Details of a Researcher - Nakasako, Masayoshi

Papers - Nakasako, Masayoshi

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Cryo-EM and crystal structure analyses reveal the indirect role played by Trp89 in glutamate dehydrogenase enzymatic reactions.

Wakabayashi, T., Matsui, Y. and Nakasako, M.

The FEBS Journal (Wiley & Sons) in press ( in press ) in press 2025.02

Research paper (scientific journal), Joint Work, Corresponding author, Accepted

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Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm

Kochi Sato and Masayoshi Nakasako

Biophysics and Physicobiology (The Biophysical Society of Japan) 22 e220004(1) - e220004(17) 2025.01

Research paper (scientific journal), Joint Work, Corresponding author, Accepted

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CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase

Taiki Wakabayashi, Mao Oide and Masayoshi Nakasako

Scientific Reports (Springer-Nature) 14 11165(1) - 11165(16) 2024.05

Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

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Protocol using similarity score and improved shrink-wrap algorithm for better convergence of phase-retrieval calculation in X-ray diffraction imaging

Syouyo Yoshida Kosei Harada So Uezu, Yuki Takayama and Masayoshi Nakasako

Journal of Synchrotron Radiation (Wiley & Sons) 31 113 - 128 2023.11

Research paper (scientific journal), Joint Work, Corresponding author, Accepted

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Similarity score for screening phase-retrieved maps in X-ray diffraction imaging – characterization in reciprocal space

Yuki Takayama and Masayoshi Nakasako

Journal of Synchrotron Radiation (Wiley & Sons) 31 95 - 112 2023.11

Research paper (scientific journal), Joint Work, Corresponding author, Accepted

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Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy

Taiki Wakabayashi, Mao Oide, Takayuki Kato and Masayoshi Nakasako

The FEBS Journal (Wiley & Sons) 290 5514 - 5535 2023.09

Research paper (scientific journal), Corresponding author, Accepted

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Ultrastructure and fractal property of chromosomes in close‑to‑native yeast nuclei visualized using X‑ray laser diffraction

So Uezu, TakahiroYamamoto, Mao Oide, YukiTakayama, Koji Okajima, Amane Kobayashi, Masaki Yamamoto, Masayoshi Nakasako

Scientifc Reports (Springer-Nature) 13 10802(1) - 10802(14) 2023.07

Research paper (scientific journal), Joint Work, Corresponding author, Accepted

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Prediction of hydrophilic and hydrophobic hydration structure of protein by neural network optimized using experimental data

Kochi Sato, Mao Oide, Masayoshi Nakasako

Scientifc Reports | (Springer-Nature) 13 2183 (1-15) 2023.02

Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

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Deducing Free-Energy Landscape of Biomolecular Dynamics from Cryo-Electron Microscopy Images

Mao Oide and Masayoshi Nakasako

Journal of the Crystallographic Society of Japan ( The Crystallographic Society of Japan) 64 ( 4 ) 300 - 305 2022.12

Research paper (scientific journal), Joint Work, Last author, Accepted

Development of Coherent X-ray Diffraction Imaging at SPring-8

Yuki TAKAYAMA and Masayoshi NAKASAKO

日本結晶学会誌 (日本結晶学会) 64 ( 1 ) 41 - 49 2022.03

Research paper (scientific journal), Last author, Corresponding author, Accepted

Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free-electron laser

A. Kobayashi, Y. Takayama, T. Hirakawa, K. Okajima, M. Oide, T. Oroguchi, Y. Inui, M. Yamamoto, S. Matsunaga and M. Nakasako

Scientific Reports (Springer-Nature) in press ( 1 ) in press 2021.02

Research paper (scientific journal), Joint Work, Accepted

Visualization of intracellular structures and their spatial organization inside cells without any modification is essential to understand the mechanisms underlying the biological functions of cells. Here, we investigated the intracellular structure of cyanobacteria Prochlorococcus in the interphase by X-ray diffraction imaging using X-ray free-electron laser. A number of diffraction patterns from single cells smaller than 1 µm in size were collected with high signal-to-noise ratio with a resolution of up to 30 nm. From diffraction patterns, a set of electron density maps projected along the direction of the incident X-ray were retrieved with high reliability. The most characteristic structure found to be common among the cells was a C-shaped arrangement of 100-nm sized high-density spots, which surrounded a low-density area of 100 nm. Furthermore, a three-dimensional map reconstructed from the projection maps of individual cells was non-uniform, indicating the presence of common structures among cyanobacteria cells in the interphase. By referring to the fluorescent images for distributions of thylakoid membranes, nucleoids, and carboxysomes, we inferred and represented their spatial arrangements in the three-dimensional map. The arrangement allowed us to discuss the relevance of the intracellular organization to the biological functions of cyanobacteria.

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Red light‑induced structure changes in phytochrome A from Pisum sativum

Mao Oide and Masayoshi Nakasako

Scientific Reports (Springer-Nature) 11 ( 1 ) 2827(1) - 2827(11) 2021.02

Research paper (scientific journal), Joint Work, Accepted

Phytochrome A (phyA) is a photoreceptor protein of plants that regulates the red/far-red light photomorphogenic responses of plants essential for growth and development. PhyA, composed of approximately 1100 amino acid residues, folds into photosensory and output signaling modules. The photosensory module covalently binds phytochromobilin as a chromophore for photoreversible interconversion between inactive red light-absorbing (Pr) and active far-red light-absorbing (Pfr) forms to act as a light-driven phosphorylation enzyme. To understand the molecular mechanism in the initial process of photomorphogenic response, we studied the molecular structures of large phyA (LphyA) from Pisum sativum, which lacks the 52 residues in the N-terminal, by small-angle X-ray scattering combined with multivariate analyses applied to molecular models predicted from the scattering profiles. According to our analyses, Pr was in a dimer and had a four-leaf shape, and the subunit was approximated as a bent rod of 175 × 50 Å. The scattering profile of Pfr was calculated from that recorded for a mixture of Pr and Pfr under red-light irradiation by using their population determined from the absorption spectrum. The Pfr dimer exhibited a butterfly shape composed of subunits with a straight rod of 175 × 50 Å. The shape differences between Pr and Pfr indicated conformational changes in the Pr/Pfr interconversion which would be essential to the interaction with protein molecules involved in transcriptional control.

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Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data of Hyper-thermostable Glutamate Dehydrogenase

Oroguchi T., Oide M., Wakabayashi T., Nakasako M.

Journal of Physical Chemistry B (Journal of Physical Chemistry B) 124 ( 39 ) 8479 - 8494 2020.10

ISSN 15206106

© 2020 American Chemical Society. Molecular dynamics (MD) simulations in biophysically relevant time scales of microseconds is a powerful tool for studying biomolecular processes, but results often display force field dependency. Therefore, assessment of force field accuracy using experimental data of biomolecules in solution is essential for simulation studies. Here, we propose the use of structural models obtained via cryo-electron microscopy (cryoEM), which provides biomolecular structures in vitreous ice mimicking the environment in solution. The accuracy of the AMBER (ff99SB-ILDN-NMR, ff14SB, ff15ipq, and ff15FB) and CHARMM (CHARMM22 and CHARMM36m) force fields was assessed by comparing their MD trajectories with the cryoEM data of thermostable hexameric glutamate dehydrogenase (GDH), which included a cryoEM map at a resolution of approximately 3 Å and structure models of subunits reflecting metastable conformations in domain motion occurring in GDH. In the assessment, we validated the force fields with respect to the reproducibility and stability of secondary structures and intersubunit interactions in the cryoEM data. Furthermore, we evaluated the force fields regarding the reproducibility of the energy landscape in the domain motion expected from the cryoEM data. As a result, among the six force fields, ff15FB and ff99SB-ILDN-NMR displayed good agreement with the experiment. The present study demonstrated the advantages of the high-resolution cryoEM map and suggested the optimal force field to reproduce experimentally observed protein structures.

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Domain organization in plant blue-light receptor phototropin2 of arabidopsis thaliana studied by small-angle x-ray scattering

Nakasako M., Oide M., Takayama Y., Oroguchi T., Okajima K.

