Research Summary

Selected Publications

• 1. Ishimaru, H., Nishimura, M., Tjan, L. H., Sutandhio, S., Marini, M. I., Effendi, G. B., Shigematsu, H., Kato, K., Hasegawa, N., Aoki, K., Kurahashi, Y., Furukawa, K., Shinohara, M., Nakamura, T., Arii, J., Nagano, T., Nakamura, S., Sano, S., Iwata, S., Okamura, S., and Mori, Y.:
  "Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants."
  Journal of Virology 97(6), e0028623 (2023).
• 2. Abe, K., Ozako, M., Inukai, M., Matsuyuki, Y., Kitayama, S., Kanai, C., Nagai, C., Gopalasingam, C. C., Gerle, C., Shigematsu, H., Umekubo, N., Yokoshima, S., and Yoshimori, A.:
  "Deep learning driven de novo drug design based on gastric proton pump structures"
  Communications Biology 6, 956 (2023).
• 3. Sakaniwa, K., Fujimura, A., Shibata, T., Shigematsu, H., Ekimoto, T., Yamamoto, M., Ikeguchi, M., Miyake, K., Ohto, U., and Shimizu, T.:
  "TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction"
  Nature Communications 14, 164 (2023).
• 4. Nishida, Y., Yanagisawa, S., Morita, R., Shigematsu, H., Shinzawa-Itoh, K., Yuki, H., Ogasawara, S., Shimuta, K., Iwamoto, T., Nakabayashi, C., Matsumura, W., Kato, H.,　Gopalasingam, C., Nagao, T., Qaqorh, T., Takahashi, Y., Yamazaki, S., Kamiya, K., Harada,R., Mizuno, N., Takahashi, H., Akeda, Y., Ohnishi, M., Ishii, Y., Kumasaka, T., Murata, T., Muramoto, K., Tosha, T., Shiro, Y., Honma, T., Shigeta, Y., Kubo, M., Takashima, S., and Shintani, Y.:
  "Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases"
  Nature Communications 13, 7591 (2022).
• 5. Gerle, C., Kishikawa, J.I., Yamaguchi, T., Nakanishi, A., Çoruh, O., Makino, F., Miyata, T., Kawamoto, A., Yokoyama, K., Namba, K., and Kurisu, G.:
  "Structures of multisubunit membrane complexes with the CRYO ARM 200"
  Microscopy 71(5), 249-261 (2022).
• 6. Yoshimi, K., Takeshita, K., Kodera, N., Shibumura, S., Yamauchi, Y., Omatsu, M., Umeda, K., Kunihiro, Y., Yamamoto, M., and Mashimo, T.:
  "Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3"
  Nature Communications 13(1), 4917 (2022).
• 7. Gopalasingam, C.C., and Hasnain, S.S.:
  "Frontiers in metalloprotein crystallography and cryogenic electron microscopy"
  Current Opinion in Structural Biology 75, 102420 (2022).
• 8. Tanaka, S., Morita, M., Yamagishi, T., Madapally, H.V., Hayashida, K., Khandelia, H., Gerle, C., Shigematsu, H., Oshima, A., and Abe, K.:
  "Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump"
  Journal of Medicinal Chemistry 65(11), 7843-7853 (2022).
• 9. Baba, S., Matsuura, H., Kawamura, T., Sakai, N., Nakamura, Y., Kawano, Y., Mizuno, N., Kumasaka, T., Yamamoto, M., and Hirata, K.:
  "Guidelines for de novo phasing using multiple small-wedge data collection"
  Journal of Synchrotron Radiation 28, 1284-1295 (2021).
• 10. Yamamoto, M., Hirata, K., Yamashita, K., Hasegawa, K., Ueno, G., Ago, H., and Kumasaka, T.:
  "Protein microcrystallography using synchrotron radiation"
  IUCrJ 4(5), 529-539 (2017).

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