Publishing type：Research paper (scientific journal)   Publisher：American Physical Society (APS)  

DOI： 10.1103/physrevmaterials.8.l052601

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Other Link： http://harvest.aps.org/v2/journals/articles/10.1103/PhysRevMaterials.8.L052601/fulltext

Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.chemmater.4c00355

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.carbon.2024.119075

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpclett.4c00319

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.mseb.2023.116579

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.cgd.2c01537

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acsabm.2c01033

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.cartre.2023.100246

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcb.2c06329

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography (IUCr)  

The double-crystal configuration is useful for the evaluation of strain and defects in single crystals. In this study, rocking curve measurements by X-ray topography in the double-crystal configuration were demonstrated using perfect crystals of the protein glucose isomerase (GI). The setup enables precise evaluation of perfection in protein crystals with the nearly nondispersive X-ray optics. It reveals the uniform perfection of GI crystals according to the theory of X-ray diffraction. It is expected that unknown imperfections in various protein crystals of lower quality will be revealed by the nondispersive configuration using perfect protein crystals.

DOI： 10.1107/s1600576722007130

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.cplett.2022.140094

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

We report two organic crystals of 2,2′:6′,2′′-terpyridine derivatives each substituted with luminescent naphthyl and anthryl moieties, displaying multi-faceted flexible bending with elasticity in response to mechanical stress.

DOI： 10.1039/d2ce01167k

Scopus

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Society of Materials Science, Japan  

DOI： 10.2472/jsms.71.749

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Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences  

Significance

Growing high-quality protein crystals is a prerequisite for the structure analysis of proteins by X-ray diffraction. However, dislocation-free perfect protein crystals such as silicon and diamond are limited to two kinds of protein crystals. We wonder whether other high-quality or dislocation-free protein crystals still exhibit some imperfection. Here, we explore the existence of twisting as a cause of imperfection in high-quality protein crystals by X-ray topography with synchrotron radiation. The magnitude of twisting is quite small and cannot be detected by conventional techniques as optical and electron microscopy. The formation of twisting may be related to the geometric frustration mechanism proposed as a primary mechanism of twisting. This finding provides insights on high-quality protein crystals with the ubiquity of twisting.

DOI： 10.1073/pnas.2120846119

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

A long alkyl-chained organic molecule has been crystallized into elastically or plastically deformable bending types depending on the recrystallization solvent.

DOI： 10.1039/d2cc00663d

Scopus

PubMed

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Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography (IUCr)  

The characterization of crystal defects induced by irradiation, such as X-rays, charged particles and neutrons, is important for understanding radiation damage and the associated generation of defects. Radiation damage to protein crystals has been measured using various methods. Until now, these methods have focused on decreased diffraction intensity, volume expansion of unit cells and specific damage to side chains. Here, the direct observation of specific crystal defects, such as dislocations, induced by X-ray irradiation of protein crystals at room temperature is reported. Dislocations are induced even by low absorbed doses of X-ray irradiation. This study revealed that for the same total absorbed dose, the formation of defects appears to critically depend on the dose rate. The relationship between dislocation energy and dose energy was analyzed based on dislocation theory associated with elasticity theory for crystalline materials. This demonstration of the crystal defects induced by X-ray irradiation could help to understand the underlying mechanisms of X-ray-induced radiation damage.

DOI： 10.1107/s205979832101281x

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acsanm.1c02977

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Authorship：Lead author  

DOI： 10.19009/jjacg.48-2-02

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

It is important to reveal the exact cause of poor diffractivity in protein crystals in order to determine the accurate structure of protein molecules. It is shown that there is a large amount of local strain in subgrains of glucose isomerase crystals even though the overall crystal quality is rather high, as shown by clear equal-thickness fringes in X-ray topography. Thus, a large stress is exerted on the subgrains of protein crystals, which could significantly lower the resistance of the crystals to radiation damage. It is also demonstrated that this local strain can be reduced through the introduction of dislocations in the crystal. This suggests that the introduction of dislocations in protein crystals can be effective in enhancing the crystal quality of subgrains of protein crystals. By exploiting this effect, the radiation damage in subgrains could be decreased, leading to the collection of X-ray diffraction data sets with high diffractivity.