International Journal of Molecular Sciences (International Journal of Molecular Sciences) 21 ( 18 ) 6638(1) - 6638(21) 2020.09

ISSN 16616596

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Phototropin2 (phot2) is a blue-light (BL) receptor protein that regulates the BL-dependent activities of plants for efficient photosynthesis. Phot2 is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) to absorb BL, and a kinase domain. Photo-activated LOV domains, especially LOV2, play a major role in photo-dependent increase in the phosphorylation activity of the kinase domain. The atomic details of the overall structure of phot2 and the intramolecular mechanism to convert BL energy to a phosphorylation signal remain unknown. We performed structural studies on the LOV fragments LOV1, LOV2, LOV2-linker, and LOV2-kinase, and full-length phot2, using small-angle X-ray scattering (SAXS). The aim of the study was to understand structural changes under BL irradiation and discuss the molecular mechanism that enhance the phosphorylation activity under BL. SAXS is a suitable technique for visualizing molecular structures of proteins in solution at low resolution and is advantageous for monitoring their structural changes in the presence of external physical and/or chemical stimuli. Structural parameters and molecular models of the recombinant specimens were obtained from SAXS profiles in the dark, under BL irradiation, and after dark reversion. LOV1, LOV2, and LOV2-linker fragments displayed minimal structural changes. However, BL-induced rearrangements of functional domains were noted for LOV2-kinase and full-length phot2. Based on the molecular model together with the absorption measurements and biochemical assays, we discuss the intramolecular interactions and domain motions necessary for BL-enhanced phosphorylation activity of phot2.

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Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo-electron microscopy

Oide M., Kato T., Oroguchi T., Nakasako M.

FEBS Journal (FEBS Journal) 287 ( 16 ) 3472 - 3493 2020.08

ISSN 1742464X

© 2020 Federation of European Biochemical Societies Analysis of the conformational changes of protein is important to elucidate the mechanisms of protein motions correlating with their function. Here, we studied the spontaneous domain motion of unliganded glutamate dehydrogenase from Thermococcus profundus using cryo-electron microscopy and proposed a novel method to construct free-energy landscape of protein conformations. Each subunit of the homo-hexameric enzyme comprises nucleotide-binding domain (NAD domain) and hexamer-forming core domain. A large active-site cleft is situated between the two domains and varies from open to close according to the motion of a NAD domain. A three-dimensional map reconstructed from all cryo-electron microscopy images displayed disordered volumes of NAD domains, suggesting that NAD domains in the collected images adopted various conformations in domain motion. Focused classifications on NAD domain of subunits provided several maps of possible conformations in domain motion. To deduce what kinds of conformations appeared in EM images, we developed a novel analysis method that describe the EM maps as a linear combination of representative conformations appearing in a 200-ns molecular dynamics simulation as reference. The analysis enabled us to estimate the appearance frequencies of the representative conformations, which illustrated a free-energy landscape in domain motion. In the open/close domain motion, two free-energy basins hindered the direct transformation from open to closed state. Structure models constructed for representative EM maps in classifications demonstrated the correlation between the energy landscape and conformations in domain motion. Based on the results, the domain motion in glutamate dehydrogenase and the analysis method to visualize conformational changes and free-energy landscape were discussed. Database: The EM maps of the four conformations were deposited to Electron Microscopy Data Bank (EMDB) as accession codes EMD-9845 (open), EMD-9846 (half-open1), EMD-9847 (half-open2), and EMD-9848 (closed), respectively. In addition, the structural models built for the four conformations were deposited to the Protein Data Bank (PDB) as accession codes 6JN9 (open), 6JNA (half-open1), 6JNC (half-open2), and 6JND (closed), respectively.

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Methods and application of coherent X-ray diffraction imaging of noncrystalline particles

Nakasako M., Kobayashi A., Takayama Y., Asakura K., Oide M., Okajima K., Oroguchi T., Yamamoto M.

Biophysical Reviews (Biophysical Reviews) 12 ( 2 ) 541 - 567 2020.04

ISSN 18672450

© 2020, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature. Microscopic imaging techniques have been developed to visualize events occurring in biological cells. Coherent X-ray diffraction imaging is one of the techniques applicable to structural analyses of cells and organelles, which have never been crystallized. In the experiment, a single noncrystalline particle is illuminated by an X-ray beam with almost complete spatial coherence. The structure of the particle projected along the direction of the beam is, in principle, retrieved from a finely recorded diffraction pattern alone by using iterative phase-retrieval algorithms. Here, we describe fundamental theory and experimental methods of coherent X-ray diffraction imaging and the recent application in structural studies of noncrystalline specimens by using X-rays available at Super Photon Ring of 8-Gev and SPring-8 Angstrom Compact Free Electron Laser in Japan.

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特別企画試料環境シリーズ(7) 第4回「温度」 4-1 蛋白質結晶の低温X線回折実験～低温 1～

中迫雅由、高山裕貴、山本雅貴

放射光 (日本放射光学会) 33 ( 2 ) 101 - 111 2020.01

Research paper (scientific journal), Joint Work, Accepted

Molecular shape under far-red light and red light-induced association of Arabidopsis phytochrome B

Mao Oide, Takaaki Hikima, Tomotaka Oroguchi, Takayuki Kato, Yuhki Yamaguchi, Shizue Yoshihara, Masaki Yamamoto, Masayoshi Nakasako and Koji Okajima

The FEBS Journal (Federation of European Biochemical Societies) 287 ( 8 ) 1612 - 1625 2019.10

Research paper (scientific journal), Joint Work, Accepted, ISSN 1742464X

© 2019 Federation of European Biochemical Societies Phytochrome B (phyB) is a plant photoreceptor protein that regulates various photomorphogenic responses to optimize plant growth and development. PhyB exists in two photoconvertible forms: a red light-absorbing (Pr) and a far-red light-absorbing (Pfr) form. Therefore, to understand the mechanism of phototransformation, the structural characterization of full-length phyB in these two forms is necessary. Here, we report the molecular structure of Arabidopsis thaliana phyB in Pr form and the molecular properties of the Pfr form determined by small-angle X-ray scattering coupled with size-exclusion chromatography. In solution, the Pr form associated as a dimer with a radius of gyration of 50 Å. The molecular shape was a crossed shape, in which the orientation of the photosensory modules differed from that in the crystal structure of dimeric photosensory module. PhyB exhibited structural reversibility in the Pfr-to-Pr phototransformation and thermal reversion from Pfr to Pr in the dark. In addition, Pfr only exhibited nonspecific association, which distinguished molecular properties of Pfr form from those of the inactive Pr form.

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Dipole–dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic Stokes shift of lysozyme

Asahi Fukuda, Tomotaka Oroguchi and Masayoshi Nakasako

Biochimica et Biophysica Acta - General Subjects (Elsevier) 1864 ( 2 ) 129406(1) - 129406(11) 2019.08

Research paper (scientific journal), Joint Work, Accepted, ISSN 03044165

© 2019 Elsevier B.V. The fluorescence intensity of tryptophan residues in hen egg-white lysozyme was measured up to 500 ps after the excitation by irradiation pulses at 290 nm. From the time-dependent variation of fluorescence intensity in a wavelength range of 320–370 nm, the energy relaxation in the dynamic Stokes shift was reconstructed as the temporal variation in wavenumber of the estimated fluorescence maximum. The relaxation was approximated by two exponential curves with decay constants of 1.2 and 26.7 ps. To interpret the relaxation, a molecular dynamics simulation of 75 ns was conducted for lysozyme immersed in a water box. From the simulation, the energy relaxation in the electrostatic interactions of each tryptophan residue was evaluated by using a scheme derived from the linear response theory. Dipole–dipole interactions between each of the Trp62 and Trp123 residues and hydration water molecules displayed an energy relaxation similar to that experimentally observed regarding time constants and magnitudes. The side chains of these residues were partly or fully exposed to the solvent. In addition, by inspecting the variation in dipole moments of the hydration water molecules around lysozyme, it was suggested that the observed relaxation could be attributed to the orientational relaxation of hydration water molecules participating in the hydrogen-bond network formed around each of the two tryptophan residues.

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高分子材料における異方性のテラヘルツセンシング

渡邉紳一, 岡野真人, 中迫雅由

レーザー研究 (一般社団法人レーザー学会) 47 ( 1月 ) 21 - 26 2019.01

Research paper (bulletin of university, research institution), Joint Work, Accepted

Apparatus and procedure in tomography X-ray diffraction imaging for biological cells at cryogenic temperature using synchrotron X-ray radiation

A. Kobayashi, Y. Takayama, K. Okajima, M. Oide, T. Yamamoto, Y. Sekiguchi, T. Oroguchi, M. Nakasako*, Y. Kohmura, M. Yamamoto, T. Hoshi and Y. Torizuka

Journal of Synchrotron Radiation (Journal of Synchrotron Radiation) 25 ( 6 ) 1803 - 1818 2018.11

Research paper (scientific journal), Joint Work, Accepted, ISSN 09090495

Â© International Union of Crystallography, 2018 X-ray diffraction imaging is a technique for visualizing the structure of biological cells. In X-ray diffraction imaging experiments using synchrotron radiation, cryogenic conditions are necessary in order to reduce radiation damage in the biological cells. Frozen-hydrated biological specimens kept at cryogenic temperatures are also free from drying and bubbling, which occurs in wet specimens under vacuum conditions. In a previous study, the diffraction apparatus KOTOBUKI-1 [Nakasako et al. (2013), Rev. Sci. Instrum. 84, 093705] was constructed for X-ray diffraction imaging at cryogenic temperatures by utilizing a cryogenic pot, which is a cooling device developed in low-temperature physics. In this study a new cryogenic pot, suitable for tomography experiments, has been developed. The pot can rotate a biological cell over an angular range of Â±170Â° against the direction of the incident X-ray beam. Herein, the details and the performance of the pot and miscellaneous devices are reported, along with established experimental procedures including specimen preparation. The apparatus has been used in tomography experiments for visualizing the three-dimensional structure of a Cyanidioschyzon merolae cell with an approximate size of 5 Âµm at a resolution of 136 nm. Based on the experimental results, the necessary improvements for future experiments and the resolution limit achievable under experimental conditions within a maximum tolerable dose are discussed.

