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352 results on '"Nango, Eriko"'

1. Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate

Author

Bertrand, Quentin, Nogly, Przemyslaw, Nango, Eriko, Kekilli, Demet, Khusainov, Georgii, Furrer, Antonia, James, Daniel, Dworkowski, Florian, Skopintsev, Petr, Mous, Sandra, Martiel, Isabelle, Börjesson, Per, Ortolani, Giorgia, Huang, Chia-Ying, Kepa, Michal, Ozerov, Dmitry, Brünle, Steffen, Panneels, Valerie, Tanaka, Tomoyuki, Tanaka, Rie, Tono, Kensuke, Owada, Shigeki, Johnson, Philip J. M., Nass, Karol, Knopp, Gregor, Cirelli, Claudio, Milne, Christopher, Schertler, Gebhard, Iwata, So, Neutze, Richard, Weinert, Tobias, and Standfuss, Jörg

Published
2024
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2. Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography

Author

Maity, Basudev, Shoji, Mitsuo, Luo, Fangjia, Nakane, Takanori, Abe, Satoshi, Owada, Shigeki, Kang, Jungmin, Tono, Kensuke, Tanaka, Rie, Pham, Thuc Toan, Kojima, Mariko, Hishikawa, Yuki, Tanaka, Junko, Tian, Jiaxin, Nagama, Misaki, Suzuki, Taiga, Noya, Hiroki, Nakasuji, Yuto, Asanuma, Asuka, Yao, Xinchen, Iwata, So, Shigeta, Yasuteru, Nango, Eriko, and Ueno, Takafumi

Published
2024
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3. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.

Author

Kubo, Minoru, Nomura, Takashi, Sugahara, Michihiro, Owada, Shigeki, Barad, Benjamin, Ito, Kazutaka, Bhowmick, Asmit, Carbajo, Sergio, Hino, Tomoya, Holton, James, Im, Dohyun, ORiordan, Lee, Tanaka, Tomoyuki, Tanaka, Rie, Sierra, Raymond, Yumoto, Fumiaki, Tono, Kensuke, Iwata, So, Wolff, Alexander, Nango, Eriko, Sauter, Nicholas, Brewster, Aaron, Fraser, James, Thompson, Michael, and Young, Iris

Subjects
Crystallography, X-Ray, Models, Molecular, Temperature, Proteins, Molecular Conformation, Protein Conformation
Abstract

Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

Published
2023

4. Optical control of ultrafast structural dynamics in a fluorescent protein.

Author

Hutchison, Christopher, Baxter, James, Fitzpatrick, Ann, Dorlhiac, Gabriel, Fadini, Alisia, Perrett, Samuel, Maghlaoui, Karim, Lefèvre, Salomé, Cordon-Preciado, Violeta, Ferreira, Josie, Chukhutsina, Volha, Garratt, Douglas, Barnard, Jonathan, Galinis, Gediminas, Glencross, Flo, Morgan, Rhodri, Stockton, Sian, Taylor, Ben, Yuan, Letong, Romei, Matthew, Lin, Chi-Yun, Marangos, Jon, Schmidt, Marius, Chatrchyan, Viktoria, Buckup, Tiago, Morozov, Dmitry, Park, Jaehyun, Park, Sehan, Eom, Intae, Kim, Minseok, Jang, Dogeun, Choi, Hyeongi, Hyun, HyoJung, Park, Gisu, Nango, Eriko, Tanaka, Rie, Owada, Shigeki, Tono, Kensuke, DePonte, Daniel, Carbajo, Sergio, Seaberg, Matt, Aquila, Andrew, Boutet, Sebastien, Barty, Anton, Iwata, So, Boxer, Steven, Groenhof, Gerrit, and van Thor, Jasper

Subjects
Motion, Vibration, Rhodopsin, Hydrogen Bonding
Abstract

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Published
2023

6. Oxygen-evolving photosystem II structures during S1–S2–S3 transitions

Author

Li, Hongjie, Nakajima, Yoshiki, Nango, Eriko, Owada, Shigeki, Yamada, Daichi, Hashimoto, Kana, Luo, Fangjia, Tanaka, Rie, Akita, Fusamichi, Kato, Koji, Kang, Jungmin, Saitoh, Yasunori, Kishi, Shunpei, Yu, Huaxin, Matsubara, Naoki, Fujii, Hajime, Sugahara, Michihiro, Suzuki, Mamoru, Masuda, Tetsuya, Kimura, Tetsunari, Thao, Tran Nguyen, Yonekura, Shinichiro, Yu, Long-Jiang, Tosha, Takehiko, Tono, Kensuke, Joti, Yasumasa, Hatsui, Takaki, Yabashi, Makina, Kubo, Minoru, Iwata, So, Isobe, Hiroshi, Yamaguchi, Kizashi, Suga, Michihiro, and Shen, Jian-Ren

Published
2024
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7. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography

Author

Wolff, Alexander M., Nango, Eriko, Young, Iris D., Brewster, Aaron S., Kubo, Minoru, Nomura, Takashi, Sugahara, Michihiro, Owada, Shigeki, Barad, Benjamin A., Ito, Kazutaka, Bhowmick, Asmit, Carbajo, Sergio, Hino, Tomoya, Holton, James M., Im, Dohyun, O’Riordan, Lee J., Tanaka, Tomoyuki, Tanaka, Rie, Sierra, Raymond G., Yumoto, Fumiaki, Tono, Kensuke, Iwata, So, Sauter, Nicholas K., Fraser, James S., and Thompson, Michael C.

