TOHOKU UNIVERSITY Researchers

Details of the Researcher

Home

日本語 English

Eriko Nango

Section

Institute of Multidisciplinary Research for Advanced Materials

Job title

Professor

Degree

博士（理学）(東京工業大学)
修士（理学）（東京工業大学）

researchmap

https://researchmap.jp/read0205389

J-GLOBAL ID

200901039012093006

Profile

Research History 10

2020/07 - Present

東北大学国際放射光イノベーション・スマート研究センター　教授（兼任）
2020/04 - Present

Tohoku University　Institute of Multidisciplinary Research for Advanced Materials　Professor
2021/04 - 2025/03

RIKEN　RIKEN SPring-8 Center
2019/12 - 2020/03

Kyoto University　Department of Cell Biology, Graduate School of Medicine　Project associate professor
2019/04 - 2019/11

Kyoto University　Department of Cell Biology, Graduate School of Medicine　Assistant Professor
2013 - 2019/03

理化学研究所　放射光科学総合研究センター　研究員
2010 - 2013

理化学研究所　放射光科学総合研究センター　リサーチアソシエイト
2007 - 2010

東京工業大学大学院　理工学研究科　助教
2004 - 2007

東京工業大学理工学研究科助手
2001 - 2004

日本学術振興会特別研究員DC1

Show all Show first 5

Education 2

Tokyo Institute of Technology　Science of Engineering　Chemistry

1999 - 2004
Tokyo Institute of Technology　School of Science

1995 - 1999

Committee Memberships 7

日本学術会議　連携会員

2023/11 - Present
SPring-8ユーザー協同体（SPRUC）　幹事

2022/04 - Present
日本結晶学会　評議員

2022/04 - Present
日本蛋白質科学会　代議員

2022/04 - Present
日本生物物理学会　理事

2021/04 - Present
さきがけ「細胞の動的高次構造体」　領域アドバイザー

2020/04 - Present
大阪大学蛋白質研究所専門委員会　専門委員

2021/04 - 2023/03

Show all ︎Show first 5

Professional Memberships 4

日本化学会
PROTEIN SCIENCE SOCIETY OF JAPAN
THE BIOPHYSICAL SOCIETY OF JAPAN
日本結晶学会

Research Interests 8

酵素反応解析
タンパク質結晶構造解析
レチナールタンパク質
シリアルフェムト秒結晶構造解析
X線自由電子レーザー
Biochemistry of biosubstances in general
Natural Organic compounds
Biological Organic Chemistry

Research Areas 6

Life sciences / Biophysics /
Life sciences / Structural biochemistry /
Life sciences / Bioorganic chemistry /
Nanotechnology/Materials / Structural/physical organic chemistry /
Energy / Quantum beam science /
Nanotechnology/Materials / Molecular biochemistry /

Awards 6

第４１回井上学術賞

2024/12　公益財団法人井上科学振興財団　光感受性タンパク質の動的構造と分子機構解明
第三回長倉三郎賞

2023/12　日本化学会
第41回学術賞

2023/12　日本化学会
Japan Academy Medal

2022/01　The Japan academy　Molecular Movie Analysis of Proteins Using X-Ray Free Electron Laser
JSPS Prize

2021/12　Japan Society for the Promotion of Science　Molecular Movie Analysis of Proteins Using X-Ray Free Electron Laser
第3回保井コノ賞

2019/03　お茶の水女子大学　X線自由電子レーザーによるタンパク質の動的構造と機能発現機構の解析

Show all ︎Show 5

Papers 107

Rapid and reversible fluorescent probe enables repeated snapshot imaging of AMPA receptors during synaptic plasticity. International-journal

Kyohei Soga, Takaaki Fujiwara, Mayu Nakagawa, Akihiro Shibata, Hansel Adriel, Kenji Yatsuzuka, Wataru Kakegawa, Michisuke Yuzaki, Itaru Hamachi, Eriko Nango, Shigeki Kiyonaka

Science advances　11　(23)　eadt6683　2025/06/06

DOI： 10.1126/sciadv.adt6683 　

More details Close

The subcellular localization of neurotransmitter receptors is strictly regulated in neurons. Changes in the trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors (AMPARs) play an essential role in synaptic plasticity, which is the cellular basis of learning and memory. To explore receptor trafficking, genetically encoded approaches (e.g., the fusion of fluorescent proteins to receptors) are often used. However, concerns remain that genetic approaches cannot fully reproduce the receptor functions that are inherent to neurons. Herein, we report on PFQX1(AF488), a fluorescent probe for the visualization of cell-surface AMPARs without any genetic manipulation to neurons. The rapid and reversible staining features of this probe enabled snapshot imaging, which showed the accumulation of native AMPARs in dendritic spines during synaptic plasticity. Moreover, the mechanism of this synaptic accumulation, for which genetically encoded approaches have given controversial results, was revealed by integrating two chemical methods: PFQX1(AF488) and covalent chemical labeling.
Capturing structural intermediates in an animal-like cryptochrome photoreceptor by time-resolved crystallography. International-journal

Manuel Maestre-Reyna, Yuhei Hosokawa, Po-Hsun Wang, Martin Saft, Nicolas Caramello, Sylvain Engilberge, Sophie Franz-Badur, Eka Putra Gusti Ngurah Putu, Mai Nakamura, Wen-Jin Wu, Hsiang-Yi Wu, Cheng-Chung Lee, Wei-Cheng Huang, Kai-Fa Huang, Yao-Kai Chang, Cheng-Han Yang, Meng-Iao Fong, Wei-Ting Lin, Kai-Chun Yang, Yuki Ban, Tomoki Imura, Atsuo Kazuoka, Eisho Tanida, Shigeki Owada, Yasumasa Joti, Rie Tanaka, Tomoyuki Tanaka, Jungmin Kang, Fangjia Luo, Kensuke Tono, Stephan Kiontke, Lukas Korf, Yasufumi Umena, Takehiko Tosha, Yoshitaka Bessho, Eriko Nango, So Iwata, Antoine Royant, Ming-Daw Tsai, Junpei Yamamoto, Lars-Oliver Essen

Science advances　11　(20)　eadu7247　2025/05/16

DOI： 10.1126/sciadv.adu7247 　

More details Close

Animal-like cryptochromes are photoreceptors that control circadian rhythm and signaling in many eukaryotes. Transient photoreduction of the cryptochrome flavin chromophore initiated signaling via a poorly understood mechanism. By serial femtosecond crystallography (SFX), we show that the photoreduction mechanism of Chlamydomonas reinhardtii cryptochrome involves three loci [carboxyl-terminal region, a transient protonation pathway, and flavin adenine dinucleotide (FAD)-binding site] acting in unison to accomplish three effects: radical pair stabilization, protonation of FAD radical, and formation of the signaling state. Using 19 time-resolved SFX snapshots between 10 nanoseconds and 233 milliseconds, we found that light-driven FAD•-/tyrosyl-373 radical pair (RP) formation primes α22 unfolding. Electron transfer-dependent protonation of aspartate-321 by tyrosine-373 is the epicenter of unfolding by disrupting salt bridges between α22 and the photolyase homology region. Before helix unfolding, another pathway opens transiently for FAD•- protonation and RP stabilization. This link between RP formation and conformational changes provides a structural basis for signaling by animal-like cryptochromes.
Redox-State-Dependent Structural Changes within a Prokaryotic 6-4 Photolyase. International-journal

Po-Hsun Wang, Yuhei Hosokawa, Jessica C Soares, Hans-Joachim Emmerich, Valeri Fuchs, Nicolas Caramello, Sylvain Engilberge, Andrea Bologna, Christian Joshua Rosner, Mai Nakamura, Mohamed Watad, Fangjia Luo, Shigeki Owada, Takehiko Tosha, Jungmin Kang, Kensuke Tono, Yoshitaka Bessho, Eriko Nango, Antonio J Pierik, Antoine Royant, Ming-Daw Tsai, Junpei Yamamoto, Manuel Maestre-Reyna, Lars-Oliver Essen

Journal of the American Chemical Society　147　(19)　16084-16098　2025/05/14

DOI： 10.1021/jacs.4c18116 　

More details Close

Photolyases repair UV damage to DNA by using absorbed blue light. Within the photolyase/cryptochrome superfamily (PCSf), a major subgroup consists of prokaryotic (6-4) photolyases. These enzymes rely on flavin adenine dinucleotide (FAD) as a catalytic cofactor, besides an ancillary antenna chromophore, and a [4Fe-4S] cluster with yet unknown function. For the prokaryotic 6-4 photolyase of Caulobacter crescentus, we investigated structural changes associated with its different redox states by damage-free crystallography using X-ray free-electron lasers. EPR and optical spectroscopy confirmed redox-dependent structural transitions, including the formation of an oxidized [4Fe-4S]3+ cluster with the dynamic cleavage of a single iron-sulfur bond. Photoreduction to the catalytic FADH- state alters the flavin binding site at the proximal aromatic pair Y390/F394 that is part of the electron transport pathway. Upon oxidation, the observable structural transitions of the protein matrix around the [4Fe-4S] cluster may affect DNA binding and are consistent with the much-debated role of the iron-sulfur cluster in DNA-binding proteins for quenching electron holes.
Time-resolved small-angle X-ray scattering system development for the biological macromolecules at SACLA: A pilot study

Nobutaka Shimizu, Fangjia Luo, Tomoyuki Tanaka, Kensuke Tono, Keiko Yatabe, So Iwata, Eriko Nango

Biophysics and Physicobiology　2025/03/27

DOI： 10.2142/biophysico.bppb-v22.0007 　
Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate. International-journal Peer-reviewed

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

Nature communications　15　(1)　10278-10278　2024/11/27

DOI： 10.1038/s41467-024-54422-8 　

More details Close

Time-resolved serial crystallography at X-ray Free Electron Lasers offers the opportunity to observe ultrafast photochemical reactions at the atomic level. The technique has yielded exciting molecular insights into various biological processes including light sensing and photochemical energy conversion. However, to achieve sufficient levels of activation within an optically dense crystal, high laser power densities are often used, which has led to an ongoing debate to which extent photodamage may compromise interpretation of the results. Here we compare time-resolved serial crystallographic data of the bacteriorhodopsin K-intermediate collected at laser power densities ranging from 0.04 to 2493 GW/cm2 and follow energy dissipation of the absorbed photons logarithmically from picoseconds to milliseconds. Although the effects of high laser power densities on the overall structure are small, in the upper excitation range we observe significant changes in retinal conformation and increased heating of the functionally critical counterion cluster. We compare light-activation within crystals to that in solution and discuss the impact of the observed changes on bacteriorhodopsin biology.
Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography Peer-reviewed

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

Nature Communications　15　(1)　2024/06/29
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41467-024-49814-9 　

eISSN： 2041-1723

More details Close

Abstract Determining short-lived intermediate structures in chemical reactions is challenging. Although ultrafast spectroscopic methods can detect the formation of transient intermediates, real-space structures cannot be determined directly from such studies. Time-resolved serial femtosecond crystallography (TR-SFX) has recently proven to be a powerful method for capturing molecular changes in proteins on femtosecond timescales. However, the methodology has been mostly applied to natural proteins/enzymes and limited to reactions promoted by synthetic molecules due to structure determination challenges. This work demonstrates the applicability of TR-SFX for investigations of chemical reaction mechanisms of synthetic metal complexes. We fix a light-induced CO-releasing Mn(CO)₃ reaction center in porous hen egg white lysozyme (HEWL) microcrystals. By controlling light exposure and time, we capture the real-time formation of Mn-carbonyl intermediates during the CO release reaction. The asymmetric protein environment is found to influence the order of CO release. The experimentally-observed reaction path agrees with quantum mechanical calculations. Therefore, our demonstration offers a new approach to visualize atomic-level reactions of small molecules using TR-SFX with real-space structure determination. This advance holds the potential to facilitate design of artificial metalloenzymes with precise mechanisms, empowering design, control and development of innovative reactions.
Structural basis for the minimal bifunctional alginate epimerase AlgE3 from Azotobacter chroococcum. International-journal Peer-reviewed

Takaaki Fujiwara, Eriko Mano, Eriko Nango

FEBS letters　598　(11)　1422-1437　2024/06

DOI： 10.1002/1873-3468.14886 　

More details Close

Among the epimerases specific to alginate, some of them in Azotobacter genera convert β-d-mannuronic acid to α-l-guluronic acid but also have lyase activity to degrade alginate. The remarkable characteristics of these epimerases make it a promising enzyme for tailoring alginates to meet specific demands. Here, we determined the structure of the bifunctional mannuronan C-5 epimerase AlgE3 from Azotobacter chroococcum (AcAlgE3) in complex with several mannuronic acid oligomers as well as in apo form, which allowed us to elucidate the binding manner of each mannuronic acid oligomer, and the structural plasticity, which is dependent on calcium ions. Moreover, a comprehensive analysis of the lyase activity profiles of AcAlgE3 combined with structural characteristics explained the preference for different chain length oligomers.
Crystal structure reveals the binding mode and selectivity of a photoswitchable ligand for the adenosine A2A receptor. International-journal Peer-reviewed

Tsuyoshi Araya, Yuya Matsuba, Harufumi Suzuki, Tomohiro Doura, Nipawan Nuemket, Eriko Nango, Masaki Yamamoto, Dohyun Im, Hidetsugu Asada, Shigeki Kiyonaka, So Iwata

Biochemical and biophysical research communications　695　149393-149393　2024/02/05

DOI： 10.1016/j.bbrc.2023.149393 　

More details Close

Rational synthetic expansion of photoresponsive ligands is important for photopharmacological studies. Adenosine A2A receptor (A2AR) is stimulated by adenosine and related in Parkinson's disease and other diseases. Here, we report the crystal structure of the A2AR in complex with the novel photoresponsive ligand photoNECA (blue) at 3.34 Å resolution. PhotoNECA (blue) was designed for this structural study and the cell-based assay showed a photoresponsive and receptor selective characteristics of photoNECA (blue) for A2AR. The crystal structure explains the binding mode, photoresponsive mechanism and receptor selectivity of photoNECA (blue). Our study would promote not only the rational design of photoresponsive ligands but also dynamic structural studies of A2AR.
Oxygen-evolving photosystem II structures during S1-S2-S3 transitions. International-journal Peer-reviewed

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

Nature　2024/01/31

DOI： 10.1038/s41586-023-06987-5 　

More details Close

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.
Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. International-journal International-coauthorship Peer-reviewed