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Classification of ab initio models of proteins restored from small-angle X-ray scattering

Mao Oide, Yuki Sekiguchi, Asahi Fukuda, Koji Okajima, Tomotaka Oroguchi and Masayoshi Nakasako

Journal of Synchrotron Radiation (Journal of Synchrotron Radiation) 25 ( 5 ) 1379 - 1388 2018.08

Research paper (scientific journal), Joint Work, Accepted, ISSN 09090495

© International Union of Crystallography, 2018 In structure analyses of proteins in solution by using small-angle X-ray scattering (SAXS), the molecular models are restored by using ab initio molecular modeling algorithms. There can be variation among restored models owing to the loss of phase information in the scattering profiles, averaging with regard to the orientation of proteins against the direction of the incident X-ray beam, and also conformational fluctuations. In many cases, a representative molecular model is obtained by averaging models restored in a number of ab initio calculations, which possibly provide nonrealistic models inconsistent with the biological and structural information about the target protein. Here, a protocol for classifying predicted models by multivariate analysis to select probable and realistic models is proposed. In the protocol, each structure model is represented as a point in a hyper-dimensional space describing the shape of the model. Principal component analysis followed by the clustering method is applied to visualize the distribution of the points in the hyper-dimensional space. Then, the classification provides an opportunity to exclude nonrealistic models. The feasibility of the protocol was examined through the application to the SAXS profiles of four proteins.

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水和構造に制御される蛋白質のドメイン運動

苙口友隆，中迫雅由

生物物理 58 ( 4 ) 204 - 206 2018.08

Research paper (scientific journal), Joint Work, Accepted

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Growth of cuprous oxide particles in liquid-phase synthesis investigated by X-ray laser diffraction

Oroguchi Tomotaka, Yoshidome Takashi, Yamamoto Takahiro, Nakasako Masayoshi

Nano Letters (ACS) 18 ( 8 ) 5192 - 5197 2018.07

Joint Work, Accepted, ISSN 15306984

Copyright © 2018 American Chemical Society. Cuprous oxide (Cu2O) particles obtained by surfactant-assisted liquid-phase synthesis have cuboid shapes but the internal structures are difficult to be visualized by electron microscopy. Herein, we investigated the internal structures of numerous individual Cu2O particles with submicrometer dimensions by X-ray diffraction imaging (XDI) using X-ray free-electron laser (XFEL) pulses. The reconstructed two-dimensional electron density maps, which displayed inhomogeneous internal structures, were divided into five classes characterized by the positions and shapes of high and low electron density areas. Further analysis of the maps in each class by a manifold learning algorithm revealed that the internal structures of Cu2O particles varied in correlation with total electron density while retaining the characteristics within each class. On the basis of the analyses, we proposed a growth mechanism to yield the inhomogeneity in the internal structures of Cu2O particles in surfactant-mediated liquid-phase synthesis.

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生物細胞の低温Ｘ線回折イメージング

中迫雅由，高山裕貴，小林周，山本隆寛，大出真央，岡島公司，苙口友隆，山本雅貴

放射光 31 ( 3 ) 189 - 201 2018.06

Research paper (scientific journal), Joint Work, Accepted

Coherent X-ray DIFFRACTION IMAGINg of Cyanidioschyzon merolae

Sekiguchi Y., Kobayashi A., Takayama Y., Oide M., Fukuda A., Yamamoto T., Okajima K., Oroguchi T., Hirakawa T., Inui Y., Matsunaga S., Yamamoto M., Nakasako M.

Cyanidioschyzon merolae: A New Model Eukaryote for Cell and Organelle Biology (Cyanidioschyzon merolae: A New Model Eukaryote for Cell and Organelle Biology) 153 - 173 2018.03

ISSN 9789811061004

© Springer Nature Singapore Pte Ltd. 2017. Coherent X-ray diffraction imaging (CXDI) is a lensless imaging technique for visualizing the structures of noncrystalline particles at a resolution of several tens of nanometers. The targets are particles with dimensions in the sub-micrometer to micrometer range. We carried out CXDI experiments at 66 K to investigate the internal structures of a whole frozen-hydrated cell and a chloroplast of Cyanidioschyzon merolae and a cyanobacteria cell by using coherent X-ray light sources, such as synchrotron and X-ray free-electron laser facilities. Owing to the short wavelength of the X-rays used (0.225 nm), the absorption and multiple scattering of X-rays inside the specimens were negligible. Diffraction patterns from each specimen particle adsorbed onto a thin membrane were collected at resolutions better than 50 μm -1 in reciprocal space. Therefore, structures of specimen particles can be illustrated at a resolution higher than 200 nm in real space. The most probable electron density map was retrieved from each diffraction pattern. Theinternal structures of the specimens are described here, particularly the structural correlation of the chloroplast of C. merolae and the cyanobacteria cell. Based on the experimental results, we discuss the feasibility of CXDI in the structural analyses of biological cells and cellular organelles.

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Blue-light excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis

Mao Oide, Koji Okajima, Hirofumi Nakagami, Takayuki Kato, Yuki Sekiguchi, Tomotaka Oroguchi, Takaaki Hikima, Masaki Yamamoto, and Masayoshi Nakasako

The Journal of Biological Chemistry (Journal of Biological Chemistry) 293 ( 3 ) 963 - 972 2018.01

Research paper (scientific journal), Joint Work, Accepted, ISSN 00219258

© 2018 by The American Society for Biochemistry and Molecular Biology, Inc. Phototropin2 (phot2) is a blue-light (BL) receptor that regulates BL-dependent activities for efficient photosynthesis in plants. phot2 comprises two BL-receiving light-oxygen-voltage–sensing domains (LOV1 and LOV2) and a kinase domain. BL-excited LOV2 is thought to be primarily responsible for the BL-dependent activation of the kinase. However, the molecular mechanisms by which small BL-induced conformational changes in the LOV2 domain are transmitted to the kinase remain unclear. Here, we used full-length wild-type and mutant phot2 proteins from Arabidopsis to study their molecular properties in the dark and under BL irradiation. Phosphoryl-ation assays and absorption measurements indicated that the LOV1 domain assists the thermal relaxation of BL-excited LOV2 and vice versa. Using small-angle X-ray scattering and electron microscopy, we observed that phot2 forms a dimer and has a rod shape with a maximum length of 188 Å and a radius of gyration of 44 Å. Under BL, phot2 displayed large conformational changes that bent the rod shape. By superimposing the crystal structures of the LOV1 dimer, LOV2, and a homology model of the kinase to the observed changes, we inferred that the BL-dependent change consisted of positional shifts of both LOV2 and the kinase relative to LOV1. Furthermore, phot2 mutants lacking the photocycle in LOV1 or LOV2 still exhibited conformational changes under BL, suggesting that LOV1 and LOV2 cooperatively contribute to the conformational changes that activate the kinase. These results suggest that BL-activated LOV1 contributes to the kinase activity of phot2. We discuss the possible intramolecular interactions and signaling mechanisms in phot2.

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Shot-by-shot characterization of focused X-ray free electron laser pulses

Amane Kobayashi, Yuki Sekiguchi, Tomotaka Oroguchi, Masaki Yamamoto, and Masayoshi Nakasako

Scientific Reports (Nature publishing) 8 ( 1 ) 831 (1-13) 2018.01

Research paper (scientific journal), Joint Work, Accepted

© 2018 The Author(s). X-ray free electron lasers (XFEL) provide intense and almost coherent X-ray pulses. They are used for various experiments investigating physical and chemical properties in materials and biological science because of their complete coherence, high intensity, and very short pulse width. In XFEL experiments, specimens are irradiated by XFEL pulses focused by mirror optics. The focused pulse is too intense to measure its coherence by placing an X-ray detector on the focal spot. Previously, a method was proposed for evaluating the coherence of focused pulses from the visibility of the diffraction intensity of colloidal particles by the speckle visibility spectroscopy (SVS). However, the visibility cannot be determined exactly because the diffraction intensity is integrated into each finite size detector pixel. Here, we propose a method to evaluate the coherence of each XFEL pulse by using SVS in combination with a theory for exact sampling of the diffraction pattern and a technique of multiplying the diffraction data by a Gaussian masks, which reduces the influence of data missing in small-angle regions due to the presence of a direct beamstop. We also introduce a method for characterizing the shot-by-shot size of each XFEL pulse by analysing the X-ray irradiated area.

