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22 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3 [Next/Last]

Instruments / Technical Area	Publication Details	Published
	Compact tape-driven sample delivery system for serial femtosecond crystallography Jungmin Kang , Yoshiaki Shimazu , Fangjia Luo , Ayumi Yamashita , Tomoyuki Tanaka , Yuichi Inubushi , Kensuke Tono , Nipawan Nuemket , Allen M. Orville , So Iwata , Eriko Nango , Makina Yabashi Journal Of Applied Crystallography 59 DOI: 10.1107/S1600576726000063 Open Access Show Abstract ▼ Abstract: We have developed a compact tape drive (CoT) with on-demand sample delivery for time-resolved serial femtosecond crystallography (SFX) experiments, which can deliver sample droplets and/or initiate reactions with a drop-on-drop strategy. Two disposable piezoelectric injectors are positioned in tandem along the tape to produce a queue of nanolitre-scale droplets. X-ray free-electron laser pulses arrive perpendicular to and pass through the broad face of the tape. The pulse is synchronized and aligned to the droplets, thereby enabling highly efficient SFX data collection. The tape transport speed and the delivery distance can be varied to control the mixing time from approximately 130 ms to tens of seconds. We conducted time-resolved SFX experiments utilizing a basic enzymatic reaction model of hen egg white lysozyme (HEWL) and N-acetyl-D-glucosamine (GlcNAc) to demonstrate the drop-on-drop capabilities of the CoT, and the full binding process of GlcNAc to HEWL was observed at 1.3–9.7 s.	Apr 2026
I24-Microfocus Macromolecular Crystallography	Integrated structural dynamics uncover a new B12 photoreceptor activation mode Ronald Rios-Santacruz , Harshwardhan Poddar , Kevin Pounot , Derren J. Heyes , Nicolas Coquelle , Megan J. Mackintosh , Linus O. Johannissen , Sara Schianchi , Laura N. Jeffreys , Elke De Zitter , Rory Munro , Martin Appleby , Danny Axford , Emma V. Beale , Matthew J. Cliff , María C. Dávila-Miliani , Sylvain Engilberge , Guillaume Gotthard , Kyprianos Hadjidemetriou , Samantha J. O. Hardman , Sam Horrell , Jochen S. Hub , Kotone Ishihara , Sofia Jaho , Gabriel Karras , Machika Kataoka , Ryohei Kawakami , Thomas Mason , Hideo Okumura , Shigeki Owada , Robin L. Owen , Antoine Royant , Annica Saaret , Michiyo Sakuma , Muralidharan Shanmugam , Hiroshi Sugimoto , Kensuke Tono , Ninon Zala , John H. Beale , Takehiko Tosha , Jacques-Philippe Colletier , Matteo Levantino , Sam Hay , Pawel M. Kozlowski , David Leys , Nigel S. Scrutton , Martin Weik , Giorgio Schirò Nature 47 DOI: 10.1038/s41586-025-10074-2 Diamond Proposal Number(s): [24447, 31850] Show Abstract ▼ Abstract: Photoreceptor proteins regulate fundamental biological processes such as vision, photosynthesis and circadian rhythms1. A large photoreceptor subfamily uses vitamin B12 derivatives for light sensing2, contrasting with the well-established mode of action of these organometallic derivatives in thermally activated enzymatic reactions3. The exact molecular mechanism of B12 photoreception and how this differs from the thermal pathways remains unknown. Here we provide a detailed description of photoactivation in the prototypical B12 photoreceptor CarH4,5 from nanoseconds to seconds, combining time-resolved and temperature-resolved structural and spectroscopic methods with quantum chemical calculations. Building on the crystal structures of the initial tetrameric dark and final monomeric light-activated states5, our structural snapshots of key intermediates in the truncated B12-binding domain illustrate how photocleavage of a cobalt–carbon (Co–C) bond within the B12 chromophore adenosylcobalamin triggers a series of structural changes that propagate throughout CarH. Breakage of the photolabile Co–C5′ bond leads to the formation of a previously unknown adduct that links the C4′ position of the adenosyl moiety to the Co ion and can subsequently be cleaved thermally over longer timescales to allow release of the adenosyl group, ultimately causing tetramer dissociation4,5. This adduct, which differentiates CarH from thermally activated B12 enzymes, steers the photoactivation pathway and acts as the molecular bridge between photochemical and photobiological timescales. The biological relevance of our study is corroborated by kinetic data on full-length CarH in the presence of DNA. Our results offer a spatiotemporal understanding of CarH photoactivation and pave the way for designing B12-dependent photoreceptors for optogenetic applications.	Feb 2026
