotani, A., Ikeda, M., Terazawa, Y., Shirouzu, M., Stefanov, V., Sakurai, T., and Yokoyama, S. "Content of intrinsic disorder influences the outcome of cell-free protein synthesis", Sci Rep, 5, 14079 (2015).

Yoshida, H., Park, SY., Oda, T., Akiyoshi, T., Sato, M., Shirouzu, M., Tsuda, K., Kuwasako, K., Unzai, S., Muto, Y., Urano, T., and Obayashi, E. "A novel 3' splice site recognition by the two zinc fingers in the U2AF small subunit", Genes Dev., 29 (15), 1649–1660 (2015).

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Morikawa, M., Yajima, H., Nitta, R., Inoue, S., Ogura, T., Sato, C., and Hirokawa, N. "X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding", EMBO J., 34 (9), 1270–1286 (2015).

Suzuki, M., Sasabe, J., Miyoshi, Y., Kuwasako, K., Muto, Y., Hamase, K., Matsuoka, M., Imanishi, N., and Aiso, S. "Glycolytic flux controls D-serine synthesis through glyceraldehyde-3-phosphate dehydrogenase in astrocytes", Proc. Natl. Acad. Sci. U.S.A., 112 (17), E2217–2224 (2015).

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Tochio, N., Umehara, T., Nakabayashi, K., Yoneyama, M., Tsuda, K., Shirouzu, M., Koshiba, S., Watanabe, S., Kigawa, T., Sasazuki, T., Shirasawa, S., and Yokoyama, S. "Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT", J. Struct. Funct. Genomics, 16 (2), 55–65 (2015).

Terasawa, K., Rajapakshe, A. R., Podyma-Inoue, K. A., Mishima-Tsumagari, C., Yanagishita, M., and Hara-Yokoyama, M. "Preferential recognition of isocitrate dehydrogenase by a rabbit monoclonal antibody (ab124797) against the C-terminal peptide of RANKL", J. Immunol. Methods, 420, 1–10 (2015).

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Kanamori, T., Ohzeki, H., Masaki, Y., Ohkubo, A., Takahashi, M., Tsuda, K., Ito, T., Shirouzu, M., Kuwasako, K., Muto, Y., Sekine, M., and Seio, K. "Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation", Chembiochem, 16 (1), 167–176 (2015).

Nishii, W., Kukimoto-Niino, M., Terada, T., Shirouzu, M., Muramatsu, T., Kojima, M., Kihara, H., and Yokoyama, S. "A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis", Nat. Chem. Biol., 11 (1), 46–51 (2015).

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Niwa, H., Mikuni, J., Sasaki, S., Tomabechi, Y., Honda, K., Ikeda, M., Ohsawa, N., Wakiyama, M., Handa, N., Shirouzu, M., Honma, T., Tanaka, A., and Yokoyama, S. "Crystal structures of the S6K1 kinase domain in complexes with inhibitors", J. Struct. Funct. Genomics, 15 (3), 153–164 (2014).

Yanagisawa, T., Takahashi, M., Mukai, T., Sato, S., Wakamori, M., Shirouzu, M., Sakamoto, K., Umehara, T., and Yokoyama, S. "Multiple site-specific installations of Nε-monomethyl-L-lysine into histone proteins by cell-based and cell-free protein synthesis", Chembiochem, 15 (12), 1830–1838 (2014).

Hato, M., Hosaka, T., Tanabe, H., Kitsunai, T., and Yokoyama, S. "A new manual dispensing system for in meso membrane protein crystallization with using a stepping motor-based dispenser", J. Struct. Funct. Genomics, 15 (3), 165–171 (2014).

Kusano, S., Kukimoto-Niino, M., Satta, Y., Ohsawa, N., Uchikubo-Kamo, T., Wakiyama, M., Ikeda, M., Terada, T., Yamamoto, K., Nishimura, Y., Shirouzu, M., Sasazuki, T., and Yokoyama, S. "Structural basis for the specific recognition of the major antigenic peptide from the Japanese cedar pollen allergen Cry j 1 by HLA-DP5", J. Mol. Biol., 426 (17), 3016–3027 (2014).

Takeo, K., Tanimura, S., Shinoda, T., Osawa, S., Zahariev, I. k., Takegami, N., Ishizuka-Katsura, Y., Shinya, N., Takagi-Niidome, S., Tominaga, A., Ohsawa, N., Kimura-Someya, T., Shirouzu, M., Yokoshima, S., Yokoyama, S., Fukuyama, T., Tomita, T., and Iwatsubo, T. "Allosteric regulation of γ-secretase activity by a phenylimidazole-type γ-secretase modulator", Proc. Natl. Acad. Sci. U.S.A., 111 (29), 10544–10549 (2014).

Shoji, S., Muto, Y., Ikeda, M., He, F., Tsuda, K., Ohsawa, N., Akasaka, R., Terada, T., Wakiyama, M., Shirouzu, M., and Yokoyama, S. "The zinc-binding region (ZBR) fragment of Emi2 can inhibit APC/C by targeting its association with the coactivator Cdc20 and UBE2C-mediated ubiquitylation", FEBS Open Bio, 4 (1), 689–703 (2014).

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Iba, Y., Fujii, Y., Ohshima, N., Sumida, T., Kubota-Koketsu, R., Ikeda, M., Wakiyama, M., Shirouzu, M., Okada, J., Okuno, Y., Kurosawa, Y., and Yokoyama, S. "Conserved neutralizing epitope at globular head of hemagglutinin in H3N2 influenza viruses", J. Virol., 88 (13), 7130–7144 (2014).

Tagami, S., Sekine, SI., Minakhin, L., Esyunina, D., Akasaka, R., Shirouzu, M., Kulbachinskiy, A., Severinov, K., and Yokoyama, S. "Structural basis for promoter specificity switching of RNA polymerase by a phage factor", Genes Dev., 28 (5), 521–531 (2014).

Parker, L. J., Taruya, S., Tsuganezawa, K., Ogawa, N., Mikuni, J., Honda, K., Tomabechi, Y., Handa, N., Shirouzu, M., Yokoyama, S., and Tanaka, A. "Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002", Acta Crystallogr. D Biol. Crystallogr., 70 (2), 392–404 (2014).

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