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Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

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science Advances 2025年第22期11卷 eadp2665页

作者： Luisa Sauthof Michal Szczepek Andrea Schmidt Asmit Bhowmick Medhanjali Dasgupta Megan J. Mackintosh Sheraz Gul Franklin D. Fuller Ruchira Chatterjee Iris D. Young Norbert Michael Nicolas Andreas Heyder Brian Bauer Anja Koch Isabel Bogacz In-Sik Kim Philipp S. Simon Agata Butryn Pierre Aller Volha U. Chukhutsina James M. Baxter Christopher D. M. Hutchison Dorothee Liebschner Billy Poon Nicholas K. Sauter Mitchell D. Miller George N. Roberto Alonso-Mori Mark S. Hunter Alexander Batyuk Shigeki Owada Kensuke Tono Rie Tanaka Jasper J. van Thor Norbert Krauß Tilman Lamparter Aaron S. Brewster Igor Schapiro Allen M. Orville Vittal K. Yachandra Junko Yano Peter Hildebrandt Jan F. Kern Patrick Scheerer Charité–Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin Institute of Medical Physics and Biophysics Group Structural Biology of Cellular Signaling Charitéplatz 1 D-10117 Berlin Germany. Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA. Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry The Hebrew University of Jerusalem Jerusalem 9190401 Israel. Linac Coherent Light Source (LCLS) SLAC National Accelerator Laboratory 2575 Sand Hill Road MS103 Menlo Park CA 94025 USA. Technische Universität Berlin Institut für Chemie Sekr. PC 14 Straße des 17. Juni 135 Berlin D-10623 Germany. Diamond Light Source Ltd. Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK. Research Complex at Harwell Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0FA UK. Imperial College London Life Sciences Department South Kensington Campus London SW7 2AZ UK. Rice University Department of Biosciences 6100 Main Street Houston TX 77005 USA. Japan Synchrotron Radiation Research Institute Kouto 1-1-1 Sayo Hyogo 679-5198 Japan. RIKEN SPring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan. Department of Cell Biology Graduate School of Medicine Kyoto University Yoshidakonoecho Sakyo-ku Kyoto 606-8501 Japan. Karlsruhe Institute of Technology (KIT) Joseph Gottlieb Kölreuter Institute of Plant Science (JKIP) Fritz Haber Weg 4 D-76131 Karlsruhe Germany. Department of Physics Technical University Dortmund Dortmund Germany. Research Center Chemical Sciences and Sustainability University Alliance Ruhr 44801 Bochum Germany.

The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.

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Analysis of the synchrotron radiation from segmented undulator in double-mini beta function 8

Analysis of the synchrotron radiation from segmented undulat...

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8th International Particle Accelerator Conference, IPAC 2017

作者： Luo, H.W. Chung, T.Y. Hwang, C.S. Lee, C.H. Graduate Program in Science and Technology of Synchrotron Light Source National Tsing Hua University Hsinchu Taiwan National Synchrotron Radiation Research Center Hsinchu Taiwan Department of Electrophysics National Chiao Tung University Hsinchu Taiwan Department of Engineering and System Science National Tsing Hua University Hsinchu Taiwan

ISBN: (纸本)9783954501823

Three long straight sections with double-mini beta-y lattice were created in the Taiwan Photon source (TPS) for which the effects of focusing elements and phase shifters between the collinear undulators result in incorrect calculations of the brilliance while assuming a Gaussian-approximation. Therefore, an on-axis Wigner distribution function (WDF), which includes effects of wave phenomena, is a natural way to measure the intensity of synchrotron radiation and is used in this article as the definition of brilliance. © 2017 CC-BY-3.0 and by the respective authors