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

Science advances　9　(49)　eadh4179　2023/12/08

DOI： 10.1126/sciadv.adh4179 　

More details Close

Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.
Visualizing the DNA repair process by a photolyase at atomic resolution. International-journal Peer-reviewed

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

Science (New York, N.Y.)　382　(6674)　eadd7795　2023/12

DOI： 10.1126/science.add7795 　

More details Close

Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.
Optical control of ultrafast structural dynamics in a fluorescent protein. International-journal Peer-reviewed

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

Nature chemistry　15　(11)　1607-1615　2023/11

DOI： 10.1038/s41557-023-01275-1 　

More details Close

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.
A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography. International-journal Peer-reviewed

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

Journal of applied crystallography　56　(Pt 5)　1361-1370　2023/10/01

DOI： 10.1107/S1600576723006428 　

More details Close

Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.
Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography Peer-reviewed

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

Nature Chemistry　2023/09/18
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41557-023-01329-4 　

ISSN： 1755-4330

eISSN： 1755-4349

More details Close

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.
Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins. International-journal

Eriko Nango, So Iwata

Current opinion in structural biology　81　102629-102629　2023/08

DOI： 10.1016/j.sbi.2023.102629 　

More details Close

Microbial rhodopsin is a membrane protein with a domain of seven-transmembrane helices and a retinal chromophore. The main function of this protein is to perform light-induced ion transport, either actively or passively, by acting as pumps, channels, and light sensors. It is widely used for optogenetic application to control the activity of specific cells in living tissues by light. Time-resolved serial femtosecond crystallography (TR-SFX) with the use of X-ray free electron lasers is an effective technique for capturing dynamic ion transport and efflux structures across membranes with high spatial and temporal resolutions. Here, we outline recent TR-SFX studies of microbial rhodopsins, including a pump and a channel. We also discuss differences and similarities observed in the structural dynamics derived from the TR-SFX structures.
Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism Peer-reviewed

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

Journal of the American Chemical Society　145　(29)　15796-15808　2023/07/07
Publisher: American Chemical Society (ACS)
DOI： 10.1021/jacs.3c02313 　

ISSN： 0002-7863

eISSN： 1520-5126
Ambient temperature structure of phosphoketolase from Bifidobacterium longum determined by serial femtosecond X-ray crystallography Peer-reviewed

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

Acta Crystallographica Section D Structural Biology　79　(4)　290-303　2023/03/28
Publisher: International Union of Crystallography (IUCr)
DOI： 10.1107/s2059798323001638 　

ISSN： 2059-7983

More details Close

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 (P_i) 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 P_i in the second step.
Ultrafast structural changes direct the first molecular events of vision Peer-reviewed

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

Nature　615　(7954)　939-944　2023/03/22
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41586-023-05863-6 　

ISSN： 0028-0836

eISSN： 1476-4687

More details Close

Abstract Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)¹. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation², 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 temperature³ 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.
Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase. International-journal Peer-reviewed

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

Acta crystallographica. Section D, Structural biology　78　(Pt 12)　1428-1438　2022/12/01

DOI： 10.1107/S2059798322010385 　

More details Close

The mechanisms by which enzymes promote catalytic reactions efficiently through their structural changes remain to be fully elucidated. Recent progress in serial femtosecond X-ray crystallography (SFX) using X-ray free-electron lasers (XFELs) has made it possible to address these issues. In particular, mix-and-inject serial crystallography (MISC) is promising for the direct observation of structural changes associated with ongoing enzymic reactions. In this study, SFX measurements using a liquid-jet system were performed on microcrystals of bacterial copper amine oxidase anaerobically premixed with a substrate amine solution. The structure determined at 1.94 Å resolution indicated that the peptidyl quinone cofactor is in equilibrium between the aminoresorcinol and semiquinone radical intermediates, which accumulate only under anaerobic single-turnover conditions. These results show that anaerobic conditions were well maintained throughout the liquid-jet SFX measurements, preventing the catalytic intermediates from reacting with dioxygen. These results also provide a necessary framework for performing time-resolved MISC to study enzymic reaction mechanisms under anaerobic conditions.
Excited-state intermediates in a designer protein encoding a phototrigger caught by an X-ray free-electron laser. International-journal Peer-reviewed

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

Nature chemistry　14　(9)　1054-1060　2022/09

DOI： 10.1038/s41557-022-00992-3 　

More details Close

One of the primary objectives in chemistry research is to observe atomic motions during reactions in real time. Although X-ray free-electron lasers (XFELs) have facilitated the capture of reaction intermediates using time-resolved serial femtosecond crystallography (TR-SFX), only a few natural photoactive proteins have been investigated using this method, mostly due to the lack of suitable phototriggers. Here we report the genetic encoding of a xanthone amino acid (FXO), as an efficient phototrigger, into a rationally designed human liver fatty-acid binding protein mutant (termed XOM), which undergoes photo-induced C-H bond transformation with high selectivity and quantum efficiency. We solved the structures of XOM before and 10-300 ns after flash illumination, at 1.55-1.70 Å resolutions, and captured the elusive excited-state intermediates responsible for precise C-H bond activation. We expect that most redox enzymes can now be investigated by TR-SFX, using our method, to reveal reaction intermediates key for their efficiency and selectivity.
Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre Peer-reviewed

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

Acta Crystallographica Section D Structural Biology　78　(6)　698-708　2022/05/25
Publisher: International Union of Crystallography (IUCr)
DOI： 10.1107/s2059798322004144 　

ISSN： 2059-7983

More details Close

Serial crystallography is a rapidly growing method that can yield structural insights from microcrystals that were previously considered to be too small to be useful in conventional X-ray crystallography. Here, conditions for growing microcrystals of the photosynthetic reaction centre of Blastochloris viridis within a lipidic cubic phase (LCP) crystallization matrix that employ a seeding protocol utilizing detergent-grown crystals with a different crystal packing are described. LCP microcrystals diffracted to 2.25 Å resolution when exposed to XFEL radiation, which is an improvement of 0.15 Å over previous microcrystal forms. Ubiquinone was incorporated into the LCP crystallization media and the resulting electron density within the mobile Q_B pocket is comparable to that of other cofactors within the structure. As such, LCP microcrystallization conditions will facilitate time-resolved diffraction studies of electron-transfer reactions to the mobile quinone, potentially allowing the observation of structural changes associated with the two electron-transfer reactions leading to complete reduction of the ubiquinone ligand.
Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme Peer-reviewed

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

NATURE CHEMISTRY　2022/04

DOI： 10.1038/s41557-022-00922-3 　

ISSN： 1755-4330

eISSN： 1755-4349
Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers. International-journal Peer-reviewed

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

Proceedings of the National Academy of Sciences of the United States of America　119　(9)　2022/03/01

DOI： 10.1073/pnas.2117433119 　

More details Close

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

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

IUCrJ　9　(Pt 1)　134-145　2022/01/01

DOI： 10.1107/S2052252521011611 　

More details Close

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 mono-acyl-glycerol 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 hy-droxy-propyl methyl-cellulose 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 from the transporter.
スフィンゴシン-1-リン酸受容体におけるバイアスドアゴニズム機構

前田信太郎, 椎村祐樹, 浅田秀基, 平田邦生, Luo Fangjia, 南後恵理子, 井上飛鳥, 青木淳賢, 岩田想, 萩原正敏

日本生化学会大会プログラム・講演要旨集　94回　[1T15m-207)]　2021/11
Publisher: (公社)日本生化学会
Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase

Takeshi Murakawa, Mamoru Suzuki, Toshi Arima, Michihiro Sugahara, Tomoyuki Tanaka, Rie Tanaka, So Iwata, Eriko Nango, Kensuke Tono, Hideyuki Hayashi, Kenji Fukui, Takato Yano, Katsuyuki Tanizawa, Toshihide Okajima

Acta Crystallographica Section F Structural Biology Communications　77　(10)　356-363　2021/10/01
Publisher: International Union of Crystallography (IUCr)
DOI： 10.1107/s2053230x21008967 　

eISSN： 2053-230X

More details Close

Recent advances in serial femtosecond X-ray crystallography (SFX) using X-ray free-electron lasers have paved the way for determining radiation-damage-free protein structures under nonfreezing conditions. However, the large-scale preparation of high-quality microcrystals of uniform size is a prerequisite for SFX, and this has been a barrier to its widespread application. Here, a convenient method for preparing high-quality microcrystals of a bacterial quinoprotein enzyme, copper amine oxidase from <italic>Arthrobacter globiformis</italic>, is reported. The method consists of the mechanical crushing of large crystals (5–15 mm³), seeding the crushed crystals into the enzyme solution and standing for 1 h at an ambient temperature of ∼26°C, leading to the rapid formation of microcrystals with a uniform size of 3–5 µm. The microcrystals diffracted X-rays to a resolution beyond 2.0 Å in SFX measurements at the SPring-8 Angstrom Compact Free Electron Laser facility. The damage-free structure determined at 2.2 Å resolution was essentially identical to that determined previously by cryogenic crystallography using synchrotron X-ray radiation.
The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. International-journal Peer-reviewed

Andrea Cellini, Weixiao Yuan Wahlgren, Léocadie Henry, Suraj Pandey, Swagatha Ghosh, Leticia Castillon, Elin Claesson, Heikki Takala, Joachim Kübel, Amke Nimmrich, Valentyna Kuznetsova, Eriko Nango, So Iwata, Shigeki Owada, Emina A Stojković, Marius Schmidt, Janne A Ihalainen, Sebastian Westenhoff

Acta crystallographica. Section D, Structural biology　77　(Pt 8)　1001-1009　2021/08/01

DOI： 10.1107/S2059798321005830 　

More details Close

(6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 Å resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 Å resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.
Endogenous agonist-bound S1PR3 structure reveals determinants of G protein-subtype bias. International-journal Peer-reviewed

Shintaro Maeda, Yuki Shiimura, Hidetsugu Asada, Kunio Hirata, Fangjia Luo, Eriko Nango, Nobuo Tanaka, Masayasu Toyomoto, Asuka Inoue, Junken Aoki, So Iwata, Masatoshi Hagiwara

Science advances　7　(24)　2021/06

DOI： 10.1126/sciadv.abf5325 　

More details Close

Sphingosine-1-phosphate (S1P) regulates numerous important physiological functions, including immune response and vascular integrity, via its cognate receptors (S1PR1 to S1PR5); however, it remains unclear how S1P activates S1PRs upon binding. Here, we determined the crystal structure of the active human S1PR3 in complex with its natural agonist S1P at 3.2-Å resolution. S1P exhibits an unbent conformation in the long tunnel, which penetrates through the receptor obliquely. Compared with the inactive S1PR1 structure, four residues surrounding the alkyl tail of S1P (the "quartet core") exhibit orchestrating rotamer changes that accommodate the moiety, thereby inducing an active conformation. In addition, we reveal that the quartet core determines G protein selectivity of S1PR3. These results offer insight into the structural basis of activation and biased signaling in G protein-coupled receptors and will help the design of biased ligands for optimized therapeutics.
Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography Peer-reviewed

Hongjie Li, Yoshiki Nakajima, Takashi Nomura, Michihiro Sugahara, Shinichiro Yonekura, Siu Kit Chan, Takanori Nakane, Takahiro Yamane, Yasufumi Umena, Mamoru Suzuki, Tetsuya Masuda, Taiki Motomura, Hisashi Naitow, Yoshinori Matsuura, Tetsunari Kimura, Kensuke Tono, Shigeki Owada, Yasumasa Joti, Rie Tanaka, Eriko Nango, Fusamichi Akita, Minoru Kubo, So Iwata, Jian-Ren Shen, Michihiro Suga

IUCrJ　8　(3)　431-443　2021/05/01
Publisher: International Union of Crystallography (IUCr)
DOI： 10.1107/s2052252521002177 　

eISSN： 2052-2525

More details Close

Photosystem II (PSII) catalyzes light-induced water oxidation through an S<italic> _i </italic>-state cycle, leading to the generation of di-oxygen, protons and electrons. Pump–probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S₁-to-S₂ transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S₂-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S₁-to-S₂ transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. International-journal Peer-reviewed

Kazumasa Oda, Takashi Nomura, Takanori Nakane, Keitaro Yamashita, Keiichi Inoue, Shota Ito, Johannes Vierock, Kunio Hirata, Andrés D Maturana, Kota Katayama, Tatsuya Ikuta, Itsuki Ishigami, Tamaki Izume, Rie Umeda, Ryuun Eguma, Satomi Oishi, Go Kasuya, Takafumi Kato, Tsukasa Kusakizako, Wataru Shihoya, Hiroto Shimada, Tomoyuki Takatsuji, Mizuki Takemoto, Reiya Taniguchi, Atsuhiro Tomita, Ryoki Nakamura, Masahiro Fukuda, Hirotake Miyauchi, Yongchan Lee, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Michihiro Sugahara, Tetsunari Kimura, Tatsuro Shimamura, Takaaki Fujiwara, Yasuaki Yamanaka, Shigeki Owada, Yasumasa Joti, Kensuke Tono, Ryuichiro Ishitani, Shigehiko Hayashi, Hideki Kandori, Peter Hegemann, So Iwata, Minoru Kubo, Tomohiro Nishizawa, Osamu Nureki

eLife　10　2021/03/23

DOI： 10.7554/eLife.62389 　

More details Close

Channelrhodopsins (ChRs) are microbial light-gated ion channels utilized in optogenetics to control neural activity with light . Light absorption causes retinal chromophore isomerization and subsequent protein conformational changes visualized as optically distinguished intermediates, coupled with channel opening and closing. However, the detailed molecular events underlying channel gating remain unknown. We performed time-resolved serial femtosecond crystallographic analyses of ChR by using an X-ray free electron laser, which revealed conformational changes following photoactivation. The isomerized retinal adopts a twisted conformation and shifts toward the putative internal proton donor residues, consequently inducing an outward shift of TM3, as well as a local deformation in TM7. These early conformational changes in the pore-forming helices should be the triggers that lead to opening of the ion conducting pore.
High-resolution crystal structures of transient intermediates in the phytochrome photocycle. International-journal Peer-reviewed