DOI： 10.1107/s2059798321001820

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Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

<p>Slip systems in triclinic hen egg-white lysozyme (Tri-HEWL) crystals, which is one of typical protein crystals, were identified by the indentation method and the surface energy estimation using phenomenological macro-bond methods.</p>

DOI： 10.1039/d1ce00241d

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Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography (IUCr)  

X-ray topography is a useful and nondestructive method for direct observation of crystal defects in nearly perfect single crystals. The grown-in dislocations from the cross-linked seed crystal in tetragonal hen egg-white lysozyme crystals were successfully characterized by digital X-ray topography. Digital X-ray topographs with various reflections were easily obtained by reconstruction of sequential rocking-curve images. The Burgers vector of the dislocation is different from those reported previously. Interestingly, one of the dislocations had a bent shape. The preferred direction of the dislocation line was analysed by the estimated dislocation energy based on the dislocation theory. The dislocation energy can be estimated by the dislocation theory even in protein crystals composed of macromolecules.

DOI： 10.1107/s1600576720015356

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.carbon.2020.07.061

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

Knowledge of X-ray diffraction in macromolecular crystals is important for not only structural analysis of proteins but also diffraction physics. Dynamical diffraction provides evidence of perfect crystals. Until now, clear dynamical diffraction in protein crystals has only been observed in glucose isomerase crystals. We wondered whether there were other protein crystals with high quality that exhibit dynamical diffraction. Here we report the observation of dynamical diffraction in thin ferritin crystals by rocking-curve measurement and imaging techniques such as X-ray topography. It is generally known that in the case of thin crystals it is difficult to distinguish whether dynamical diffraction occurs from only rocking-curve profiles. Therefore, our results clarified that dynamical diffraction occurs in thin protein crystals because fringe contrasts similar to <italic>Pendellösung</italic> fringes were clearly observed in the X-ray topographic images. For macromolecular crystallography, it is hard to obtain large crystals because they are difficult to crystallize. For thin crystals, dynamical diffraction can be demonstrated by analysis of the equal-thickness fringes observed by X-ray topography.

DOI： 10.1107/s2052252520007393

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

DOI： 10.1021/acs.cgd.9b01084

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.actamat.2018.06.018

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：National Academy of Sciences  

High-quality protein crystals meant for structural analysis by X-ray diffraction have been grown by various methods. The observation of dynamical diffraction in protein crystals is an interesting topic because dynamical diffraction generally occurs in perfect crystals such as Si crystals. However, to our knowledge, there is no report yet on protein crystals showing clear dynamical diffraction. We wonder whether the perfection of protein crystals might still be low compared with that of high-quality Si crystals. Here, we present observations of the oscillatory profile of rocking curves for protein crystals such as glucose isomerase crystals. The oscillatory profiles are in good agreement with those predicted by the dynamical theory of diffraction. We demonstrate that dynamical diffraction occurs even in protein crystals. This suggests the possibility of the use of dynamical diffraction for the determination of the structure and charge density of proteins.

DOI： 10.1073/pnas.1720098115

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

Vickers microindentation hardness of protein crystals was investigated on the (110) habit plane of tetragonal hen egg-white lysozyme crystals containing intracrystalline water at controlled relative humidity. The time evolution of the hardness of the crystals exposed to air with different humidities exhibits three stages such as the incubation, transition, and saturation stages. The hardness in the incubation stage keeps a constant value of 16 MPa, which is independent of the humidity. The incubation hardness can correspond to the intrinsic one in the wet condition. The increase of the hardness in the transition and saturation stages is well fitted with the single exponential curve, and is correlated with the reduction of water content in the crystal by the evaporation. The saturated maximum hardness also strongly depends on the water content equilibrated with the humidity. The slip traces corresponding to the 1 (1) over bar0 [110] slip system around the indentation marks are observed in not only incubation but also saturation stages. It is suggested that the plastic deformation in protein crystals by the indentation can be attributed to dislocation multiplication and motion inducing the slip. The indentation hardness in protein crystals is discussed in light of dislocation mechanism with Peierls stress and intracrystalline water.

DOI： 10.3390/cryst7110339

Web of Science

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

High quality glucose isomerase (GI) single crystals are grown by using chemical cross-linked seed crystals. The crystal structure is an orthorhombic system in which the molecular arrangement is close to a body-centered cubic (bcc) one. The crystal defects, especially dislocations, in GI crystals are experimentally characterized by synchrotron monochromatic-beam X-ray topography. Two straight dislocations are clearly observed, which originate from the interface between the cross-linked seed crystal and the grown crystal. From the invisibility criterion of the dislocation images, it is experimentally identified that they are close to be of pure edge character with the Burgers vector of [1 1 1] which is typical one in bcc metal crystals. Moreover, bead-like contrasts along the dislocation images and the equal-thickness fringes, related to Pendellosung fringes, at crystal edges are clearly observed, which have never been observed in other protein crystals so far. These contrasts can attributed to the dynamical diffraction effect which has been often observed in high-quality crystals such as Si. Thus it seems that the perfection of GI crystals shown in this paper is extremely high compared with other protein crystals reported so far.

