Language：English   Publisher：Journal of Physics: Conference Series  

The identification of protein crystals naturally occurring inside cells and organisms has opened a window for a new type of macromolecular crystallography (MX) and structural biology, referred to as in vivo MX. In the past decade, there have been efforts to obtain deeper insights into the yet uncontrollable events dictating in vivo crystal growth, by further developing sample handling and delivery procedures and applying these techniques to the structure determination and analysis of readily available ivMX systems. To facilitate the use of ivMX by the larger community, milestones for the implementation of a complete pipeline have been set at Synchrotron SOLEIL (France).

DOI： 10.1088/1742-6596/2380/1/012138

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

X-ray crystallography has revolutionized our understanding of biological macromolecules by elucidating their three-dimensional structures. However, the use of X-rays in this technique raises concerns about potential damage to the protein crystals, which results in a quality degradation of the diffraction data even at very low temperatures. Since such damage can occur on the micro- to millisecond timescale, a development in its real-time measurement has been expected. Here, we introduce diffracted X-ray blinking (DXB), which was originally proposed as a method to analyze the intensity fluctuations of diffraction of crystalline particles, to small-angle X-ray scattering (SAXS) of a lysozyme single-crystal. This novel technique, called the small-angle X-ray blinking (SAXB) method, analyzes the fluctuation in SAXS intensity reflecting the domain fluctuation in the protein crystal caused by the X-ray irradiation, which could be correlated with the X-ray-induced damage on the crystal. There was no change in the protein crystal’s domain dynamics between the first and second X-ray exposures at 95K, each of which lasted 0.7 s. On the other hand, its dynamics at 295K increased remarkably. The SAXB method further showed a dramatic increase in domain fluctuations with an increasing dose of X-ray radiation, indicating the significance of this method.

DOI： 10.3390/ijms242316640

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (other academic)   Publisher：J-STAGE  

Conversion to amyloid-like fibrils and/or aggregation of numerous soluble proteins is associated with several pathologies such as amyotrophic lateral sclerosis (ALS), Alzheimer’s, and Parkinson’s diseases. Cu, Zn-superoxide dismutase (SOD1) is an important anti-oxidative enzyme that protects cells. Mutations of the gene coding for SOD1 cause familial ALS. We found that the self-assembly of amyloid-like fibrils by SOD1 in certain conditions was accompanied by the formation of hydrogels rather than precipitation, notably when the concentration of the protein was sufficiently high. The structure of the hydrogels and pathogenic SOD1 fibrils remains unknown.

DOI： 10.18957/rr.11.2.164

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

Cyclic-olefin-copolymer (COC)-based microfluidic devices are increasingly becoming the center of highly valuable research for in situ X-ray measurements due to their compatibility with X-rays, biological compounds, chemical resistance, optical properties, low cost, and simplified handling. COC microfluidic devices present potential solutions to challenging biological applications such as protein binding, folding, nucleation, growth kinetics, and structural changes. In recent years, the techniques applied to manufacturing and handling these devices have capitalized on enormous progress toward small-scale sample probing. Here, we describe the new and innovative design aspects, fabrication, and experimental implementation of low-cost and micron-sized X-ray-compatible microfluidic sample environments that address diffusion-based crystal formation for crystallographic characterization. The devices appear fully compatible with crystal growth and subsequent X-ray diffraction experiments, resulting in remarkably low background data recording. The results highlighted in this research demonstrate how the engineered microfluidic devices allow the recording of accurate crystallographic data at room temperature and structure determination at high resolution.

DOI： 10.3390/mi13081365

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1088/1742-6596/2380/1/012138

Language：English   Publishing type：Research paper (international conference proceedings)  

A proposal for a high brilliance upgrade to the SOLEIL synchrotron radiation source is expected to increase the beam brightness by > 50 times on beamlines used for life sciences. At the same time revolutions in Cryo-electron microscopy and the prediction of protein folds, and accessibile super resolution microscopy techniques have changed the way we look at an integrative approach. The combined expertise of the life sciences beamline teams at SOLEIL form the HelioBiology section, which has been, for the last 4 years, developing a post-upgrade approach to structural biology. This approach will be presented, paying particular attention to facilities that are novel to SOLEIL including in- vivo crystallisation [1] , microfluidic devices and their synchrotron applications [2], and concrete efforts towards an integrated approach to structural problems including the addition of new methods, such as cryo-electron microscopy and soft X-ray end cryo-electron tomography. Recent examples will illustrate opportunities for integrated studies at SOLEIL and elsewhere, and some potential evolutions discussed. This work is presented on behalf of the members of the HelioBio scientific section at SOLEIL (https://www.synchrotron-soleil.fr/en/research/house-research/biology-health-heliobio).

DOI： 10.1107/S2053273322093159

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Association for the Advancement of Science (AAAS)  

Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light-absorbing) and Pfr (far-red light-absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator XccBphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.

DOI： 10.1126/sciadv.abh1097

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Red/far-red light-sensing bacteriophytochrome photoreceptor (BphP) pathways play key roles in bacterial physiology and ecology. These bilin-binding proteins photoswitch between two states, Pr (red absorbing) and Pfr (far-red absorbing). The isomerization of the chromophore and the downstream structural changes result in the light signal transduction. The agricultural pathogen Xanthomonas campestris pv. campestris (Xcc) code for a single bathy-like type BphP (XccBphP), previously shown to negatively regulate several light-mediated biological processes involved in virulence. Here, we generated three different full-length variants with single amino acid changes within its GAF domain that affect the XccBphP photocycle favouring its Pr state: L193Q, L193N and D199A. While D199A recombinant protein locks XccBphP in a Pr-like state, L193Q and L193N exhibit a significant enrichment of the Pr form in thermal equilibrium. The X-ray crystal structures of the three variants were solved, resembling the wild-type protein in the Pr state. Finally, we studied the effects of altering the XccBphP photocycle on the exopolysaccharide xanthan production and stomatal aperture assays as readouts of its bacterial signalling pathway. Null-mutant complementation assays show that the photoactive Pr-favoured XccBphP variants L193Q and L193N tend to negatively regulate xanthan production in vivo. In addition, our results indicate that strains expressing these variants also promote stomatal apertures in challenged plant epidermal peels, compared to wild-type Xcc. The findings presented in this work provide new evidence on the Pr state of XccBphP as a negative regulator of the virulence-associated mechanisms by light in Xcc.

DOI： 10.1111/febs.15883

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/febs.15883

Language：English   Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography (IUCr)  

The undulator beamline PROXIMA-1 at Synchrotron SOLEIL scheduled its first users in March 2008. The endstation is dedicated to biomolecular crystallography experiments, with a layout designed to favour anomalous data recording and studies of crystals with large cell dimensions. In 12 years, the beamline has accommodated 4267 shifts of 8 h and more than 6300 visitors. By the end of 2020, it saw 1039 identified published scientific papers referring to 1415 coordinates deposited in the Protein Data Bank. The current paper describes the PROXIMA-1 beamline, including the recent specific implementations developed for the sample environment. The setup installed in the experimental station contains numerous beam-shaping equipment, a chi-geometry three-axis goniometer, a single-photon-counting pixel-array X-ray detector, combined with a medium-throughput sample exchange robot. As part of a standard experimental scheme, PROXIMA-1 can also be accessed via `mail-in' services or remotely.