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Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acid side chains in molecular dynamics simulation

Tomotaka Oroguchi and M. Nakasako

Scientific Reports (Nature Publishing) 7 15859 (1-14) 2017.11

Joint Work, Accepted

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A protocol for searching most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting relationship between convergence of retrieved phase and success of calculation

Yuki Sekiguchi, Saki Hashimoto, Amane Kobayashi, Tomotaka Oroguchi and Masayoshi Nakasako

Journal of Synchrotron Radiation 24 1024 - 1038 2017.09

Research paper (scientific journal), Joint Work, Accepted

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Controlled Terahertz Birefringence in Stretched Poly(lactic acid) Films Investigated by Terahertz Time-Domain Spectroscopy and Wide-Angle X‑ray Scattering

Hotsumi Iwasaki, Madoka Nakamura, Nozomu Komatsubara, Makoto Okano, Masayoshi Nakasako, Harumi Sato and Shinichi Watanab

Journal of Physical Chemistry B 121 6951 - 6957 2017.07

Research paper (scientific journal), Joint Work, Accepted

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Blue-light-excited LOV2 triggers a rearrangement of the kinase domain to induce phosphorylation activity in Arabidopsis phototropin1

Mao Oide, Koji Okajima, Sachiko Kashojiya, Yuki Takayama, Tomotaka Oroguchi, Takaaki Hikima, Masaki Yamamoto, and Masayoshi Nakasako

Journal of Biological Chemistry 291 ( 38 ) 19975 - 19984 2016.09

Joint Work, Accepted

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Common structural features of toxic intermediates from alpha-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging

H. Kameda, S. Usugi, M. Kobayashi, N. Fukui, S. Lee, K. Hongo, T. Mizobata, Y. Sekiguchi, Y. Masaki3, A. Kobayashi, T. Oroguchi, M. Nakasako, Y. Takayama, M. Yamamoto, and Y. Kawata

Journal of Biochemistry (Tokyo) 161 55 - 65 2016.08

Research paper (scientific journal), Joint Work, Accepted

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Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using X-ray free electron laser at SACLA

Amane Kobayashi, Yuki Sekiguchi, Tomotaka Oroguchi, Koji Okajima, Asahi Fukuda, Mao Oide, Masaki Yamamoto and Masayoshi Nakasako

Journal of Synchrotron Radiation 23 975 - 989 2016.06

Joint Work, Accepted

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Changes in hydration structure are necessary for collective motions of a multi-domain protein

Tomotaka Oroguchi and Masayoshi Nakasako

Scientific Reports 6 26302 (14 pages) 2016.05

Joint Work, Accepted

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TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA

Amane Kobayashi, Yuki Sekiguchi, Yuki Takayama, Tomotaka Oroguchi, Keiya Shirahama,　Yasufumi Torizuka, Masahiro Manoda, Masayoshi Nakasako, Masaki Yamamoto

Review of Scientific Instruments 87 053109 (15 pages) 2016.05

Joint Work, Accepted

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Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate analysis

Yuki Sekiguchi, Tomotaka Oroguchi, and Masayoshi Nakasako

Journal of Synchrotron Radiation 23 312 - 323 2015.12

Research paper (scientific journal), Joint Work, Accepted

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金コロイド粒子を利用した非結晶生体試料の高分解能・高精度コヒーレントX線回折イメージング

高山裕貴、眞木さおり、苙口友隆、中迫雅由、米倉功治

Isotope News 739 ( 11 ) 9 - 14 2015.11

Research paper (scientific journal), Joint Work, Accepted

Classification of projection images of proteins with structural polymorphism by manifold: A simulation study for X-ray free-electron laser diffraction imaging

Takashi Yoshidome, Tomotaka Oroguchi, Masayoshi Nakasako, and Mitsunori Ikeguchi

Physical Review E 92 ( 3 ) 032710 - 13 pages 2015.09

Research paper (scientific journal), Joint Work, Accepted

Access to Document (DOI)

X-ray structure analyses of biological molecules and particles in Japan - A brief history and future prospect -

中迫雅由、山本雅貴

日本物理学会誌 70 ( 9 ) 702 - 712 2015.09

Structure of thermophilic F1-ATPase inhibited by ε-subunit: Deeper insight into ε-inhibition mechanism

Y. Shirakihara, A. Shiratori, Aya, H. Tanikawa, M. Nakasako, M. Yoshida, Masasuke, S. Toshiharu

The FEBS Journal 282 ( 15 ) 2895 - 2913 2015.08

Joint Work, Accepted

Cryogenic coherent X-ray diffraction imaging for biological non-crystalline particles using the KOTOBUKI-1 diffraction apparatus at SACLA

Tomotaka Oroguchi, Yuki Sekiguchi, Amane Kobayashi, Yu Masaki, Asahi Fukuda, Saki Hashimoto, Masayoshi Nakasako, Yuichi Ichikawa, Hitoshi Kurumizaka, Mitsuhiro Shimizu, Yayoi Inui, Sachihiro Matsunaga, Takayuki Kato, Keiichi Namba, Keiichi Yamaguchi, Kazuo Kuwata, Hiroshi Kameda, Naoya Fukui, Yasushi Kawata, Takashi Kameshima, Yuki Takayama, Koji Yonekura, Masaki Yamamoto

Journal of Physics B: Atomic, Molecular and Optical Physics 48 ( 18 ) 184003 - (11pages) 2015.07

Research paper (scientific journal), Joint Work, Accepted

Access to Document (DOI)

Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser

Yuki Takayama, Yayoi Inui Yuki Sekiguchi1, Amane Kobayashi, Tomotaka Oroguchi, Masaki Yamamoto, Sachihiro Matsunaga and Masayoshi Nakasako

Plant Cell Physiology 56 ( 7 ) 1272 - 1286 2015.07

Joint Work, Accepted

Access to Document (DOI)

Signal enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects

Yuki Takayama, Saori Maki-Yonekura, Tomotaka Oroguchi, Masayoshi Nakasako and Koji Yonekura

Scientific Reports 5 8074 2015.01

Research paper (scientific journal), Accepted

Access to Document (DOI)

Dark-field phase retrieval under the constraint of the Friedel symmetry in coherent X-ray diffraction imaging

Amane Kobayashi, Yuki Sekiguchi, Yuki Takayama, Tomotaka Oroguchi, and Masayoshi Nakasako

Optics Express 22 27892 - 27909 2014.11

Research paper (scientific journal), Joint Work, Accepted

IDATEN and G-SITENNO: GUI assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA

Yuki Sekiguchi, Masaki Yamamoto, Tomotaka Oroguchi, Yuki Takayama, Shigeyuki Suzuki and Masayoshi Nakasako

Journal of Synchrotron Radiation 21 1378 - 1383 2014.10

Research paper (scientific journal), Joint Work, Accepted

Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses

Rui Xu, Huaidong Jiang, Changyong Song, Jose A. Rodriguez, Zhifeng Huang, Chien-Chun Chen, Daewoong Nam, Jaehyun Park, Marcus Gallagher-Jones Sangsoo Kim, Sunam Kim, Akihiro Suzuki, Yuki Takayama, Tomotaka Oroguchi, Yukio Takahashi, Jiadong Fan, Yunfei Zou, Takaki Hatsui, Yuichi Inubushi, Takashi Kameshima, Koji Yonekura, Kensuke Tono, Tadashi Togashi, Takahiro Sato, Masaki Yamamoto, Masayoshi Nakasako, Makina Yabashi, Tetsuya Ishikawa & Jianwei Miao

Nature Communications DOI: 10.1038/ncomms5061 1 - 9 2014.06

Joint Work, Accepted

Access to Document (DOI)

Data processing software suite SITENNO for coherent X-ray diffraction imaging using X-ray free electron laser SACLA

Yuki Sekiguchi, Tomotaka Oroguchi, Yuki Takayama and Masayoshi Nakasako

Journal of Synchrotron Radiation 21 ( 4 ) 600 - 612 2014.03

Research paper (scientific journal), Joint Work, Accepted

Ｘ線自由電子レーザーを用いた非結晶粒子のコヒーレントＸ線回折イメージング実験

中迫雅由、苙口友隆、関口優希、小林　周、橋本早紀、山本雅貴、引間孝明、米倉功治、高山裕貴、眞木さおり、高橋幸生、鈴木明大、松永幸大、乾弥生、星　貴彦

日本結晶学会誌 56 ( 1 ) 27-35 2014.03

Research paper (scientific journal), Joint Work, Accepted

Light-induced conformational changes of LOV (Light Oxygen Voltage-sensing domain) 1 and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin

K. Okajima, Y. Aihara, Y. Takayama, M. Nakajima, S. Kashojiya, T. Hikima, T. Oroguchi, A. Kobayashi, Y. Sekiguchi, M. Yamamoto, T. Suzuki, A. Nagatani, M. Nakasako and S. Tokutomi

Journal of Biological Chemistry 289 ( 1 ) 413-422 2014.01

Research paper (scientific journal), Joint Work, Accepted

Coherent Diffraction Imaging Analysis of Shape-Controlled Nanoparticles with Focused Hard X-ray Free-Electron Laser Pulses

Yukio Takahashi, Akihiro Suzuki, Nobuyuki Zettsu, Tomotaka Oroguchi, Yuki Takayama, Yuki Sekiguchi, Amane Kobayashi, Masaki Yamamoto, and Masayoshi Nakasako

Nano Letter 13 ( 12 ) 6028–6032 2013.11

Research paper (scientific journal), Joint Work, Accepted

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging

Masayoshi Nakasako, Yuki Takayama,Tomotaka Oroguchi,Yuki Sekiguchi, Amane Kobayashi, Keiya Shirahama, Masaki Yamamoto, Takaaki Hikima, Koji Yonekura, Saori Maki-Yonekura, Yoshiki Kohmura, Yuichi Inubushi, Yukio Takahashi , Akihiro Suzuki, Sachihiro Matsunaga, Yayoi Inui, Kensuke Tono, Takashi Kameshima, Yasumasa Joti, Takahiko Hoshi

Review of Scientific Instruments 84 ( 9 ) 093705 (11 pages) 2013.09

Research paper (scientific journal), Joint Work, Accepted

Application of empirical hydration distribution functions around polar atoms for assessing hydration structures of proteins

Daisuke Matsuoka, Masayoshi Nakasako

Chemical Physics 419 59-64 2013.07

Research paper (scientific journal), Joint Work, Accepted

先端的Ｘ線光源による細胞の空間階層イメージング（特集号依頼、表紙図提供）

中迫雅由、山本雅貴

パリティ 28 ( 7 ) 16-19 2013.06

Research paper (scientific journal), Joint Work, Accepted

Three-dimensional structure determination protocol for noncrystalline biomolecules using x-ray free-electron laser diffraction imaging

Tomotaka Oroguchi and Masayoshi Nakasako

Physical Review E 87 022712 (15 pages) 2013.02

Research paper (scientific journal), Joint Work, Accepted

蛋白質水和構造の実験研究

中迫雅由、苙口友隆、高山裕貴、中島真、松井夕花

アンサンブル 15 7-18 2013.01

Research paper (scientific journal), Joint Work, Accepted

コヒーレントX線回折イメージング構造解析理論の開発と展望

中迫雅由、苙口友隆、高山裕貴、小林周、児玉渉、坂本啓太、吉留崇、池口満徳

放射光 26 ( 1 ) 11-25 2013.01

Research paper (scientific journal), Joint Work, Accepted

蛋白質極性原子周辺の水分子分布　－データベース解析と水和構造予測―

松岳大輔、中迫雅由

アンサンブル 15 19-27 2013.01

Research paper (scientific journal), Joint Work, Accepted

非結晶粒子のコヒーレントＸ線回折イメージング

中迫雅由，高山裕貴，苙口友隆，白濱圭也，関口優希，山本雅貴，米倉功治，引間孝明，眞木‐さおり，高橋幸生，鈴木明大，松永幸大，加藤翔一，星貴彦

レーザー研究 40 680-86 2012.11

Research paper (scientific journal), Single Work, Accepted

Ｘ線自由電子レーザーを用いた非結晶粒子のコヒーレントＸ線回折イメージング実験

オプトロニクス 368 ( 8 ) 101-106 2012.08

Research paper (scientific journal), Single Work, Accepted

Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent x-ray diffraction microscopy

Yuki Takayama & Masayoshi Nakasako

Review of Scientific Instruments 83 ( 5 ) 054301 (6 pages) 2012.05

Research paper (scientific journal), Joint Work, Accepted

A few low-frequency normal modes predominantly contribute to conformational responses of hen egg white lysozyme in the tetragonal crystal to variations of molecular packing controlled by environmental humidity

Yuki Takayama & Masayoshi Nakasako

Biophysical Chemistry 159 237-246 2011.12

Research paper (scientific journal), Joint Work, Accepted

Ｘ線自由電子レーザー(XFEL)の生命科学での利用

中迫雅由、山本雅貴

日本生物物理学会誌 51 ( 6 ) 278-281 2011.11

Research paper (scientific journal), Joint Work, Accepted

生命には何故水が必要なのか－蛋白質の機能と水和構造の相関

中迫雅由、松岳大輔

日本応用物理学会誌 80 ( 10 ) 903-907 2011.10

Research paper (scientific journal), Joint Work, Accepted

Application of a real-space three-dimensional image reconstruction method in the structural analysis of non-crystalline biological macromolecules enveloped by water in coherent X-ray diffraction microscopy

Wataru Kodama & Masayoshi Nakasako

Physical Review E 84 021902 (15 pages) 2011.08

Research paper (scientific journal), Joint Work, Accepted

New monoclinic form of bovine pancreatic ribonuclease A from a salt solution and comparison of intermolecular interactions in ribonucleases A

H.Takusagawaa, S. Yamamuraa, S. Endoa, Y. Sugawaraa,T. Inagakib & M. Nakasakob

Journal of Crystal Growth 319 ( 1 ) 49-56 2011.02

Research paper (scientific journal), Single Work, Accepted

Light-induced movement of the LOV2 domain in an Asp720Asn-mutated LOV2-kinase fragment of Arabidopsis phototropin 2

Y. Takayama, M. Nakasako, K. Okajima, A. Iwata, S. Kashojiya, Y. Matsui, S. Tokutomi

Biochemistry 50 1174-1183 2011.01

Research paper (scientific journal), Joint Work, Accepted

Redox-dependent domain rearrangement of protein disulfide isomerase from a thermophilic fungus

Masayoshi Nakasako, Aya Maeno, Eiji Kurimoto, Takushi Harada, Yoshiki Yamaguchi, Toshihiko Oka, Yuki Takayama, Aya Iwata, Koichi Kato

Biochemistry 49 ( 32 ) 6953–6962 2010.07

Research paper (scientific journal), Joint Work, Accepted

Prediction of Hydration Structures around Hydrophilic Surfaces of Proteins by using the Empirical Hydration Distribution Functions from a Database Analysis

Daisuke Matsuoka and Masayoshi Nakasako

Journal of Physical Chemistry B 114 4562-4663 2010.03

Research paper (scientific journal), Single Work, Accepted

Redox-dependent domain rearrangement of protein disulfide isomerase coupled with exposure of its substrate-binding hydrophobic surface

Olivier Serve, Yukiko Kamiya, Aya Maeno3, Michiko Nakano, Chiho Murakami, Hiroaki Sasakawa, Yoshiki Yamaguchi, Takushi Harada, Eiji Kurimoto, Maho Yagi-Utsumi, Tsuyoshi Iguchi, Kenji Inaba, Jun Kikuchi, Osamu Asami, Tsutomu Kajino, Toshihiko Oka, Masayoshi Nakasako, and Koichi Kato

Journal of Molecular Biology 396 ( 2 ) 361-374 2010.02

Research paper (scientific journal), Joint Work, Accepted

Structural basis for inverting the enantioselectivity of arylmalonate decarboxylase revealed by the structural analysis of the Gly74Cys/Cys188Ser mutant in the liganded form

Rika Obata and Masayoshi Nakasako

Biochemsitry 49 1963-1969 2010.02

Research paper (scientific journal), Single Work, Accepted

Probability distribution of hydration water molecules around polar protein atoms obtained by a database analysis

Daisuke Matsuoka, Masayoshi Nakasako

Journal of Physical Chemistry B 113 ( 32 ) 11274–11292 2009.07

Research paper (scientific journal), Single Work, Accepted

Hydartion structure changes around proteins at work

NAKASAKO MASAYOSHI

日本結晶学会誌 51 ( 1 ) 37-39 2009.02

Research paper (scientific journal), Single Work, Accepted

Structural basis of LOV1-dimerization of Arabidopsis phototropin 1 and 2 (cover illustration of the issue)

Masayoshi Nakasako, Kazunori Zikihara, Daisuke Matsuoka, Hitomi Katsura, Satoru Tokutomi

Journal of Molecular Biology 381 ( 3 ) 718-733 2008.09

Research paper (scientific journal), Joint Work, Accepted

Crystallization and preliminary X-ray diffraction experiments of LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana

M. Nakasako,a+ M. Hirata, N. Shimizu, S. Hosokawa, D. Matsuoka, T. Oka, M. Yamamoto and S. Tokutomi

Acta Crystallographica Section F 64 617-621 2008.07

Research paper (scientific journal), Joint Work, Accepted

Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus

Masayoshi Nakasako, Rika Obata, Ryosuke Okubo, Shyuichi Nakayama, Kenji Miyamoto and Hiromichi Ohta

Acta Crystallographica Section F 64 610-613 2008.07

Research paper (scientific journal), Joint Work, Accepted

Investigation of hydration structures of proteins

NAKASAKO MASAYOSHI

Molecular Science Journal 2 ( 1 ) A0022 2008.02

Research paper (scientific journal), Single Work, Accepted

非弾性散乱の生物への応用について

城地保昌、中迫雅由、難波啓一

日本結晶学会誌 50 ( 1 ) 78-82 2008.01

Research paper (scientific journal), Single Work, Accepted

Crystal Structures of Blasticidin S Deaminase (BSD): Implications for Dynamic Properties of Catalytic Zinc

Takashi Kumasaka, Masaki Yamamoto, Makio Furuichi, Masayoshi Nakasako, Aik-Hong Teh, Makoto Kimura, Isamu Yamaguchi, Tatzuo Ueki

Journal of Biological Chemistry 228 37103-37111 2007.12

Research paper (scientific journal), Joint Work, Accepted

タンパク質の水和水と機能

肥後順一、中迫雅由

日本生物物理学会誌”生物物理” 46 ( 4 ) 220-223 2006.07

Research paper (scientific journal), Joint Work

Discovery of MBI-D Resistant Buster Compounds: Inquiry of Effective Compound among Derivatives of MBI-D Products

Yoshio Kurahashi, Shinzo Kagabu, Naoki Yamada, Yu Mitsugi, Maiko Shimizu, Masayoshi Nakasako and Isamu Yamaguchi

Journal of Pestiside Science 31 ( 2 ) 85-94 2006.05

Research paper (scientific journal), Joint Work, Accepted

A fluorescent antibiotic resistance marker fir rapid production of transgenic rice plants

T. Ochiai-Fukuda, N. Takahashi-Ando, S. Ohsato, T. Igawa, K. Kadokura, H. Hamamoto, M. Nakasako, T. Kudo, T. SHibata, I. Yamaguchi and M. Kimura

Journal of Biotechnology 122 ( 4 ) 521-527 2006.04

Research paper (scientific journal), Joint Work

LOV Photoreceptors in Plants; Molecular Structure, Photoreaction and Signal Transduction

D. Matsuoka, M. Nakasko and S. Tokutomi

Proceedings of the 15th International Symposium on Flavins and Flavoproteins (Nishino, T. ed) (Architect Tokyo) 557-567 2005.12

Research paper (scientific journal), Joint Work, Accepted

Conformational dynamics of complementary determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten (cover illustration of the issue)

M. Nakasako, T. Oka, M. Masumo, H. Takahashi, I. Shimada, Y. Yamaguchi, K. Kato and Y. Arata

Journal of Molecular Biology 351 627-640 2005.07

Research paper (scientific journal), Joint Work, Accepted

タンパク質の水和構造 (Cover illustration)

中迫雅由、肥後順一

現代化学 413 48-54 2005.07

Research paper (scientific journal), Joint Work

Patterns and networks of hydrogen-bonds in the hydration structure of human lysozyme

T. Yokomizo, M. Nakasako and J. Higo

Chemical Physics Letters 410 31-35 2005.06

Research paper (scientific journal), Joint Work, Accepted

Quaternary structure of LOV-domain containing polypeptides of Arabidopsis FKF1 protein

M.Nakasako, D. Matsuoka, K. Zikihara and S. Tokutomi

FEBS Letters 579 ( 5 ) 1067-1071 2005.02

Research paper (scientific journal), Joint Work, Accepted

Light-induced global structural changes of phytochrome A regulating photomorphogenesis in plants

M.Nakasako, T. Iwata, K. Inoue and S. Tokutomi

The FEBS Journal 272 ( 3 ) 603-612 2005.02

Research paper (scientific journal), Single Work, Accepted

Hydrogen-bond patterns in the hydration structure of a protein

T. Yokomizo, M. Nakasako, T. Yamazaki, H. Shindo and J. Higo

Chemical Physics Letters 401 ( 4-6 ) 332-336 2005.01

Research paper (scientific journal), Single Work, Accepted

Light-induced structural changes of LOV-domain containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering

M. Nakasako, T. Iwata, D. Matsuoka and S. Tokutomi

Biochemistry 43 ( 47 ) 14881-14890 2004.12

Research paper (scientific journal), Joint Work, Accepted

30年後の放射光生命科学実験に期待すること生きた細胞を原子分解能でリアルタイムに観察する

中迫雅由

放射光 17 ( 5 ) 268 2004.09

Research paper (scientific journal), Single Work

Water-protein interactions from high-resolution protein crystallography

M. Nakasako

Philosophical Transaction B Royal Society London B359 1191-1206 2004.08

Research paper (scientific journal), Single Work, Accepted

Enzymatic characterization of scytalone dehydratase Val75Met variant found in melanin biosynthesis inhibitor (MBI) resistant strains of the rice blast fungus

N. Yamada, T. Motoyama, M. Nakasako, S. Kagabu, T. Kudo & I. Yamaguchi

Bioscience, Biotechnology & Biochemistry Vol. 68 615-621 2004.03

Research paper (scientific journal), Joint Work, Accepted

Carpropamid ((1RS, 3SR )-2, 2-dichloro-N-
[(R )-1-(4-chlorophenyl)ethyl]-1-ethyl-3-methylcyclopropanecarboxamide) is a potent chemical against the rice blast fungus, Pyricularia oryzae. In 2001, isolates of the fungus with reduced sensitivity to this fungicide appeared in Saga Prefecture of Japan and were regarded as a potential threat to rice protection by carpropamid. The cause of the resistance has been identified genetically as a point mutation resulting in the Val75Met change in scytalone dehydratase, the primary target of the fungicide. We constructed an overexpression system of the variant enzyme and characterized the kinetics in the catalysis and the inhibition by carpropamid isomers. The variant enzyme retained a significant level of enzymatic activity. Inhibition of the variant enzyme by carpropamid was more than 200-fold reduced in comparison with that of the wild-type. Based on the results, here we propose possible mechanisms of the carpropamid-resistance of the variant enzyme in retaining the normal enzymatic activity.

Molecular structures and light-induced changes in LOV fragments of phot1 and phot2

Nakasako M, Iwata T, Matsuoka D, Inoue K, Tokutomi S

PLANT AND CELL PHYSIOLOGY Vol. 45 S86-S86 Suppl 2004

Research paper (scientific journal), Joint Work

低温ヘリウムガス吹き付け型結晶冷却装置の開発

中迫雅由、澤野成民、河本正秀

放射光 Vol. 15 163-166 2002.05

Joint Work

タンパク質の水和構造

中迫雅由、肥後順一

現代化学 ( No. 374 ) 24-30 2002.05

Research paper (scientific journal), Joint Work

極低温Ｘ線結晶構造解析と分子動力学計算による蛋白質の水和構造解析について最近の知見を平易にまとめた。２つの実験手法は、蛋白質の水和構造についてまったく新しい見方を提供している。特に、結晶解析で見出されたドメイン運動と水和構造変化の協奏や、分子動力学計算で観測される溶媒双極子場は、水溶液中での蛋白質の動力学や相互作用に新たな視点をもたらすものである。

Roles of hydration water molecules in molecular packing of the killer toxin from Pichia farinosa in its crystalline state investigated by cryogenic X-ray crystallography

M. Nakasako, F. Tsuchiya and Y. Arata

Biophysical Chemistry Vol. 95 211-225 2002.03

Research paper (scientific journal), Joint Work, Accepted

極低温Ｘ線結晶構造解析によって、酵母由来キラートキシンの水和構造を調べ、同蛋白質が機能発現する際の会合状態形成に水和水が大きな寄与をする可能性を指摘した。また、結晶内での蛋白質間相互作用を媒介している水分子の距離分布は、液体論から導かれた閉鎖空間中での溶媒分子の距離分布関数によって近似的に記述可能であることが示された。

An open-flow helium cryostat for cryogenic X-ray diffraction experiments

M. Nakasako, M. Sawano and M. Kawamoto

Review of Scientific Instruments Vol. 73 1318-1320 2002.03

Research paper (scientific journal), Joint Work, Accepted

Crystallization of scytalone dehydratase F162A mutant in the unligated state and a preliminary X-ray diffraction study at 37 K

T. Motoyama, M. Nakasako and I. Yamaguchi

Acta Crystallographica Sect. D Vol. 58 148-150 2002.02

Research paper (scientific journal), Joint Work, Accepted

Structural characteristics in protein hydration investigated by cryogenic X-ray crystal structure analyses