	Guanosine hydrogel as a new injection matrix for protein serial X-ray crystallography Alessia Pepe , Ronald Rios-Santacruz , Sara Schianchi , Jovana Vitas , Elena Andreeva , Jacques-Philippe Colletier , Nicolas Coquelle , Elke De Zitter , Shibom Basu , Daniele De Sanctis , Julien Orlans , Ninon Zala , Kyprianos Hadjidemetriou , Kensuke Tono , Takehiko Tosha , Bruce Doak , Robert Shoeman , Martin Weik , Paolo Mariani , Giorgio Schirò Journal Of Applied Crystallography 59 DOI: 10.1107/S1600576725011276 Show Abstract ▼ Abstract: Serial X-ray crystallography is the method of choice for protein structural studies at X-ray free-electron lasers and is increasingly widely used at third- and fourth-generation synchrotron facilities. Sample delivery is a critical step in serial crystallography experiments, and the definition and control of delivery methods is especially important for time-resolved studies. Extruding protein crystals embedded in viscous matrices as a thin, stable jet is a delivery method that ensures low sample consumption. However, it requires specific characteristics, such as a constant speed, chemical compatibility and, for laser-triggered dynamic studies, optical transparency. Here, we present a new transparent carrier matrix for protein serial crystallography, based on a guanosine hydrogel. Crystal stability in the hydrogel, in terms of morphology, size and diffraction quality, along with optical properties, injection characteristics and X-ray background were tested at the ESRF synchrotron and compared with other commonly used matrices. Additionally, we present a high-quality serial femtosecond crystallography dataset collected at the Spring-8 Angstrom Compact Free-Electron Laser (Japan) using hen egg-white lysozyme microcrystals embedded in the hydrogel. The results establish that this new injection matrix is a suitable alternative to existing carriers. The main advantage is its stability, so that the composition of the aqueous phase inside the hydrogel can be easily modified and adapted to the crystallization conditions of the embedded crystals.	Feb 2026
I24-Microfocus Macromolecular Crystallography	Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide Peter Smyth , Sofia Jaho , Lewis J. Williams , Gabriel Karras , Ann Fitzpatrick , Amy J. Thompson , Sinan Battah , Danny Axford , Sam Horrell , Marina Lucic , Kotone Ishihara , Machika Kataoka , Hiroaki Matsuura , Kanji Shimba , Kensuke Tono , Takehiko Tosha , Hiroshi Sugimoto , Shigeki Owada , Michael A. Hough , Jonathan A. R. Worrall , Robin L. Owen Iucrj 12 DOI: 10.1107/S2052252525006645 Diamond Proposal Number(s): [18565, 28583, 27313] Open Access Show Abstract ▼ Abstract: Time-resolved X-ray crystallography is undergoing a renaissance due to the development of serial crystallography at synchrotron and XFEL beamlines. Crucial to such experiments are efficient and effective methods for uniformly initiating time-dependent processes within microcrystals, such as ligand binding, enzymatic reactions or signalling. A widely applicable approach is the use of photocaged substrates, where the photocage is soaked into the crystal in advance and then activated using a laser pulse to provide uniform initiation of the reaction throughout the crystal. This work characterizes photocage release of nitric oxide and binding of this ligand to two heme protein systems, cytochrome c′-β and dye-decolourizing peroxidase B using a fixed target sample delivery system. Laser parameters for photoactivation are systematically explored, and time-resolved structures over timescales ranging from 100 µs to 1.4 s using synchrotron and XFEL beamlines are described. The effective use of this photocage for time-resolved crystallography is demonstrated and appropriate illumination conditions for such experiments are determined.	Sep 2025