DOI： 10.1107/s1600577521002605

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

A microfluidic laboratory recently opened at Synchrotron SOLEIL, dedicated to in-house research and external users. Its purpose is to provide the equipment and expertise that allow the development of microfluidic systems adapted to the beamlines of SOLEIL as well as other light sources. Such systems can be used to continuously deliver a liquid sample under a photon beam, keep a solid sample in a liquid environment or provide a means to track a chemical reaction in a time-resolved manner. The laboratory provides all the amenities required for the design and preparation of soft-lithography microfluidic chips compatible with synchrotron-based experiments. Three examples of microfluidic systems that were used on SOLEIL beamlines are presented, which allow the use of X-ray techniques to study physical, chemical or biological phenomena.

DOI： 10.1107/S1600577519015042

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Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Part of collection (book)  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

In cellulo crystallization is a developing technique to provide crystals for protein structure determination, particularly for proteins that are difficult to prepare by in vitro crystallization. This method has a key advantage: it requires neither a protein purification step nor a crystallization step. However, there is still no systematic strategy for improving the technique of in cellulo crystallization because the process occurs spontaneously. Here we report a protocol to produce and extract in cellulo crystals of human lysosomal neuraminidase-1 (NEU1) in human cultured cells. Overexpression of NEU1 protein by the retransfection of cells pretransfected with neu1-overexpressing plasmid improved the efficiency of NEU1 crystallization. Microscopic analysis revealed that NEU1 proteins were not crystallized in the lysosome but in the endoplasmic reticulum (ER). Screening of the buffer conditions used to extract crystals from cells further improved the crystal yield. The optimal pH was 7.0, which corresponds to the pH in the ER. Use of a high-yield flask with a large surface area also yielded more crystals. These optimizations enabled us to execute a serial femtosecond crystallography experiment with a sufficient number of crystals to generate a complete data set. Optimization of the in cellulo crystallization method was thus shown to be possible.

DOI： 10.1021/acsabm.9b00686

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Language：English   Publisher：NATURE PUBLISHING GROUP  

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

DOI： 10.1038/s41467-019-12151-3

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2 nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4 nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.

DOI： 10.1038/s41467-019-10448-x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF - the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community.

DOI： 10.1107/S1600577519001267

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Single molecule dynamics studies have begun to use quantum probes. Single particle analysis using cryo-transmission electron microscopy has dramatically improved the resolution when studying protein structures and is shifting towards molecular motion observations. X-ray free-electron lasers are also being explored as routes for determining single molecule structures of biological entities. Here, we propose a new X-ray single molecule technology that allows observation of molecular internal motion over long time scales, ranging from milliseconds up to 103 seconds. Our method uses both low-dose monochromatic X-rays and nanocrystal labelling technology. During monochromatic X-ray diffraction experiments, the intensity of X-ray diffraction from moving single nanocrystals appears to blink because of Brownian motion in aqueous solutions. X-ray diffraction spots from moving nanocrystals were observed to cycle in and out of the Bragg condition. Consequently, the internal motions of a protein molecule labelled with nanocrystals could be extracted from the time trajectory using this diffracted X-ray blinking (DXB) approach. Finally, we succeeded in distinguishing the degree of fluctuation motions of an individual acetylcholine-binding protein (AChBP) interacting with acetylcholine (ACh) using a laboratory X-ray source.

DOI： 10.1038/s41598-018-35468-3

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Language：English   Publisher：SPRINGER  

The function of a protein dictates its physical state in a cell. Evolution has imparted selection pressure on proteins to maximize their function and minimize cell death. Most of the proteins exist in their soluble form inside or outside the cells. However, a small fraction of proteins in the total protein pool crystallizes with functional consequence. These in vivo-grown protein crystals perform a diversity of functions, ranging from food storage to defense. Sometimes limited by the volume of the cells and the cellular concentration of proteins, these crystals are very small in size. Hence, it has been difficult to carry out conventional X-ray crystallography on these crystals. With the advent of microcrystallography, it is now possible to study the structures of these tiny crystals. In this review, some of the diverse examples of in vivo crystals and the new approaches towards microcrystallography are summarized.

DOI： 10.1007/s41745-018-0086-0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.

DOI： 10.1002/cm.21378

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

The success of diffraction experiments from weakly scattering samples strongly depends on achieving an optimal signal-to-noise ratio. This is particularly important in single-particle imaging experiments where diffraction signals are typically very weak and the experiments are often accompanied by significant background scattering. A simple way to tremendously reduce background scattering by placing an aperture downstream of the sample has been developed and its application in a single-particle X-ray imaging experiment at FLASH is demonstrated. Using the concept of a post-sample aperture it was possible to reduce the background scattering levels by two orders of magnitude.

DOI： 10.1107/S1600577517011961

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography ({IUCr})  

A microfluidic platform was used to address the problems of obtaining diffraction-quality crystals and crystal handling during transfer to the X-ray diffractometer. Crystallization conditions of a protein of pharmaceutical interest were optimized and X-ray data were collected both in situ and ex situ.

DOI： 10.1107/S2053230X17013826

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Human parainfluenza viruses represent a leading cause of lower respiratory tract disease in children, with currently no available approved drug or vaccine. The viral surface glycoprotein haemagglutinin-neuraminidase (HN) represents an ideal antiviral target. Herein, we describe the first structure-based study on the rearrangement of key active site amino acid residues by an induced opening of the 216-loop, through the accommodation of appropriately functionalised neuraminic acid-based inhibitors. We discovered that the rearrangement is influenced by the degree of loop opening and is controlled by the neuraminic acid's C-4 substituent's size (large or small). In this study, we found that these rearrangements induce a butterfly effect of paramount importance in HN inhibitor design and define criteria for the ideal substituent size in two different categories of HN inhibitors and provide novel structural insight into the druggable viral HN protein.

DOI： 10.1038/s41598-017-04656-y

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1140/epjp/i2017-11403-3

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Other Link： http://link.springer.com/article/10.1140/epjp/i2017-11403-3/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

Indolone-N-oxides have antiplasmodial properties against Plasmodium falciparum at the erythrocytic stage, with IC50 values in the nanomolar range. The mechanism of action of indolone derivatives involves the production of free radicals, which follows their bioreduction by an unknown mechanism. In this study, we hypothesized that human quinone reductase 2 (hQR2), known to act as a flavin redox switch upon binding to the broadly used antimalarial chloroquine, could be involved in the activity of the redox-active indolone derivatives. Therefore, we investigated the role of hQR2 in the reduction of indolone derivatives. We analyzed the interaction between hQR2 and several indolone-type derivatives by examining enzymatic kinetics, the substrate/protein complex structure with X-ray diffraction analysis, and the production of free radicals with electron paramagnetic resonance. The reduction of each compound in cells overexpressing hQR2 was compared to its reduction in naïve cells. This process could be inhibited by the specific hQR2 inhibitor, S29434. These results confirmed that the anti-malarial activity of indolone-type derivatives was linked to their ability to serve as hQR2 substrates and not as hQR2 inhibitors as reported for chloroquine, leading to the possibility that substrate of hQR2 could be considered as a new avenue for the design of new antimalarial compounds.