Published
2023
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8. Mapping Protein Dynamics at High Spatial Resolution with Temperature-Jump X-ray Crystallography

Author

Wolff, Alexander M, Nango, Eriko, Young, Iris D, Brewster, Aaron S, Kubo, Minoru, Nomura, Takashi, Sugahara, Michihiro, Owada, Shigeki, Barad, Benjamin A, Ito, Kazutaka, Bhowmick, Asmit, Carbajo, Sergio, Hino, Tomoya, Holton, James M, Im, Dohyun, O’Riordan, Lee J, Tanaka, Tomoyuki, Tanaka, Rie, Sierra, Raymond G, Yumoto, Fumiaki, Tono, Kensuke, Iwata, So, Sauter, Nicholas K, Fraser, James S, and Thompson, Michael C

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Generic health relevance
Abstract

Summary Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the sub-millisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature-jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

Published
2022

9. Ultrafast structural changes direct the first molecular events of vision

Author

Gruhl, Thomas, Weinert, Tobias, Rodrigues, Matthew J., Milne, Christopher J., Ortolani, Giorgia, Nass, Karol, Nango, Eriko, Sen, Saumik, Johnson, Philip J. M., Cirelli, Claudio, Furrer, Antonia, Mous, Sandra, Skopintsev, Petr, James, Daniel, Dworkowski, Florian, Båth, Petra, Kekilli, Demet, Ozerov, Dmitry, Tanaka, Rie, Glover, Hannah, Bacellar, Camila, Brünle, Steffen, Casadei, Cecilia M., Diethelm, Azeglio D., Gashi, Dardan, Gotthard, Guillaume, Guixà-González, Ramon, Joti, Yasumasa, Kabanova, Victoria, Knopp, Gregor, Lesca, Elena, Ma, Pikyee, Martiel, Isabelle, Mühle, Jonas, Owada, Shigeki, Pamula, Filip, Sarabi, Daniel, Tejero, Oliver, Tsai, Ching-Ju, Varma, Niranjan, Wach, Anna, Boutet, Sébastien, Tono, Kensuke, Nogly, Przemyslaw, Deupi, Xavier, Iwata, So, Neutze, Richard, Standfuss, Jörg, Schertler, Gebhard, and Panneels, Valerie

Published
2023
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11. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Author

Wolff, Alexander M, Young, Iris D, Sierra, Raymond G, Brewster, Aaron S, Martynowycz, Michael W, Nango, Eriko, Sugahara, Michihiro, Nakane, Takanori, Ito, Kazutaka, Aquila, Andrew, Bhowmick, Asmit, Biel, Justin T, Carbajo, Sergio, Cohen, Aina E, Cortez, Saul, Gonzalez, Ana, Hino, Tomoya, Im, Dohyun, Koralek, Jake D, Kubo, Minoru, Lazarou, Tomas S, Nomura, Takashi, Owada, Shigeki, Samelson, Avi J, Tanaka, Tomoyuki, Tanaka, Rie, Thompson, Erin M, van den Bedem, Henry, Woldeyes, Rahel A, Yumoto, Fumiaki, Zhao, Wei, Tono, Kensuke, Boutet, Sebastien, Iwata, So, Gonen, Tamir, Sauter, Nicholas K, Fraser, James S, and Thompson, Michael C

Subjects
Inorganic Chemistry, Chemical Sciences, 1.4 Methodologies and measurements, microcrystals, batch crystallization, serial crystallography, MicroED, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Condensed Matter Physics, Physical Chemistry (incl. Structural), Physical chemistry, Condensed matter physics
Abstract

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

Published
2020

12. Excited-state intermediates in a designer protein encoding a phototrigger caught by an X-ray free-electron laser

Author

Liu, Xiaohong, Liu, Pengcheng, Li, Hongjie, Xu, Zhen, Jia, Lu, Xia, Yan, Yu, Minling, Tang, Wenqin, Zhu, Xiaolei, Chen, Chao, Zhang, Yuanlin, Nango, Eriko, Tanaka, Rie, Luo, Fangjia, Kato, Koji, Nakajima, Yoshiki, Kishi, Shunpei, Yu, Huaxin, Matsubara, Naoki, Owada, Shigeki, Tono, Kensuke, Iwata, So, Yu, Long-Jiang, Shen, Jian-Ren, and Wang, Jiangyun

Published
2022
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13. TURNING UP THE HEAT ON DYNAMIC PROTEINS: OBSERVING MOLECULAR MOTION IN REAL TIME WITH TEMPERATURE-JUMP X-RAY CRYSTALLOGRAPHY

Author

Thompson, Michael, Wolff, Alexander, Nango, Eriko, Kubo, Minoru, Young, Iris, Nakane, Takanori, Sugahara, Michihiro, Tanaka, Rie, Ito, Kazutaka, Brewster, Aaron, Owada, Shigeki, Yumoto, Fumiaki, Sauter, Nicholas, Tono, Kensuke, Iwata, So, and Fraser, James

Subjects
Biochemistry and Cell Biology, Computation Theory and Mathematics, Other Information and Computing Sciences, Biophysics, Biochemistry and cell biology, Medicinal and biomolecular chemistry
Published
2019

14. Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme

Author

Maestre-Reyna, Manuel, Yang, Cheng-Han, Nango, Eriko, Huang, Wei-Cheng, Ngurah Putu, Eka Putra Gusti, Wu, Wen-Jin, Wang, Po-Hsun, Franz-Badur, Sophie, Saft, Martin, Emmerich, Hans-Joachim, Wu, Hsiang-Yi, Lee, Cheng-Chung, Huang, Kai-Fa, Chang, Yao-Kai, Liao, Jiahn-Haur, Weng, Jui-Hung, Gad, Wael, Chang, Chiung-Wen, Pang, Allan H., Sugahara, Michihiro, Owada, Shigeki, Hosokawa, Yuhei, Joti, Yasumasa, Yamashita, Ayumi, Tanaka, Rie, Tanaka, Tomoyuki, Luo, Fangjia, Tono, Kensuke, Hsu, Kai-Cheng, Kiontke, Stephan, Schapiro, Igor, Spadaccini, Roberta, Royant, Antoine, Yamamoto, Junpei, Iwata, So, Essen, Lars-Oliver, Bessho, Yoshitaka, and Tsai, Ming-Daw