I19-Small Molecule Single Crystal Diffraction	Supramolecular support of cuprophilic network bonding in 2-D copper n-alkanethiolates Maggie C. Willson , Daniel W. Paley , Elyse A. Schriber , Daniel J. Rosenberg , Daniel M. Tchon , Patience A. Kotei , Komal Rani , Cynthia Melendrez , Matthias Zeller , Tarun Kaushik , Qiaoling Fan , Chamathka Dehiwala Liyanage , Jungmin Kang , Ichiro Inoue , Kensuke Tono , Yuichi Inubushi , Aaron S. Brewster , J. Nathan Hohman Inorganic Chemistry DOI: 10.1021/acs.inorgchem.5c02024 Diamond Proposal Number(s): [35300] Show Abstract ▼ Abstract: The development of heterogeneous materials, catalysts, and semiconductors is often reliant on precise control of self-assembly and crystal packing. Many new materials are initially synthesized as microcrystalline powders, making them incompatible with typical methods of structure determination, such as single-crystal X-ray diffraction. This resultant lack of structural information has made thorough investigation into the effect of metal substitution on crystal structure in metal–organic chalcogenolates (MOChas) challenging. Here, we use small molecule serial femtosecond crystallography (smSFX) to present the structures of four copper n-alkanethiolates: CuSC4, CuSC5, CuSC6, and CuSC7. Divergent patterns of alkyl chain packing are identified from microcrystalline powders via smSFX. An odd–even effect in crystal packing has been identified and attributed to different orientations of symmetry elements in the even- and odd-numbered chains. This results in minute changes in the azimuthal organization of the even-numbered chains and the network of cuprophilic interactions. Additionally, we present a synthesis of crystalline gold n-alkanethiolates to provide the first comparison between three d10 coinage metals (Cu, Ag, and Au) and their resultant n-alkanethiolates.	Aug 2025
	Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes 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. Phillips , 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 Science Advances 11 DOI: 10.1126/sciadv.adp2665 Open Access Show Abstract ▼ Abstract: 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.	May 2025
I19-Small Molecule Single Crystal Diffraction	Ligand-mediated quantum yield enhancement in 1-D silver organothiolate metal–organic chalcogenolates Mariya Aleksich , Yeongsu Cho , Daniel W. Paley , Maggie C. Willson , Hawi N. Nyiera , Patience A. Kotei , Vanessa Oklejas , David W. Mittan-Moreau , Elyse A. Schriber , Kara Christensen , Ichiro Inoue , Shigeki Owada , Kensuke Tono , Michihiro Sugahara , Satomi Inaba-Inoue , Mohammad Vakili , Christopher J. Milne , Fabio Dallantonia , Dmitry Khakhulin , Fernando Ardana-Lamas , Frederico Lima , Joana Valerio , Huijong Han , Tamires Gallo , Hazem Yousef , Oleksii Turkot , Ivette J. Bermudez Macias , Thomas Kluyver , Philipp Schmidt , Luca Gelisio , Adam R. Round , Yifeng Jiang , Doriana Vinci , Yohei Uemura , Marco Kloos , Adrian P. Mancuso , Mark Warren , Nicholas K. Sauter , Jing Zhao , Tess Smidt , Heather J. Kulik , Sahar Sharifzadeh , Aaron S. Brewster , J. Nathan Hohman Advanced Functional Materials 17 DOI: 10.1002/adfm.202414914 Diamond Proposal Number(s): [35300] Show Abstract ▼ Abstract: X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. The proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.	Dec 2024
I24-Microfocus Macromolecular Crystallography	A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography James Birch , Tristan O. C. Kwan , Peter J. Judge , Danny Axford , Pierre Aller , Agata Butryn , Rosana 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 DOI: 10.1107/S1600576723006428 Diamond Proposal Number(s): [19152] Open Access Show Abstract ▼ Abstract: 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.	Oct 2023
I03-Macromolecular Crystallography	Optical control of ultrafast structural dynamics in a fluorescent protein Christopher D. M. Hutchison , James 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 4 DOI: 10.1038/s41557-023-01275-1 Diamond Proposal Number(s): [22819, 17221] Open Access Show Abstract ▼ Abstract: The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump–probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.	Aug 2023
I23-Long wavelength MX	Serial femtosecond crystallography reveals that photoactivation in a fluorescent protein proceeds via the hula twist mechanism 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 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 DOI: 10.1021/jacs.3c02313 Diamond Proposal Number(s): [23620] Open Access Show Abstract ▼ Abstract: Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements.	Jul 2023

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