关键词： synchrotron radiation

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Presolar stardust in asteroid Ryugu

arXiv

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arXiv 2022年

作者： Barosch, Jens Nittler, Larry R. Wang, Jianhua O'D. Alexander, Conel M. De Gregorio, Bradley T. Engrand, Cécile Kebukawa, Yoko Nagashima, Kazuhide Stroud, Rhonda M. Yabuta, Hikaru Abe, Yoshinari Aléon, Jérôme Amari, Sachiko Amelin, Yuri Bajo, Ken-Ichi Bejach, Laure Bizzarro, Martin Bonal, Lydie Bouvier, Audrey Carlson, Richard W. Chaussidon, Marc Choi, Byeon-Gak Cody, George D. Dartois, Emmanuel Dauphas, Nicolas Davis, Andrew M. Dazzi, Alexandre Deniset-Besseau, Ariane Rocco, Tommaso Di Duprat, Jean Fujiya, Wataru Fukai, Ryota Gautam, Ikshu Haba, Makiko K. Hashiguchi, Minako Hibiya, Yuki Hidaka, Hiroshi Homma, Hisashi Hoppe, Peter Huss, Gary R. Ichida, Kiyohiro Iizuka, Tsuyoshi Ireland, Trevor R. Ishikawa, Akira Ito, Motoo Itoh, Shoichi Kamide, Kanami Kawasaki, Noriyuki Kilcoyne, David A.L. Kita, Noriko T. Kitajima, Kouki Kleine, Thorsten Komatani, Shintaro Komatsu, Mutsumi Krot, Alexander N. Liu, Ming-Chang Martins, Zita Masuda, Yuki Mathurin, Jérémie McKeegan, Kevin D. Montagnac, Gilles Morita, Mayu Mostefaoui, Smail Motomura, Kazuko Moynier, Frédéric Nakai, Izumi Nguyen, Ann N. Ohigashi, Takuji Okumura, Taiga Onose, Morihiko Pack, Andreas Park, Changkun Piani, Laurette Qin, Liping Quirico, Eric Remusat, Laurent Russell, Sara S. Sakamoto, Naoya Sandford, Scott A. Schönbächler, Maria Shigenaka, Miho Suga, Hiroki Tafla, Lauren Takahashi, Yoshio Takeichi, Yasuo Tamenori, Yusuke Tang, Haolan Terada, Kentaro Terada, Yasuko Usui, Tomohiro Verdier-Paoletti, Maximilien Wada, Sohei Wadhwa, Meenakshi Wakabayashi, Daisuke Walker, Richard J. Yamashita, Katsuyuki Yamashita, Shohei Yin, Qing-Zhu Yokoyama, Tetsuya Yoneda, Shigekazu Young, Edward D. Yui, Hiroharu Zhang, Ai-Cheng Abe, Masanao Miyazaki, Akiko Nakato, Aiko Nakazawa, Satoru Nishimura, Masahiro Okada, Tatsuaki Saiki, Takanao Tanaka, Satoshi Terui, Fuyuto Tsuda, Yuichi Watanabe, Seiichiro Yada, Toru Yogata, Kasumi Yoshikawa, Makoto Nakamura, Tomoki Naraoka, Hiroshi Noguchi, Takaaki Okazaki, Ryuji Sakamoto, Kanako Tachibana, Shogo Yurimoto, Hisayoshi Earth and Planets Laboratory Carnegie Institution of Washington 5241 Broad Branch Rd. NW WashingtonDC20015 United States Materials Science and Technology Division US Naval Research Laboratory WashingtonDC20375 United States IJCLab UMR 9012 Université Paris-Saclay CNRS Orsay91405 France Faculty of Engineering Yokohama National University Kanagawa Yokohama240-8501 Japan Hawai‘i Institute of Geophysics and Planetology University of Hawai‘i at Mānoa HonoluluHI96822 United States Department of Earth and Planetary Systems Science Hiroshima University Higashi-Hiroshima Hiroshima739-8526 Japan Graduate School of Engineering Materials Science and Engineering Tokyo Denki University Tokyo120-8551 Japan Institut de Mineralogie Physique des Materiaux et de Cosmochimie Museum National d'Histoire Naturelle CNRS Sorbonne Université Paris75231 France McDonnell Center for the Space Sciences and Physics Department Washington University St. LouisMO63130 United States Geochemical Research Center The University of Tokyo Bunkyo-ku Tokyo113-0033 Japan Guangzhou Institute of Geochemistry Chinese Academy of Sciences GD Guangzhou510640 China Department of Natural History Sciences Hokkaido University Sapporo060-0810 Japan Centre for Star and Planet Formation Globe Institute University of Copenhagen Copenhagen1350 Denmark Institut de Planétologie et d'Astrophysique Université Grenoble Alpes Grenoble38000 France Bayerisches Geoinstitut Universität Bayreuth Bayreuth95447 Germany Institut de Physique du Globe de Paris Université de Paris CNRS Paris75005 France Department of Physics and Astronomy Seoul National University Seoul08826 Korea Republic of UMR 8214 Université Paris-Saclay CNRS Orsay91405 France Department of the Geophysical Sciences Enrico Fermi Institute The University of Chicago ChicagoIL60637 United States UMR 8000 Université Paris-Saclay CNRS Orsay91405 France Faculty of Geosciences and Geography University of Göttingen Götti