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

Structure (London, England : 1993)　2021/03/20

DOI： 10.1016/j.str.2021.03.004 　

More details Close

Phytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting Pr state and the light-activated Pfr state. Light signals are transduced as structural change through the entire protein to modulate its activity. It is unknown how the Pr-to-Pfr interconversion occurs, as the structure of intermediates remains notoriously elusive. Here, we present short-lived crystal structures of the photosensory core modules of the bacteriophytochrome from myxobacterium Stigmatella aurantiaca captured by an X-ray free electron laser 5 ns and 33 ms after light illumination of the Pr state. We observe large structural displacements of the covalently bound bilin chromophore, which trigger a bifurcated signaling pathway that extends through the entire protein. The snapshots show with atomic precision how the signal progresses from the chromophore, explaining how plants, bacteria, and fungi sense red light.
Structure of the dopamine D2 receptor in complex with the antipsychotic drug spiperone Peer-reviewed

Dohyun Im, Asuka Inoue, Takaaki Fujiwara, Takanori Nakane, Yasuaki Yamanaka, Tomoko Uemura, Chihiro Mori, Yuki Shiimura, Kanako Terakado Kimura, Hidetsugu Asada, Norimichi Nomura, Tomoyuki Tanaka, Ayumi Yamashita, Eriko Nango, Kensuke Tono, Francois Marie Ngako Kadji, Junken Aoki, So Iwata, Tatsuro Shimamura

Nature Communications　11　(1)　2020/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41467-020-20221-0 　

eISSN： 2041-1723

More details Close

<title>Abstract</title>In addition to the serotonin 5-HT_2A receptor (5-HT_2AR), the dopamine D₂ receptor (D₂R) is a key therapeutic target of antipsychotics for the treatment of schizophrenia. The inactive state structures of D₂R have been described in complex with the inverse agonists risperidone (D₂R_ris) and haloperidol (D₂R_hal). Here we describe the structure of human D₂R in complex with spiperone (D₂R_spi). In D₂R_spi, the conformation of the extracellular loop (ECL) 2, which composes the ligand-binding pocket, was substantially different from those in D₂R_ris and D₂R_hal, demonstrating that ECL2 in D₂R is highly dynamic. Moreover, D₂R_spi exhibited an extended binding pocket to accommodate spiperone’s phenyl ring, which probably contributes to the selectivity of spiperone to D₂R and 5-HT_2AR. Together with D₂R_ris and D₂R_hal, the structural information of D₂R_spi should be of value for designing novel antipsychotics with improved safety and efficacy.
Isoprenoid-chained lipid EROCOC17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography International-journal Peer-reviewed

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

Scientific Reports　10　(1)　19305-19305　2020/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-020-76277-x 　

eISSN： 2045-2322

More details Close

<title>Abstract</title> In meso crystallization of membrane proteins relies on the use of lipids capable of forming a lipidic cubic phase (LCP). However, almost all previous crystallization trials have used monoacylglycerols, with 1-(<italic>cis</italic>-9-octadecanoyl)-<italic>rac</italic>-glycerol (MO) being the most widely used lipid. We now report that EROCOC₁₇₊₄ mixed with 10% (w/w) cholesterol (Fig. 1) serves as a new matrix for crystallization and a crystal delivery medium in the serial femtosecond crystallography of Adenosine A_2A receptor (A_2AR). The structures of EROCOC₁₇₊₄-matrix grown A_2AR crystals were determined at 2.0 Å resolution by serial synchrotron rotation crystallography at a cryogenic temperature, and at 1.8 Å by LCP-serial femtosecond crystallography, using an X-ray free-electron laser at 4 and 20 °C sample temperatures, and are comparable to the structure of the MO-matrix grown A_2AR crystal (PDB ID: 4EIY). Moreover, X-ray scattering measurements indicated that the EROCOC₁₇₊₄/water system did not form the crystalline L_C phase at least down to − 20 °C, in marked contrast to the equilibrium MO/water system, which transforms into the crystalline L_C phase below about 17 °C. As the L_C phase formation within the LCP-matrix causes difficulties in protein crystallography experiments in meso, this feature of EROCOC₁₇₊₄ will expand the utility of the in meso method.
The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser International-journal Peer-reviewed

Elin Claesson, Weixiao Yuan Wahlgren, Heikki Takala, Suraj Pandey, Leticia Castillon, Valentyna Kuznetsova, Léocadie Henry, Matthijs Panman, Melissa Carrillo, Joachim Kübel, Rahul Nanekar, Linnéa Isaksson, Amke Nimmrich, Andrea Cellini, Dmitry Morozov, Michał Maj, Moona Kurttila, Robert Bosman, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, So Iwata, Shigeki Owada, Keith Moffat, Gerrit Groenhof, Emina A Stojković, Janne A Ihalainen, Marius Schmidt, Sebastian Westenhoff

eLife　9　2020/03/31
Publisher: eLife Sciences Publications, Ltd
DOI： 10.7554/elife.53514 　

eISSN： 2050-084X

More details Close

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.
A tool for visualizing protein motions in time-resolved crystallography Peer-reviewed

Cecilia Wickstrand, Gergely Katona, Takanori Nakane, Przemyslaw Nogly, Joerg Standfuss, Eriko Nango, Richard Neutze

Structural Dynamics　7　(2)　024701-024701　2020/03
Publisher: AIP Publishing
DOI： 10.1063/1.5126921 　

eISSN： 2329-7778
Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals Peer-reviewed

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

IUCrJ　7　(2)　306-323　2020/03/01
Publisher: International Union of Crystallography (IUCr)
DOI： 10.1107/s205225252000072x 　

eISSN： 2052-2525

More details Close

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.
Pump-Probe Time-Resolved Serial Femtosecond Crystallography at SACLA: Current Status and Data Collection Strategies Peer-reviewed

Eriko Nango, Minoru Kubo, Kensuke Tono, So Iwata

Applied Sciences　9　(24)　5505-5505　2019/12/14
Publisher: MDPI AG
DOI： 10.3390/app9245505 　

eISSN： 2076-3417

More details Close

Structural information on protein dynamics is a critical factor in fully understanding the protein functions. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) is a recently established technique for visualizing the structural changes or reactions in proteins that are at work with high spatial and temporal resolution. In the pump-probe method, protein microcrystals are continuously delivered from an injector and exposed to an X-ray free-electron laser (XFEL) pulse after a trigger to initiate a reaction, such as light, chemicals, temperature, and electric field, which affords the structural snapshots of intermediates that occur in the protein. We are in the process of developing the device and techniques for pump-probe TR-SFX while using XFEL produced at SPring-8 Angstrom Compact Free-Electron Laser (SACLA). In this paper, we described our current development details and data collection strategies for the optical pump X-ray probe TR-SFX experiment at SACLA and then reported the techniques of in crystallo TR spectroscopy, which is useful in clarifying the nature of reaction that takes place in crystals in advance.
Improvement of Production and Isolation of Human Neuraminidase-1 in Cellulo Crystals

Kotaro Koiwai, Jun Tsukimoto, Tetsuya Higashi, Fumitaka Mafuné, Ken Miyajima, Takanori Nakane, Naohiro Matsugaki, Ryuichi Kato, Serena Sirigu, Arjen Jakobi, Matthias Wilmanns, Michihiro Sugahara, Tomoyuki Tanaka, Kensuke Tono, Yasumasa Joti, Makina Yabashi, Osamu Nureki, Eiichi Mizohata, Toru Nakatsu, Eriko Nango, So Iwata, Leonard M. G. Chavas, Toshiya Senda, Kohji Itoh, Fumiaki Yumoto

ACS Applied Bio Materials　2　(11)　4941-4952　2019/11/18
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acsabm.9b00686 　

ISSN： 2576-6422

eISSN： 2576-6422
Toward G protein-coupled receptor structure-based drug design using X-ray lasers. International-journal Peer-reviewed

Ishchenko A, Stauch B, Han GW, Batyuk A, Shiriaeva A, Li C, Zatsepin N, Weierstall U, Liu W, Nango E, Nakane T, Tanaka R, Tono K, Joti Y, Iwata S, Moraes I, Gati C, Cherezov V

IUCrJ　6　(Pt 6)　1106-1119　2019/11

DOI： 10.1107/S2052252519013137 　

More details Close

Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.
Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation Peer-reviewed

Cecilia Wickstrand, Przemyslaw Nogly, Eriko Nango, So Iwata, Jörg Standfuss, Richard Neutze

Annual Review of Biochemistry　88　(1)　59-83　2019/06/20
Publisher: Annual Reviews
DOI： 10.1146/annurev-biochem-013118-111327 　

ISSN： 0066-4154

eISSN： 1545-4509

More details Close

Directional transport of protons across an energy transducing membrane—proton pumping—is ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all- trans retinal chromophore being photoisomerized to a 13- cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive.
Improving High Viscosity Extrusion of Microcrystals for Time-resolved Serial Femtosecond Crystallography at X-ray Lasers

Daniel James, Tobias Weinert, Petr Skopintsev, Antonia Furrer, Dardan Gashi, Tomoyuki Tanaka, Eriko Nango, Przemyslaw Nogly, Joerg Standfuss

Journal of Visualized Experiments　(144)　2019/02/28
Publisher: MyJove Corporation
DOI： 10.3791/59087 　

eISSN： 1940-087X
High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure Peer-reviewed

Shimazu Y, Tono K, Tanaka T, Yamanaka Y, Nakane T, Mori C, Terakado Kimura K, Fujiwara T, Sugahara M, Tanaka R, Doak RB, Shimamura T, Iwata S, Nango E, Yabashi M

J. Appl. Cryst.　52　(6)　1280-1288　2019
Publisher: International Union of Crystallography (IUCr)
DOI： 10.1107/S1600576719012846 　

eISSN： 1600-5767

More details Close

A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A_2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump–probe techniques.
High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures. International-journal Peer-reviewed

Sanchez JC, Carrillo M, Pandey S, Noda M, Aldama L, Feliz D, Claesson E, Wahlgren WY, Tracy G, Duong P, Nugent AC, Field A, Šrajer V, Kupitz C, Iwata S, Nango E, Tanaka R, Tanaka T, Fangjia L, Tono K, Owada S, Westenhoff S, Schmidt M, Stojković EA

Struct Dyn.　6　(5)　054701-054701　2019

DOI： 10.1063/1.5120527 　

More details Close

Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the mechanisms by which these natural photoswitches can control single cell development, although the role of BphPs in vivo remains largely unknown. BphPs are dimeric proteins that consist of a photosensory core module (PCM) and an enzymatic domain, often a histidine kinase. The PCM is composed of three domains (PAS, GAF, and PHY). It holds a covalently bound open-chain tetrapyrrole (biliverdin, BV) chromophore. Upon absorption of light, the double bond between BV rings C and D isomerizes and reversibly switches the protein between Pr and Pfr states. We report crystal structures of the wild-type and mutant (His275Thr) forms of the canonical BphP from the nonphotosynthetic myxobacterium Stigmatella aurantiaca (SaBphP2) in the Pr state. Structures were determined at 1.65 Å and 2.2 Å (respectively), the highest resolution of any PCM construct to date. We also report the room temperature wild-type structure of the same protein determined at 2.1 Å at the SPring-8 Angstrom Compact free electron LAser (SACLA), Japan. Our results not only highlight and confirm important amino acids near the chromophore that play a role in Pr-Pfr photoconversion but also describe the signal transduction into the PHY domain which moves across tens of angstroms after the light stimulus.
Time-resolved serial femtosecond crystallography studies at an X-ray free electron laser reveals structural changes in bacteriorhodopsin Peer-reviewed

Richard Neutze, Eriko Nango, Tomoyuki Tanaka, Takanori Nakane, So Iwata, Antoine Royant, Jörg St, fuss, Przemyslaw Nogly, Cecilia Wickstr

Biochimica et Biophysica Acta (BBA) - Bioenergetics　1859　2018/09
Publisher: Elsevier {BV}
DOI： 10.1016/j.bbabio.2018.09.087 　

ISSN： 0005-2728
Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome International-journal Peer-reviewed

Woitowich Nicole C, Halavaty Andrei S, Waltz Patricia, Kupitz Christopher, Valera Joseph, Tracy Gregory, Gallagher Kevin D, Claesson Elin, Nakane Takanori, Pandey Suraj, Nelson Garrett, Tanaka Rie, Nango Eriko, Mizohata Eiichi, Owada Shigeki, Tono Kensure, Joti Yasumasa, Nugent Angela C, Patel Hardik, Mapara Ayesha, Hopkins James, Duong Phu, Bizhga Dorina, Kovaleva Svetlana E, St Peter Rachael, Hernandez Cynthia N, Ozarowski Wesley B, Roy-Chowdhuri Shatabdi, Yang Jay-How, Edlund Petra, Takala Heikki, Ihalainen Janne, Brayshaw Jennifer, Norwood Tyler, Poudyal Ishwor, Fromme Petra, Spence John C. H, Moffat Keith, Westenhoff Sebastian, Schmidt Marius, Stojkovic Emina A

IUCRJ　5　(Pt 5)　619-634　2018/09

DOI： 10.1107/S2052252518010631 　

ISSN： 2052-2525
Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser Peer-reviewed

Nogly Przemyslaw, Weinert Tobias, James Daniel, Carbajo Sergio, Ozerov Dmitry, Furrer Antonia, Gashi Dardan, Borin Veniamin, Skopintsev Petr, Jaeger Kathrin, Nass Karol, Bath Petra, Bosman Robert, Koglin Jason, Seaberg Matthew, Lane Thomas, Kekilli Demet, Brunle 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, Standfuss Jorg

SCIENCE　361　(6398)　145-+　2018/07/13

DOI： 10.1126/science.aat0094 　

ISSN： 0036-8075
Three-dimensional Movie of Chemical Reactions in Proteins Captured by X-ray Free Electron Lasers Invited

Nango Eriko

JOURNAL OF SYNTHETIC ORGANIC CHEMISTRY JAPAN　76　(7)　734-739　2018/07

DOI： 10.5059/yukigoseikyokaishi.76.734 　

ISSN： 0037-9980

eISSN： 1883-6526
Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology Peer-reviewed

Eiichi Mizohata, Takanori Nakane, Yohta Fukuda, Eriko Nango, So Iwata

Biophysical Reviews　10　(2)　209-218　2018/04/01
Publisher: Springer Verlag
DOI： 10.1007/s12551-017-0344-9 　

ISSN： 1867-2469 1867-2450
Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA. International-journal Peer-reviewed

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

Structure (London, England : 1993)　26　(1)　7-19　2018/01/02

DOI： 10.1016/j.str.2017.11.005 　

ISSN： 0969-2126
XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction Peer-reviewed

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

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　114　(51)　13357-13362　2017/12