DOI： 10.1016/j.jcrysgro.2016.10.047

Web of Science

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

We show that the extinction effect explained by the dynamical theory of diffraction must be considered even in the case of protein crystals. Equal-thickness fringes, which are attributed to the Pendellosung effect, were clearly observed in the region of a tapered glucose isomerase crystal with wedge-like edges using X-ray topography carried out with a beam of monochromatic synchrotron radiation. This indicates that the perfection of this glucose isomerase crystal is high enough to produce this dynamical theory-related effect: this surely leads to difficulty in the collection of accurate integrated intensities of diffraction spots for Xray structural analysis. Therefore, it is important to determine whether the crystal quality of a protein crystal under analysis is adequate to obtain accurate three-dimensional structures of protein molecules for X-ray structural analyses. We show that X-ray diffraction rocking-curve measurements can provide clues for this determination.

DOI： 10.1021/acs.cgd.6b00457

Web of Science

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Language：Japanese   Publisher：The Japanese Association for Crystal Growth  

<p>  Synchrotron X-ray topography is one of the most powerful methods for the observation and characterization of crystal defects, especially dislocations, in crystals. For protein crystals, larger crystals with millimeter size are required to obtain clear topographic contrasts of dislocations. In this review, various types of dislocations such as straight, loop, and curved ones are identified for large crystals of hen egg-white lysozyme and glucose isomerase (GI). Pendellösung fringes which have been seen in high quality Si crystals are also observed in GI crystals with high quality. In addition, digital topography with X-ray CCD camera is shown with the analysis of local rocking curves in protein crystals. The digital topography shows promising for the evaluation of not only the distribution but also the misorientation of subgrains with strain in protein crystals.</p>

DOI： 10.19009/jjacg.43.2_101

CiNii Books

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Hardness and slip systems by an indentation method were investigated on different habit planes of orthorhombic hen egg-white lysozyme (O-HEWL) crystals containing water. A dependence of the hardness on the water-evaporation time exhibits three stages as incubation, transition and saturated ones, as tetragonal (T)-HEWL crystals reported previously. The hardness values of (110), (010) and (011) habit planes of O-HEWL in the incubation stage or wet condition exhibits 6, 8 and 10MPa, respectively. The hardness depends on indented planes but it is independent of the air-humidity and crystal volumes. These values correspond to the intrinsic hardness for O-HEWL crystals containing water. In the incubation stage, the slip traces are clearly observed around the indentation mark and the corresponding six kinds of slip systems are identified to be {011}&lt;100&gt;, {110}&lt;110&gt;, {011}&lt;011&gt;, {110}&lt;001&gt;, {100}&lt;001&gt; and {010}&lt;001&gt;.

DOI： 10.1080/14786435.2016.1219074

Web of Science

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Language：Japanese   Publisher：The Physical Society of Japan  

&lt;p&gt;我々は、これまでタンパク質結晶の塑性といった力学的性質の先導的な研究を行い、その塑性変形のメカニズムが転位の運動によるものであることを報告してきた。タンパク質結晶のひとつであるグルコースイソメラーゼ結晶は擬BCC構造をもつ。今回、グルコースイソメラーゼ結晶に導入された転位のX線トポグラフィ観察とキャラクタリゼーションに初めて成功した。発表ではBCC金属との比較と、タンパク質結晶のすべり変形の一般性について議論する。&lt;/p&gt;

DOI： 10.11316/jpsgaiyo.72.1.0_2739

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Language：Japanese   Publisher：The Physical Society of Japan  

DOI： 10.11316/jpsgaiyo.72.2.0_2268

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Language：Japanese   Publisher：一般社団法人 日本物理学会  

DOI： 10.11316/jpsgaiyo.71.1.0_2765

CiNii Books

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Language：Japanese   Publisher：一般社団法人 日本物理学会  

DOI： 10.11316/jpsgaiyo.70.2.0_2441

CiNii Books

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

CiNii Books

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Language：Japanese   Publisher：一般社団法人 日本物理学会  

CiNii Books

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Event date： 2022.5

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Event date： 2019.12

Presentation type：Oral presentation (invited, special)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Poster presentation  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Poster presentation  

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Language：English   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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