Article
Chemistry, Multidisciplinary
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
Summary: The study successfully captured the structural dynamics of light-sensitive proteins during the S-1 to S-2 transition using pump-probe time-resolved serial femtosecond crystallography (TR-SFX), while also avoiding the influence of light contamination, revealing key structural changes important for the water-splitting reaction.
Article
Chemistry, Multidisciplinary
Raphael de Wijn, Diogo V. M. Melo, Faisal H. M. Koua, Adrian P. Mancuso
Summary: This perspective review discusses emerging techniques and future opportunities for time-resolved serial femtosecond crystallography experiments using high repetition rate XFEL sources. The efficient use of these sources for pump-probe experiments and mix-and-inject experiments is highlighted. The development of photocaged compounds is also being explored to expand the application of time-resolved serial femtosecond crystallography.
APPLIED SCIENCES-BASEL
(2022)
Article
Multidisciplinary Sciences
P. Mehrabi, R. Buecker, G. Bourenkov, H. M. Ginn, D. von Stetten, H. M. Mueller-Werkmeister, A. Kuo, T. Morizumi, B. T. Eger, W-L Ou, S. Oghbaey, A. Sarracini, J. E. Besaw, O. Pare-Labrosse, S. Meier, H. Schikora, F. Tellkamp, A. Marx, D. A. Sherrell, D. Axford, R. L. Owen, O. P. Ernst, E. F. Pai, E. C. Schulz, R. J. D. Miller
Summary: This study systematically compared crystallographic diffraction data collected by SFX and SSX methods for myoglobin and fluoroacetate dehalogenase, finding that approximately 5000 room-temperature diffraction images are sufficient for reasonable data statistics regardless of the radiation source. The data suggest that the quality of diffraction data obtained from these samples is more related to the properties of the crystals rather than the radiation source.
Article
Biochemical Research Methods
Kyprianos Hadjidemetriou, Nicolas Coquelle, Thomas R. M. Barends, Elke De Zitter, Ilme Schlichting, Jacques-Philippe Colletier, Martin Weik
Summary: By combining various techniques, researchers have elucidated the catalytic mechanism of fatty-acid photodecarboxylase, which converts free fatty acids into hydrocarbon compounds. The study faced challenges and further experiments are needed to identify the photoproducts and their movements during the catalytic cycle.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Maximilian Wranik, Tobias Weinert, Chavdar Slavov, Tiziana Masini, Antonia Furrer, Natacha Gaillard, Dario Gioia, Marco Ferrarotti, Daniel James, Hannah Glover, Melissa Carrillo, Demet Kekilli, Robin Stipp, Petr Skopintsev, Steffen Brunle, Tobias Muhlethaler, John Beale, Dardan Gashi, Karol Nass, Dmitry Ozerov, Philip J. M. Johnson, Claudio Cirelli, Camila Bacellar, Markus Braun, Meitian Wang, Florian Dworkowski, Chris Milne, Andrea Cavalli, Josef Wachtveitl, Michel O. O. Steinmetz, Jorg Standfuss
Summary: Photopharmacology utilizes chemical triggers to change ligand affinities and biological activity by light, which is important for understanding ligand-protein binding and release processes.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Izumi Ishigami, Sergio Carbajo, Nadia Zatsepin, Masahide Hikita, Chelsie E. Conrad, Garrett Nelson, Jesse Coe, Shibom Basu, Thomas Grant, Matthew H. Seaberg, Raymond G. Sierra, Mark S. Hunter, Petra Fromme, Raimund Fromme, Denis L. Rousseau, Syun-Ru Yeh
Summary: Cytochrome c oxidase (CcO) is a hemeprotein that reduces dioxygen to water. It has a unique structure with a binuclear center composed of a copper atom and a heme iron. In the CO complex of CcO, the CO molecule dissociates from the heme iron and moves to a temporary binding site between the copper atom and the heme iron. This new structure provides insight into the ligand dissociation trajectory and protein dynamics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Eike C. Schulz, Briony A. Yorke, Arwen R. Pearson, Pedram Mehrabi