Published
2022
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15. Mapping Enzyme Motions in Real Time Using Time-Resolved Temperature-Jump X-Ray Crystallography and SAXS/WAXS

Author

Thompson, Michael, Wolff, Alexander, Barad, Benjamin, Nango, Eriko, Kubo, Minoru, Sugahara, Michihiro, Cho, Hynu Sun, Brewster, Aaron, Young, Iris, Schotte, Friedrich, Tanaka, Rie, Tono, Kensuke, Iwata, So, Sauter, Nicholas, Anfinrud, Philip, and Fraser, James

Subjects
Biochemistry and Cell Biology, Computation Theory and Mathematics, Other Information and Computing Sciences, Biophysics, Biochemistry and cell biology, Medicinal and biomolecular chemistry
Published
2018

17. High-resolution crystal structures of transient intermediates in the phytochrome photocycle

Author

Carrillo, Melissa, Pandey, Suraj, Sanchez, Juan, Noda, Moraima, Poudyal, Ishwor, Aldama, Luis, Malla, Tek Narsingh, Claesson, Elin, Wahlgren, Weixiao Yuan, Feliz, Denisse, Šrajer, Vukica, Maj, Michał, Castillon, Leticia, Iwata, So, Nango, Eriko, Tanaka, Rie, Tanaka, Tomoyuki, Fangjia, Luo, Tono, Kensuke, Owada, Shigeki, Westenhoff, Sebastian, Stojković, Emina A., and Schmidt, Marius

Published
2021
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18. XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

Author

Thomaston, Jessica L, Woldeyes, Rahel A, Nakane, Takanori, Yamashita, Ayumi, Tanaka, Tomoyuki, Koiwai, Kotaro, Brewster, Aaron S, Barad, Benjamin A, Chen, Yujie, Lemmin, Thomas, Uervirojnangkoorn, Monarin, Arima, Toshi, Kobayashi, Jun, Masuda, Tetsuya, Suzuki, Mamoru, Sugahara, Michihiro, Sauter, Nicholas K, Tanaka, Rie, Nureki, Osamu, Tono, Kensuke, Joti, Yasumasa, Nango, Eriko, Iwata, So, Yumoto, Fumiaki, Fraser, James S, and DeGrado, William F

Subjects
Chemical Sciences, Physical Chemistry, Emerging Infectious Diseases, Infectious Diseases, Influenza, Pneumonia & Influenza, Amino Acid Motifs, Hydrogen Bonding, Ion Channel Gating, Molecular Dynamics Simulation, Protein Domains, Protons, Static Electricity, Temperature, Viral Matrix Proteins, XFEL, proton channel, influenza, membrane protein
Abstract

The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged in "wires" inside the channel pore have been proposed to play a role in both the conduction of protons to the four gating His37 residues and the stabilization of multiple positive charges within the channel. To visualize the solvent in the pore of the channel at room temperature while minimizing the effects of radiation damage, data were collected to a resolution of 1.4 Å using an X-ray free-electron laser (XFEL) at three different pH conditions: pH 5.5, pH 6.5, and pH 8.0. Data were collected on the Inwardopen state, which is an intermediate that accumulates at high protonation of the His37 tetrad. At pH 5.5, a continuous hydrogen-bonded network of water molecules spans the vertical length of the channel, consistent with a Grotthuss mechanism model for proton transport to the His37 tetrad. This ordered solvent at pH 5.5 could act to stabilize the positive charges that build up on the gating His37 tetrad during the proton conduction cycle. The number of ordered pore waters decreases at pH 6.5 and 8.0, where the Inwardopen state is less stable. These studies provide a graphical view of the response of water to a change in charge within a restricted channel environment.

Published
2017

19. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

Author

Nogly, Przemyslaw, Panneels, Valerie, Nelson, Garrett, Gati, Cornelius, Kimura, Tetsunari, Milne, Christopher, Milathianaki, Despina, Kubo, Minoru, Wu, Wenting, Conrad, Chelsie, Coe, Jesse, Bean, Richard, Zhao, Yun, Båth, Petra, Dods, Robert, Harimoorthy, Rajiv, Beyerlein, Kenneth R, Rheinberger, Jan, James, Daniel, DePonte, Daniel, Li, Chufeng, Sala, Leonardo, Williams, Garth J, Hunter, Mark S, Koglin, Jason E, Berntsen, Peter, Nango, Eriko, Iwata, So, Chapman, Henry N, Fromme, Petra, Frank, Matthias, Abela, Rafael, Boutet, Sébastien, Barty, Anton, White, Thomas A, Weierstall, Uwe, Spence, John, Neutze, Richard, Schertler, Gebhard, and Standfuss, Jörg

Subjects
Chemical Sciences, Physical Chemistry, Bioengineering, Nanotechnology, Bacteriorhodopsins, Crystallography, X-Ray, Feasibility Studies, Lasers, Lipids, Protein Conformation, Synchrotrons, Time Factors, Viscosity, X-Ray Absorption Spectroscopy
Abstract

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.