DOI： 10.1073/pnas.1705624114 　

ISSN： 0027-8424
Two-colour serial femtosecond crystallography dataset from gadoteridol-derivatized lysozyme for MAD phasing Peer-reviewed

Alexander Gorel, Koji Motomura, Hironobu Fukuzawa, R. Bruce Doak, Marie Luise Gruenbein, Mario Hilpert, Ichiro Inoue, Marco Kloos, Gabriela Nass Kovacs, Eriko Nango, Karol Nass, Christopher M. Roome, Robert L. Shoeman, Rie Tanaka, Kensuke Tono, Lutz Foucar, Yasumasa Joti, Makina Yabashi, So Iwata, Kiyoshi Ueda, Thomas R. M. Barends, Ilme Schlichting

SCIENTIFIC DATA　4　170188　2017/12

DOI： 10.1038/sdata.2017.188 　

ISSN： 2052-4463
A large-scale expression strategy for multimeric extracellular protein complexes using Drosophila S2 cells and its application to the recombinant expression of heterodimeric ligand-binding domains of taste receptor Peer-reviewed

Atsuko Yamashita, Eriko Nango, Yuji Ashikawa

PROTEIN SCIENCE　26　(11)　2291-2301　2017/11

DOI： 10.1002/pro.3271 　

ISSN： 0961-8368

eISSN： 1469-896X
Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate Peer-reviewed

Takehiko Tosha, Takashi Nomura, Takuma Nishida, Naoya Saeki, Kouta Okubayashi, Raika Yamagiwa, Michihiro Sugahara, Takanori Nakane, Keitaro Yamashita, Kunio Hirata, Go Ueno, Tetsunari Kimura, Tamao Hisano, Kazumasa Muramoto, Hitomi Sawai, Hanae Takeda, Eiichi Mizohata, Ayumi Yamashita, Yusuke Kanematsu, Yu Takano, Eriko Nango, Rie Tanaka, Osamu Nureki, Osami Shoji, Yuka Ikemoto, Hironori Murakami, Shigeki Owada, Kensuke Tono, Makina Yabashi, Masaki Yamamoto, Hideo Ago, So Iwata, Hiroshi Sugimoto, Yoshitsugu Shiro, Minoru Kubo

NATURE COMMUNICATIONS　8　2017/11

DOI： 10.1038/s41467-017-01702-1 　

ISSN： 2041-1723
Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability Peer-reviewed

Alexander Gorel, Koji Motomura, Hironobu Fukuzawa, R. Bruce Doak, Marie Luise Gruenbein, Mario Hilpert, Ichiro Inoue, Marco Kloos, Gabriela Kovacsova, Eriko Nango, Karol Nass, Christopher M. Roome, Robert L. Shoeman, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Makina Yabashi, So Iwata, Lutz Foucar, Kiyoshi Ueda, Thomas R. M. Barends, Ilme Schlichting

NATURE COMMUNICATIONS　8　2017/10

DOI： 10.1038/s41467-017-00754-7 　

ISSN： 2041-1723
Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography Peer-reviewed

Keitaro Yamashita, Naoyuki Kuwabara, Takanori Nakane, Tomohiro Murai, Eiichi Mizohata, Michihiro Sugahara, Dongqing Pan, Tetsuya Masuda, Mamoru Suzuki, Tomomi Sato, Atsushi Kodan, Tomohiro Yamaguchi, Eriko Nango, Tomoyuki Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Hiroshi Manya, Tamao Endo, Ryuichi Kato, Toshiya Senda, Hiroaki Kato, So Iwata, Hideo Ago, Masaki Yamamoto, Fumiaki Yumoto, Toru Nakatsu

IUCRJ　4　639-647　2017/09

DOI： 10.1107/S2052252517008557 　

ISSN： 2052-2525
Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA Peer-reviewed

Minoru Kubo, Eriko Nango, Kensuke Tono, Tetsunari Kimura, Shigeki Owada, Changyong Song, Fumitaka Mafune, Ken Miyajima, Yoshihiro Takeda, Jun-ya Kohno, Naoya Miyauchi, Takanori Nakane, Tomoyuki Tanaka, Takashi Nomura, Jan Davidsson, Rie Tanaka, Michio Murata, Takashi Kameshima, Takaki Hatsui, Yasumasa Joti, Richard Neutze, Makina Yabashi, So Iwata

JOURNAL OF SYNCHROTRON RADIATION　24　1086-1091　2017/09

DOI： 10.1107/S160057751701030X 　

ISSN： 1600-5775
Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation Peer-reviewed

Hisashi Naitow, Yoshinori Matsuura, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Rie Tanaka, Tomoyuki Tanaka, Michihiro Sugahara, Jun Kobayashi, Eriko Nango, So Iwata, Naoki Kunishima

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY　73　702-709　2017/08

DOI： 10.1107/S2059798317008919 　

ISSN： 2059-7983
Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature Peer-reviewed

Rebecka Andersson, Cecilia Safari, Robert Dods, Eriko Nango, Rie Tanaka, Ayumi Yamashita, Takanori Nakane, Kensuke Tono, Yasumasa Joti, Petra Bath, Elin Dunevall, Robert Bosman, Osamu Nureki, So Iwata, Richard Neutze, Gisela Branden

SCIENTIFIC REPORTS　7　2017/07

DOI： 10.1038/s41598-017-04817-z 　

ISSN： 2045-2322
Structural basis for perception of diverse chemical substances by T1r taste receptors Peer-reviewed

Nipawan Nuemket, Norihisa Yasui, Yuko Kusakabe, Yukiyo Nomura, Nanako Atsumi, Shuji Akiyama, Eriko Nango, Yukinari Kato, Mika K. Kaneko, Junichi Takagi, Maiko Hosotani, Atsuko Yamashita

NATURE COMMUNICATIONS　8　2017/05

DOI： 10.1038/ncomms15530 　

ISSN： 2041-1723
Hydroxyethyl cellulose matrix applied to serial crystallography Peer-reviewed

Michihiro Sugahara, Takanori Nakane, Tetsuya Masuda, Mamoru Suzuki, Shigeyuki Inoue, Changyong Song, Rie Tanaka, Toru Nakatsu, Eiichi Mizohata, Fumiaki Yumoto, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Keiji Numata, Eriko Nango, So Iwata

SCIENTIFIC REPORTS　7　2017/04

DOI： 10.1038/s41598-017-00761-0 　

ISSN： 2045-2322
Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL Peer-reviewed

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

NATURE　543　(7643)　131-+　2017/03

DOI： 10.1038/nature21400 　

ISSN： 0028-0836

eISSN： 1476-4687
Atomic resolution structure of serine protease proteinase K at ambient temperature Peer-reviewed

Tetsuya Masuda, Mamoru Suzuki, Shigeyuki Inoue, Changyong Song, Takanori Nakane, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Bunzo Mikami, Osamu Nureki, Keiji Numata, So Iwata, Michihiro Sugahara

SCIENTIFIC REPORTS　7　2017/03

DOI： 10.1038/srep45604 　

ISSN： 2045-2322
Serial Femtosecond Crystallography at SACLA: Current Situation and Future Prospects

Eriko NANGO, Takanori NAKANE, So IWATA

Nihon Kessho Gakkaishi　59　(1)　12-17　2017
Publisher: The Crystallographic Society of Japan
DOI： 10.5940/jcrsj.59.12 　

ISSN： 0369-4585 1884-5576

eISSN： 1884-5576

More details Close

Intense, femtosecond X-ray pulses from X-ray free electron laser （XFEL） have enabled acquisition of diffraction patterns from protein microcrystals before the onset of radiation damage. Although a single-shot exposure of XFEL destroys a crystal, diffraction by XFEL terminates before movements of atoms become significant. Thus, XFEL allows determination of damage free structures at room temperature. In serial femtosecond crystallography, fresh microcrystals are continuously delivered by an injector to the XFEL interaction zone. When combined with an excitation laser in a pump-probe setting, this technique is of great utility for time-resolved experiments in measuring ultra-fast reactions in proteins. We will describe current situation of SFX experiments at SACLA and future prospects.
A three-dimensional movie of structural changes in bacteriorhodopsin Peer-reviewed

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

SCIENCE　354　(6319)　1552-1557　2016/12

DOI： 10.1126/science.aah3497 　

ISSN： 0036-8075

eISSN： 1095-9203
Taste substance binding to the ligand-binding domains of T1r taste receptor heterodimer Peer-reviewed

Atsuko Yamashita, Eriko Nango, Shuji Akiyama, Saori Maki-Yonekura, Yuji Ashikawa, Yuko Kusakabe, Elena Krayukhina, Takahiro Maruno, Susumu Uchiyama, Nipawan Nuemket, Koji Yonekura, Madoka Shimizu, Nanako Atsumi, Norihisa Yasui, Takaaki Hikima, Masaki Yamamoto, Yuji Kobayashi

CHEMICAL SENSES　41　(9)　E176-E177　2016/11

ISSN： 0379-864X

eISSN： 1464-3553
Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent Peer-reviewed

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

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　113　(46)　13039-13044　2016/11

DOI： 10.1073/pnas.1602531113 　

ISSN： 0027-8424
The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography Peer-reviewed

Petra Edlund, Heikki Takala, Elin Claesson, Leocadie Henry, Robert Dods, Heli Lehtivuori, Matthijs Panman, Kanupriya Pande, Thomas White, Takanori Nakane, Oskar Berntsson, Emil Gustavsson, Petra Bath, Vaibhav Modi, Shatabdi Roy-Chowdhury, James Zook, Peter Berntsen, Suraj Pandey, Ishwor Poudyal, Jason Tenboer, Christopher Kupitz, Anton Barty, Petra Fromme, Jake D. Koralek, Tomoyuki Tanaka, John Spence, Mengning Liang, Mark S. Hunter, Sebastien Boutet, Eriko Nango, Keith Moffat, Gerrit Groenhof, Janne Ihalainen, Emina A. Stojkovic, Marius Schmidt, Sebastian Westenhoff

SCIENTIFIC REPORTS　6　2016/10

DOI： 10.1038/srep35279 　

ISSN： 2045-2322
Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography Peer-reviewed

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

NATURE COMMUNICATIONS　7　2016/08

DOI： 10.1038/ncomms12314 　

ISSN： 2041-1723
Data processing pipeline for serial femtosecond crystallography at SACLA. International-journal

Takanori Nakane, Yasumasa Joti, Kensuke Tono, Makina Yabashi, Eriko Nango, So Iwata, Ryuichiro Ishitani, Osamu Nureki

Journal of applied crystallography　49　(Pt 3)　1035-1041　2016/06/01

ISSN： 0021-8898

More details Close

A data processing pipeline for serial femtosecond crystallography at SACLA was developed, based on Cheetah [Barty et al. (2014). J. Appl. Cryst.47, 1118-1131] and CrystFEL [White et al. (2016). J. Appl. Cryst.49, 680-689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runs CrystFEL for indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime.
Data processing pipeline for serial femtosecond crystallography at SACLA Peer-reviewed

Takanori Nakane, Yasumasa Joti, Kensuke Tono, Makina Yabashi, Eriko Nango, So Iwata, Ryuichiro Ishitani, Osamu Nureki

JOURNAL OF APPLIED CRYSTALLOGRAPHY　49　1035-1041　2016/06

DOI： 10.1107/S1600576716005720 　

ISSN： 1600-5767
Taste substance binding elicits conformational change of taste receptor T1r heterodimer extracellular domains Peer-reviewed

Eriko Nango, Shuji Akiyama, Saori Maki-Yonekura, Yuji Ashikawa, Yuko Kusakabe, Elena Krayukhina, Takahiro Maruno, Susumu Uchiyama, Nipawan Nuemket, Koji Yonekura, Madoka Shimizu, Nanako Atsumi, Norihisa Yasui, Takaaki Hikima, Masaki Yamamoto, Yuji Kobayashi, Atsuko Yamashita

SCIENTIFIC REPORTS　6　2016/05

DOI： 10.1038/srep25745 　

ISSN： 2045-2322
Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography Peer-reviewed

Yohta Fukuda, Ka Man Tse, Mamoru Suzuki, Kay Diederichs, Kunio Hirata, Takanori Nakane, Michihiro Sugahara, Eriko Nango, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Changyong Song, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Hiroyoshi Matsumura, Tsuyoshi Inoue, So Iwata, Eiichi Mizohata

JOURNAL OF BIOCHEMISTRY　159　(5)　527-538　2016/05

DOI： 10.1093/jb/mvv133 　

ISSN： 0021-924X

eISSN： 1756-2651
Microcrystal delivery by pulsed liquid droplet for serial femtosecond crystallography Peer-reviewed

Fumitaka Mafune, Ken Miyajima, Kensuke Tono, Yoshihiro Takeda, Jun-ya Kohno, Naoya Miyauchi, Jun Kobayashi, Yasumasa Joti, Eriko Nango, So Iwata, Makina Yabashi

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY　72　520-523　2016/04

DOI： 10.1107/S2059798316001480 　

ISSN： 2059-7983
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography (vol 113, pg 2928, 2016) Peer-reviewed

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

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　113　(15)　E2207-E2207　2016/04

DOI： 10.1073/pnas.1604061113 　

ISSN： 0027-8424
Oil-free hyaluronic acid matrix for serial femtosecond crystallography Peer-reviewed

Michihiro Sugahara, Changyong Song, Mamoru Suzuki, Tetsuya Masuda, Shigeyuki Inoue, Takanori Nakane, Fumiaki Yumoto, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Keiji Numata, So Iwata

SCIENTIFIC REPORTS　6　2016/04

DOI： 10.1038/srep24484 　

ISSN： 2045-2322
Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP Peer-reviewed

Jacques-Philippe Colletier, Michel Sliwa, Francois-Xavier Gallat, Michihiro Sugahara, Virginia Guillon, Giorgio Schiro, Nicolas Coquelle, Joyce Woodhouse, Laure Roux, Guillaume Gotthard, Antoine Royant, Lucas Martinez Uriarte, Cyril Ruckebusch, Yasumasa Joti, Martin Byrdin, Eiichi Mizohata, Eriko Nango, Tomoyuki Tanaka, Kensuke Tono, Makina Yabashi, Virgile Adam, Marco Cammarata, Ilme Schlichting, Dominique Bourgeois, Martin Weik

JOURNAL OF PHYSICAL CHEMISTRY LETTERS　7　(5)　882-887　2016/03

DOI： 10.1021/acs.jpclett.5b02789 　

ISSN： 1948-7185
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography Peer-reviewed