Summary: With advancements in X-ray sources, equipment, and data-analysis tools, time-resolved crystallographic experiments are becoming more accessible to a wider user base. This article highlights the key factors that need to be considered when planning and conducting a time-resolved structural study, with a focus on synchrotron-based experiments.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Maximilian Wranik, Michal W. Kepa, Emma V. Beale, Daniel James, Quentin Bertrand, Tobias Weinert, Antonia Furrer, Hannah Glover, Dardan Gashi, Melissa Carrillo, Yasushi Kondo, Robin T. Stipp, Georgii Khusainov, Karol Nass, Dmitry Ozerov, Claudio Cirelli, Philip J. M. Johnson, Florian Dworkowski, John H. Beale, Scott Stubbs, Thierry Zamofing, Marco Schneider, Kristina Krauskopf, Li Gao, Oliver Thorn-Seshold, Christoph Bostedt, Camila Bacellar, Michel O. Steinmetz, Christopher Milne, Jorg Standfuss
Summary: This study presents a new device for sample delivery at X-ray free-electron lasers (XFELs), which significantly reduces sample exchange time and user workload. The device was used to study protein structures and identified low occupancy ligands, which can be valuable for drug design.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
J. Mia Lahey-Rudolph, Robert Schonherr, Miriam Barthelmess, Pontus Fischer, Carolin Seuring, Armin Wagner, Alke Meents, Lars Redecke
Summary: This study presents an efficient approach for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micrometre-sized crystals of the protein HEX-1 on a fixed target. Compared with liquid-jet injection systems, the increased hit rates and reduced background scattering allowed for the elucidation of the HEX-1 structure. The results demonstrate that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection and offers huge potential for straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
Article
Chemistry, Physical
Cecilia M. Casadei, Ahmad Hosseinizadeh, Spencer Bliven, Tobias Weinert, Jorg Standfuss, Russell Fung, Gebhard F. X. Schertler, Robin Santra
Summary: Low-pass spectral analysis (LPSA) is an effective algorithm for retrieving dynamics in model data affected by incompleteness and weighting errors. In this study, LPSA is applied to experimental time-resolved crystallography data and the parametric sensitivity is analyzed. The presence of high-frequency contamination in dynamical modes is investigated using synthetic data with various uncertainties and errors. A method is proposed to handle missing observations and improved dynamics retrieval is achieved.
STRUCTURAL DYNAMICS-US
(2023)
Article
Multidisciplinary Sciences
Oliver F. Harder, Sarah V. Barrass, Marcel Drabbels, Ulrich J. Lorenz
Summary: Microsecond time-resolved cryo-EM allows for observation of fast protein dynamics, as demonstrated by the contraction of the CCMV capsid induced by a pH jump.
NATURE COMMUNICATIONS
(2023)
Article
Crystallography
Oleksii Turkot, Fabio Dall'Antonia, Richard J. Bean, Juncheng E, Hans Fangohr, Danilo E. Ferreira de Lima, Sravya Kantamneni, Henry J. Kirkwood, Faisal H. M. Koua, Adrian P. Mancuso, Diogo V. M. Melo, Adam Round, Michael Schuh, Egor Sobolev, Raphael de Wijn, James J. Wrigley, Luca Gelisio
Summary: Researchers have developed a semi-automated pipeline called EXtra-Xwiz to streamline and accelerate the analysis of serial femtosecond crystallography (SFX) data, which is crucial for experiments with high data complexity like the European XFEL.
Article
Biology
Juliane John, Oskar Aurelius, Vivek Srinivas, Patricia Saura, In-Sik Kim, Asmit Bhowmick, Philipp S. Simon, Medhanjali Dasgupta, Cindy Pham, Sheraz Gul, Kyle D. Sutherlin, Pierre Aller, Agata Butryn, Allen M. Orville, Mun Hon Cheah, Shigeki Owada, Kensuke Tono, Franklin D. Fuller, Alexander Batyuk, Aaron S. Brewster, Nicholas K. Sauter, Vittal K. Yachandra, Junko Yano, Ville Ri Kaila, Jan Kern, Hugo Lebrette, Martin Hogbom
Summary: Redox reactions play a central role in biochemistry and are controlled by protein structural changes. In this study, the authors utilized femtosecond crystallography to examine the structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b-NrdI complex. They found that the flavin in the complex is under steric strain, which likely affects its redox properties and promotes superoxide generation. The redox state of the flavin also controls a binding site that is linked to the channel responsible for transporting superoxide species. These findings have important implications for understanding the control of reactive oxygen species and radical generation in protein R2b.