M. Nakasako

Journal of Biological Physics Vol. 28 129-137 2002

Research paper (scientific journal), Single Work, Accepted

Nonlinear temperature dependence of crystal structure of Lysozyme: Correlation between coordinate shifts and thermal factors

Y. Joti, M. Nakasako, A. Kidera and N. Go

Acta Crystallographica Section D Vol. 58 1421-1432 2002

Research paper (scientific journal), Joint Work, Accepted

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between and crystal-water sites, solvent-density and solvent-dipole

J. Higo and M. Nakasako

Journal of Computational Chemistry Vol. 23 1323-1336 2002

Research paper (scientific journal), Joint Work, Accepted

筋小胞体カルシウムポンプの構造決定

豊島　近、中迫雅由、野村博美、小川治夫

蛋白質・核酸・酵素 Vol. 46 1374-1380 2001.11

Joint Work

筋小胞体カルシウムポンプの構造決定

豊島　近、中迫雅由、野村博美、小川治夫

放射光 Vol. 14 204-210 2001.06

Joint Work

Large-scale networks of hydration water molecules around proteins investigated by cryogenic X-ray crystallography

M. Nakasako

Cellular and Molecular Biology Vol. 47 767-790 2001.06

Research paper (scientific journal), Single Work, Accepted

極低温Ｘ線結晶構造解析による蛋白質の水和構造解析について最近の知見をまとめた。同手法の有効性について解説し、９種類の蛋白質の解析結果からの蛋白質表面での水和水分布の特徴、水和水の水素結合形態と水素結合数蛋白質表面からの距離分布を高い統計精度で明らかにした。また、アミノ酸残基の極性原子団や疎水性側鎖周辺での水和構造の特徴を調べるとともに、水和水と蛋白質表面の極性原子団によって構成される大規模な水素結合ネットワークの特徴を蛋白質の動的構造との関連で考察した。水分子が蛋白質の立体構造形成に果たす役割についてもレビンタール逆説との関連で議論した。

Large-scale domain movements and hydration structure changes in the active-site cleft in unligated glutamate dehydrogenase from Thermococcus profundus: studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering”

M. Nakasako, T. Fujisawa, S. Adachi, T. Kudo and S. Higuchi

Biochemistry Vol. 40 3069-3079 2001.04

Research paper (scientific journal), Joint Work, Accepted

極低温Ｘ線結晶構造解析によって、超高度好熱菌のグルタミン酸脱水素酵素六量体の結晶構造解析を2.2オングストローム分解能で行った。各サブユニットは六量体ドメインと補酵素結合ドメインによって形成されているが、６つのサブユニットでこれらドメインの立体配置がすべて異なっており、結晶化に際してドメイン運動が固定されたものと考えられた。各サブユニットの水和構造を詳細に比較した結果、活性クレフトの水和水がドメイン運動に連動して水和サイト間を移動していることが明らかとなった。この実験結果は、蛋白質の動的ドメイン運動に水和水分子が直接かかわっていることを実験的に示した最初の例である。

Fe-type Nitrile Hydratase

I. Endo, M. Nojiri, M. Tsujimura, M. Nakasako, S. Nagashima, M. Yohda and M. Odaka

Journal of Inorganic Biochemistry Vol. 83 247-253 2001.04

Research paper (scientific journal), Joint Work, Accepted

Development of an open-flow cryostat utilizing helium gas

M. Nakasako, M. Sawano and M. Kawamoto

The Rigaku Journal Vol. 18 47-53 2001

Research paper (conference, symposium, etc.), Joint Work

低温ヘリウムガス吹き付け型結晶冷却装置の開発

中迫雅由、澤野成民、河本正秀

理学電機ジャーナル Vol. 32 8-15 2001

Research paper (scientific journal), Joint Work

筋小胞体カルシウムポンプの構造決定

豊島　近、中迫雅由、野村博美、小川治夫

SPring-8 利用者情報 Vol. 5 389-393 2001

Research paper (scientific journal), Joint Work

Detailed characterization of the cooperative mechanism of Ca2+ binding and catalytic activation in the Ca2+ transport (SERCA) ATPase

Z. Zhang, D.Lewis, C. Strock, G. Inesi, M. Nakasako, H. Nomura and C. Toyoshima

Biochemistry Vol. 39 8758-8767 2000.12

Research paper (scientific journal), Joint Work, Accepted

筋小胞体カルシウムポンプのカルシウム結合様態を調べるためにカルシウム結合アミノ酸残基に部位特異的変異を導入し、それらのカルシウム結合活性を測定することで各アミノ酸残基の機能上の役割分担を解析した。その結果、第一の結合部位を形成するアミノ酸残基によるカルシウム結合が最初に起こり、それに誘起された構造変化が第二の結合部位形成を促すことが明らかとなった。さらに、この結果を、カルシウム結合状態にある筋小胞体カルシウムポンプの結晶構造と合わせて議論した。

筋小胞体カルシウムポンプの結晶構造解析

中迫雅由、野村博美、小川治夫、豊島　近

日本結晶学会誌 Vol. 42 478-485 2000.12

Research paper (scientific journal), Joint Work

Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution

C. Toyoshima, M. Nakasako, H. Nomura and H. Ogawa

Nature Vol. 405 647-655 2000.06

Research paper (scientific journal), Joint Work

重原子多重同型法を用いたＸ線結晶構造解析により、カルシウム結合状態にある筋小胞体カルシウムポンプの結晶構造を2.6オングストローム分解能で明らかにした。同蛋白質は、１０本の膜貫通へリックス、ＡＴＰ結合ドメイン、リン酸化ドメイン、制御ドメインから形成されていた。２個のカルシウムイオンが４本の膜貫通へリックスで形成された空隙に結合していた。また、カルシウム非結合状態尾低分解能構造モデルとの比較から、カルシウム輸送サイクルにおいて大規模なドメイン運動が生じることが示唆された。

Crystallization and preliminary X-ray diffraction studies of hyperthermostable glutamate dehydrogenase from Thermococcus profundus

S. Higuchi, M. Nakasako and T. Kudo

Acta Crystallographica Sect. D Vol. 55 1917-1919 1999.12

Research paper (scientific journal), Joint Work, Accepted

Tertiary and quaternary structures of photoreactive Fe-type nitrile hydratase from Rhodococcus sp. N-771: Roles of hydration water molecules in stabilizing the structures and the structural origin for the substrate specificity of the enzyme

M. Nakasako, M. Odaka, M. Yohda, N. Dohmae, K. Takio, N. Kamiya and I. Endo

Biochemistry Vol. 38 9887-9898 1999.09

Research paper (scientific journal), Joint Work, Accepted

ロドコッカスの光応答性酵素鉄型ニトリルヒドラターゼには多数の水分子が吸着している。これら水分子の高次構造および活性中心構造形成への役割を詳細に検討し、準弾性光散乱実験により、生理的条件下での高次構造を明らかにした。また、酵素外部から活性中心に至る狭い通路が同酵素の基質選択性に大きく寄与していることを指摘した。さらに、光照射下で結晶のＸ線回折実験から、解析に用いた結晶では分子間相互作用によって蛋白質内部振動が抑制され、一酸化窒素分子が活性中心から光解離できないことが示された。

The pH-dependent structural variation of　complementarity-　determining region H3 in the Fv fragment from an anti-dansyl monoclonal antibody, IgG2a(s)

M. Nakasako, H. Takahashi, N. Shimba, I. Shimada and Y. Arata

Journal of Molecular Biology Vol. 291 117-134 1999.07

Research paper (scientific journal), Joint Work, Accepted

抗ダンシル抗体ＦｖフラグメントのＸ線結晶構造解析を1.6オングストローム分解能で行った。異なるｐＨ条件で結晶化したフラグメントの構造解析の結果、抗原認識領域のＨ３ループがｐＨに応じて大規模な構造することが明らかとなった。ＮＭＲによるヒスチジン残基のｐＨ滴定の結果からはまさにＨ３のヒスチジン残基のみが２つの結晶化条件のｐＨを境にしてその荷電状態を変化させることが明らかとなった。ｐＨに依存した局所的な構造変化を結晶構造解析とＮＭＲによって調べた最初の例である。

Large-scale networks of hydration water molecules around b-trypsin revealed by cryogenic X-ray crystal structure analyses

M. Nakasako

Journal of Molecular Biology Vol. 289 547-564 1999.06

Research paper (scientific journal), Single Work, Accepted

極低温Ｘ線結晶構造解析によって、３種類結晶系におけるトリプシンの水和構造を明らかにした。水和構造解析に特化したプログラムにより、水和水を蛋白質との相互作用や配置に応じて分類し、水和構造の特徴づけを試みた。水和水分子の蛋白質表面からの距離分布、水和水が蛋白質表面の極性原子団とともに形成する大規模な水素結合ネットワーク、疎水性表面の水和形態などについて、共通した構造的特徴を明らかにした。また、蛋白質の折れ畳み、ダイナミクスや分子認識における水分子の寄与について議論した。極低温Ｘ線結晶構造解析が蛋白質水和構造解析の有力な手段であることを示した最初の論文である。

