RIKEN SPring-8 Center Molecular Movie Analysis Team

Research Summary

It was extremely challenging to capture the structural changes and reactions with high temporal and spatial resolution at the moment of protein functioning. Recently, X-ray free electron lasers (XFEL), having ultrahigh brightness and ultrashort pulse characteristics, have allowed for the observation of the dynamic structural changes of proteins as a molecular movie. Our team aims to establish various reaction initiation methods and develop related devices for molecular movie analysis using XFEL while cooperating with groups both inside and outside the facility. The developed techniques will then be applied to various proteins, including receptors and enzymes, to reveal the underlying mechanisms of their functions.

Main Research Fields

• Biology

Related Research Fields

• Engineering
• Chemistry
• Complex Systems
• Structural biochemistry
• Quantum beam science

Keywords

• Serial femtosecond crystallography
• X-ray free electron laser
• Dynamic structure of protein
• Photoreceptor protein
• Enzymatic reaction analysis

Selected Publications

• 1. Carrillo, M., Pandey, S., Sanchez1, J., Noda1, M., Poudyal, I., Aldama, L., Malla, T. N., Claesson, E., Wahlgren, W. Y., Feliz, D., Šrajer, V., Maj, M., Castillon, L., Iwata, S., Nango, E., Tanaka, R., Tanaka, T., Luo, F., Tono, K., Owada, S., Westenhoff, S., Stojković, E. A., Schmidt, M.:
  "High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle."
  Structure 29, 743-754 (2021)
• 2. Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A. D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T. & Nureki, O.:
  "Time-Resolved Serial Femtosecond Crystallography Reveals Early Structural Changes in Channelrhodopsin."
  ELife 10, 62389 (2021)
• 3. Claesson, E., Wahlgren, W. Y., Takala, H., Pandey, S., Castillon, L., Kuznetsova, V., Henry, L., Panman, M., Carrillo, M., Kubel, J., Nanekar, R., Isaksson, L., Nimmrich, A., Cellini, A., Morozov, D., Maj, M., Kurttila, M., Bosman, R., Nango, E., Tanaka, R., Tanaka, T., Fangjia, L., Iwata, S., Owada, S., Moffat, K., Groenhof, G., Stojkovic, E. A., Ihalainen, J. A., Schmidt, M. & Westenhoff, S.:
  "The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser"
  Elife 9, 53514 (2020)
• 4. Wickstrand, C., Katona, G., Nakane, T., Nogly, P., Standfuss, J., Nango, E. & Neutze, R.:
  "A tool for visualizing protein motions in time-resolved crystallography."
  Struct Dyn 7, 024701 (2020)
• 5. Nango, E.^*, Kubo, M.^*, Tono, K., Iwata, S.:
  "Pump-Probe Time-Resolved Serial Femtosecond Crystallography at SACLA: Current Status and Data Collection Strategies."
  Appl. Sci. 9(24), 5505 (2019)
• 6. Shimazua, Y., Tono, K.^*, Tanaka, T., Yamanaka, Y., Nakane, T., Mori, C., Kimura, T. K., Fujiwara, T., Sugahara, M., Tanaka, R., Doak, R. B., Shimamura, T., Iwata, S., Nango, E.^* and Yabashi, M.:
  "High-viscosity sample injection device for serial femtosecond crystallography at atmospheric pressure."
  J. Appl. Cryst. 52, 1280–1288 (2019)
• 7. Nogly, P., Weinert, T., James, D., Carbajo, S., Ozerov, D., Furrer, A., Gashi, D., Borin, V., Skopintsev, P., Jaeger, K., Nass, K., Båth, P., Bosman, R., Koglin, J., Seaberg, M., Lane, T., Kekilli, D., Brünle, S., Tanaka, T., Wu, W., Milne, C., White, T., Barty, A., Weierstall, U., Panneels, V., Nango, E., Iwata, S., Hunter, M., Schapiro, I., Schertler, G., Neutze, R., and Standfuss, J.:
  "Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser."
  Science 261, 145-152 (2018)
• 8. Kubo, M., Nango, E.^*, Tono, K.^*, Kimura, T., Owada, S., Song, C., Mafuné, F., Miyajima, K., Takeda, Y., Kohno, J. Y., Miyauchi, N., Nakane, T., Tanaka, T., Nomura, T., Davidsson, J., Tanaka, R., Murata, M., Kameshima, T., Hatsui, T., Joti, Y., Neutze, R., Yabashi, M. and Iwata, S.:
  "Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA."
  J. Synchrotron Radiat. 24, 1086-1091 (2017)
• 9. Suga, M., Akita, F., Sugahara, M., Kubo, M., Nakajima, Y., Nakane, T., Yamashita, K., Umena, Y., Nakabayashi, M., Yamane, T., Nakano, T., Suzuki, M., Masuda, T., Inoue, S., Kimura, T., Nomura, T., Yonekura, S., Yu, L. J., Sakamoto, T., Motomura, T., Chen, J. H., Kato, Y., Noguchi, T., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Nango, E., Tanaka, R., Naitow, H., Matsuura, Y., Yamashita, A., Yamamoto, M., Nureki, O., Yabashi, M., Ishikawa, T., Iwata, S. and Shen, J. R.:
  "Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL."
  Nature 543, 131–135 (2017)
• 10. Nango, E., Royant, A., Kubo, M., Nakane, T., Wickstrand, C., Kimura, T., Tanaka, T., Tono, K., Song, C., Tanaka, R., Arima, T., Yamashita, A., Kobayashi, J., Hosaka, T., Mizohata, E., Nogly, P., Sugahara, M., Nam, D., Nomura, T., Shimamura, T., Im, D., Fujiwara, T., Yamanaka, Y., Jeon, B., Nishizawa, T., Oda, K., Fukuda, M., Andersson, R., Bath, P., Dods, R., Davidsson, J., Matsuoka, S., Kawatake, S., Murata, M., Nureki, O., Owada, S., Kameshima, T., Hatsui, T., Joti, Y., Schertler, G., Yabashi, M., Bondar, A. N., Standfuss, J., Neutze, R. and Iwata, S.:
  "A three-dimensional movie of structural changes in bacteriorhodopsin."
  Science 354, 1552-1557 (2016)

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