DOI： 10.3390/molecules22020210

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Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S2053273317093962

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DOI： 10.1107/S205327331708696X

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Synthetic biology (or chemical biology) is a growing field to which the chemical synthesis of proteins, particularly enzymes, makes a fundamental contribution. However, the chemical synthesis of catalytically active proteins (enzymes) remains poorly documented because it is difficult to obtain enough material for biochemical experiments. We chose calstabin, a 107-amino-acid proline isomerase, as a model. We synthesized the enzyme using the native chemical ligation approach and obtained several tens of milligrams. The polypeptide was refolded properly, and we characterized its biophysical properties, measured its catalytic activity, and then crystallized it in order to obtain its tridimensional structure after X-ray diffraction. The refolded enzyme was compared to the recombinant, wild-type enzyme. In addition, as a first step of validating the whole process, we incorporated exotic amino acids into the N-terminus. Surprisingly, none of the changes altered the catalytic activities of the corresponding mutants. Using this body of techniques, avenues are now open to further obtain enzymes modified with exotic amino acids in a way that is only barely accessible by molecular biology, obtaining detailed information on the structure-function relationship of enzymes reachable by complete chemical synthesis.

DOI： 10.1002/pro.3051

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Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.

DOI： 10.1107/S2052252516008903

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Language：English   Publisher：INT UNION CRYSTALLOGRAPHY  

DOI： 10.1107/S205327331609690X

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

DOI： 10.1063/1.4921220

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Other Link： http://aip.scitation.org/doi/10.1063/1.4921220

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DOI： 10.1063/1.4922648

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Other Link： http://aip.scitation.org/doi/10.1063/1.4922648

Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

Human parainfluenza virus type 3 (hPIV-3) is one of the leading causes for lower respiratory tract disease in children, with neither an approved antiviral drug nor vaccine available to date. Understanding the catalytic mechanism of human parainfluenza virus haemagglutinin-neuraminidase (HN) protein is key to the design of specific inhibitors against this virus. Herein, we used (1) H NMR spectroscopy, X-ray crystallography, and virological assays to study the catalytic mechanism of the HN enzyme activity and have identified the conserved Tyr530 as a key amino acid involved in catalysis. A novel 2,3-difluorosialic acid derivative showed prolonged enzyme inhibition and was found to react and form a covalent bond with Tyr530. Furthermore, the novel derivative exhibited enhanced potency in virus blockade assays relative to its Neu2en analogue. These outcomes open the door for a new generation of potent inhibitors against hPIV-3 HN.

DOI： 10.1002/anie.201412243

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

Serial femtosecond crystallography on in vivo grown crystals at SACLA - developments and results

DOI： 10.1107/S2053273315097831

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The European X-ray Free-Electron Laser (XFEL.EU) [1] will provide ultra-short, highly-intense, coherent x-ray pulses at an unprecedented repetition rate, transforming experiments in many scientific areas, including serial femtosecond crystallography (SFX). For the purpose of SFX experiments at the XFEL.EU, a dedicated endstation is being developed to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument [2]. The setup will refocus the beam spent by SPB into a second interaction region, thereby enabling two parallel experiments. In order to overcome various challenges in XFEL crystallography, and to optimize the output for SFX experiments at XFEL.EU, the Adaptive Gain Integrating Pixel Detector (AGIPD) [3] is currently under development and is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX apparatus. The AGIPD is a hybrid-pixel detector with pixels of 200 x 200 micron^2 each. The gain of each single pixel dynamically and independently adapts to the incoming signal. Thus, diffraction patterns of high dynamic range can be recorded, with the measured signal within a single data frame ranging from single photons and up to 1e+4 photons at 12 keV. Moreover, the AGIPD is designed to store over 350 data frames from successive pulses prior to digitization and read-out, thereby enabling operation at the European XFEL with its challenging repetition rate with 10 Hz pulse trains and a 4.5 MHz intra-train repetition rate. Furthermore, the incorporation of a veto system in AGIPD will allow one to potentially store only the frames that contain diffraction data from actual crystal hits, which ultimately increases the efficiency of the detector and DAQ systems dramatically. In the present work, we will review the design of the 4Mpix AGIPD for the SFX apparatus and discuss simulations and tests of its expected performance under the conditions foreseen for SFX experiments at the XFEL.EU.

DOI： 10.1107/s205327331409305x

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The Serial Femtosecond Crystallography (SFX) user's consortium apparatus is to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument of the European X-ray Free-Electron Laser facility (XFEL.EU) [1, 2]. The XFEL.EU will provide ultra-short, highly intense, coherent X-ray pulses at an unprecedented repetition rate. The experimental setup and methodological approaches of many scientific areas will be transformed, including structural biology that could potentially overcome common problems and bottlenecks encountered in crystallography, such as creating large crystals, dealing with radiation damage, or understanding sub-picosecond time-resolved phenomena. The key concept of the SFX method is based on the kinetic insertion of protein crystal samples in solution via a gas dynamic virtual nozzle jet and recording diffraction signals of individual, randomly oriented crystals passing through the XFEL beam, as first demonstrated by Chapman et al. [3]. The SFX-apparatus will refocus the beam spent by the SPB instrument into a second interaction region, in some cases enabling two parallel experiments. The planned photon energy range at the SPB instrument is from 3 to 16 keV. The Adaptive Gain Integrating Pixel Detector (AGIPD) is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX-apparatus. The AGIPD is designed to store over 350 data frames from successive pulses, and aims to collect more than 3,000 images per second. Together with the implementation of automated procedures for sample exchange and injection, high-throughput nanocrystallography experiments can be integrated at the SFX-apparatus. In this work, we review the overall design of the SFX-apparatus and discuss the main parameters and challenges

DOI： 10.1107/s2053273314082515

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC  

The serendipitous discovery of the spontaneous growth of protein crystals inside cells has opened the field of crystallography to chemically unmodified samples directly available from their natural environment. On the one hand, through in vivo crystallography, protocols for protein crystal preparation can be highly simplified, although the technique suffers from difficulties in sampling, particularly in the extraction of the crystals from the cells partly due to their small sizes. On the other hand, the extremely intense X-ray pulses emerging from X-ray free-electron laser (XFEL) sources, along with the appearance of serial femtosecond crystallography (SFX) is a milestone for radiation damage-free protein structural studies but requires micrometre-size crystals. The combination of SFX with in vivo crystallography has the potential to boost the applicability of these techniques, eventually bringing the field to the point where in vitro sample manipulations will no longer be required, and direct imaging of the crystals from within the cells will be achievable. To fully appreciate the diverse aspects of sample characterization, handling and analysis, SFX experiments at the Japanese SPring-8 angstrom compact free-electron laser were scheduled on various types of in vivo grown crystals. The first experiments have demonstrated the feasibility of the approach and suggest that future in vivo crystallography applications at XFELs will be another alternative to nano-crystallography.

DOI： 10.1098/rstb.2013.0497

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Authorship：Lead author,　Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

Small Angle X-ray and Neutron Scattering from Solutions of Biological Macromolecules is a superb book that efficiently summarises both SAXS (small-angle X-ray scattering) and SANS (small-angle neutron scattering) techniques in a flow driven by the ambition to bring readers from an inexperienced background to a good practical knowledge and understanding of these scattering methods.

DOI： 10.1107/s1399004714005719

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley-VCH (Germany)  

3-Fluorosialosyl fluorides are inhibitors of sialidases that function by the formation of a long-lived covalent active-site adduct and have potential as therapeutics if made specific for the pathogen sialidase. Surprisingly, human Neu2 and the Trypanosoma cruzi trans-sialidase are inactivated more rapidly by the reagent with an equatorial fluorine at C3 than by its axial epimer, with reactivation following the same pattern. To explore a possible stereoelectronic basis for this, rate constants for spontaneous hydrolysis of the full series of four 3-fluorosialosyl fluorides were measured, and ground-state energies for each computed. The alpha (equatorial) anomeric fluorides hydrolyze more rapidly than their beta anomers, consistent with their higher ground-state energies. However ground-state energies do not explain the relative spontaneous reactivities of the 3-fluoro-epimers. The three-dimensional structures of the two 3-fluoro-sialosyl enzyme intermediates of human Neu2 were solved, revealing key stabilizing interactions between Arg21 and the equatorial, but not the axial, fluorine. Because of changes in geometry these interactions will increase at the transition state, likely explaining the difference in reaction rates.

