Nihon Kessho Gakkaishi
Online ISSN : 1884-5576
Print ISSN : 0369-4585
ISSN-L : 0369-4585
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Displaying 1-20 of 20 articles from this issue
Preface
Special Issue Graph Theory Meets Crystallography
  • Tomoyasu YOKOYAMA, Kazuhide ICHIKAWA, Hisashi NAITO
    2024 Volume 66 Issue 2 Pages 60-70
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    The crystal structure can be thought of as consisting of space-filling polyhedra, which affect material properties such as ionic conductivity and dielectric constant. However, most conventional methods of crystal structure prediction use random structure generation methods that do not take space-filling polyhedra into account, contributing to the inefficiency of materials development. In this work, we propose a crystal structure generation method based on discrete geometric analysis of polyhedra information. In our method, the shape and connectivity of a space-filling polyhedron are represented as a dual periodic graph, and the crystal structure is generated by the standard realization of this graph. We demonstrate that this method can correctly generate face-centered cubic, hexagonal close-packed, and body-centered cubic structures from dual periodic graphs. This work is a first step toward generating undiscovered crystal structures based on the target polyhedra, leading to major advances in materials design in areas including electronics and energy storage.

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Current Topics in Crystallography
Review Articles
  • Tetsuya ISHIKAWA
    2024 Volume 66 Issue 2 Pages 79-86
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    X-ray crystallography has significantly changed with the advancement of X-ray light sources, particularly since synchrotron radiation X-ray sources emerged in the 1970s. Over the years, the author has been proud to contribute indirectly to the progress of crystallography by supporting the development of synchrotron radiation facilities. In this paper, the relationship between the evolution of light sources and crystallography at the Photon Factory, SPring-8, and SACLA will be discussed, all of which the author was involved in constructing. The future of crystallography in the upcoming SPring-8-II project is also discussed.

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  • Masahiro FUJIHASHI
    2024 Volume 66 Issue 2 Pages 87-93
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    Enzymes are tremendous catalysts. Protein crystallography widely and deeply contributes to the elucidation of their reaction mechanism as well as to the exploration and modification of useful enzymes. Structure analysis of orotidine monophosphate decarboxylase(ODCase), which is one of the most proficient enzymes, also elucidates its reaction mechanism, in which the substrate distortion largely contributes to the catalysis. The distortion destabilizes the enzyme-substrate complex but not the transition state complex, to increase both kcat/KM and kcat along with transition state stabilization. Besides, this review focuses on the pyrophosphate dependent kinases(PPi-kinases)as an example of the exploration and modification of useful enzymes. Kinases typically transfer a phosphate group from a nucleoside triphosphate such as ATP to a suitable acceptor molecule, but rarely utilize pyrophosphate as a phosphate donor. We have identified several PPi-kinases based on the structural features elucidated by crystallographic analysis. Crystallographic data also enabled us to alter the product of a PPi-kinase by replacing the ligand recognition residues. The combination of crystallography-based methodology with AlphaFold2/AlphaFold3 prediction promises further discovery of novel enzymes and the alternation of the enzymatic reactions.

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  • Yuki TAKAYAMA
    2024 Volume 66 Issue 2 Pages 94-102
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    We developed a hard X-ray coherent diffraction imaging(CDI)system dedicated for visualization of spatio-temporally hierarchical structures of thick objects under atmospheric condition. CDI is a lens-less nanoimaging technique, where a set of coherent diffraction patterns of the imaging target is collected and subjected to iterative phase retrieval calculation to reconstruct both absorption and phase images of the target. Spatial resolutions of ~10 nm for two-dimensional projection and ~20 nm for three-dimensional computed tomography were achieved. In addition, we extended the method to dynamic nanoimaging and demonstrated capability of capturing nanodynamics at frame rates of 10~100 fps.

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Article
  • Youichi OKIMOTO, Tatsuo FUJII, Naoshi IKEDA
    2024 Volume 66 Issue 2 Pages 103-108
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    Mixed-valence ferrites RFe2O4(R=trivalent rare earth ions)consist of an equal number of Fe2+ and Fe3+ in a triangular lattice. The Fe2+ and Fe3+ exhibit long-range charge ordering at room temperature. It has long been pointed out that the charge ordering breaks the inversion symmetry of the crystal, and RFe2O4 has been a candidate for electronic ferroelectric material at room temperature. We report here our recent success in synthesizing RFe2O4 single crystals with high chemical stoichiometry by the floating zone method and high-quality thin films by the magnetron sputtering technique. We also describe the details of the synthesis of RFe2O4 crystals mentioning the history of RFe2O4 research so far. We will also report on the observation of electronic ferroelectric polarization in RFe2O4 through neutron scattering measurements and second harmonic generation measurements using the obtained single crystals, and our recent attempts at ultrafast optical control of the electric polarization in RFe2O4.