Published
2016

21. Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase

Author

Safari, Cecilia, primary, Ghosh, Swagatha, additional, Andersson, Rebecka, additional, Johannesson, Jonatan, additional, Båth, Petra, additional, Uwangue, Owens, additional, Dahl, Peter, additional, Zoric, Doris, additional, Sandelin, Emil, additional, Vallejos, Adams, additional, Nango, Eriko, additional, Tanaka, Rie, additional, Bosman, Robert, additional, Börjesson, Per, additional, Dunevall, Elin, additional, Hammarin, Greger, additional, Ortolani, Giorgia, additional, Panman, Matthijs, additional, Tanaka, Tomoyuki, additional, Yamashita, Ayumi, additional, Arima, Toshi, additional, Sugahara, Michihiro, additional, Suzuki, Mamoru, additional, Masuda, Tetsuya, additional, Takeda, Hanae, additional, Yamagiwa, Raika, additional, Oda, Kazumasa, additional, Fukuda, Masahiro, additional, Tosha, Takehiko, additional, Naitow, Hisashi, additional, Owada, Shigeki, additional, Tono, Kensuke, additional, Nureki, Osamu, additional, Iwata, So, additional, Neutze, Richard, additional, and Brändén, Gisela, additional

Published
2023
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22. Visualizing the DNA repair process by a photolyase at atomic resolution

Author

Maestre-Reyna, Manuel, primary, Wang, Po-Hsun, additional, Nango, Eriko, additional, Hosokawa, Yuhei, additional, Saft, Martin, additional, Furrer, Antonia, additional, Yang, Cheng-Han, additional, Gusti Ngurah Putu, Eka Putra, additional, Wu, Wen-Jin, additional, Emmerich, Hans-Joachim, additional, Caramello, Nicolas, additional, Franz-Badur, Sophie, additional, Yang, Chao, additional, Engilberge, Sylvain, additional, Wranik, Maximilian, additional, Glover, Hannah Louise, additional, Weinert, Tobias, additional, Wu, Hsiang-Yi, additional, Lee, Cheng-Chung, additional, Huang, Wei-Cheng, additional, Huang, Kai-Fa, additional, Chang, Yao-Kai, additional, Liao, Jiahn-Haur, additional, Weng, Jui-Hung, additional, Gad, Wael, additional, Chang, Chiung-Wen, additional, Pang, Allan H., additional, Yang, Kai-Chun, additional, Lin, Wei-Ting, additional, Chang, Yu-Chen, additional, Gashi, Dardan, additional, Beale, Emma, additional, Ozerov, Dmitry, additional, Nass, Karol, additional, Knopp, Gregor, additional, Johnson, Philip J. M., additional, Cirelli, Claudio, additional, Milne, Chris, additional, Bacellar, Camila, additional, Sugahara, Michihiro, additional, Owada, Shigeki, additional, Joti, Yasumasa, additional, Yamashita, Ayumi, additional, Tanaka, Rie, additional, Tanaka, Tomoyuki, additional, Luo, Fangjia, additional, Tono, Kensuke, additional, Zarzycka, Wiktoria, additional, Müller, Pavel, additional, Alahmad, Maisa Alkheder, additional, Bezold, Filipp, additional, Fuchs, Valerie, additional, Gnau, Petra, additional, Kiontke, Stephan, additional, Korf, Lukas, additional, Reithofer, Viktoria, additional, Rosner, Christian Joshua, additional, Seiler, Elisa Marie, additional, Watad, Mohamed, additional, Werel, Laura, additional, Spadaccini, Roberta, additional, Yamamoto, Junpei, additional, Iwata, So, additional, Zhong, Dongping, additional, Standfuss, Jörg, additional, Royant, Antoine, additional, Bessho, Yoshitaka, additional, Essen, Lars-Oliver, additional, and Tsai, Ming-Daw, additional

Published
2023
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24. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser

Author

Nogly, Przemyslaw, Weinert, Tobias, James, Daniel, Carbajo, Sergio, Ozerov, Dmitry, Furrer, Antonia, Gashi, Dardan, Borin, Veniamin, Skopintsev, Petr, Jaeger, Kathrin, Nass, Karol, Båth, Petra, Bosman, Robert, Koglin, Jason, Seaberg, Matthew, Lane, Thomas, Kekilli, Demet, Brünle, Steffen, Tanaka, Tomoyuki, Wu, Wenting, Milne, Christopher, White, Thomas, Barty, Anton, Weierstall, Uwe, Panneels, Valerie, Nango, Eriko, Iwata, So, Hunter, Mark, Schapiro, Igor, Schertler, Gebhard, Neutze, Richard, and Standfuss, Jörg

Published
2018

25. Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA

Author

Suno, Ryoji, Kimura, Kanako Terakado, Nakane, Takanori, Yamashita, Keitaro, Wang, Junmei, Fujiwara, Takaaki, Yamanaka, Yasuaki, Im, Dohyun, Horita, Shoichiro, Tsujimoto, Hirokazu, Tawaramoto, Maki S., Hirokawa, Takatsugu, Nango, Eriko, Tono, Kensuke, Kameshima, Takashi, Hatsui, Takaki, Joti, Yasumasa, Yabashi, Makina, Shimamoto, Keiko, Yamamoto, Masaki, Rosenbaum, Daniel M., Iwata, So, Shimamura, Tatsuro, and Kobayashi, Takuya

Published
2018
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26. A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography

Author

Birch, James, primary, Kwan, Tristan O. C., additional, Judge, Peter J., additional, Axford, Danny, additional, Aller, Pierre, additional, Butryn, Agata, additional, Reis, Rosana I., additional, Bada Juarez, Juan F., additional, Vinals, Javier, additional, Owen, Robin L., additional, Nango, Eriko, additional, Tanaka, Rie, additional, Tono, Kensuke, additional, Joti, Yasumasa, additional, Tanaka, Tomoyuki, additional, Owada, Shigeki, additional, Sugahara, Michihiro, additional, Iwata, So, additional, Orville, Allen M., additional, Watts, Anthony, additional, and Moraes, Isabel, additional

Published
2023
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27. Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism

Author

Fadini, Alisia, primary, Hutchison, Christopher D.M., additional, Morozov, Dmitry, additional, Chang, Jeffrey, additional, Maghlaoui, Karim, additional, Perrett, Samuel, additional, Luo, Fangjia, additional, Kho, Jeslyn C.X., additional, Romei, Matthew G., additional, Morgan, R. Marc L., additional, Orr, Christian M., additional, Cordon-Preciado, Violeta, additional, Fujiwara, Takaaki, additional, Nuemket, Nipawan, additional, Tosha, Takehiko, additional, Tanaka, Rie, additional, Owada, Shigeki, additional, Tono, Kensuke, additional, Iwata, So, additional, Boxer, Steven G., additional, Groenhof, Gerrit, additional, Nango, Eriko, additional, and van Thor, Jasper J., additional

Published
2023
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29. Isoprenoid-chained lipid EROCOC17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography

Author

Ihara, Kentaro, Hato, Masakatsu, Nakane, Takanori, Yamashita, Keitaro, Kimura-Someya, Tomomi, Hosaka, Toshiaki, Ishizuka-Katsura, Yoshiko, Tanaka, Rie, Tanaka, Tomoyuki, Sugahara, Michihiro, Hirata, Kunio, Yamamoto, Masaki, Nureki, Osamu, Tono, Kensuke, Nango, Eriko, Iwata, So, and Shirouzu, Mikako

Published
2020
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30. Oxygen-evolving photosystem II structures during S1–S2–S3 transitions.

Author

Li, Hongjie, Nakajima, Yoshiki, Nango, Eriko, Owada, Shigeki, Yamada, Daichi, Hashimoto, Kana, Luo, Fangjia, Tanaka, Rie, Akita, Fusamichi, Kato, Koji, Kang, Jungmin, Saitoh, Yasunori, Kishi, Shunpei, Yu, Huaxin, Matsubara, Naoki, Fujii, Hajime, Sugahara, Michihiro, Suzuki, Mamoru, Masuda, Tetsuya, and Kimura, Tetsunari

Abstract

Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0–4) at the Mn4CaO5 cluster1–3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4–7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O–O bond formation.Serial femtosecond crystallography reveals the structural dynamics of photosystem II during the S-state transitions that produce dioxygen, providing insight into electron transfer, water insertion, proton release and O–O bond formation on sub-microsecond timescales. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Serial femtosecond crystallography reveals that photoactivation in a fluorescent protein proceeds via the hula twist mechanism

Author

Fadini, Alisia, Hutchison, Christopher D. M., Morozov, Dmitry, Chang, Jeffrey, Maghlaoui, Karim, Perrett, Samuel, Luo, Fangjia, Kho, Jeslyn C. X., Romei, Matthew G., Morgan, R. Marc L., Orr, Christian M., Cordon-Preciado, Violeta, Fujiwara, Takaaki, Nuemket, Nipawan, Tosha, Takehiko, Tanaka, Rie, Owada, Shigeki, Tono, Kensuke, Iwata, So, Boxer, Steven G., Groenhof, Gerrit, Nango, Eriko, van Thor, Jasper J., and Biotechnology and Biological Sciences Research Council (BBSRC)

Subjects
fluoresenssi, proteiinit, valokemia, General Chemistry, 03 Chemical Sciences
Abstract

Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements. peerReviewed

Published
2023

34. Ultrafast structural changes direct the first molecular events of vision

Author

60452330, Gruhl, Thomas, Weinert, Tobias, Rodrigues, Matthew J., Milne, Christopher J., Ortolani, Giorgia, Nass, Karol, Nango, Eriko, Sen, Saumik, Johnson, Philip J. M., Cirelli, Claudio, Furrer, Antonia, Mous, Sandra, Skopintsev, Petr, James, Daniel, Dworkowski, Florian, Båth, Petra, Kekilli, Demet, Ozerov, Dmitry, Tanaka, Rie, Glover, Hannah, Bacellar, Camila, Brünle, Steffen, Casadei, Cecilia M., Diethelm, Azeglio D., Gashi, Dardan, Gotthard, Guillaume, Guixà-González, Ramon, Joti, Yasumasa, Kabanova, Victoria, Knopp, Gregor, Lesca, Elena, Ma, Pikyee, Martiel, Isabelle, Mühle, Jonas, Owada, Shigeki, Pamula, Filip, Sarabi, Daniel, Tejero, Oliver, Tsai, Ching-Ju, Varma, Niranjan, Wach, Anna, Boutet, Sébastien, Tono, Kensuke, Nogly, Przemyslaw, Deupi, Xavier, Iwata, So, Neutze, Richard, Standfuss, Jörg, Schertler, Gebhard, Panneels, Valerie, 60452330, Gruhl, Thomas, Weinert, Tobias, Rodrigues, Matthew J., Milne, Christopher J., Ortolani, Giorgia, Nass, Karol, Nango, Eriko, Sen, Saumik, Johnson, Philip J. M., Cirelli, Claudio, Furrer, Antonia, Mous, Sandra, Skopintsev, Petr, James, Daniel, Dworkowski, Florian, Båth, Petra, Kekilli, Demet, Ozerov, Dmitry, Tanaka, Rie, Glover, Hannah, Bacellar, Camila, Brünle, Steffen, Casadei, Cecilia M., Diethelm, Azeglio D., Gashi, Dardan, Gotthard, Guillaume, Guixà-González, Ramon, Joti, Yasumasa, Kabanova, Victoria, Knopp, Gregor, Lesca, Elena, Ma, Pikyee, Martiel, Isabelle, Mühle, Jonas, Owada, Shigeki, Pamula, Filip, Sarabi, Daniel, Tejero, Oliver, Tsai, Ching-Ju, Varma, Niranjan, Wach, Anna, Boutet, Sébastien, Tono, Kensuke, Nogly, Przemyslaw, Deupi, Xavier, Iwata, So, Neutze, Richard, Standfuss, Jörg, Schertler, Gebhard, and Panneels, Valerie

Abstract

Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs). A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.