We have conducted a NanoSIMS-based search for presolar material in samples recently returned from C-type asteroid Ryugu as part of JAXA’s Hayabusa2 mission. We report the detection of all major presolar grain types with O- and C-anomalous isotopic compositions typically identified in carbonaceous chondrite meteorites: 1 silicate, 1 oxide, 1 O-anomalous supernova grain of ambiguous phase, 38 SiC, and 16 carbonaceous grains. At least two of the carbonaceous grains are presolar graphites, whereas several grains with moderate C isotopic anomalies are probably organics. The presolar silicate was located in a clast with a less altered lithology than the typical extensively aqueously altered Ryugu matrix. The matrix-normalized presolar grain abundances in Ryugu are 4.8 !".$%&.' ppm for O-anomalous grains, 25 !(%$ ppm for SiC grains and 11 !)%(ppm for carbonaceous grains. Ryugu is isotopically and petrologically similar to carbonaceous Ivuna-type (CI) chondrites. To compare the in situ presolar grain abundances of Ryugu with CI chondrites, we also mapped Ivuna and Orgueil samples and found a total of 15 SiC grains and 6 carbonaceous grains. No O-anomalous grains were detected. The matrix-normalized presolar grain abundances in the CI chondrites are similar to those in Ryugu: 23 !$%' ppm SiC and 9.0 !).$%(.& ppm carbonaceous grains. Thus, our results provide further evidence in support of the Ryugu-CI connection. They also reveal intriguing hints of small-scale heterogeneities in the Ryugu samples, such as locally distinct degrees of alteration that allowed the preservation of delicate presolar material. Copyright © 2022, The Authors. All rights reserved.

关键词： Silicon carbide

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Electronic correlation determining correlated plasmons in Sb-doped Bi2Se3

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Physical Review B 2019年第11期100卷 115109-115109页

作者： P. K. Das T. J. Whitcher M. Yang X. Chi Y. P. Feng W. Lin J. S. Chen I. Vobornik J. Fujii K. A. Kokh O. E. Tereshchenko C. Z. Diao Jisoo Moon Seongshik Oh A. H. Castro-Neto M. B. H. Breese A. T. S. Wee A. Rusydi Singapore Synchrotron Light Source National University of Singapore 5 Research Link 117603 Singapore Centre for Advanced 2D Materials National University of Singapore 6 Science Drive 2 117546 Singapore Institute of Materials Research and Engineering A*STAR (Agency for Science Technology and Research) 2 Fusionopolis Way 138634 Singapore Department of Physics National University of Singapore 2 Science Drive 3 117576 Singapore Department of Materials Science and Engineering National University of Singapore 117575 Singapore Istituto Officina dei Materiali (IOM)–CNR Laboratorio TASC Area Science Park S.S.14 Km 163.5 I-34149 Trieste Italy V. S. Sobolev Institute of Geology and Mineralogy Novosibirsk 630090 Russia Novosibirsk State University Novosibirsk 630090 Russia A. V. Rzhanov Institute of Semiconductor Physics Novosibirsk 630090 Russia Department of Physics & Astronomy Rutgers The State University of New Jersey 136 Frelinghuysen Road Piscataway New Jersey 08854 USA NUSSNI-NanoCore National University of Singapore 117576 Singapore NUS Graduate School for Integrative Sciences and Engineering 117456 Singapore

Electronic correlation is believed to play an important role in exotic phenomena such as insulator-metal transition, colossal magnetoresistance, and high-temperature superconductivity in correlated electron systems. Recently, it has been shown that electronic correlation may also be responsible for the formation of unconventional plasmons. Herewith, using a combination of angle-dependent spectroscopic ellipsometry, angle resolved photoemission spectroscopy, and Hall measurements, all as a function of temperature supported by first-principles calculations, the existence of low-loss high-energy correlated plasmons accompanied by spectral weight transfer, a fingerprint of electronic correlation, in topological insulator (Bi0.8Sb0.2)2Se3 is revealed. Upon cooling, the density of free charge carriers in the surface states decreases whereas that in the bulk states increases, and the recently reported correlated plasmons are key to explaining this phenomenon. Our result shows the importance of electronic correlation in determining correlated plasmons and opens an alternative path in engineering plasmonic-based topologically insulating devices.