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Special Issue Structural Biology of SARS-CoV-2
  • Shunsuke KITA, Taiyo SOMEYA, Tomo NOMAI, Yuki ANRAKU, Katsumi MAENAKA
    2024 Volume 66 Issue 2 Pages 109-114
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    SARS-CoV-2 spike protein plays an important role in invading host cells. Spike protein is one of the targets of neutralizing antibodies, and thus is well studied for vaccine design and development of therapeutic antibodies. Here we review our research regarding the structure analysis of SARS-CoV-2 spike protein and spike-antibody complex with X-ray crystallography and cryo-EM.

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  • Akifumi HIGASHIURA, Akima YAMAMOTO, Takemasa SAKAGUCHI, Tomoharu YASUD ...
    2024 Volume 66 Issue 2 Pages 115-120
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    Here, we analyzed broadly neutralizing antibodies isolated from long-term hospitalized convalescent patients of early SARS-CoV-2 strains. Antibodies named NCV2SG48 and NCV2SG53 are highly potent to broad SARS-CoV-2 variants. To reveal the mode of action, we determined the crystal structure of the Fab fragment of NCV2SG48 or NCV2SG53 in a complex with RBD of the S proteins from the Wuhan-Hu-1 and Omicron BA.1.

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  • Shiho YAMAMOTO, Yuto UNOH, Shota UEHARA, Teruhisa KATO, Yuki TACHIBANA
    2024 Volume 66 Issue 2 Pages 121-126
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    We pursued structure-based drug design(SBDD)targeting the 3CL protease of SARS-CoV-2 in order to develop a COVID-19 therapeutic drug. Through virtual screening using our in-house compound library, we identified hit compounds and optimized them while leveraging the co-crystal structure with the 3CL protease. As a result, we successfully achieved over 600-fold improvement in enzyme inhibition activity within a short period of time and finally developed ensitrelvir, which exhibited excellent antiviral activity and pharmacokinetic profile.

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  • Keishi YAMAGUCHI
    2024 Volume 66 Issue 2 Pages 127-132
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    The continuous emergence of severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)variants is still prolonging the global coronavirus disease 2019 pandemic. A dimerized variable domain of heavy chain of heavy chain antibody(VHH)P17 that has highly potent neutralizing activity against SARS-CoV-2 has been reported but the mode of interaction with the epitope remains unclear. Here, we report the complex structure of monomerized P17 bound to the SARS-CoV-2 receptor binding domain(RBD). The structure revealed details of the binding interface and showed that P17 had an appropriate linker length to have an avidity effect. Furthermore, we identified mutations that decrease the binding affinity of P17 and proposed methods for the acquisition of affinity toward the Omicron RBD.

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  • Jun-ichi KISHIKAWA
    2024 Volume 66 Issue 2 Pages 133-137
    Published: May 31, 2024
    Released on J-STAGE: June 12, 2024
    JOURNAL FREE ACCESS

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolves continuously under the humoral immune pressure. As the result, the many variants displaying immune evasion and antibody escape have emerged. An engineered angiotensin-converting enzyme 2 (ACE2) decoy which has higher affinity for the spike protein of SARS-CoV-2 could offer alternative way to neutralize SARS-CoV-2. In this study, we showed that ACE2 decoy capture spike proteins more readily than wild-type ACE2 by single particle cryo-EM. We also demonstrated that the ACE2 decoy retains neutralization activity against Omicron subvariants, which are resistant to antibodies. Furthermore, in SARS-CoV-2 infected rodents, inhalation of aerosolized ACE2 decoys was 20-fold efficient in its therapeutic effect than the intravenous administration. In addition, it is also demonstrated that ACE2 decoy has therapeutic effect for cynomolgus macaques. In this manuscript, in addition to these results, the structural analysis of spiked proteins by Cryo-EM will also be presented.

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