Published
2023

35. A three-dimensional movie of structural changes in bacteriorhodopsin

Author

Nango, Eriko, Royant, Antoine, Kubo, Minora, Nakane, Takanori, Wickstrand, Cecilia, Kimura, Tetsunari, Tanaka, Tomoyuki, Tono, Kensuke, Song, Changyong, Tanaka, Rie, Arima, Toshi, Yamashita, Ayumi, Kobayashi, Jun, Hosaka, Toshiaki, Mizohata, Eiichi, Nogly, Przemyslaw, Sugahara, Michihiro, Nam, Daewoong, Nomura, Takashi, Shimamura, Tatsuro, Im, Dohyun, Fujiwara, Takaaki, Yamanaka, Yasuaki, Jeon, Byeonghyun, Nishizawa, Tomohiro, Oda, Kazumasa, Fukuda, Masahiro, Andersson, Rebecka, Båth, Petra, Dods, Robert, Davidsson, Jan, Matsuoka, Shigeru, Kawatake, Satoshi, Murata, Michio, Nureki, Osamu, Owada, Shigeki, Kameshima, Takashi, Hatsui, Takaki, Joti, Yasumasa, Schertler, Gebhard, Yabashi, Makina, Bondar, Ana-Nicoleta, Standfuss, Jörg, Neutze, Richard, and Iwata, So

Published
2016

36. Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

Author

(中根崇智), Takanori Nakane, Hanashima, Shinya, Suzuki, Mamoru, Saiki, Haruka, Hayashi, Taichi, Kakinouchi, Keisuke, Sugiyama, Shigeru, Kawatake, Satoshi, Matsuoka, Shigeru, Matsumori, Nobuaki, Nango, Eriko, Kobayashi, Jun, Shimamura, Tatsuro, Kimura, Kanako, Mori, Chihiro, Kunishima, Naoki, Sugahara, Michihiro, Takakyu, Yoko, Inoue, Shigeyuki, Masuda, Tetsuya, Hosaka, Toshiaki, Tono, Kensuke, Joti, Yasumasa, Kameshima, Takashi, Hatsui, Takaki, Yabashi, Makina, Inoue, Tsuyoshi, Nureki, Osamu, Iwata, So, Murata, Michio, and (溝端栄一), Eiichi Mizohata

Published
2016

37. Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography

Author

Fukuda, Yohta, Tse, Ka Man, Nakane, Takanori, Nakatsu, Toru, Suzuki, Mamoru, Sugahara, Michihiro, Inoue, Shigeyuki, Masuda, Tetsuya, Yumoto, Fumiaki, Matsugaki, Naohiro, Nango, Eriko, Tono, Kensuke, Joti, Yasumasa, Kameshima, Takashi, Song, Changyong, Hatsui, Takaki, Yabashi, Makina, Nureki, Osamu, Murphy, Michael E. P., Inoue, Tsuyoshi, Iwata, So, and Mizohata, Eiichi

Published
2016

40. Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase

Author

Murakawa, Takeshi, primary, Suzuki, Mamoru, additional, Fukui, Kenji, additional, Masuda, Tetsuya, additional, Sugahara, Michihiro, additional, Tono, Kensuke, additional, Tanaka, Tomoyuki, additional, Iwata, So, additional, Nango, Eriko, additional, Yano, Takato, additional, Tanizawa, Katsuyuki, additional, and Okajima, Toshihide, additional

Published
2022
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41. ULTRAFAST STRUCTURAL CHANGES DIRECT THE FIRST MOLECULAR EVENTS OF VISION

Author

Gruhl, Thomas, primary, Weinert, Tobias, additional, Rodrigues, Matthew, additional, Milne, Christopher J, additional, Ortolani, Giorgia, additional, Nass, Karol, additional, Nango, Eriko, additional, Sen, Saumik, additional, Johnson, Philip J M, additional, Cirelli, Claudio, additional, Furrer, Antonia, additional, Mous, Sandra, additional, Skopintsev, Petr, additional, James, Daniel, additional, Dworkowski, Florian, additional, Båth, Petra, additional, Kekilli, Demet, additional, Ozerov, Dmitry, additional, Tanaka, Rie, additional, Glover, Hannah, additional, Bacellar, Camila, additional, Brünle, Steffen, additional, Casadei, Cecilia M, additional, Diethelm, Azeglio D, additional, Gashi, Dardan, additional, Gotthard, Guillaume, additional, Guixà-González, Ramon, additional, Joti, Yasumasa, additional, Kabanova, Victoria, additional, Knopp, Gregor, additional, Lesca, Elena, additional, Ma, Pikyee, additional, Martiel, Isabelle, additional, Mühle, Jonas, additional, Owada, Shigeki, additional, Pamula, Filip, additional, Sarabi, Daniel, additional, Tejero, Oliver, additional, Tsai, Ching-Ju, additional, Varma, Niranjan, additional, Wach, Anna, additional, Boutet, Sébastien, additional, Tono, Kensuke, additional, Nogly, Przemyslaw, additional, Deupi, Xavier, additional, Iwata, So, additional, Neutze, Richard, additional, Standfuss, Jörg, additional, Schertler, Gebhard FX, additional, and Panneels, Valerie, additional

Published
2022
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42. In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?