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

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　113　(11)　2928-2933　2016/03

DOI： 10.1073/pnas.1517770113 　

ISSN： 0027-8424
5B35: Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA Peer-reviewed

Nakane T, Hanashima S, Suzuki M, Saiki H, Hayashi T, Kakinouchi K, Sugiyama S, Kawatake S, Matsuoka S, Matsumori N, Nango E, Kobayashi J, Shimamura T, Kimura K, Mori C, Kunishima N, Sugahara M, Takakyu Y, Inoue S, Masuda T, Hosaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Inoue T, Nureki O, Iwata S, Murata M, Mizohata E

Worldwide Protein Data Bank　2016

DOI： 10.2210/pdb5b35/pdb 　
4YSD: Room temperature structure of copper nitrite reductase from Geobacillus thermodenitrificans Peer-reviewed

Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E

Worldwide Protein Data Bank　2016

DOI： 10.2210/pdb4ysd/pdb 　
4YSA: Completely oxidized structure of copper nitrite reductase from Geobacillus thermodenitrificans Peer-reviewed

Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E

Worldwide Protein Data Bank　2016

DOI： 10.2210/pdb4ysa/pdb 　
5D4I: Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography Peer-reviewed

Fukuda Y, Tse KM, Nakane T, Nakatsu T, Suzuki M, Sugahara M, Inoue S, Masuda T, Yumoto F, Matsugaki N, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Murphy MEP, Inoue T, Iwata S, Mizohata E

Worldwide Protein Data Bank　2016

DOI： 10.2210/pdb5d4i/pdb 　
Native sulfur/chlorine SAD phasing for serial femtosecond crystallography Peer-reviewed

Takanori Nakane, Changyong Song, Mamoru Suzuki, Eriko Nango, Jun Kobayashi, Tetsuya Masuda, Shigeyuki Inoue, Eiichi Mizohata, Toru Nakatsu, Tomoyuki Tanaka, Rie Tanaka, Tatsuro Shimamura, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, So Iwata, Michihiro Sugahara

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　71　2519-2525　2015/12

DOI： 10.1107/S139900471501857X 　

ISSN： 1399-0047
An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography Peer-reviewed

Keitaro Yamashita, Dongqing Pan, Tomohiko Okuda, Michihiro Sugahara, Atsushi Kodan, Tomohiro Yamaguchi, Tomohiro Murai, Keiko Gomi, Naoki Kajiyama, Eiichi Mizohata, Mamoru Suzuki, Eriko Nango, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Jaehyun Park, Changyong Song, Takaki Hatsui, Makina Yabashi, So Iwata, Hiroaki Kato, Hideo Ago, Masaki Yamamoto, Toru Nakatsu

SCIENTIFIC REPORTS　5　2015/09

DOI： 10.1038/srep14017 　

ISSN： 2045-2322
Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laser Peer-reviewed

Kensuke Tono, Eriko Nango, Michihiro Sugahara, Changyong Song, Jaehyun Park, Tomoyuki Tanaka, Rie Tanaka, Yasumasa Joti, Takashi Kameshima, Shun Ono, Takaki Hatsui, Eiichi Mizohata, Mamoru Suzuki, Tatsuro Shimamura, Yoshiki Tanaka, So Iwata, Makina Yabashi

JOURNAL OF SYNCHROTRON RADIATION　22　532-537　2015/05

DOI： 10.1107/S1600577515004464 　

ISSN： 1600-5775
Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data) Peer-reviewed

Yamashita K, Pan D, Okuda T, Sugahara M, Kodan A, Yamaguchi T, Murai T, Gomi K, Kajiyama N, Mizohata E, Suzuki M, Nango E, Tono K, Joti Y, Kameshima T, Park J, Song C, Hatsui T, Yabashi M, Iwata S, Kato H, Ago H, Yamamoto M, Nakatsu T

Worldwide Protein Data Bank　2015

DOI： 10.2210/pdb5d9c/pdb 　
Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature Peer-reviewed

Yamashita K, Pan D, Okuda T, Sugahara M, Kodan A, Yamaguchi T, Murai T, Gomi K, Kajiyama N, Mizohata E, Suzuki M, Nango E, Tono K, Joti Y, Kameshima T, Park J, Song C, Hatsui T, Yabashi M, Iwata S, Kato H, Ago H, Yamamoto M, Nakatsu T

Worldwide Protein Data Bank　2015

DOI： 10.2210/pdb5d9d/pdb 　
4YOP: CRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME Peer-reviewed

Nakane T, Song C, Suzuki M, Nango E, Kobayashi J, Masuda T, Inoue S, Mizohata E, Nakatsu T, Tanaka T, Tanaka R, Shimamura T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Nureki O, Iwata S, Sugahara M

Worldwide Protein Data Bank　2015

DOI： 10.2210/pdb4yop/pdb 　
Grease matrix as a versatile carrier of proteins for serial crystallography Peer-reviewed

Michihiro Sugahara, Eiichi Mizohata, Eriko Nango, Mamoru Suzuki, Tomoyuki Tanaka, Tetsuya Masudala, Rie Tanaka, Tatsuro Shimamura, Yoshiki Tanaka, Chiyo Suno, Kentaro Ihara, Dongqing Pan, Keisuke Kakinouchi, Shigeru Sugiyama, Michio Murata, Tsuyoshi Inoue, Kensuke Tono, Changyong Song, Jaehyun Park, Takashi Kameshima, Takaki Hatsui, Yasumasa Joti, Makina Yabashi, So Iwata

NATURE METHODS　12　(1)　61-63　2015/01

DOI： 10.1038/NMETH.3172 　

ISSN： 1548-7091

eISSN： 1548-7105
Protein structure analyses using X-ray free-electron lasers Invited Peer-reviewed

Eiichi MIZOHATA, Eriko NANGO, Michihiro SUGAHARA, Mamoru SUZUKI, So IWATA

日本結晶学会誌　56　(4)　241-246　2014/08
Publisher: The Crystallographic Society of Japan
DOI： 10.5940/jcrsj.56.241 　

ISSN： 0369-4585

eISSN： 1884-5576

More details Close

X-ray free-electron laser (XFEL) source produces X-ray pulses more than a billion times brighter than the most powerful synchrotron source. The extremely intense X-ray pulses emerging from XFEL source, along with the appearance of serial femtosecond X-ray crystallography (SFX) technique enabled us to reveal radiation damage-free protein structures from nano-/micro-crystals. Current state of protein structure analyses using XFEL is described.
In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology? Peer-reviewed

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

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES　369　(1647)　2014/07

DOI： 10.1098/rstb.2013.0497 　

ISSN： 0962-8436

eISSN： 1471-2970
Thaumatin structure determined by SPring-8 Angstrom Compact free electron Laser (SACLA) Peer-reviewed

Masuda T, Nango E, Sugahara M, Mizohata E, Tanaka T, Tanaka R, Suzuki M, Mikami B, Iwata S

Worldwide Protein Data Bank　2014

DOI： 10.2210/pdb3wxs/pdb 　
Serial femtosecond X-ray structure of human fatty acid-binding protein type-3 (FABP3) in complex with stearic acid (C18:0) determined using X-ray free-electron laser at SACLA Peer-reviewed

Mizohata E, Suzuki M, Kakinouchi K, Sugiyama S, Murata M, Sugahara M, Nango E, Tanaka T, Tanaka R, Tono K, Song C, Hatsui T, Joti Y, Yabashi M, Iwata S

Worldwide Protein Data Bank　2014

DOI： 10.2210/pdb3wxq/pdb 　
創薬ターゲット蛋白質のXFELによる迅速構造解析法の開発

南後恵理子

日本結晶学会誌　56　(Supplement)　s18-s18　2014
Publisher: The Crystallographic Society of Japan
DOI： 10.5940/jcrsj.56.s18 　

ISSN： 0369-4585

eISSN： 1884-5576
SACLAを利用したXFEL微結晶構造解析

溝端栄一, 鈴木守, 南後恵理子, 森田能次, 垣之内啓介, 田中里枝, 登野健介, 城地保昌, 亀島敬, Jaehyun Park, Changyong Song, 初井宇記, 矢橋牧名, Thomas A White, 北郷悠, 大洞光司, 石田英子, 廣瀬未果, 杉山成, 村田道雄, 林高史, 高木淳一, 井上豪, 岩田想

日本結晶学会年会講演要旨集　2013　2013/10
Structure of Thermus thermophilus homoisocitrate dehydrogenase in complex with a designed inhibitor Peer-reviewed

Eriko Nango, Takashi Yamamoto, Takashi Kumasaka, Tadashi Eguchi

JOURNAL OF BIOCHEMISTRY　150　(6)　607-614　2011/12

DOI： 10.1093/jb/mvr097 　

ISSN： 0021-924X

eISSN： 1756-2651
Crystallization and preliminary X-ray analysis of isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii Peer-reviewed

Takeshi Hoshino, Eriko Nango, Seiki Baba, Tadashi Eguchi, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　67　101-103　2011/01

DOI： 10.1107/S1744309110046944 　

ISSN： 1744-3091
Roles of a 20 kDa Protein Associated with a Carbocycle-Forming Enzyme Involved in Aminoglycoside Biosynthesis in Primary and Secondary Metabolism

Hideyuki Tamegai, Hiroshi Sawada, Eriko Nango, Rie Aoki, Haruka Hirakawa, Teruhiko Iino, Tadashi Eguchi

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　74　(6)　1215-1219　2010/06

DOI： 10.1271/bbb.90961 　

ISSN： 0916-8451

eISSN： 1347-6947
Crystal structure of 3-isopropylmalate dehydrogenase in complex with NAD(+) and a designed inhibitor

Eriko Nango, Takashi Yamamoto, Takashi Kumasaka, Tadashi Eguchi

BIOORGANIC & MEDICINAL CHEMISTRY　17　(22)　7789-7794　2009/11

DOI： 10.1016/j.bmc.2009.09.025 　

ISSN： 0968-0896
Crystallization and preliminary X-ray analysis of vicenisaminyltransferase VinC

Eriko Nango, Atsushi Minami, Takashi Kumasaka, Tadashi Eguchi

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　64　(6)　558-560　2008/06

DOI： 10.1107/S1744309108014681 　

ISSN： 1744-3091
Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD(+)

Eriko Nango, Takashi Kumasaka, Toshifumi Hirayama, Nobuo Tanaka, Tadashi Eguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　70　(2)　517-527　2008/02

DOI： 10.1002/prot.21526 　

ISSN： 0887-3585
糖質環化酵素の構造と機能の解明バイオマスから化学工業資源へ Invited

南後恵理子, 江口正

バイオサイエンスとインダストリー　66　(2)　61-64　2008
Publisher: 東京 : バイオインダストリー協会
ISSN： 0914-8981
Crystallization and X-ray analysis of 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics

E Nango, T Kumasaka, T Sato, N Tanaka, KA Katsumi, T Eguchi

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　61　(7)　709-711　2005/07

DOI： 10.1107/S1744309105018841 　

ISSN： 1744-3091
Active site mapping of 2-deoxy-scyllo-inosose synthase, the key starter enzyme for the biosynthesis of 2-deoxystreptamine. Mechanism-based inhibition and identification of lysine-141 as the entrapped nucleophile

E Nango, T Eguchi, K Kakinuma

JOURNAL OF ORGANIC CHEMISTRY　69　(3)　593-600　2004/02

DOI： 10.1021/jo034706y 　

ISSN： 0022-3263
Reaction stereochemistry of 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine

E Nango, F Kudo, T Eguchi, K Kakinuma

CHEMISTRY LETTERS　32　(5)　438-439　2003/05

DOI： 10.1246/cl.2003.438 　

ISSN： 0366-7022

eISSN： 1348-0715
Identification of L-glutamine: 2-deoxy-scyllo-inosose aminotransferase required for the biosynthesis of butirosin in Bacillus circulans Peer-reviewed

H Tamegai, E Nango, M Kuwahara, H Yamamoto, Y Ota, H Kuriki, T Eguchi, K Kakinuma

JOURNAL OF ANTIBIOTICS　55　(8)　707-714　2002/08

DOI： 10.7164/antibiotics.55.707 　

ISSN： 0021-8820
Significance of the 20-kDa subunit of heterodimeric 2-deoxy-scyllo-inosose synthase for the biosynthesis of butirosin antibiotics in Bacillus circulans Peer-reviewed

H Tamegai, E Nango, A Koike-Takeshita, F Kudo, K Kakinuma

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　66　(7)　1538-1545　2002/07

DOI： 10.1271/bbb.66.1538 　

ISSN： 0916-8451

eISSN： 1347-6947
An expeditious chemo-enzymatic route from glucose to catechol by the use of 2-deoxy-scyllo-inosose synthase Peer-reviewed

K Kakinuma, E Nango, F Kudo, Y Matsushima, T Eguchi

TETRAHEDRON LETTERS　41　(12)　1935-1938　2000/03

DOI： 10.1016/S0040-4039(00)00064-2 　

ISSN： 0040-4039

Show all ︎Show first 5

Misc. 77

Interview 動くタンパク質を動画で観る : X線自由電子レーザーが捉える化学反応

南後恵理子

現代化学 = Chemistry today　(642)　22-27　2024/09
Publisher: 東京 : 東京化学同人
ISSN： 0386-961X
特集高速分子動画:動的構造からタンパク質分子制御へ Ⅰ.高速分子動画装置の開発時分割実験のための多様な反応誘起システムの開発

南後恵理子

生体の科学　75　(3)　197-201　2024/06/15
Publisher: 株式会社医学書院
DOI： 10.11477/mf.2425201852 　

ISSN： 0370-9531

eISSN： 1883-5503
3 GeV高輝度放射光施設NanoTerasuが拓く創薬研究

山田悠介, 山本雅貴, 南後恵理子

ファルマシア　60　(8)　753-757　2024
Publisher: 公益社団法人日本薬学会
DOI： 10.14894/faruawpsj.60.8_753 　

ISSN： 0014-8601

eISSN： 2189-7026

More details Close

NanoTerasuは東北大学の青葉山キャンパス内に設立された3 GeV高輝度放射光施設であり、2024年から運用を開始した。筆者らは現在、NanoTerasuにおいてタンパク質結晶構造解析用の実験ステーションの整備に取り組んでいる。本稿では、NanoTerasuの概要から医学・薬学分野で期待される様々な実験手法について紹介する。
X線自由電子レーザーで捉えたビフィズス菌酵素の常温構造—特集多様化するバイオテクノロジーと光技術