DOI： 10.1002/anie.201309675

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

Photon Factory Automated Mounting system (PAM) protein crystal exchange systems are available at the following Photon Factory macromolecular beamlines: BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. The beamline AR-NE3A has been constructed for high-throughput macromolecular crystallography and is dedicated to structure-based drug design. The PAM liquid-nitrogen Dewar can store a maximum of three SSRL cassettes. Therefore, users have to interrupt their experiments and replace the cassettes when using four or more of them during their beam time. As a result of investigation, four or more cassettes were used in AR-NE3A alone. For continuous automated data collection, the size of the liquid-nitrogen Dewar for the AR-NE3A PAM was increased, doubling the capacity. In order to check the calibration with the new Dewar and the cassette stand, calibration experiments were repeatedly performed. Compared with the current system, the parameters of the novel system are shown to be stable.

DOI： 10.1107/S0909049513021067

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

The macromolecular crystallography (MX) beamline AR-NW12A is evolving from its original design of high-throughput crystallography to a multi-purpose end-station. Among the various options to be implemented, great efforts were made in making available high-pressure MX (HPMX) at the beamline. High-pressure molecular biophysics is a developing field that attracts the interest of a constantly growing scientific community. A plethora of activities can benefit from high pressure, and investigations have been performed on its applicability to study multimeric complex assemblies, compressibility of proteins and their crystals, macromolecules originating from extremophiles, or even the trapping of higher-energy conformers for molecules of biological interest. Recent studies using HPMX showed structural hydrostatic-pressure-induced changes in proteins. The conformational modifications could explain the enzymatic mechanism differences between proteins of the same family, living at different environmental pressures, as well as the initial steps in the pressure-denaturation process that have been attributed to water penetration into the protein interior. To facilitate further HPMX, while allowing access to various individualized set-ups and experiments, the AR-NW12A sample environment has been revisited. Altogether, the newly added implementations will bring a fresh breath of life to AR-NW12A and allow the MX community to experiment in a larger set of fields related to structural biology.

DOI： 10.1107/S0909049513020797

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BL-17A is a macromolecular crystallography beamline dedicated to diffraction experiments conducted using micro-crystals and structure determination studies using a lower energy X-ray beam. In these experiments, highly accurate diffraction intensity measurements are definitively important. Since this beamline was constructed, the beamline apparatus has been improved in several ways to enable the collection of accurate diffraction data. The stability of the beam intensities at the sample position was recently improved by modifying the monochromator. The diffractometer has also been improved. A new detector table was installed to prevent distortions in the diffractometer's base during the repositioning of the diffractometer detector. A new pinhole system and an on-axis viewing system were installed to improve the X-ray beam profile at the sample position and the centering of tiny crystal samples.

DOI： 10.1107/S0909049513022875

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：IOP Publishing  

The exponential growth of protein crystallography can be observed in the continuously increasing demand for synchrotron beam time, both from academic and industrial users. Nowadays, the screening of a profusion of sample crystals for more and more projects is being implemented by taking advantage of fully automated procedures at every level of the experiments. The insertion device AR-NW12A beamline is one of the five macromolecular crystallography (MX) beamlines at the Photon Factory (PF). Currently the oldest MX beamline operational at the High Energy Accelerator Research Organization (KEK), the end-station was launched in 2001 as part of an upgrade of the PF Advanced Ring. Since its commissioning, AR-NW12A has been operating as a high-throughput beamline, slowly evolving to a multipurpose end-station for MX experiments. The development of the beamline took place about a decade ago, in parallel with a drastic development of protein crystallography and more general synchrotron technology. To keep the beamline up-to-date and competitive with other MX stations in Japan and worldwide, new features have been constantly added, with the goal of user friendliness of the various beamline optics and other instruments. Here we describe the evolution of AR-NW12A for its tenth anniversary. We also discuss the plans for upgrades for AR-NW12A, the future objectives in terms of the beamline developments, and especially the strong desire to open the beamline to a larger user community. © Published under licence by IOP Publishing Ltd.

DOI： 10.1088/1742-6596/425/1/012008

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Other Link： http://stacks.iop.org/1742-6596/425/i=1/a=012008?key=crossref.51e8bce4e1903fbc177b2d861ae7b433

Language：English   Publishing type：Research paper (scientific journal)   Publisher：IOP Publishing  

Data Management System at the Photon Factory Macromolecular Crystallography Beamline

DOI： 10.1088/1742-6596/425/1/012017

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：IOP Publishing  

Current status and future prospects of an automated sample exchange system PAM for protein crystallography

DOI： 10.1088/1742-6596/425/1/012014

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Biophysical Society of Japan General Incorporated Association  

Promotion of the Platform for Drug discovery, Informatics, and Structural life science (PDIS) project at Photon Factory in KEK

DOI： 10.2142/biophys.53.S106_1

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Language：Japanese   Publisher：The Crystallographic Society of Japan  

Fully automated data collection and processing system has been developed on macromolecular crystallography beamlines at the Photon Factory. In this system, the sample exchange, centering and data collection are sequentially performed for all samples stored in the sample exchange system at a beamline without any manual operations. Data processing of collected data sets is also performed automatically. These results are stored into the database system, and users can monitor the progress and results of automated experiment via a Web browser.

DOI： 10.5940/jcrsj.54.359

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Other Link： https://jlc.jst.go.jp/DN/JALC/10013526589?from=CiNii

Language：English   Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography (IUCr)  

AR-NW12A is an in-vacuum undulator beamline optimized for high-throughput macromolecular crystallography experiments as one of the five macromolecular crystallography (MX) beamlines at the Photon Factory. This report provides details of the beamline design, covering its optical specifications, hardware set-up, control software, and the latest developments for MX experiments. The experimental environment presents state-of-the-art instrumentation for high-throughput projects with a high-precision goniometer with an adaptable goniometer head, and a UV-light sample visualization system. Combined with an efficient automounting robot modified from the SSRL SAM system, a remote control system enables fully automated and remote-access X-ray diffraction experiments. © 2012 International Union of Crystallography.

DOI： 10.1107/s0909049512009727

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Hydrostatic pressure induces structural changes in proteins, including denaturation, the mechanism of which has been attributed to water penetration into the protein interior. In this study, structures of 3-isopropylmalate dehydrogenase (IPMDH) from Shewanella oneidensis MR-1 were determined at about 2 Å resolution under pressures ranging from 0.1 to 650 MPa using a diamond anvil cell (DAC). Although most of the protein cavities are monotonically compressed as the pressure increases, the volume of one particular cavity at the dimer interface increases at pressures over 340 MPa. In parallel with this volume increase, water penetration into the cavity could be observed at pressures over 410 MPa. In addition, the generation of a new cleft on the molecular surface accompanied by water penetration could also be observed at pressures over 580 MPa. These water-penetration phenomena are considered to be initial steps in the pressure-denaturation process of IPMDH.