Author

Gallat, François-Xavier, Matsugaki, Naohiro, Coussens, Nathan P., Yagi, Koichiro J., Boudes, Marion, Higashi, Tetsuya, Tsuji, Daisuke, Tatano, Yutaka, Suzuki, Mamoru, Mizohata, Eiichi, Tono, Kensuke, Joti, Yasumasa, Kameshima, Takashi, Park, Jaehyun, Song, Changyong, Hatsui, Takaki, Yabashi, Makina, Nango, Eriko, Itoh, Kohji, Coulibaly, Fasséli, Tobe, Stephen, Ramaswamy, S., Stay, Barbara, Iwata, So, and Chavas, Leonard M. G.

Published
2014

43. Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers

Author

60452330, Hosaka, Toshiaki, Nomura, Takashi, Kubo, Minoru, Nakane, Takanori, Fangjia, Luo, Sekine, Shun-ichi, Ito, Takuhiro, Murayama, Kazutaka, Ihara, Kentaro, Ehara, Haruhiko, Kashiwagi, Kazuhiro, Katsura, Kazushige, Akasaka, Ryogo, Hisano, Tamao, Tanaka, Tomoyuki, Tanaka, Rie, Arima, Toshi, Yamashita, Ayumi, Sugahara, Michihiro, Naitow, Hisashi, Matsuura, Yoshinori, Yoshizawa, Susumu, Tono, Kensuke, Owada, Shigeki, Nureki, Osamu, Kimura-Someya, Tomomi, Iwata, So, Nango, Eriko, Shirouzu, Mikako, 60452330, Hosaka, Toshiaki, Nomura, Takashi, Kubo, Minoru, Nakane, Takanori, Fangjia, Luo, Sekine, Shun-ichi, Ito, Takuhiro, Murayama, Kazutaka, Ihara, Kentaro, Ehara, Haruhiko, Kashiwagi, Kazuhiro, Katsura, Kazushige, Akasaka, Ryogo, Hisano, Tamao, Tanaka, Tomoyuki, Tanaka, Rie, Arima, Toshi, Yamashita, Ayumi, Sugahara, Michihiro, Naitow, Hisashi, Matsuura, Yoshinori, Yoshizawa, Susumu, Tono, Kensuke, Owada, Shigeki, Nureki, Osamu, Kimura-Someya, Tomomi, Iwata, So, Nango, Eriko, and Shirouzu, Mikako

Abstract

Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10-µs and 1-ms time points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied by a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3.

Published
2022

44. Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX

Author

50710787, 60452330, 90204487, Pan, Dongqing, Oyama, Ryo, Sato, Tomomi, Nakane, Takanori, Mizunuma, Ryo, Matsuoka, Keita, Joti, Yasumasa, Tono, Kensuke, Nango, Eriko, Iwata, So, Nakatsu, Toru, Kato, Hiroaki, 50710787, 60452330, 90204487, Pan, Dongqing, Oyama, Ryo, Sato, Tomomi, Nakane, Takanori, Mizunuma, Ryo, Matsuoka, Keita, Joti, Yasumasa, Tono, Kensuke, Nango, Eriko, Iwata, So, Nakatsu, Toru, and Kato, Hiroaki

Abstract

CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open–close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 mono­acyl­glycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hy­droxy­propyl methyl­cellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates fr

Published
2022

45. Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography

Author

Wolff, Alexander M, Wolff, Alexander M, Nango, Eriko, Young, Iris D, Brewster, Aaron S, Kubo, Minoru, Nomura, Takashi, Sugahara, Michihiro, Owada, Shigeki, Barad, Benjamin A, Ito, Kazutaka, Bhowmick, Asmit, Carbajo, Sergio, Hino, Tomoya, Holton, James M, Im, Dohyun, O’Riordan, Lee J, Tanaka, Tomoyuki, Tanaka, Rie, Sierra, Raymond G, Yumoto, Fumiaki, Tono, Kensuke, Iwata, So, Sauter, Nicholas K, Fraser, James S, Thompson, Michael C, Wolff, Alexander M, Wolff, Alexander M, Nango, Eriko, Young, Iris D, Brewster, Aaron S, Kubo, Minoru, Nomura, Takashi, Sugahara, Michihiro, Owada, Shigeki, Barad, Benjamin A, Ito, Kazutaka, Bhowmick, Asmit, Carbajo, Sergio, Hino, Tomoya, Holton, James M, Im, Dohyun, O’Riordan, Lee J, Tanaka, Tomoyuki, Tanaka, Rie, Sierra, Raymond G, Yumoto, Fumiaki, Tono, Kensuke, Iwata, So, Sauter, Nicholas K, Fraser, James S, and Thompson, Michael C

Abstract

Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to trigger conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the sub-millisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature-jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

Published
2022

46. Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography

Author

Wolff, Alexander, Wolff, Alexander, Nango, Eriko, Young, Iris, Brewster, Aaron, Kubo, Minoru, Nomura, Takashi, Sugahara, Michihiro, Owada, Shigeki, Barad, Benjamin, Ito, Kazutaka, Bhowmick, Asmit, Carbajo, Sergio, Hino, Tomoya, Holton, James, Im, Dohyun, O’Riordan, Lee, Tanaka, Tomoyuki, Tanaka, Rie, Sierra, Raymond, Yumoto, Fumiaki, Tono, Kensuke, Iwata, So, Sauter, Nicholas, Fraser, James, Thompson, Michael, Wolff, Alexander, Wolff, Alexander, Nango, Eriko, Young, Iris, Brewster, Aaron, Kubo, Minoru, Nomura, Takashi, Sugahara, Michihiro, Owada, Shigeki, Barad, Benjamin, Ito, Kazutaka, Bhowmick, Asmit, Carbajo, Sergio, Hino, Tomoya, Holton, James, Im, Dohyun, O’Riordan, Lee, Tanaka, Tomoyuki, Tanaka, Rie, Sierra, Raymond, Yumoto, Fumiaki, Tono, Kensuke, Iwata, So, Sauter, Nicholas, Fraser, James, and Thompson, Michael