中田國夫, 柏木立己, 南後恵理子, 岩田想

光アライアンス / 光アライアンス編集委員会編　34　(10)　1-4　2023/10
Publisher: 東京 : 日本工業出版
ISSN： 0917-026X
室温構造解析・時分割構造解析に向けたSPring-8構造生物学ビームラインの高度化

矢野直峰, 馬場清喜, 奥村英夫, 河村高志, 村上博則, 増永拓也, NIPAWAN Nuemket, NIPAWAN Nuemket, KANG Jungmin, 保坂俊彰, 長谷川和也, 山本雅貴, 南後恵理子, 熊坂崇

日本結晶学会年会講演要旨集　2023　2023
変容

南後恵理子

生物物理　63　(3)　133-133　2023
Publisher: 一般社団法人日本生物物理学会
DOI： 10.2142/biophys.63.133 　

ISSN： 0582-4052

eISSN： 1347-4219
X線自由電子レーザーによるタンパク質分子動画解析—Molecular movie analysis of proteins by X-ray free electron lasers—光・量子デバイス研究会・量子ビームによるナノ構造・界面形成とバイオメディカル応用

南後恵理子

電気学会研究会資料. OQD = The papers of technical meeting on optical and quantum devices, IEE Japan / 光・量子デバイス研究会 [編]　2022　(45-51)　23-26　2022/12/27
Publisher: 東京 : 電気学会
Molecular Movies using X-ray Free Electron Lasers: Recent Advances and Future Prospects

NANGO Eriko, FUJIWARA Takaaki, FANGJIA Luo, IWATA So

Nihon Kessho Gakkaishi　64　(4)　290-293　2022/12/15
Publisher: The Crystallographic Society of Japan
DOI： 10.5940/jcrsj.64.290 　

ISSN： 0369-4585

eISSN： 1884-5576

More details Close

Conventional X-ray protein crystallography captures only “static” structures due to the limitation of temporal resolution. Recently, X-ray free electron lasers（XFEL）enabled to capture dynamic structures at the atomic level with time resolutions of several tenth femtoseconds. We have been working on the development of serial femtosecond crystallography（SFX）, which is a protein structure determination technique, at SACLA and successfully obtained “molecular movies” of various proteins by combining an X-ray free electron laser with a reaction trigger. This technique is suitable for tracking fast reactions such as chemical reactions because of its high temporal resolution. We will describe current advances and future prospects of molecular movies using XFEL.
X線自由電子レーザーを用いたタンパク質分子動画解析—Protein Molecular Movie Analysis Using X-Ray Free Electron Lasers—光による化学反応の観測および制御の進展

南後恵理子

光学 = Japanese journal of optics : publication of the Optical Society of Japan　51　(1)　2-7　2022/01
Publisher: 東京 : 日本光学会
ISSN： 0389-6625
New Technologies that Propel Biophysics

ANDO Toshio, ITO Yutaka, SUGITA Yuji, NANGO Eriko, YASUNAGA Takuo, OKADA Yasushi, KANDA Genki N.

Seibutsu Butsuri　61　(2)　111-118　2021
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.61.111 　

ISSN： 0582-4052

eISSN： 1347-4219
二液混合シリアルフェムト秒結晶構造解析による酵素反応追跡

南後恵理子, 南後恵理子, LUO Fangjia, LUO Fangjia, 木村哲就, 菅原道泰, 中根崇智, 鈴木守, 桝田哲哉, 溝端栄一, 登野健介, 登野健介, 岩田想, 岩田想

日本結晶学会年会講演要旨集　2021　2021
受容体タンパク質を用いた味覚感知初反応の解析と応用

山下敦子, 芦川雄二, 南後恵理子, 安井典久

バイオサイエンスとインダストリー　79　(2)　86-89　2021
Publisher: 東京 : バイオインダストリー協会
ISSN： 0914-8981
The Ca²⁺-binding photoprotein aequorin stabilizes a peroxidized state

船橋俊也, 南後恵理子, 南後恵理子, 岩田想, 岩田想, 加藤博章, 加藤博章, 中津亨, 中津亨

日本薬学会年会要旨集(Web)　141st　2021

ISSN： 0918-9823
タンパク質の分子動画はどのようにして得られるのか

南後恵理子

アンサンブル　23　(3)　156-160　2021
Publisher: 分子シミュレーション学会
DOI： 10.11436/mssj.23.156 　

ISSN： 1884-6750

eISSN： 1884-5088

More details Close

<tt>最近利用が可能となった</tt>X <tt>線自由電子レーザーは，高輝度フェムト秒パルスの特性を有し，素早く変化するタンパク質の構造を高い空間・時間分解能で捉えることが期待されている．本稿では，</tt>X <tt>線自由電子レーザーを用いたタンパク質結晶構造解析であるシリアルフェムト秒結晶構造解析について取り上げ，分子動画としてどのように構造変化を捉えているのか実験方法を中心に紹介する</tt><tt>． </tt>
X線自由電子レーザーによる分子動画解析

南後恵理子, 南後恵理子, 岩田想, 岩田想

生体分子科学討論会講演要旨集　47th　2021
微小結晶を利用したRas caged-GTP時分割測定の試み

河村高志, 槇野義輝, 長谷川和也, 中根崇智, 馬場清喜, 南後恵理子, 南後恵理子, 田中里枝, 田中里枝, 岩田想, 岩田想, 島扶美, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム(Web)　33rd　2020
X線自由電子レーザーを用いたタンパク質分子動画解析

南後恵理子

東北大学多元物質科学研究所研究発表会講演予稿集　20th　2020
高速分子動画:タンパク質が機能する際の構造変化を可視化する

南後恵理子

日本分子生物学会年会プログラム・要旨集(Web)　43rd　2020
SACLA,SPring-8並びにNMRを用いた低分子量Gタンパク質RasのGTP加水分解過程における動的構造解析

佐伯茉帆, 槇野義輝, 松本篤幸, 河村高志, 南後恵理子, 熊坂崇, 島扶美

日本分子生物学会年会プログラム・要旨集(Web)　43rd　2020
X線自由電子レーザーによるチャネルロドプシンの時分割構造解析

小田和正, 野村高志, 野村高志, 中根崇智, 中根崇智, 西澤知宏, 久保稔, 久保稔, 南後恵理子, 南後恵理子, 島村達郎, 石神一貴, 生田達也, 井爪珠希, 江熊龍雲, 岩田想, 岩田想, 濡木理

日本細胞生物学会大会(Web)　71st　2019
X線自由電子レーザーによるチャネルロドプシンの時分割構造解析

小田和正, 野村高志, 野村高志, 中根崇智, 西澤知宏, 久保稔, 久保稔, 南後恵理子, 南後恵理子, 島村達郎, 岩田想, 濡木理

日本結晶学会年会講演要旨集　2019　2019
Time Resolved Crystallography Using X-ray Free Electron Laser on Photoreactive Membrane Proteins

IWATA So, NANGO Eriko

Seibutsu Butsuri　58　(1)　017-021　2018
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.58.017 　 10.2142/biophys.59.205_references_DOI_4EXMEzZXNnD2QvtkJST7yCsvUHq 　

ISSN： 0582-4052

eISSN： 1347-4219

More details Close

At SACLA, we are developing a data collection system focusing on dynamic crystallography putting a particular effort on membrane proteins. An experimental system for pump-probe experiments based on serial femtosecond crystallography using a viscous material injector has been developed. We used time-resolved serial femtosecond crystallography to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. The cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons. We have also applied this system to study the light-induced structural changes and the site of O=O bond formation in photosystem II.
光修復酵素DNAフォトリアーゼのXFEL結晶構造解析

別所義隆, 別所義隆, 山元淳平, 田中里枝, 田中里枝, 南後恵理子, 南後恵理子, 岩田想, 岩田想, TSAI Ming-Daw, ESSEN Lars-Oliver, MAESTRE-REYNA Manuel

日本蛋白質科学会年会プログラム・要旨集　18th　2018
Time Resolved Crystallography Using X-ray Free Electron Laser on Photoreactive Membrane Proteins

岩田想, 岩田想, 南後恵理子

生物物理(Web)　58　(1)　2018

ISSN： 1347-4219
XFEL分子動画が捉えたタンパク質構造変化

南後恵理子, 南後恵理子, 岩田想, 岩田想

日本蛋白質科学会年会プログラム・要旨集　18th　2018
X線自由電子レーザーで捉えたバクテリオロドプシンの構造変化過程

田中智之, 田中智之, 南後恵理子, 南後恵理子, 岩田想, 岩田想

日本結晶学会年会講演要旨集　2018　2018
SACLA産学連携プログラム/産業利用推進プログラムを通じて

高橋瑞稀, 南後恵理子, 国島直樹, 登野健介, 登野健介, 城地保昌, 城地保昌, 半沢宏之, 岩田想, 岩田想

日本放射光学会年会・放射光科学合同シンポジウム(Web)　31st　2018
Microcrystal-carrier matrices for serial crystallography.

M. Sugahara, T. Nakane, E. Nango, K. Tono, M. Yabashi, S. Iwata

J. Biol. Macromol.　18　(2)　15-22　2018
A molecular movie of structural changes in the light-driven proton pump bacteriorhodopsin

E. Nango, S. Iwata

SPring-8/SACLA Research Frontiers 2017　16-17　2018
Molecular movie of structural changes in bacteriorhodopsin

262　(5)　395-399　2017/07/29
Publisher: 医歯薬出版
ISSN： 0039-2359
XFELの創薬利用を目指したタンパク質‐リガンド複合体微結晶のシリアルフェムト秒構造解析

内藤久志, 松浦祥悟, 登野健介, 登野健介, 城地保昌, 城地保昌, 亀島敬, 亀島敬, 初井宇記, 初井宇記, 矢橋牧名, 矢橋牧名, 田中里枝, 田中智之, 菅原道泰, 小林淳, 南後恵理子, 岩田想, 国島直樹

日本蛋白質科学会年会プログラム・要旨集　17th　126　2017/05/22
XFEL施設SACLAでの連続フェムト秒結晶構造解析における微結晶輸送媒体の利用

菅原道泰, 菅原道泰, 南後恵理子, 南後恵理子, 田中智之, 田中智之, 山下鮎美, 山下鮎美, 有馬登志, 有馬登志, 田中里枝, 田中里枝, 沼田圭司, 岩田想, 岩田想

日本結晶学会年会講演要旨集　2017　2017
酵素反応機構解明のためのX線自由電子レーザーを利用した時間分解結晶構造解析

當舎武彦, 西田拓真, 西田拓真, 野村高志, 佐伯直哉, 佐伯直哉, 杉本宏, 山下恵太郎, 平田邦生, 吾郷日出夫, 山本雅貴, 中根崇智, 菅原道泰, 菅原道泰, 南後恵理子, 岩田想, 岩田想, 城宜嗣, 城宜嗣, 久保稔, 久保稔

酸化反応討論会講演要旨集　50th　2017
X線自由電子レーザーによるバクテリオロドプシン構造変化の分子動画

南後恵理子, 南後恵理子, 岩田想, 岩田想

日本蛋白質科学会年会プログラム・要旨集　17th　2017
微結晶輸送媒体を利用した連続フェムト秒結晶構造解析

菅原道泰, 南後恵理子, 南後恵理子, 田中智之, 田中智之, 山本鮎美, 山本鮎美, 有馬登志, 有馬登志, 田中里枝, 田中里枝, 岩田想, 岩田想

日本蛋白質科学会年会プログラム・要旨集　17th　2017
SACLAにおけるシリアルフェムト秒結晶構造解析の現状と展望

南後恵理子, 中根崇智, 岩田想, 岩田想

日本結晶学会誌　59　(1)　2017

ISSN： 0369-4585
X線自由電子レーザーを利用した時間分解X線結晶構造解析による酵素反応の観測

當舎武彦, 西田拓真, 西田拓真, 野村高志, 佐伯直哉, 佐伯直哉, 杉本宏, 山下恵太郎, 平田邦生, 吾郷日出夫, 山本雅貴, 中根崇智, 菅原道泰, 菅原道泰, 南後恵理子, 岩田想, 岩田想, 城宜嗣, 城宜嗣, 久保稔, 久保稔, 久保稔

生体分子科学討論会講演要旨集　44th　2017
X線自由電子レーザーで捉えたバクテリオロドプシンの光反応中間体構造

南後恵理子

日本放射光学会年会・放射光科学合同シンポジウム(Web)　30th　2017
A three-dimensional movie of structural changes in bacteriorhodopsin captured by X-ray free electron lasers Invited

Nango, E, Kubo, M, Iwata, S

Journal of the Japanese Society for Synchrotron Radiation Research (in Japanese)　30　(5)　218‐227-227　2017
Publisher: 大阪 : 日本放射光学会
ISSN： 0914-9287
膜蛋白質のSFXによる迅速位相決定を志向したヨウ素含有界面活性剤の開発

中根崇智, 花島慎弥, 鈴木守, 鈴木守, 斎木悠, 林太一, 垣之内啓介, 垣之内啓介, 杉山成, 杉山成, 川竹悟史, 川竹悟史, 松岡茂, 松岡茂, 松森信明, 南後恵理子, 小林淳, 島村達郎, 木村香菜子, 森千寿, 国島直樹, 菅原道泰, 高久陽子, 井上茂之, 井上茂之, 桝田哲哉, 桝田哲哉, 保坂俊彰, 登野健介, 城地保昌, 亀島敬, 初井宇記, 矢橋牧名, 井上豪, 濡木理, 岩田想, 岩田想, 村田道雄, 村田道雄, 溝端栄一

日本結晶学会年会講演要旨集　2016　112　2016/11/17
高粘度結晶輸送媒体を利用したXFEL施設SACLAでの連続フェムト秒結晶構造解析

菅原道泰, 鈴木守, 鈴木守, 桝田哲哉, 桝田哲哉, 井上茂之, 井上茂之, SONG Changyong, SONG Changyong, 中根崇智, 溝端栄一, 中津亨, 中津亨, 湯本史明, 南後恵理子, 登野健介, 沼田圭司, 岩田想, 岩田想

日本結晶学会年会講演要旨集　2016　117　2016/11
Method of sample loading for serial femtosecond crystallography

菅原道泰, 登野健介, 南後恵理子, 岩田想

放射光　29　(4)　198-203　2016/07
Publisher: 日本放射光学会
ISSN： 0914-9287
X線自由電子レーザーを用いた新規タンパク質の立体構造決定