DOI： 10.1107/S0907444912001862

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Structural biology beamlines at the Photon Factory

DOI： 10.1107/S0108767312097152

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

A direct outcome of the exponential growth of macromolecular crystallography is the continuously increasing demand for synchrotron beam time, both from academic and industrial users. As more and more projects entail screening a profusion of sample crystals, fully automated procedures at every level of the experiments are being implemented at all synchrotron facilities. One of the major obstacles to achieving such automation lies in the sample recognition and centring in the X-ray beam. The capacity of UV light to specifically react with aromatic residues present in proteins or with DNA base pairs is at the basis of UV-assisted crystal centring. Although very efficient, a well known side effect of illuminating biological samples with strong UV sources is the damage induced on the irradiated samples. In the present study the effectiveness of a softer UV light for crystal centring by taking advantage of low-power light-emitting diode (LED) sources has been investigated. The use of UV LEDs represents a low-cost solution for crystal centring with high specificity.

DOI： 10.1107/S0909049510028670

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：INT UNION CRYSTALLOGRAPHY  

Low energy SAD experiments performed at the photon factory BL-1A

DOI： 10.1107/S0108767311091057

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：INT UNION CRYSTALLOGRAPHY  

Structure study of IPMDH from piezosensitive and piezophilic Shewanella species

DOI： 10.1107/S0108767311093111

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：INT UNION CRYSTALLOGRAPHY  

Structural biology and SAXS beamlines at the photon factory

DOI： 10.1107/S0108767311079669

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Potential of UV in phasing and its implementation for crystal centering at PF

DOI： 10.1107/S0108767311083425

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：PHARMACEUTICAL SOC JAPAN  

The Targeted Protein Research Program (TPRP) started in 2007 as a sequel of the Protein 3000 Project which lasted from 2002 to 2007. In the new project, four cores, Protein Production, Structure Analysis, Control of Protein Functions with Compounds, and Informatics, have been established as focus of methodology developments critical for functional and structural studies by the target protein research teams. Within the "Analysis Core" synchrotron radiation plays a pivotal role providing X-ray beams for structural analyses of the target proteins. The two large Japanese synchrotron radiation facilities, SPring-8 and Photon Factory (PF), along with three protein crystallography groups from Hokkaido, Kyoto and Osaka Universities have teamed up to develop two complementary micro-beam beamlines, one on each synchrotron site, and associated technologies for cutting edge structural biology research. At the PF, there are 5 operational beamlines which are equipped with state-of-the-art instrumentation for high-throughput protein crystallography experiments. Within the TPRP framework, the PF is developing a micro-focus beamline optimized for a lower energy single anomalous diffraction (SAD) experiment. This will be particularly useful for structure determination of difficult protein targets for which heavy atom derivatives or selenomethionine substitution does not work and other standard phasing methods fail to give structure solutions. This will augment the capabilities of the PF structural biology beamlines with similar look-and-feel experimental environments.

DOI： 10.1248/yakushi.130.631

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

With the global spread of the pandemic H1N1 and the ongoing pandemic potential of the H5N1 subtype, the influenza virus represents one of the most alarming viruses spreading worldwide. The influenza virus sialidase is an effective drug target, and a number of inhibitors are clinically effective against the virus (zanamivir, oseltamivir, peramivir). Here we report structural and biochemical studies of the human cytosolic sialidase Neu2 with influenza virus sialidase-targeting drugs and related compounds.

DOI： 10.1021/jm100078r

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The dual-specificity protein kinase monopolar spindle 1 (Mps1) is a central component of the mitotic spindle assembly checkpoint (SAC), a sensing mechanism that prevents anaphase until all chromosomes are bioriented on the metaphase plate. Partial depletion of Mps1 protein levels sensitizes transformed, but not untransformed, human cells to therapeutic doses of the anticancer agent Taxol, making it an attractive novel therapeutic cancer target. We have previously determined the X-ray structure of the catalytic domain of human Mps1 in complex with the anthrapyrazolone kinase inhibitor SP600125. In order to validate distinct inhibitors that target this enzyme and improve our understanding of nucleotide binding site architecture, we now report a biophysical and structural evaluation of the Mps1 catalytic domain in the presence of ATP and the aspecific model kinase inhibitor staurosporine. Collective in silico, enzymatic, and fluorescent screens also identified several new lead quinazoline Mps1 inhibitors, including a low-affinity compound termed Compound 4 (Cpd 4), whose interaction with the Mps1 kinase domain was further characterized by X-ray crystallography. A novel biophysical analysis demonstrated that the intrinsic fluorescence of SP600125 changed markedly upon Mps1 binding, allowing spectrophotometric displacement analysis and determination of dissociation constants for ATP-competitive Mps1 inhibitors. By illuminating the structure of the Mps1 ATP-binding site our results provide novel biophysical insights into Mps1-ligand interactions that will be useful for the development of specific Mps1 inhibitors, including those employing a therapeutically validated quinazoline template.

DOI： 10.1021/bi901970c

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：AMER INST PHYSICS  

To remotely control and automatically collect data in high-throughput X-ray data collection experiments, the Structural Biology Research Center at the Photon Factory (PF) developed and installed sample exchange robots PAM (PF Automated Mounting system) at PF macromolecular crystallography beamlines; BL-5A, BL-17A, AR-NW12A and AR-NE3A. We developed and installed software that manages the flow of the automated X-ray experiments; sample exchanges, loop-centering and X-ray diffraction data collection. The fully automated data collection function has been available since February 2009. To identify sample cassettes, PAM employs a two-dimensional bar code reader. New beamlines, BL-1A at the Photon Factory and BL32XU at SPring-8, are currently under construction as part of Targeted Proteins Research Program (TPRP) by the Ministry of Education, Culture, Sports, Science and Technology of Japan. However, different robots, PAM and SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), will be installed at BL-1A and BL32XU, respectively. For the convenience of the users of both facilities, pins and cassettes for PAM and SPACE are developed as part of the TPRP.

DOI： 10.1063/1.3463297

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Crystallographic Society of Japan  

An increasing number of Rab GTPases associated with partial dysfunction has been linked to several human diseases characterized by a diminution in vesicle transport. Due to its direct implication in human disorders, the Rab27 subfamily is considered as a standard for vesicle docking studies. By which mechanism Rab27 effectors distinguish among the pool of Rab GTPases? What is the underneath machinery rendering the interaction of eleven distinct effectors specific of Rab27 when compared to other Rabs of the secretory pathway? By solving the X-ray structures of Rab27, both in its inactive form and active form bound to the effector protein Slp2-a, attempts have been given to unravel the molecular basis of regulation of the delivering process of vesicles to fusion by the Rab27 subfamily.

DOI： 10.5940/jcrsj.51.334

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Other Link： https://jlc.jst.go.jp/DN/JALC/00346245141?from=CiNii

Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：CELL PRESS  

Rab GTPases coordinate vesicular trafficking within eukaryotic cells by collaborating with a set of effector proteins. Rab27a regulates numerous exocytotic pathways, and its dysfunction causes the Griscelli syndrome human immunodeficiency. Exophilin4/Slp2-a localizes on phosphatidylserine-enriched plasma membrane, and its N-terminal Rab27-binding domain (RBD27) specifically recognizes Rab27 on the surfaces of melanosomes and secretory granules prior to docking and fusion. To characterize the selective binding of Rab27 to 11 various effectors, we have determined the 1.8 A resolution structure of Rab27a in complex with Exophilin4 RBD27. The effector packs against the switch and interswitch elements of Rab27a, and specific affinity toward Rab27a is modulated by a shift in the orientation of the effector structural motif (S/T)(G/L)xW(F/Y)(2). The observed structural complementation between the interacting surfaces of Rab27a and Exophilin4 sheds light on the disparities among the Rab27 effectors and outlines a general mechanism for their recruitment.