Article
Chemistry, Multidisciplinary
Keondo Lee, Donghyeon Lee, Jaehyun Park, Jong-Lam Lee, Wan Kyun Chung, Yunje Cho, Ki Hyun Nam
Summary: This study introduces an upgraded inject-and-transfer system that improves beamtime efficiency for serial femtosecond crystallography. It is reported that the widely used viscous solution for protein crystallization can be stably deposited on a hydrophobic surface without any special treatment. Additionally, the development of an inject-and-diffuse method for time-resolved studies with liquid applications in the system is presented.
APPLIED SCIENCES-BASEL
(2022)
Article
Multidisciplinary Sciences
Thomas R. M. Barends, Benjamin Stauch, Vadim Cherezov, Ilme Schlichting
Summary: This article introduces the basic principles of X-ray free-electron lasers and serial crystallography, providing assistance for structural biology groups in planning and conducting SFX experiments. The main content includes microcrystal growth and characterization, sample delivery and data processing techniques, experimental preparation and operation at different stages, as well as the possibilities of SFX in various application areas.
NATURE REVIEWS METHODS PRIMERS
(2022)
Article
Materials Science, Biomaterials
Mariko Kojima, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Kunio Hirata, Keitaro Yamashita, Yuki Hishikawa, Akio Kitao, Takafumi Ueno
Summary: Protein crystals can serve as porous scaffolds for capturing exogenous molecules. Fixing target proteins in the pores of scaffold protein crystals has been challenging due to limited strategies to control protein-protein interactions. This study successfully fixes a miniprotein within a polyhedra crystal scaffold, revealing the potential of modulating intermolecular interactions for trapping various protein conformations.
BIOMATERIALS SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Shunpei Hanai, Takashi Nagata, Kota Katayama, Shino Inukai, Mitsumasa Koyanagi, Keiichi Inoue, Akihisa Terakita, Hideki Kandori
Summary: Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, typically found in vertebrates and invertebrates respectively. Bovine rhodopsin (BovRh) is an example of monostable rhodopsin with extensively studied structures and functions. On the other hand, the structures and functions of bistable rhodopsins, despite their importance in optogenetics, are less known. In this study, low-temperature Fourier transform infrared (FTIR) spectroscopy was used to compare the spectral changes of jumping spider rhodopsin-1 (SpiRh1), squid rhodopsin (SquRh), and BovRh. The analysis showed that while the chromophore distortion in the resting state is not distinctive between invertebrate and vertebrate rhodopsins, the distortion after photoisomerization is unique for BovRh. Moreover, the analysis of O-D stretching vibrations revealed unique features of protein-bound water molecules. The absence of strongly hydrogen-bonded water molecules is a distinct characteristic of animal rhodopsins compared to microbial rhodopsins.
Article
Biochemistry & Molecular Biology
Naoya Morimoto, Takashi Nagata, Keiichi Inoue
Summary: This study revealed that human and chicken RGRs form blue-absorbing pigments similar to bovine RGR, and they are bistable rhodopsins displaying a reversible photoreaction. These findings provide insight into the behavior of RGR as a retinal photoisomerase and aid in understanding its role in the visual system.
Article
Multidisciplinary Sciences
Kazuhiro Kobayashi, Kouki Kawakami, Tsukasa Kusakizako, Atsuhiro Tomita, Michihiro Nishimura, Kazuhiro Sawada, Hiroyuki H. Okamoto, Suzune Hiratsuka, Gaku Nakamura, Riku Kuwabara, Hiroshi Noda, Hiroyasu Muramatsu, Masaru Shimizu, Tomohiko Taguchi, Asuka Inoue, Takeshi Murata, Osamu Nureki
Summary: This study reports the cryogenic electron microscopy structure of a complex of Gs and the human parathyroid hormone type 1 receptor (PTHR1) bound to a PTHR1 agonist, PCO371. PCO371 binds within the intracellular pocket of PTHR1 and directly interacts with Gs. This study identifies a new and conserved intracellular agonist-binding pocket and provides evidence of a biased signaling mechanism that targets the receptor-transducer interface.