山下恵太郎, 潘東青, 奥田智彦, 菅原道泰, 小段篤史, 山口知宏, 村井智洋, 溝端栄一, 鈴木守, 南後恵理子, 登野健介, 城地保昌, 亀島敬, 初井宇記, 矢橋牧名, 岩田想, 岩田想, 加藤博章, 加藤博章, 吾郷日出夫, 山本雅貴, 中津亨, 中津亨

日本薬学会年会要旨集(CD-ROM)　136年会　(2)　249-249　2016/03
Publisher: (公社)日本薬学会
ISSN： 0918-9823
XFELと同期したパルス駆動試料インジェクターの開発

登野健介, 真船文隆, 宮島謙, 武田佳宏, 河野淳也, 宮内直弥, 小林淳, 城地保昌, 南後恵理子, 岩田想, 岩田想, 矢橋牧名, 矢橋牧名

日本放射光学会年会・放射光科学合同シンポジウム予稿集　29th　74　2016/01/09
SACLAにおけるシリアルフェムト秒X線結晶構造解析の技術開発

田中智之, 菅原道泰, 中根崇智, 木村哲就, 木村哲就, 久保稔, 久保稔, 宮島謙, 宮島謙, 登野健介, 真船文隆, 真船文隆, 南後恵理子, 南後恵理子, 岩田想, 岩田想

日本結晶学会年会講演要旨集　2016　2016
SACLAにおけるシリアルフェムト秒結晶構造解析の現状と展望

南後恵理子, 登野健介

日本結晶学会年会講演要旨集　2016　(Supplement)　s21-s21　2016
Publisher: 日本結晶学会
DOI： 10.5940/jcrsj.58.s21 　

ISSN： 0369-4585

eISSN： 1884-5576
時分割シリアルフェムト秒X線結晶構造解析によるバクテリオロドプシンの光反応中間体構造

南後恵理子, 岩田想, 南後恵理子, 岩田想

日本蛋白質科学会年会プログラム・要旨集　16th　2016
シリアルフェムト秒X線結晶構造解析のための試料調製方法

田中智之, 菅原道泰, 山下鮎美, 小林淳, 田中里枝, 登野健介, 城地保昌, 亀島敬, PARK Jaehyun, SONG Changyong, 初井宇記, 矢橋牧名, 潘東青, 島村達郎, 溝端栄一, 岩田想, 南後恵理子

日本蛋白質科学会年会プログラム・要旨集　15th　95　2015/05/26
X 線自由電子レーザーを用いたタンパク質 X 線結晶構造解析

潘東青, 中津亨, 山口知宏, 小段篤史, 小川和浩, 松嶌一樹, 山下恵太郎, 城地保昌, 登野健介, 矢橋牧名, 鈴木守, 南後恵理子, 岩田想, 加藤博章

日本薬学会第135年会　135th　2015/03/27
甘味タンパク質ソーマチンの連続フェムト秒結晶構造解析

桝田哲哉, 桝田哲哉, 南後恵理子, 菅原道泰, 鈴木守, 鈴木守, 登野健介, 城地保昌, 亀島敬, PARK Jaehyun, SONG Changyong, 初井宇記, 矢橋牧名, 大久保喬平, 三上文三, 北畠直文, 北畠直文, 谷史人, 岩田想, 岩田想

日本農芸化学会大会講演要旨集(Web)　2015　2015

ISSN： 2186-7976
時分割シリアルフェムト秒X線結晶解析法によるバクテリオロドプシン光反応中間体の構造解析

南後恵理子, NEUTZE Richard, 久保稔, 久保稔, 木村哲就, 中根崇智, ROYANT Antoine, 登野健介, 岩田想

日本結晶学会年会講演要旨集　2015　2015
SACLAによるABCトランスポーターおよびホタル・ルシフェラーゼのX線結晶構造解析(第2報)

潘東青, 中津亨, 山口知宏, 小段篤史, 小川和浩, 松嶌一樹, 山下恵太郎, 城地保昌, 登野健介, 矢橋牧名, 鈴木守, 南後恵理子, 岩田想, 加藤博章

平成26年度日本結晶学会年会　14th　2014/11/01
SACLAによるABCトランスポーターおよびホタル・ルシフェラーゼのX線結晶構造解析(第2報)

潘東青, 中津亨, 中津亨, 山口知宏, 小段篤史, 小川和浩, 松嶌一樹, 山下恵太郎, 城地保昌, 登野健介, 矢橋牧名, 鈴木守, 鈴木守, 南後恵理子, 岩田想, 岩田想, 加藤博章, 加藤博章

日本結晶学会年会講演要旨集　2014　2014
XFEL連続フェムト秒結晶構造解析:構造生物学の新時代

溝端栄一, 福田庸太, 鈴木守, 鈴木守, 南後恵理子, 菅原道泰, 矢橋牧名, 登野健介, 城地保昌, 島村達郎, PANG Dongqing, CHAVAS Leonard M.G., 西澤知宏, 松村浩由, 林高史, 的場康幸, 杉山成, 村田道雄, 高木淳一, 井上豪, 岩田想

日本蛋白質科学会年会プログラム・要旨集　14th　2014
XFELを用いた創薬ターゲット蛋白質の迅速構造解析法の開発

南後恵理子, 田中智之, 鈴木守, 鈴木守, 桝田哲哉, 桝田哲哉, 山下鮎美, 田中里枝, 登野健介, 城地保昌, 亀島敬, PARK Jaehyun, SONG Changyong, 初井宇記, 矢橋牧名, PAN Dongqing, 島村達郎, 溝端栄一, 北郷悠, 石谷隆一郎, 湯本史明, 岩田想, 岩田想

日本蛋白質科学会年会プログラム・要旨集　14th　2014
XFELを用いた迅速タンパク質構造解析システムの開発

登野健介, 岩田想, 岩田想, 田中里枝, 南後恵理子, 鈴木守, 鈴木守, SONG Changyong, PARK Jaehyun, 亀島敬, 城地保昌, 初井宇記, 矢橋牧名

日本放射光学会年会・放射光科学合同シンポジウム予稿集　27th　2014
自由電子レーザーを用いた膜蛋白質の系統的構造解析

岩田想, 岩田想, 木村香菜子, 島村達郎, 南後恵理子, 田中智之, 西澤知宏, 濡木理, 田中里枝, 鈴木守, 鈴木守, 桝田哲哉, 桝田哲哉, 菅原道泰, 登野健介, 城地保昌, 亀島敬, SONG Changyong, 初井宇記, 矢橋牧名, 山下恵太郎, 保坂俊彰, 田辺弘明, 羽藤正勝, 有馬登志, 染谷友美, 白水美香子, 潘東青, 中津亨, 加藤博章, 溝端栄一, 北郷悠, 高木淳一, 山中保明, 藤原孝彰, 山下鮎美, 小林淳

日本分子生物学会年会プログラム・要旨集(Web)　37th　2014
創薬ターゲット蛋白質の迅速構造解析法の開発~SACLAにおけるシリアルフェムト秒X線結晶構造解析~

南後恵理子, 鈴木守, 鈴木守, 田中里枝, 登野健介, 城地保昌, 亀島敬, PARK Jaehyun, SONG Changyong, 初井宇記, 矢橋牧名, 潘東青, 小段篤史, 山口知宏, 中津亨, 加藤博章, 田中良樹, 寿野千代, 伊原健太郎, 豊田洋輔, 島村達郎, 溝端栄一, 北郷悠, 高木淳一, 石谷隆一郎, 濡木理, GALLAT Francois-Xavier, 山田悠介, 松垣直宏, 湯本史明, CHAVAS Leonard M. G., 岩田想, 岩田想

日本結晶学会年会講演要旨集　2013　2013
ビセニスタチン生合成における糖転移酵素VinCの結晶構造解析

南後恵理子, 南篤志, 沼倉真理緒, 熊坂崇, 江口正

日本農芸化学会大会講演要旨集(Web)　2013　2013

ISSN： 2186-7976
創薬ターゲット蛋白質の迅速構造解析法の開発~SACLAにおけるシリアルフェムト秒X線結晶構造解析~

南後恵理子, 鈴木守, 田中里枝, 登野健介, 城地保昌, 亀島敬, PARK Jaehyun, SONG Changyong, 初井宇記, 矢橋牧名, 潘東青, 小段篤史, 山口知宏, 中津亨, 加藤博章, 田中良樹, 寿野千代, 伊原健太郎, 豊田洋輔, 島村達郎, 溝端栄一, 北郷悠, 高木淳一, 石谷隆一郎, 濡木理, GALLAT Francois‐Xavier, 山田悠介, 松垣直宏, 湯本史明, CHAVAS Leonar, M. G, 岩田想

日本結晶学会年会講演要旨集,2013,92　2014　2013
理研ターゲットタンパクビームラインBL32XUの現状

平田邦生, 河野能顕, 橋本浩一, 上野剛, 引間孝明, 村上博則, 南後恵理子, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　25th　2012
タンパク質微小結晶自動凍結装置の開発

引間孝明, 橋本浩一, 村上博則, 河野能顕, 上野剛, 平田邦生, 南後恵理子, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　25th　2012
メタン生成古細菌由来イソペンテニル二リン酸異性化酵素の構造解析

星野武司, 南後恵理子, 馬場清喜, 江口正, 熊坂崇

日本化学会講演予稿集　91st　(4)　2011

ISSN： 0285-7626
タンパク質試料結晶の放射線損傷とうまく付き合うために

平田邦生, 河野能顕, 橋本浩一, 上野剛, 引間孝明, 村上博則, 南後恵理子, 長谷川和也, 奥村英夫, 熊坂崇, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2011　2011
アミノグリコシド抗生物質生合成に関与する糖質環化酵素20kDaサブユニットの生理的意義

為我井秀行, 澤田博司, 南後恵理子, 青木里恵, 平川暖果, 飯野煕彦, 江口正

日本農芸化学会大会講演要旨集　2010　2010
メタン生成古細菌由来イソペンテニル二リン酸異性化酵素の構造解析

星野武司, 南後恵理子, 馬場清喜, 江口正, 熊坂崇

日本結晶学会年会講演要旨集　2010　2010
必須アミノ酸生合成経路におけるβ-脱炭酸脱水素酵素-阻害剤複合体構造解析

南後恵理子, 南後恵理子, 山本崇史, 熊坂崇, 江口正

日本放射光学会年会・放射光科学合同シンポジウム予稿集　23rd　2009
糖質環化酵素の構造と機能の解明--バイオマスから化学工業資源へ—Structure and mechanism of 2-deoxy-scyllo-inosose synthase: bioconversion of sugar to versatile chemicals

南後恵理子, 江口正

バイオサイエンスとインダストリー / バイオサイエンスとインダストリー編集委員会編　66　(2)　60-64　2008/02
Publisher: 東京 : バイオインダストリー協会
ISSN： 0914-8981
β-脱炭酸脱水素酵素の阻害剤設計

江口正, 山本崇史, 南後恵理子, 熊坂崇

天然有機化合物討論会講演要旨集　50th　2008
ブチロシン生合成におけるアミノ基転移酵素BtrBの機能解析

遠藤由美恵, 為我井秀行, 沼倉真理緒, 工藤史貴, 南後恵理子, 江口正

日本化学会講演予稿集　87th　(2)　2007

ISSN： 0285-7626
ブチロシン生合成における2-デオキシ-scyllo-イノソース合成酵素の基質認識機構-基質グルコース-6リン酸1位に関して-

玉城朱理, 南後恵理子, 江口正

日本化学会講演予稿集　87th　(2)　2007

ISSN： 0285-7626
Functional analysis of btrS in butirosin-biosynthetic gene cluster.

桑原三恵子, 南後恵理子, 山本英樹, 為我井秀行, 江口正, 柿沼勝己

日本化学会講演予稿集　81st　(2)　2002

ISSN： 0285-7626
2-Deoxy-scyllo-inosose synthase from Bacillius circulans. (6). Mechanism of substrate recognition analyzed with substrate analogues.

ZHEN H, 南後恵理子, 江口正, 柿沼勝己

日本化学会講演予稿集　81st　(2)　2002

ISSN： 0285-7626
2-deoxy-scyllo-inosose synthase of Bacillus circulans. (7). Signficance of Asp135 in substrate recognition.

大門静絵, 南後恵理子, 為我井秀行, 江口正, 柿沼勝己

日本化学会講演予稿集　81st　(2)　2002

ISSN： 0285-7626
アミノ配糖体抗生物質生合成における糖質環化鍵酵素2-デオキシ-scyllo-イノソース合成酵素の動的解析

南後恵理子, 為我井秀行, 桑原三恵子, 小池(竹下)あゆみ, 工藤史貴, 江口正, 柿沼勝己

天然有機化合物討論会講演要旨集　44th　2002
Biosynthesis of antibiotic butirosin: A mechanism-based inhibitor of 2-deoxy-scyllo-inosose synthase.

南後恵理子, 為我井秀行, 松島芳隆, 江口正, 柿沼勝己

日本化学会講演予稿集　80th　2001

ISSN： 0285-7626
Molecular Analysis of the Biosynthesis of 2-Deoxystreptamine-containing Antibiotics.

柿沼勝己, 工藤史貴, 太田康勝, 久力久子, 佐々木聡子, 南後恵理子, 為我井秀行, 松島芳隆, 江口正

天然有機化合物討論会講演要旨集　42nd　2000

Show all ︎Show first 5

Books and Other Publications 3

Ultrafast electronic and structural dynamics

Ueda, Kiyoshi

Springer　2024

ISBN: 9789819729135
X-ray Free Electron Lasers A Revolution in Structural Biology

Boutet, Sebastien, Fromme, Petra, Hunter, Mark S

2019
タンパク質結晶の最前線 = Frontiers of protein crystals

杉山, 成

シーエムシー出版　2013/12

ISBN: 9784781309293

Presentations 70

分子が機能する瞬間を捉える：X線自由電子レーザーによる分子動画解析 Invited

南後恵理子

日本化学会第105春季年会　2025/03/26
X線自由電子レーザーによるタンパク質の動的構造と反応可視化 Invited

南後恵理子

東京大学物性研究所機能物性セミナー　2025/03/13
3 GeV高輝度放射光NanoTerasuが拓く創薬研究 Invited

南後恵理子

第32回地域を活かす科学技術政策研修会　2025/01/22
Three-dimensional molecular movies of structural changes in proteins captured by X-ray free electron lasers Invited

Eriko Nango

IPR International Conference　2025/01/17
Beyond "Molecular Movies": How can TR-SFX contribute to protein design?