DOI： 10.1016/j.str.2008.07.015

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

Chromosomal instability can result from defective control of checkpoints and is associated with malignant cell growth. Monopolar spindle 1 (Mps1) is a dual-specificity protein kinase that has important roles in the prevention of aneuploidy during the cell cycle and might therefore be a potential target for new therapeutic agents in the treatment of cancer. To gain insights into the molecular mechanism of Mps1 inhibition by small molecules, we determined the x-ray structure of Mps1, both alone and in complex with the ATP-competitive inhibitor SP600125. Mps1 adopts a classic protein kinase fold, with the inhibitor sitting in the ATP-binding site where it is stabilized by hydrophobic interactions. We identified a secondary pocket, not utilized by SP600125, which might be exploited for the rational design of specific Mps1 inhibitors. These structures provide important insights into the interaction of this protein kinase with small molecules and suggest potential mechanisms for Mps1 regulation.

DOI： 10.1074/jbc.M803026200

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By switching between GTP-active and GDP-inactive conformations, small Ras GTPases partly regulate membrane trafficking, cell growth and cytoskeleton dynamics. Among Rab GTPases, the Rab27 subfamily, which comprises Rab27a and Rab27b, controls the proper targeting of secretory vesicles to the plasma membrane. GppNHp-bound Rab27a in complex with the Rab27-binding domain of exophilin4/Slp2-a effector has been purified and crystallized for structural studies. The crystals belong to space group P2(1)2(1)2(1) and a complete data set was collected to a resolution of 1.8 A. Eventually, the structural characterization of the Rab27a-exophilin4/Slp2-a complex will clarify Rab27 recognition by its effectors prior to vesicle tethering and docking.

DOI： 10.1107/S1744309108009251

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Atomic model of Rab27a: Exophilin4/Slp2-a complex: Structural studies on vesicular transport

DOI： 10.1107/S0108767308089344

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Members of the Rab family of small GTPases regulate membrane traffic within the cell by recruiting their specific effectors in a nucleotide-dependent manner. The Rab27 subfamily consists of Rab27a and Rab27b, which share 70% sequence identity. By interacting with a large set of effector proteins such as melanophilin and granuphilin, both Rab27a and Rab27b regulate the exocytosis of secretory lysosomes. Here, the crystal structures of mouse Rab27b in complex with GDP have been determined in three distinct crystal lattices. Surprisingly, Rab27b-GDP exists in an open conformation with protruding switch and interswitch regions, which are stabilized through dimerization by means of domain-swapping in the crystals. In contrast, small-angle X-ray scattering measurements showed an extended monomer form of Rab27b in solution. The observed dimer formation of Rab27b-GDP in the crystals would restrain the highly flexible switch regions. Possible biological implications of this atypical structure of Rab27b and its plausible influence in effector interaction are discussed.

DOI： 10.1107/S0907444907019725

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：INT UNION CRYSTALLOGRAPHY  

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed. PXS can set up 7680 drops for vapour diffusion per hour, which includes time for replenishing supplies such as disposable tips and crystallization plates. Images of the crystallization drops are automatically recorded according to a preprogrammed schedule and can be viewed by users remotely using web-based browser software. A number of protein crystals were successfully produced and several protein structures could be determined directly from crystals grown by PXS. In other cases, X-ray quality crystals were obtained by further optimization by manual screening based on the conditions found by PXS.

DOI： 10.1107/S0907444906023821

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Society for Biochemistry and Molecular Biology, Inc.  

Gangliosides play key roles in cell differentiation, cell-cell interactions, and transmembrane signaling. Sialidases hydrolyze sialic acids to produce asialo compounds, which is the first step of degradation processes of glycoproteins and gangliosides. Sialidase involvement has been implicated in some lysosomal storage disorders such as sialidosis and galactosialidosis. Neu2 is a recently identified human cytosolic sialidase. Here we report the first high resolution x-ray structures of mammalian sialidase, human Neu2, in its apo form and in complex with an inhibitor, 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA). The structure shows the canonical six-blade beta-propeller observed in viral and bacterial sialidases with its active site in a shallow crevice. In the complex structure, the inhibitor lies in the catalytic crevice surrounded by ten amino acids. In particular, the arginine triad, conserved among sialidases, aids in the proper positioning of the carboxylate group of DANA within the active site region. The tyrosine residue, Tyr(334), conserved among mammalian and bacterial sialidases as well as in viral neuraminidases, facilitates the enzymatic reaction by stabilizing a putative carbonium ion in the transition state. The loops containing Glu(111) and the catalytic aspartate Asp(46) are disordered in the apo form but upon binding of DANA become ordered to adopt two short alpha-helices to cover the inhibitor, illustrating the dynamic nature of substrate recognition. The N-acetyl and glycerol moieties of DANA are recognized by Neu2 residues not shared by bacterial sialidases and viral neuraminidases, which can be regarded as a key structural difference for potential drug design against bacteria, influenza, and other viruses.

DOI： 10.1074/jbc.M411506200

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Event date： 2023.8

Language：English   Presentation type：Poster presentation  

Venue：Melbourne   Country：Australia  

In recent years, a new branch of macromolecular crystallography (MX) is emerging that focuses on protein crystals naturally occurring inside cells and organisms. This field of research is in turn named in cellulo or in vivo MX (ivMX), mostly depending on whether the crystals appear inside or outside cells. One of the motivations for studying these rare phenomena lies in their applicability to developing high throughput pipelines and revolutionizing the currently implemented workflows. The classical MX pipelines are composed of multiple interdependent steps. After overexpressing the protein of interest in heterologous expression systems, the samples are extensively purified to obtain a highly homogenous, concentrated, and stable sample solution. Prior to obtaining crystals of the purified protein, the sample solution is submitted to an empirical and semi-rational crystallization screening process that is time-consuming, costly, and with no insurance of success and crystallization. When considering ivMX, all the steps of sample purification and crystallization are removed and left to be done by the organism overexpressing the protein of interest. The ivMX involves proteins that eventually present post-translational modifications, another difference compared to the in vitro MX that commonly clips out these modifications for homogeneity. Only a few modified protein structures prepared through in vitro pipelines are deposited in the PDB, although these modifications are often key to the proteins' functions. Numerous efforts from various groups worldwide have been provided to obtain deeper insights into the yet uncontrollable events dictating natural crystal growth. One of these efforts led to the initiation of a platform at Synchrotron SOLEIL (France). To facilitate the use of ivMX by the larger community and in particular in Japan, milestones for the implementation of a complete pipeline have been set at Nagoya University and will be presented. The ivMX platform is part of the Next-BINDS national project and is aimed to open to general users in the coming year.

