RIKEN SPring-8 Center Life Science Research Infrastructure Group
Group Director: Masaki Yamamoto (Ph.D.)
Research Summary
Macromolecular crystallography (MX) of difficult target such as membrane proteins has been successfully achieved by using bright light source of SPring-8. To emphasize the application of structural analysis such as better understanding of life and drug discovery, our group advance the research facilities (SPring-8 and SACLA) for MX or small angle X-ray scattering (Bio-SAXS). Moreover, we facilitate the use of electron cryo-microscopy (cryo-EM) to expect synergy on structural biology activity in addition to those techniques using X-ray. Our group tackle with new structural life science for complex structure-function analysis by combining such state-of-the-art analytical techniques.
Main Research Fields
- Biology
Related Research Fields
- Chemistry
- Engineering
- Biological Sciences
- Agricultural Sciences
- Medicine, Dentistry & Pharmacy
- Structural biochemistry
- Biophysics
- Drug development chemistry
Keywords
- Structural life Science
- Structural Biology
- Correlative Structural Analysis
- Drug Discovery
- Structural Dynamics
Selected Publications
- 1.
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). - 2.
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). - 3.
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). - 4.
Gopalasingam, C.C., and Hasnain, S.S.:
"Frontiers in metalloprotein crystallography and cryogenic electron microscopy"
Current Opinion in Structural Biology 75, 102420 (2022). - 5.
Kutsukawa, R., Imaizumi, R., Suenaga-Hiromori, M., Takeshita, K., Sakai, N., Misawa, S., Yamamoto, M., Yamaguchi, H., Miyagi-Inoue, Y., Waki, T., Kataoka, K., Nakayama, T., Yamashita, S., and Takahashi, S.:
"Structure-based engineering of a short-chain cis-prenyltransferase to biosynthesize nonnatural all-cis-polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain-length determination"
The FEBS Journal 289(15), (2022). - 6.
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). - 7.
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). - 8.
Tojo, S., Zhang, Z., Matsui, H., Tahara, M., Ikeguchi, M., Kochi, M., Kamada, M., Shigematsu, H., Tsutsumi, A., Adachi, N., Shibata, T., Yamamoto, M., Kikkawa, M., Senda, T., Isobe, Y., Ohto, U., and Shimizu T.:
"Structural analysis reveals TLR7 dynamics underlying antagonism"
Nature Communications 11(1), 5204 (2020). - 9.
Gopalasingam, C.C., Johnson, R.M., Chiduza, G.N., Tosha, T., Yamamoto, M., Shiro, Y., Antonyuk, S.V., Muench, S.P., and Hasnain, S.S.:
"Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo–electron microscopy"
Science Advances 5(8), eaax1803 (2019). - 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).
Related Links
Lab Members
Principal investigator
- Masaki Yamamoto
- Group Director
Core members
- Kohei Takeshita
- Research Scientist
- Christoph Gerle
- Research Scientist
- Hiroaki Matsuura
- Postdoctoral Researcher
- Chai Gopalasingam
- Postdoctoral Researcher
Contact Information
Structural Biology Facility,
1-1-1 Kouto, Sayo-cho,
Sayo-gun, Hyogo,
679-5148 Japan
Tel: +81-(0)791-58-2839
Fax: +81-(0)791-58-2834
Email: yamamoto [at] riken.jp
Organization
- SR Life Science Instrumentation Team
- Masaki Yamamoto (Ph.D.)