Article
Neurosciences
Andrew M. Stern, Yang Yang, Shanxue Jin, Keitaro Yamashita, Angela L. Meunier, Wen Liu, Yuqi Cai, Maria Ericsson, Lei Liu, Michel Goedert, Sjors H. W. Scheres, Dennis J. Selkoe
Summary: A study has found that Aβ fibrils are present in aqueous extracts from AD brains, indicating their pathological nature. This finding has important implications for understanding and treating AD.
Article
Multidisciplinary Sciences
Andriko von Kugelgen, Sofie van Dorst, Keitaro Yamashita, Danielle L. Sexton, Elitza I. Tocheva, Garib Murshudov, Vikram Alva, Tanmay A. M. Bharat ab
Summary: Using electron cryomicroscopy, we have revealed that the surface layer (S-layer) of the radiotolerant bacterium Deinococcus radiodurans is formed by the Hexagonally Packed Intermediate-layer (HPI) protein. The HPI protein forms an array of immunoglobulin-like folds within the S-layer, resulting in a highly interconnected, stable sheet-like structure. Our study also shows the structure of the cellular S-layer and highlights the similarities between the S-layer of D. radiodurans and immunoglobulin-like domain-containing S-layers from monoderm bacteria and archaea, which have implications for the evolution of immunoglobulin-based molecular recognition systems in eukaryotes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Keitaro Yamashita, Marcin Wojdyr, Fei Long, Robert A. Nicholls, Garib N. Murshudov
Summary: Macromolecular refinement uses experimental data and prior chemical knowledge to fit an atomic structural model into the data, while ensuring chemical plausibility. In CCP4 suite, the Monomer Library stores the chemical knowledge in restraint dictionaries. Recently, this part of CCP4 has been overhauled, allowing for increased flexibility and easier experimentation.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Jon Agirre, Mihaela Atanasova, Haroldas Bagdonas, Charles B. Ballard, Arnaud Basle, James Beilsten-Edmands, Rafael J. Borges, David G. Brown, J. Javier Burgos-Marmol, John M. Berrisford, Paul S. Bond, Iracema Caballero, Lucrezia Catapano, Grzegorz Chojnowski, Atlanta G. Cook, Kevin D. Cowtan, Tristan I. Croll, Judit E. Debreczeni, Nicholas E. Devenish, Eleanor J. Dodson, Tarik R. Drevon, Paul Emsley, Gwyndaf Evans, Phil R. Evans, Maria Fando, James Foadi, Luis Fuentes-Montero, Elspeth F. Garman, Markus Gerstel, Richard J. Gildea, Kaushik Hatti, Maarten L. Hekkelman, Philipp Heuser, Soon Wen Hoh, Michael A. Hough, Huw T. Jenkins, Elisabet Jimenez, Robbie P. Joosten, Ronan M. Keegan, Nicholas Keep, Eugene B. Krissinel, Petr Kolenko, Oleg Kovalevskiy, Victor S. Lamzin, David M. Lawson, Andrey A. Lebedev, Andrew G. W. Leslie, Bernhard Lohkamp, Fei Long, Martin Maly, Airlie J. McCoy, Stuart J. McNicholas, Ana Medina, Claudia Millan, James W. Murray, Garib N. Murshudov, Robert A. Nicholls, Martin E. M. Noble, Robert Oeffner, Navraj S. Pannu, James M. Parkhurst, Nicholas Pearce, Joana Pereira, Anastassis Perrakis, Harold R. Powell, Randy J. Read, Daniel J. Rigden, William Rochira, Massimo Sammito, Filomeno Sanchez Rodriguez, George M. Sheldrick, Kathryn L. Shelley, Felix Simkovic, Adam J. Simpkin, Pavol Skubak, Egor Sobolev, Roberto A. Steiner, Kyle Stevenson, Ivo Tews, Jens M. H. Thomas, Andrea Thorn, Josep Trivino Valls, Ville Uski, Isabel Uson, Alexei Vagin, Sameer Velankar, Melanie Vollmar, Helen Walden, David Waterman, Keith S. Wilson, Martyn D. Winn, Graeme Winter, Marcin Wojdyr, Keitaro Yamashita
Summary: The Collaborative Computational Project No. 4 (CCP4) is an international collective led by the UK, dedicated to the development, testing, distribution, and promotion of software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs, unified by familiar execution routines, common libraries, and graphical interfaces. This article serves as a general literature citation for the use of the CCP4 software suite, providing an overview of its recent changes, new features, and future developments, while also highlighting the individual programs within the suite and providing up-to-date references for crystallographers worldwide.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Seiya Tajima, Yoon Seok Kim, Masahiro Fukuda, Youngju Jo, Peter Y. Wang, Joseph M. Paggi, Masatoshi Inoue, Eamon F. X. Byrne, Koichiro E. Kishi, Seiwa Nakamura, Charu Ramakrishnan, Shunki Takaramoto, Takashi Nagata, Masae Konno, Masahiro Sugiura, Kota Katayama, Toshiki E. Matsui, Keitaro Yamashita, Suhyang Kim, Hisako Ikeda, Jaeah Kim, Hideki Kandori, Ron O. Dror, Keiichi Inoue, Karl Deisseroth, Hideaki E. Kato
Summary: KCR channelrhodopsins exhibit a distinctive mechanism for K+ selectivity, involving the formation of an asymmetric selectivity gate and a distinct dehydration pathway. The discovery of this mechanism provides a framework for studying ion-channel selectivity and advancing optogenetic applications.