Event date： 2023.7

Language：Japanese   Presentation type：Poster presentation  

Venue：Nagoya Congress Center   Country：Japan  

The global situation that requires sustainable food is becoming more and more urgent. The current food system, which is based on industrialized agriculture, has a significant impact on the environment and human health. Industrialized agriculture has contributed to climate change, forest destruction, water pollution, and soil deterioration. In addition, the current food system is not fair when considering worldwide distribution. Many people around the world still have no access to sufficient nutritional foods, but others overconsume food considered unhealthy. To compile with these issues, the need for a more durable food system is increasing. This includes the promotion of sustainable agricultural practices that prioritize environmental health, animal welfare, and human happiness, reducing food waste, and increasing access to nutrients for all people. Cockroaches are generally not considered a source of sustainable food. There were research and experiments, however, using cockroaches as a potential source of protein for human consumption. Cockroaches are rich in proteins and other nutrients, and they can be grown in various disfavorable environments such as from organic wastes that usually go to discharge. Cockroaches can then be considered a potential sustainable source of protein, especially in areas where conventional protein sources are rare or expensive. Nevertheless, there are concerns regarding the safety and hygiene required while using cockroaches as human food. Cockroaches can transport bacteria and other pathogens, and even if they are not expensive they need to be treated in a controlled environment to avoid risks of pollution. In addition, cultural and societal barriers remain when considering cockroaches, or more generally insects.

Event date： 2023.1

Language：Japanese   Presentation type：Oral presentation (general)  

DOI： 10.5281/zenodo.7523504

Event date： 2022.11

Language：Japanese   Presentation type：Oral presentation (general)  

DOI： 10.5281/zenodo.7471979

Event date： 2021.8

Language：English   Presentation type：Oral presentation (general)  

Event date： 2021.3

Language：English   Presentation type：Oral presentation (general)  

Venue：Nagoya University   Country：Japan  

DOI： 10.5281/zenodo.4646448

Language：English   Presentation type：Oral presentation (general)  

Venue：Nagoya University   Country：Japan  

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Other Link： https://doi.org/10.5281/zenodo.4646448

Language：Japanese   Presentation type：Public lecture, seminar, tutorial, course, or other speech  

The research in biology as a whole faces great challenges when it comes to an extensive and detailed comprehension of the molecular interactions and complex mechanisms within living systems. To image and understand such systems extends across multiple approaches at mixed scales down to chemical imaging of compartmentalised environments. Biological systems present an intricate architectural organisation, where the structural disposition of the macromolecules, their individual functions and interactions within the cellular systems, and the effects on the entire organisms need to be explored. The integration of the multiple information coming from disparate techniques arises as a key organisational step in modern biology research, calling for the implementation of shared scientific platforms. Taking this in consideration, I intend to present what are the possibilities for integrated biology at the Applied Structural Biology and Methodology research group from the Synchrotron Radiation Research Center of Nagoya University. Notably, I will attempt to highlight the opportunities that lie behind novel sample preparation methods, among which the capacity of cells to grow crystals of unmodified proteins.

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Language：English   Presentation type：Oral presentation (general)  

Country：France  

The research in biology as a whole faces great challenges when it comes to an extensive and detailed comprehension of the molecular interactions and complex mechanisms within living systems. To image and understand such systems extends across multiple approaches at mixed scales down to chemical imaging of compartmentalized environments. Biological systems present an intricate architectural organization, where the structural disposition of the macromolecules, their individual functions and interactions within the cellular systems, and the effects on the entire organisms need to be explored. The integration of the multiple information coming from disparate techniques arises as a key organizational step in modern biology research, calling for the implementation of shared scientific platforms. Taking this in consideration, I intend to present what are the possibilities for integrated biology at modern research facilities by taking advantage fo state-of- the-art instrumentations combined to the latest developments in artificial intelligence and the finest molecular dynamics projects dedicated to the field of protein structure prediction. Notably, I will attempt to highlight the opportunities that lie behind novel sample preparation methods, among which the capacity of cells to grow crystals of unmodified proteins, and how to handle these cells for experimenting at various instruments and for gaining information at different scales.

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Language：Japanese   Presentation type：Poster presentation  

The Aichi synchrotron is a 1.2 GeV synchrotron located in Nagoya suburbs. The small electron storage ring provides synchrotron light to X beamlines, operating at 300 mA on a top-up injection mode. The beamline BL2S1 is accommodated in one of the available bending magnets of Aichi synchrotron. The end-station was built and is maintained by the Nagoya University Synchrotron Radiation Research Center since 2015. By adjusting a series of dedicated optics, the beamline can accommodate various types of experiments, including single-crystal diffraction, powder diffraction, and high-pressure diffraction.
High-pressure protein x-ray crystallography (hereafter referred to HPPX) is a specific branch of macromolecular crystallography that provides mixed information of protein structures placed under various pressure conditions. Hence, the HPPX technique gives valuable insights in the hydration states at the molecular surface of the proteins, and within internal cavities. Moreover, the method can be applied for investigating the different states of biological events (e.g. enzymatic reaction mechanisms...) or for the study of the differences among deep sea and homolog ‘ambient pressure’ organisms.
In the current presentation, I will summarize the HPPX results obtained at the BL2S1 beamline during its 6 years of operation. Some emphasizes will be given on the future implementation plans of the beamline, both in terms of HPPX and for more classical experimental setups.

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Language：Japanese   Presentation type：Oral presentation (general)  

The identification of protein crystals naturally occurring inside cells and organisms has opened a window for a new type of macromolecular crystallography (MX) and structural biology, referred to as in vivo MX. In the past decade, efforts were provided in getting deeper insights into the yet uncontrollable events dictating in vivo crystal growth, by further developing sample handling and delivery procedures and applying these techniques to the structure determination and analysis of readily available ivMX systems.
To facilitate the use of ivMX by the larger community, milestones for the implementation of a complete pipeline has been set at Synchrotron SOLEIL (France). In the current presentation, I will be introducing the hows and whys of ivMX, the basics behind the platform and the promising results obtained when applied to the studies of the SARS-CoV-2 pathogen responsible of the CoViD-19.

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Language：English   Presentation type：Poster presentation  

Recent developments in ultra-brilliant synchrotron and hard X-ray free electron lasers (FEL) open very exciting possibilities in structural biology, such as serial protein crystallography (1) and time resolved structural studies of bio-macromolecules. These techniques already contribute to high impact science, yet both require high consumption of crystals and generate large data volumes for structural analysis, potentially requiring long periods of beamtime acquisition on oversubscribed central facilities. These issues can be somewhat mitigated with efficient sample delivery under the X-ray beam. Microfluidic and microscale technologies have played a critical role in facilitating both protein crystallization and structure determination (2). The transfer of microfluidic technology experiments is, however, technically challenging due to the requirement of X-ray compatibility of the different device materials. In the current presentation we will review the impact of microfluidic device technologies on protein crystal growth and X-ray diffraction analysis. We focus on applications of microfluidics for use in serial protein crystallography experiments at synchrotron sources. At Synchrotron Soleil, the microfluidic team, together with the life sciences scientists provides expertise in the design, manufacturing, and experimental implementation of microfluidic devices optimized for X-ray experiments. We also provide facilitated means of sample handling and specialized sample environments that address specific experimental conditions at synchrotrons and XFEL facilities. Finally, we are attempting to prepare standardized microfluidic trapping devices for biomacromolecular structural studies at Synchrotron Soleil and other synchrotron facilities (3).