关键词： Electronic structure Plasmons Topological insulators Angle-resolved photoemission spectroscopy Ellipsometry First-principles calculations Transport techniques

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Transition-Metal Dichalcogenides: Anisotropic Collective Charge Excitations in Quasimetallic 2D Transition-Metal Dichalcogenides (Adv. Sci. 10/2020)

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Advanced science 2020年第10期7卷 2070055-2070055页

作者： Chi Sin Tang Xinmao Yin Ming Yang Di Wu Jing Wu Lai Mun Wong Changjian Li Shi Wun Tong Yung-Huang Chang Fangping Ouyang Yuan Ping Feng Shi Jie Wang Dongzhi Chi Mark B. H. Breese Wenjing Zhang Andrivo Rusydi Andrew T. S. Wee Department of Physics Faculty of Science National University of Singapore S12 Science Drive 3 Singapore 117551 Singapore NUS Graduate School for Integrative Sciences and Engineering National University of Singapore 21 Lower Kent Ridge Singapore 119077 Singapore Singapore Synchrotron Light Source (SSLS) National University of Singapore 5 Research Link Singapore 117603 Singapore Institute of Materials Research and Engineering (IMRE) A*STAR (Agency for Science Technology and Research) 2 Fusionopolis Way Innovis Singapore 138634 Singapore International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology Shenzhen University Shenzhen 518060 China School of Physics and Electronics Central South University No. 932 South Lushan Road Changsha Hunan 410083 China Department of Materials Science & Engineering National University of Singapore 9 Engineering Drive 1 Singapore 117575 Singapore Bachelor Program in Interdisciplinary Studies National Yunlin University of Science and Technology 123 University Road Section 3 Douliou Yunlin 64002 Taiwan

In article number https://***/10.1002/advs.201902726 , Xinmao Yin, Andrew T. S. Wee, and co‐workers observe 1D mid‐IR range anisotropic plasmons in quasi‐metallic WSe 2 and MoS 2 monolayers. In‐depth analysis reveals that the long‐range inter‐chain coupling is responsible for the 1D‐charge dynamics and the plasmon energy is dictated by the effects of spin–orbit coupling. Detailed investigation into these collective modes in 2D‐chained systems opens new opportunities for novel device applications and holds significant implications to the underlying mechanism that governs superconductivity in 2D‐transition‐metal dichalcogenide systems.

关键词： anisotropic charge dynamics phase transitions plasmons spectroscopic ellipsometry transition-metal dichalcogenides

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Frontispiz: The Electrophilicity of Surface Carbon Species in the Redox Reactions of CuO-CeO2Catalysts

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Angewandte Chemie 2021年第26期133卷

作者： Liqun Kang Dr. Bolun Wang Dr. Andreas T. Güntner Siyuan Xu Xuhao Wan Yiyun Liu Sushila Marlow Yifei Ren Dr. Diego Gianolio Dr. Chiu C. Tang Dr. Vadim Murzin Dr. Hiroyuki Asakura Dr. Qian He Dr. Shaoliang Guan Dr. Juan J. Velasco-Vélez Prof. Sotiris E. Pratsinis Dr. Yuzheng Guo Dr. Feng Ryan Wang Department of Chemical Engineering University College London London WC1E 7JE UK Particle Technology Laboratory Institute of Process Engineering Department of Mechanical and Process Engineering ETH Zürich 8092 Zürich Switzerland School of Electrical Engineering and Automation Wuhan University Wuhan China Diamond Light Source Ltd Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK Deutsches Elektronen Synchrotron DESY 22607 Hamburg Germany Department of Molecular Engineering Graduate School of Engineering Kyoto University Kyotodaigaku Katsura Nishikyo-ku Kyoto 6158510 Japan Department of Materials Science and Engineering National University of Singapore Singapore 117575 Singapore HarwellXPS—The EPSRC National Facility for Photoelectron Spectroscopy Research Complex at Harwell (RCaH) Didcot OX11 0FA UK Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany

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The Electrophilicity of Surface Carbon Species in the Redox Reactions of CuO-CeO2Catalysts

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Angewandte Chemie 2021年第26期133卷

Electronic metal–support interactions (EMSI) describe the electron flow between metal sites and a metal oxide support. It is generally used to follow the mechanism of redox reactions. In this study of CuO-CeO 2 redox, an additional flow of electrons from metallic Cu to surface carbon species is observed via a combination of operando X-ray absorption spectroscopy, synchrotron X-ray powder diffraction, near ambient pressure near edge X-ray absorption fine structure spectroscopy, and diffuse reflectance infrared Fourier transform spectroscopy. An electronic metal–support–carbon interaction (EMSCI) is proposed to explain the reaction pathway of CO oxidation. The EMSCI provides a complete picture of the mass and electron flow, which will help predict and improve the catalytic performance in the selective activation of CO 2 , carbonate, or carbonyl species in C1 chemistry.

关键词： CO oxidation copper-ceria electrophilicity EMSI surface chemistry

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Frontispiece: The Electrophilicity of Surface Carbon Species in the Redox Reactions of CuO-CeO2Catalysts

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Angewandte Chemie International Edition 2021年第26期60卷

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Publisher Correction: A weak topological insulator state in quasi-one-dimensional bismuth iodide

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Nature 2020年第7819期584卷 E4页

作者： Ryo Noguchi T Takahashi K Kuroda M Ochi T Shirasawa M Sakano C Bareille M Nakayama M D Watson K Yaji A Harasawa H Iwasawa P Dudin T K Kim M Hoesch V Kandyba A Giampietri A Barinov S Shin R Arita T Sasagawa Takeshi Kondo Institute for Solid State Physics University of Tokyo Kashiwa Japan. Materials and Structures Laboratory Tokyo Institute of Technology Yokohama Japan. Department of Physics Osaka University Toyonaka Japan. National Metrology Institute of Japan National Institute of Advanced Industrial Science and Technology Tsukuba Japan. Department of Applied Physics and Quantum-Phase Electronics Center (QPEC) The University of Tokyo Tokyo Japan. Diamond Light Source Harwell Campus Didcot UK. Graduate School of Science Hiroshima University Higashi-Hiroshima Japan. DESY Photon Science Deutsches Elektronen-Synchrotron Hamburg Germany. Elettra - Sincrotrone Trieste Basovizza Italy. RIKEN Center for Emergent Matter Science (CEMS) Wako Japan. Materials and Structures Laboratory Tokyo Institute of Technology Yokohama Japan. sasagawa@msl.titech.ac.jp. Institute for Solid State Physics University of Tokyo Kashiwa Japan. kondo1215@issp.u-tokyo.ac.jp.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Applications for ultimate spatial resolution in LASER based μ-ARPES: A FeSe case study

arXiv

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arXiv 2018年

作者： Schwier, E.F. Takita, H. Mansur, W. Ino, A. Hoesch, M. Watson, M.D. Haghighirad, A.A. Shimada, K. Hiroshima Synchrotron Radiation Center Hiroshima University 2-313 Kagamiyama Higashi-Hiroshima739-0046 Japan Graduate School of Science Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima739-8526 Japan Diamond Light Source Harwell Campus DidcotOX11 0DE United Kingdom DESY Photon Science Deutsches Elektronen-Synchrotron HamburgD-22603 Germany Clarendon Laboratory Department of Physics University of Oxford Parks Road OxfordOX1 3PU United Kingdom Institute for Solid State Physics Karlsruhe Institute of Technology Karlsruhe76021 Germany

Combining Angle resolved photoelectron spectroscopy (ARPES) and a μ-focused Laser, we have performed scanning ARPES microscopy measurements of the domain population within the nematic phase of FeSe single crystals. We are able to demonstrate a variation of the domain population density on a scale of a few 10 μm while constraining the upper limit of the single domain size to less than 5 μm. This experiment serves as a demonstration of how combining the advantages of high resolution Laser ARPES and an ultimate control over the spatial dimension can improve investigations of materials by reducing the cross contamination of spectral features of different domains. Copyright © 2018, The Authors. All rights reserved.

关键词： Selenium compounds

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