Article
Chemistry, Physical
Manish Singh, Shota Ito, Shoko Hososhima, Rei Abe-Yoshizumi, Satoshi P. Tsunoda, Keiichi Inoue, Hideki Kandori
Summary: AaClR is a natural light-driven chloride pump that binds chloride ions in the resting state. It is also able to pump sulfate ions, although with lower efficiency. The photocycle dynamics of the AaClR sulfate pump resemble a non-functional cycle, but there is evidence of transient binding of sulfate ions to AaClR. The molecular mechanism of this unusual active transport by AaClR is discussed.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Keiichi Inoue
Summary: Microbial rhodopsins are photoreceptive membrane proteins that exhibit diverse photobiological functions. The chromophore of these rhodopsins, all-trans-retinal, undergoes isomerization upon photoexcitation, leading to sequential conformational changes in the protein and the emergence of active states with biological functions. Recent studies have revealed new photochemical characteristics of retinal in some microbial rhodopsins, including red-shifted absorption, isomerization to different forms, and energy transfer from a secondary chromophore. These findings challenge the established understanding of retinal photochemistry in canonical microbial rhodopsins.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Danyang Zhang, Josip Ivica, James M. Krieger, Hinze Ho, Keitaro Yamashita, Imogen Stockwell, Rozbeh Baradaran, Ondrej Cais, Ingo H. Greger
Summary: This study determines and characterizes the cryo-electron microscopy structures of GluA1/gamma 3, revealing their unique kinetic properties and synaptic signaling efficiency among AMPAR subtypes.
Article
Biophysics
Maria del Carmen Marin, Alexander L. Jaffe, Patrick T. West, Masae Konno, Jillian F. Banfield, Keiichi Inoue
Summary: Recent genomic and metagenomic analysis have identified many microbial rhodopsins with unique sequences. Functional characterization of these new microbial rhodopsins will enhance our understanding of their physiological roles.
BIOPHYSICS AND PHYSICOBIOLOGY
(2023)
Article
Chemistry, Physical
Yusuke Nakasone, Yuma Kawasaki, Masae Konno, Keiichi Inoue, Masahide Terazima
Summary: Heliorhodopsins (HeRs) are a new category of rhodopsins, which exist as dimers and have an inverted topology. This study investigated the conformational changes of HeRs using the transient grating (TG) and circular dichroism (CD) methods. The results showed that there were no significant conformation changes on the protein's surface during the early steps of the reaction, but a decrease in diffusion coefficient (D) was observed after the formation of the O intermediate. The contribution of the ICL1 helix in the conformational changes was examined. The study suggests that the hydrophilic residues in the ICL1 helix undergo structural changes during the process. Rating: 8/10
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Junko Tanaka, Satoshi Abe, Tohru Hayakawa, Mariko Kojima, Keitaro Yamashita, Kunio Hirata, Takafumi Ueno
Summary: In-cell protein crystals that spontaneously crystallize in living cells have been analyzed to understand their structures and biological functions. However, their small size has made it challenging to determine their structures. In this study, the cross-linked network of disulfide bonds within Cry1Aa crystals, a cysteine-rich protein that crystallizes in Bacillus thuringiensis, was characterized through direct X-ray crystallographic analysis using crystals purified from Bt cells.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