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Language：English   Presentation type：Poster presentation  

Synchrotron Soleil is the French national synchrotron source located on the Saclay Plateau in the Parisian suburbs. Two beamlines dedicated to the macromolecular crystallography, PROXIMA1 and PROXIMA2A, have hosted both academic and industrial users for the several years now. To cope with the COVID-19 pandemic, the development and implementation of computing tools have been accelerated to facilitate remote access. Both beamlines were the first to come back on-line host users after the lockdown in May 2020.
- The two beamlines are remotely controlled via NoMachine. - Recent developments allow users to prepare and visualize their data in EXI2 - a new version of ISPyB : http://vedette-ng.synchrotron- soleil.fr:8081/EXI2/ - XDSME and AutoPROC pipelines are available for automatic image processing and the results can be examined via EXI2. Some output results can be downloaded.
- GLOBUS is now available for data retrieval: http://globus.org
To maintain contact with our user community, we have instigated regular BAG training webinars.
Instructions and tutorials are also available on the SOLEIL website.
In view of the planned upgrade to the SOLEIL storage ring, proposals for the future of MX at SOLEIL are being prepared. These will be presented to the user community at a workshop in 2022.

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Language：English   Presentation type：Poster presentation  

Country：France  

Chemotherapy or radiobiology treatments aim at generating DNA double-strand breaks (DSBs). Tumor cells are more sensitive to DSBs than healthy cells due their phenotype and genotype[1]. One important axis in radiobiology is to combine radiation therapy with inhibitors of the DNA repair pathways to increase radio-sensitivity and overcome radiation resistance of some cancer cells[2]. Our objectives is to unveil the molecular mechanism of the NHEJ (Non Homologous End Joining) pathway and to characterize new specific inhibitors of this pathway. Ku70/Ku80 heterodimer (Ku) is a central player of the NHEJ for DSB recognition and in downstream DNA events (processing and ligation steps). Our team showed that Ku can recruit several enzymes of the NHEJ pathway through direct interactions and thus acts as a hub that coordinates the whole NHEJ[3][4][5]. Many interactions involve motifs called KBM (Ku Binding Motif). One of the enzymes is Werner (WRN) that has two KBM motifs. This protein is part of the helicase RecQ family. It is the only member of this family to have in addition to its helicase domain, an exonuclease domain. It is particularly studied in the case of Werner Syndrome, a rare autosomal- recessive inherited disease, characterised by an early aging[6]. It was also identified as a promising drug target for frequent cancers presenting local DNA instability[7], but little is known about its role in the NHEJ pathway. During my PhD, I successfully produced several WRN constructs and full-length protein and studied them by combining multiple structural approaches. I showed that WRN can adopt several oligomeric state using SAXS and SEC-MALS, and that WRN interacts directly with Ku through two peptidic motifs, located in N-terminal and C-terminal extremity. I determined the CryoEM structure of a Ku-DNA complex bound to the exonuclease domain of WRN at 3Å of resolution. We showed that Ku recruits WRN through its KBM motif and position the DNA in the exonuclease site of WRN. Our collaborators analysed by life cell imaging and enzymatic assays the Ku-WRN interaction and observed a stimulatory effect of Ku on WRN function in good agreement with our data.

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Language：Japanese   Presentation type：Oral presentation (general)  

Since 2007, the Synchrotron Radiation Research Center at Nagoya University (NUSR) worked together with the Aichi Synchrotron Center (AichiSR) to operate the Aichi synchrotron source and provide an expert service to its users. As part of its activities, the NUSR participates in the daily actions of the AichiSR, but also has its own research projects, all of which related to synchrotron radiation and oriented toward user support. By providing a large set of expertise to academic and industrial users in terms of synchrotron light source, sample preparation and data analysis, members of the NUSR are experimenting at all Japanese x-ray sources and other international facilities.
During the presentation, I would like to introduce to the audience this very peculiar, yet inspiring approach adopted by the NUSR, summarize 10 years of collaboration with the AichiSR, and present the objectives envisioned for the center in views of an evolving research community.

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Work type：Software   Location：Nagoya University BL2S1 at AichiSR  

UGUI2 is a software developed for controlling the experiments performed at the Photon Factory beamlines for structural biology. The software was modified and implemented at the Nagoya University BL2S1 beamline at AichiSR.

Work type：Artistic work  

Art work to illustrate the work done on the methane emission.

Work type：Artistic work  

Art work to illustrate the work done on the black rote disease.

Work type：Web Service  

Development and maintenance of the Home and Linked internet pages for the organized NUSR Symposium 2021

Coordination of the project related to Ferritin protein involving:
- Kono Yusuka (M1 student) for experimental protocols
- Onoda Hiroki (Assistant Professor) for assistance in the experiments

Promotion of the BL2S1 beamline operation by:
- the organization of weekly 2 hrs meetings
- the development of dedicated software for beamline control
- the execution of safety procedures

Coordination of the cohesion with the Biomolecular Physics group by:
- the organization of weekly 90 min meetings
- the organization of bi-weekly 30 min discussions with all members

Contribution to the operation, maintenance, and upgrading of the beamlines of the Aichi SR

Support for Nagoya University faculty, staff, and students using the Aichi SR beamlines

Educational guidance for students using Aichi SR

Contribution to the operation of the Aichi SR by providing education and technical guidance to Aichi SR staff and by hosting meetings of beamline supervisors at the Aichi SR

Working out on setting up international collaborations with France universities by
- discussing with the Academic research responsible person at the French Embassy in Tokyo about possibliities

Contribution to the operation, maintenance, and upgrading of the beamlines of the Aichi SR

Contribution to the operation of the Aichi SR by providing education and technical guidance to Aichi SR staff and by hosting meetings of beamline supervisors at the Aichi SR

Educational guidance for students using Aichi SR

Support for Nagoya University faculty, staff, and students using the Aichi SR beamlines

Audience： College students,　Graduate students,　Teachers,　Researchesrs

Type：Seminar, workshop

Audience： College students,　Graduate students,　Teachers,　Researchesrs

Type：Seminar, workshop

Audience： College students,　Graduate students,　Teachers,　Researchesrs

Type：Seminar, workshop

Audience： High school students,　Teachers

Type：University open house

Audience： High school students,　Teachers

Type：University open house

Audience： College students,　Graduate students,　Teachers,　Researchesrs

Type：Seminar, workshop

Audience： College students,　Graduate students,　Teachers,　Researchesrs

Type：Seminar, workshop

Audience： High school students,　College students,　Graduate students,　Teachers,　Guardians,　Researchesrs,　General,　Scientific,　Company,　Civic organization,　Governmental agency,　Media

Type：Promotional material

Description of the various activities at Nagoya University BL2S1 beamline by setting up a promotion video.

Audience： High school students,　College students,　Graduate students,　Teachers,　Guardians,　Researchesrs,　General,　Scientific,　Company,　Civic organization,　Governmental agency,　Media

Type：Promotional material

Description of the various activities within the Engineering department of Nagoya University

Audience： Company,　Media

Type：Seminar, workshop

Organization of seminars oriented toward publicizing the use of Nagoya University BL2S1 beamline at AichiSR.

Type：Peer review 

Type：Peer review 

Type：Peer review 

Type：Peer review 

Type：Peer review 

Type：Peer review 

Type：Peer review 

Type：Peer review 

Type：Competition, symposium, etc. 

Participation to the 10th conference of the AichiSR special access users.

Type：Academic society, research group, etc. 

Redundant meeting to discuss the organization within the Biomolecular Physics group.
Meeting #3: presentation by Prof. Onoda

Redundant meeting to discuss the organization within the Engineering Department of Nagoya University

Type：Academic society, research group, etc. 

Redundant meeting to discuss the organization within the Biomolecular Physics group.
Meeting #2: presentation by Prof. Umena

Type：Academic society, research group, etc. 

Redundant meeting to discuss the organization within the Biomolecular Physics group.

Type：Competition, symposium, etc. 

Type：Peer review 

Type：Peer review 

Type：Peer review 

Type：Peer review