Eriko Nango

Generative Design to Unlock the Potential of Protein Function Grant-in-Aid for Transformative Research Areas A (2024-2028) The 2nd Area Meeting　2024/12/16
Molecular movies of structural changes in proteins captured by X-ray free electron lasers Invited

Eriko Nango

The 24th RIES-HOKUDAI International Symposium 開（kai）　2024/12/10
Three-Dimensional Molecular Movies of Structural Changes in Proteins Captured by X-Ray Free Electron Lasers Invited

Eriko Nango

18th Conference of the Asian Crystallographic Association (AsCA 2024)　2024/12/03
放射光で解く機能・構造相関：分子設計への貢献 Invited

南後恵理子

東北大学Research Showcase 進化する“構造生物学”〜創薬研究への応用〜　2024/11/27
Structural Dynamics of Microbial Rhodopsins Captured by X-ray Free Electron Lasers Invited

Eriko Nango

20th International Conference on Retinal Proteins　2024/11/19
タンパク質の動的挙動を解明する：X線自由電子レーザーの挑戦 Invited

南後恵理子

日本化学会 CSJ化学フェスタ　2024/10/24
放射光で解く機能・構造相関：分子設計への貢献 Invited

南後恵理子

有機合成化学協会「ニューモダリティと有機合成化学」第12回勉強会　2024/10/07
タンパク質が機能する瞬間を捉える：X 線自由電子レーザーによる分子動画解析 Invited

南後恵理子

ブレーンストーミング2024 in 直島　2024/09/28
3GeV高輝度放射光NanoTerasuが拓く創薬研究 Invited

南後恵理子

令和６年度生命科学・創薬研究支援基盤事業公開シンポジウム　2024/09/06
タンパク質が機能する瞬間を捉える：X 線自由電子レーザーによる分子動画解析 Invited

南後恵理子

第12回Chem-Bio Joint Seminar 2024 @杜の都仙台　2024/08/27
time-resolved SFX-pump-probe approaches at SACLA Invited

Eriko Nango

UK XFEL Town Hall　2024/07/29
NanoTerasuの光で見える世界 Invited

南後恵理子

2024年度みやぎ県民大学東北大学多元物質科学研究所「生命と化学の接点」　2024/07/26
次世代放射光NanoTerasuが拓く創薬研究 Invited

南後恵理子

第3回HT研究会（ヘルステックカレッジ）　2024/07/23
Structual Dynamics of Microbial Rhodopsins Captured by X-ray Free Electron Lasers Invited

Eriko Nango

第21回IUPAB2024　2024/06/27
X 線自由電子レーザーによる光感受性タンパク質分子動画 Invited

南後恵理子

量子生命科学会第６回大会　2024/05/31
Terpen cyclase intermediates captured by serial femtosecond crystallography Invited

Eriko Nango

US-Japan seminar 2024 第10回日米生合成セミナー　2024/05/20
Time-resolved serial femtosecond crystallography for enzymatic reaction analysis Invited

Eriko Nango

The Protein Society Webinar Series　2024/04/25
X線自由電子レーザーによる時分割実験の現状と展望 Invited

南後恵理子

日本農芸化学会大会　2024/03/26
タンパク質動的解析による反応機構解明 Invited

南後恵理子

日本化学会第104春季年会　2024/03/18
Measurement systems for biomolecular movies using X-ray free electron lasers

Eriko Nango

SACLA User's Meeting 2023　2024/03/11
X線自由電子レーザーによる創薬ターゲットタンパク質のダイナミクス解析 Invited

南後恵理子

中谷財団贈呈式　2024/02/23
時分割実験のための多様な反応誘起システムの開発

南後恵理子

令和５年度新学術領域「高速分子動画」領域会議　2023/12/01
室温下のX線結晶構造解析が見せる新たな可能性 Invited

南後恵理子

日本結晶学会オンライン講演会第１回CrSJ Keynotes　2023/09/20
Seeing is believing:X線自由電子レーザーによるタンパク質分子動画解析

南後恵理子

生物物理学会若手の会夏の学校　2023/09/06
3D movies of structural changes in proteins captured by X-ray free electron lasers Invited

Eriko Nango

the 9th CWRU x Tohoku Joint Workshop　2023/08/08
Crystal Structures of AMPA Receptor Complexed With a Ligand by X-ray Free Electron Laser

Eriko Nango

Chemisutry summer school 2023 Tohoku Univ.　2023/08/08
X線自由電子レーザーによるタンパク質分子動画解析 Invited

南後恵理子

第 17 回日本分子イメージング学会総会・学術集会　2023/06/08
時分割実験のための多様な反応誘起システムの開発 Invited

南後恵理子

令和5年度「高速分子動画」シンポジウム・領域会議（横浜）　2023/05/10
Time-resolved serial femtosecond crystallography of microbial rhodopsins Invited

Eriko Nango

EMBO Workshop Time-resolved spectroscopy meets time-resolved crystallography: The future of dynamic photobiology　2023/04/19
Recent activities of biology research fields and requests for facilities Invited

Eriko Nango

SACLA User's Meeting 2023　2023/03/03
X線自由電子レーザーによるタンパク質分子動画解析 Invited

南後恵理子

2022年度iBIX-JAXA-KEK物構研-QST合同タンパク質研究会　2023/02/27
XFELによるタンパク質分子動画解析の現状と今後の展望 Invited

南後恵理子

第３６回日本放射光学会年会・放射光科学合同シンポジウム　2023/01/09
X 線自由電子レーザーによるタンパク質分子動画解析 Invited

南後恵理子

光・量子デバイス研究会　2022/12/27
3D Movies of Structural Changes in Proteins Captured by X-ray Free Electron Lasers Invited

Eriko Nango

AsBIC10(10th Asian Biological Inorganic Chemistry Conference)　2022/12/01
光解離性化合物結合型 AMPA 受容体細胞外ドメインのシリアルフェムト秒結晶構造解 Invited

南後恵理子

日本結晶学会　2022/11/26
高速分子動画計測の現状と今後の課題 Invited

南後恵理子

新学術領域会議　2022/11/22
X 線自由電子レーザーによる高時空間分解能タンパク質分子動画 Invited

南後恵理子

第８回電子状態理論シンポジウム　2022/11/16
高速分子動画法で観るタンパク質構造変化 Invited

南後恵理子

第95回日本生化学会大会　2022/11/11
Time-resolved serial femtosecond crystallography of microbial rhodopsins Invited

Eriko Nango

ICRP2022　2022/11/01
Toward understanding of enzyme reaction mechanism: serial crystallography using mixing injectors Invited

Eriko Nango

2022 SSRL/LCLS USERS' MEETING　2022/09/28
3D movies of structural changes in proteins captured by X-ray free electron lasers Invited

Eriko Nango

Sendai2022 workshop, An Update on Molecular Machines: Open Challenges and New Perspectives　2022/08/04
高速分子動画法で観るタンパク質構造変化 Invited

南後恵理子

Agtechセミナー　2022/07/07
X線自由電子レーザーを用いた膜タンパク質分子動画解析 Invited

南後恵理子

バイオインタストリー協会「発酵と代謝研究会」第１回勉強会　2022/07/06
百聞は一見に如かず：タンパク質分子動画から見えてくる世界 Invited

南後恵理子

LINK-J×東北大学次世代放射光イベント　2022/05/26
Time-resolved serial femtosecond crystallography of microbial rhodopsins Invited

Eriko Nango

“The Molecular Movies and beyond” International Symposium 2022　2022/05/13
温度ジャンプ法による分子動画解析の技術開発 Invited

南後恵理子

新学術領域「高速分子動画」国際シンポジウム・令和 4 年度領域会議　2022/05/12
百聞は一見に如かず：X線自由電子レーザーによる分子動画解析 Invited

南後恵理子

さきがけ領域会議　2022/04/29
Tracking enzymatic reactions by mix;d-inject serial femtosecond crystallography Invited

Pacifichem2021　2021/12/21
X線自由電子レーザーによるタンパク質分子動画解析 Invited

南後恵理子

日本化学会東海支部東海コンファレンス2021　2021/12/03
SACLAでの時分割構造解析 Invited

南後恵理子

よこはまNMR研究会第67回ワークショップ　2021/07/30
Protein structural;dynamics revealed by molecular movie analysis Invited

Eriko Nango

Protein Society 35th Annual Symposium　2021/07/12
高速分子動画が捉えるタンパク質構造ダイナミクス Invited

南後恵理子

日本顕微鏡学会第77回学術講演会　2021/06/14
X線自由電子レーザーによる分子動画解析 Invited

南後恵理子

第47回生体分子科学討論会　2021/06/05
Time-resolved serial femtosecond crystallography of light-sensitive proteins Invited

Belgian Crystallography Symposium　2021/03/17
Protein structural dynamics revealed by molecular movie analysis Invited

Eriko Nango, So Iwata

RIKEN BDR Symposium 2021　2021/03/03
高速分子動画：タンパク質が機能する際の構造変化を可視化する Invited

南後恵理子

第43回日本分子生物学会年会シンポジウム　2020/12/02
Protein dynamics structures revealed by time-resolved serial femtosecond crystallography Invited
A Molecular Movie of Structural Changes in the Light-Driven Proton Pump Bacteriorhodopsin International-presentation Invited

Nango Eriko

18th International Conference on Retinal Proteins　2018/09/24
A Molecular Movie of Structural Changes in the Light-Driven Proton Pump Bacteriorhodopsin International-presentation Invited

Nango Eriko

32nd Annual Symposium of the Protein Society　2018/07/09
X線自由電子レーザーで捉えたタンパク質リアルタイム動画 Invited

南後恵理子

第６回放射光産業利用支援講座～マテリアルインフォマティクスのための放射光科学と計算科学の融合技術　2018/03/16
生命を司る精密な分子機械 Invited

南後恵理子

第31回日本放射光学会年会（2018/1/8-10, つくば）市民公開講座「放射光で輝く！女性研究者」　2018/01/08
A three-dimensional movie of structural changes in bacteriorhodopsin captured by X-ray free electron lasers Invited

Nango Eriko

2017/12/04
X 線自由電子レーザーで捉えたバクテリオロドプシン構造変化の三次元動画 Invited

南後恵理子

第55回日本生物物理学会年会　2017/09/19
X線自由電子レーザーで捉えたバクテリオロドプシンの三次元動画 Invited

南後恵理子

第4回大型実験施設とスーパーコンピュータとの連携利用シンポジウム　2017/09/08
A molecular movie of structural changes in bacteriorhodopsin International-presentation Invited

Nango Eriko

24th Congress of the International Union of Crystallography　2017/08/21
A Molecular Movie of Structural Changes in the Light-Driven Proton Pump Bacteriorhodopsin International-presentation Invited

Nango Eriko

Gordon Research Conference Frontier Science with Forefront Synchrotrons and XFEL Sources　2017/07/30

Show all Show first 5

Research Projects 7

Generative design to unlock the potential of protein function

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Transformative Research Areas (A)

Institution: Kyoto University

2024/04/01 - 2029/03/31
生成的デザインのための量子ビームタンパク質分子動画解析

南後恵理子, 福田昌弘

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 学術変革領域研究(A)

Institution: 東北大学

2024/04/01 - 2029/03/31
XFEL-SFXによる化学反応解明を目指した「反応追跡結晶」の構築

上野隆史, 庄司光男, 南後恵理子

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 基盤研究(A)

Institution: 東京工業大学

2022/04/01 - 2026/03/31

More details Close

近年の結晶構造解析技術の進歩により、天然タンパク質の反応過程を原子分解能で実時間追跡することが可能となってきた。しかし、その手法を様々な化学反応へと展開するには多くの課題が残されている。本研究では人工反応の高分解能実時間構造追跡に向けた汎用性の高い分子システムの確立に向け、タンパク質結晶を用いた「反応観察結晶」の構築を目指し、結晶中に標的分子を特異的に導入し、結晶内部に一分子反応の追跡を可能とする活性部位を構築した。エックス線自由電子レーザーシリアルフェムト秒結晶解析により、反応過程で刻々と変化する構造を原子レベルで追跡し、正確な中間構造を用いた理論計算によって真の反応の追跡を達成した。
Time-resolved X-ray crystallography of light-driven ion pumps and their applications

Nango Eriko

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Tohoku University

2021/04/01 - 2024/03/31

More details Close

Retinal proteins (rhodopsin) from microorganisms are membrane proteins that perform their functions by light. A typical function is the active transport of ions in one direction by photoexcitation, transporting a variety of ions. There has been interest in the mechanism by which they transport ions with different charges unidirectionally despite their structural similarity. In this project, we have expressed and crystallized several ion-pump rhodopsins, and obtained their dynamic structures by time-resolved serial crystallography using an X-ray free electron laser.
Reaction initiation techniques in time-resolved experiments

Nango Eriko

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

2019/06/28 - 2024/03/31

More details Close

Time-resolved serial femtosecond crystallography (SFX) using an X-ray free electron laser is currently the only method that can obtain protein dynamic structures with high temporal and spatial resolution. In particular, time-resolved SFX using a pump laser has led to successful results. However, most of proteins are photo non-excitable, and it is necessary to develop a versatile reaction initiation technique. In this project, we worked on the development of a temperature jump method for SFX and "mixed and inject" SFX experiments by rapid mixing of substrates. We also developed a solution scattering method using an X-ray free electron laser to overcome the limitations imposed by crystals.
Activation mechanism of G protein-coupled receptors by X-ray free electron lasers

Nango Eriko

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

2018/04/01 - 2021/03/31

More details Close

We conducted this research to analyze dynamic structures of visual rhodopsin, which is one of G protein-coupled receptors, using X-ray free electron lasers (XFEL). So far, time-resolved crystallography using XFEL has enabled to visualize dynamic structures of several light-sensitive proteins. However, it has been challenging to measure visual rhodopsin crystals because the crystal is damaged by very weak light. It has been also challenging to obtain rhodopsin crystals diffracting with high spatial resolution. We developed a new experimental device for time-resolved serial femtosecond crystallography to transport samples discontinuously for less light contamination. We performed pump-probe type time-resolved experiments with photo-sensitive samples using the device and observed structural changes with time. In addition, various expression systems of visual rhodopsin have been examined, and crystals were obtained under several conditions.
必須アミノ酸生合成におけるβ‐脱炭酸脱水素酵素‐阻害剤複合体の精密構造解析

南後恵理子

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 若手研究(B)

Institution: 東京工業大学

2010 - 2010

Show all Show first 5