Abstract

Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to trigger conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the sub-millisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature-jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

Published
2022

47. Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL

Author

Suga, Michihiro, Akita, Fusamichi, Sugahara, Michihiro, Kubo, Minoru, Nakajima, Yoshiki, Nakane, Takanori, Yamashita, Keitaro, Umena, Yasufumi, Nakabayashi, Makoto, Yamane, Takahiro, Nakano, Takamitsu, Suzuki, Mamoru, Masuda, Tetsuya, Inoue, Shigeyuki, Kimura, Tetsunari, Nomura, Takashi, Yonekura, Shinichiro, Yu, Long-Jiang, Sakamoto, Tomohiro, Motomura, Taiki, Chen, Jing-Hua, Kato, Yuki, Noguchi, Takumi, Tono, Kensuke, Joti, Yasumasa, Kameshima, Takashi, Hatsui, Takaki, Nango, Eriko, Tanaka, Rie, Naitow, Hisashi, Matsuura, Yoshinori, Yamashita, Ayumi, Yamamoto, Masaki, Nureki, Osamu, Yabashi, Makina, Ishikawa, Tetsuya, Iwata, So, and Shen, Jian-Ren

Published
2017
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48. Ambient temperature structure of phosphoketolase from Bifidobacterium longum determined by serial femtosecond X‐ray crystallography.

Author

Nakata, Kunio, Kashiwagi, Tatsuki, Kunishima, Naoki, Naitow, Hisashi, Matsuura, Yoshinori, Miyano, Hiroshi, Mizukoshi, Toshimi, Tono, Kensuke, Yabashi, Makina, Nango, Eriko, and Iwata, So

Subjects
BIFIDOBACTERIUM longum, X-ray crystallography, THIAMIN pyrophosphate, FREE electron lasers, X-ray lasers, METABOLISM
Abstract

Phosphoketolase and transketolase are thiamine diphosphate‐dependent enzymes and play a central role in the primary metabolism of bifidobacteria: the bifid shunt. The enzymes both catalyze phosphorolytic cleavage of xylulose 5‐phosphate or fructose 6‐phosphate in the first reaction step, but possess different substrate specificity in the second reaction step, where phosphoketolase and transketolase utilize inorganic phosphate (Pi) and d‐ribose 5‐phosphate, respectively, as the acceptor substrate. Structures of Bifidobacterium longum phosphoketolase holoenzyme and its complex with a putative inhibitor, phosphoenolpyruvate, were determined at 2.5 Å resolution by serial femtosecond crystallography using an X‐ray free‐electron laser. In the complex structure, phosphoenolpyruvate was present at the entrance to the active‐site pocket and plugged the channel to thiamine diphosphate. The phosphate‐group position of phosphoenolpyruvate coincided well with those of xylulose 5‐phosphate and fructose 6‐phosphate in the structures of their complexes with transketolase. The most striking structural change was observed in a loop consisting of Gln546‐Asp547‐His548‐Asn549 (the QN‐loop) at the entrance to the active‐site pocket. Contrary to the conformation of the QN‐loop that partially covers the entrance to the active‐site pocket ('closed form') in the known crystal structures, including the phosphoketolase holoenzyme and its complexes with reaction intermediates, the QN‐loop in the current ambient structures showed a more compact conformation with a widened entrance to the active‐site pocket ('open form'). In the phosphoketolase reaction, the 'open form' QN‐loop may play a role in providing the binding site for xylulose 5‐phosphate or fructose 6‐phosphate in the first step, and the 'closed form' QN‐loop may help confer specificity for Pi in the second step. [ABSTRACT FROM AUTHOR]

Published
2023
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49. Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography

Author

Wolff, Alexander M, primary, Nango, Eriko, additional, Young, Iris D, additional, Brewster, Aaron S, additional, Kubo, Minoru, additional, Nomura, Takashi, additional, Sugahara, Michihiro, additional, Owada, Shigeki, additional, Barad, Benjamin A, additional, Ito, Kazutaka, additional, Bhowmick, Asmit, additional, Carbajo, Sergio, additional, Hino, Tomoya, additional, Holton, James M, additional, Im, Dohyun, additional, O'Riordan, Lee J, additional, Tanaka, Tomoyuki, additional, Tanaka, Rie, additional, Sierra, Raymond G, additional, Yumoto, Fumiyaki, additional, Tono, Kensuke, additional, Iwata, So, additional, Sauter, Nicholas K, additional, Fraser, James S, additional, and Thompson, Michael C, additional

Published
2022
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50. Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre

Author

Båth, Petra, primary, Banacore, Analia, additional, Börjesson, Per, additional, Bosman, Robert, additional, Wickstrand, Cecilia, additional, Safari, Cecilia, additional, Dods, Robert, additional, Ghosh, Swagatha, additional, Dahl, Peter, additional, Ortolani, Giorgia, additional, Björg Ulfarsdottir, Tinna, additional, Hammarin, Greger, additional, García Bonete, María-José, additional, Vallejos, Adams, additional, Ostojić, Lucija, additional, Edlund, Petra, additional, Linse, Johanna-Barbara, additional, Andersson, Rebecka, additional, Nango, Eriko, additional, Owada, Shigeki, additional, Tanaka, Rie, additional, Tono, Kensuke, additional, Joti, Yasumasa, additional, Nureki, Osamu, additional, Luo, Fangjia, additional, James, Daniel, additional, Nass, Karol, additional, Johnson, Philip J. M., additional, Knopp, Gregor, additional, Ozerov, Dmitry, additional, Cirelli, Claudio, additional, Milne, Christopher, additional, Iwata, So, additional, Brändén, Gisela, additional, and Neutze, Richard, additional

Published
2022
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