Specific lipid-protein interactions in a novel honeycomb lattice structure of bacteriorhodopsin

H. Sato, K. Takeda, K. Tani, T. Okada, M. Nakasako, N. Kamiya and T. Kouyama

Acta Crystallographica Sect. D Vol. 55 1251-1256 1999

Research paper (scientific journal), Joint Work, Accepted

Crystallization and preliminary X-ray diffraction studies of blasticidin S deaminase from Aspergillus terreus

M. Nakasako, M. Kimura and I. Yamaguchi

Acta Crystallographica Sect. D Vol. 55 547-548 1999

Research paper (scientific journal), Joint Work, Accepted

低温蛋白質結晶構造解析

中迫雅由

日本結晶学会誌 Vol. 41 47-56 1999

Single Work

蛋白質の水和構造

中迫雅由

日本結晶学会誌 Vol. 40 107-113 1998

Research paper (scientific journal), Single Work

Cryogenic X-ray crystal structure analysisfor the complex of scytalone dehydratase of a rice blast fungus and its tight-binding inhibitor, carpropamid: The structural basis of tight-binding inhibition

M. Nakasako, T. Motoyama, Y. Kurahashi and I. Yamaguchi

Biochemistry Vol. 37 9931-9939 1998

Research paper (scientific journal), Joint Work, Accepted

イネいもち病菌の感染においては、メラニン生合成系で合成されるカビ・メラニンが重要な役割を果たしている。本研究では、メラニン生合成系のシタロン脱水酵素と同酵素を不活化する強結合型阻害剤カルプロパミドの複合体について極低温Ｘ線結晶構造解析を行った。高分解能で得られた電子密度図を元に作成された立体構造モデルに基づいて、同酵素と阻害剤の結合様式の詳細を明らかにするとともに、強結合型阻害の立体化学的なメカニズムを考察した。また、酵素のＣ末端領域の基質結合における動的な役割について議論した。

Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms

S. Nagashima, M. Nakasako, N. Dohmae, M. Tsujimura, K. Takio, M. Odaka, M. Yohda, N. Kamiya and I. Endo

Nature Structural Biology Vol. 5 347-351 1998

Research paper (scientific journal), Joint Work, Accepted

重原子多重同型法を用いたＸ線結晶構造解析により、ロドコッカスの光応答性酵素鉄型ニトリルヒドラターゼの結晶構造を1.7オングストローム分解能で明らかにした。同酵素は２つのサブユニットが複雑に絡み合った立体構造を有し、サブユニット界面に活性中心が存在した。活性中心の鉄原子は、立爪型に配置した酵素の窒素および硫黄原子に配位していた。論文では、その構造の立体化学的詳細を報告するとともに、生物体内での一酸化窒素結合蛋白質の活性中心の構造について議論した。

Molecular action mechanism of nonfungicidal anti-blast chemicals

I. Yamaguchi, T. Motoyama and M. Nakasako

Reviews in Toxicology Vol. 2 225-230 1998

Research paper (scientific journal), Joint Work, Accepted

低温でのタンパク質Ｘ線結晶構造解析

中迫雅由

バイオサイエンスとインダストリー Vol. 56 23-26 1998

Single Work

低温蛋白質結晶解析でのCryostream Coolerの利用

中迫雅由

マックサイエンス技報 vol.9, 25-33. Vol. 9 25-33 1997

Research paper (other academic), Single Work

光応答性ニトリルヒドラターゼ

遠藤勲、尾高雅文、野口巧、星野幹雄、中迫雅由

蛋白質・核酸・酵素 Vol. 42 136-143 1997

Joint Work

蛋白質のＸ線結晶構造解析

中迫雅由

食品機械装置 Vol. 33 86-96 1996

Single Work

Cryocrystallography of 3-isopropylmalate dehydrogenase from Thurmus thermophilus and its chimeric enzyme

C. Nagata, H. Moriyama, N. Tanaka, M. Nakasako, M. Yamamoto, T. Ueki and T. Oshima

Acta Crystallographica Sect. D Vol. 52 623-630 1996

Research paper (scientific journal), Joint Work, Accepted

低温下での蛋白質Ｘ線結晶構造解析２

中迫雅由

The Journal of TARA Sakabe Project Vol. 2 87-97 1996

Research paper (scientific journal), Single Work

低温下での蛋白質Ｘ線結晶構造解析３

中迫雅由

The Journal of TARA Sakabe Project Vol. 2 114-121 1996

Single Work

蛋白質結晶の液体窒素温度への冷却方法

中迫雅由

生物物理 Vol. 36 110-111 1996

Single Work

A crystal mouting device made from a capillary tube for cryogenic macromolecular crystallography

M. Nakasako, T. Ueki, C. Toyoshima and Y. Umeda

Journal of Applied Crystallography Vol. 28 856-857 1995

Research paper (scientific journal), Joint Work, Accepted

Conceptual design of Spring-8 contract beam line for structural biology

M. Yamamoto, T. Fujisawa, M. Nakasako, T. Tanaka, T. Uruga, H. Kimura, H. Yamaoka, Y. Inoue, H. Iwasaki, T. Ishikawa, H. Kitamura and T. Ueki

Review of Scientific Instruments Vol. 66 1833-1835 1995

Research paper (scientific journal), Joint Work, Accepted

Development of cryo-cooling system for cryogenic protein crystallography at the RIKEN beamline”

M. Nakasako, M. Yamamoto, T. Uruga, C. Toyoshima, T. Ueki and H. Iwasaki

SPring-8 Annual Report Vol. 1 301 1995

Research paper (scientific journal), Joint Work, Accepted

低温下での蛋白質Ｘ線結晶構造解技術

中迫雅由

日本結晶学会誌 Vol. 37 266-270 1995

Single Work

SPring-8で実施される蛋白質のＸ線結晶構造解析に不可欠な極低温Ｘ線回折実験手法の開発経過について報告を行った。ここでは、開発の経緯、極低温に向けた蛋白質結晶の前処理方法、極低温実験手順と幾つかの予備的実験によって得られた回折強度データの統計について詳細な報告を行い、放射線損傷対策としての極低温Ｘ線回折実験手法の有効性を明らかにした。

低温下での蛋白質Ｘ線結晶構造解析1

中迫雅由

The Journal of TARA Sakabe Project Vol. 1 98-102 1995

Single Work

Crystal structure of the Fv fragment of an anti-dansyl antibody at 1.6 A resolution

M. Nakasako, S. Noguchi, Y. Satow, H. Takahashi, I. Shimada and Y. Arata

Acta Crystallographica Sect A Vol. 49 PS-03.03.07 1994.08

Research paper (scientific journal), Joint Work, Accepted

Light-induced structural change of bacteriorhodopsin

F. Tokunaga, M. Kataoka, K. Mihara, M. Nakasako and Y. Amemiya

Photomedicine and Photobiology Vol. 14 83-88 1992

Research paper (scientific journal), Joint Work, Accepted

I型フィトクロム二量体４次構造モデルの提案

中迫雅由、和田正三

植物細胞工学 Vol. 3 106-109 1991.03

Research paper (scientific journal), Joint Work

Crystallographic characterization by X-ray diffraction of the M-intermediate from the photo-cycle of bacteriorhodopsin at room temperature

M. Nakasako, M. Kataoka, Y. Amemiya and F. Tokunaga

FEBS Letters Vol. 292 73-75 1991

Research paper (scientific journal), Joint Work, Accepted

光駆動プロトンポンプであるバクテリオロドプシンにおいては、光反応中間体Ｍがその機能発現上最も重要である。Ｍ中間体を高効率で蓄積可能なアルギニン処理バクテリオロドプシンのＸ線回折実験を光照射下で行い、光照射前後での回折強度変化を見出した。さらに、フーリエ解析を行うことで、バクテリオロドプシンを構成する７本の膜貫通へリックス内、プロトンの輸送経路と考えられる領域を構成するへリックスにおいて構造変化が見出された。

Quaternary structure of pea phytochrome I dimer studied with small-angle X-ray scattering and rotary-shadowing electron microscopy

M. Nakasako, M.Wada, S. Tokutomi, K. T. Yamamoto, J. Sakai, M. Kataoka, F. Tokunaga and M. Furuya

Photochemistry and Photobiology Vol. 52 3-12 1990

Research paper (scientific journal), Joint Work, Accepted

コントラスト変調法を用いたＸ線小角散乱実験とロータリーシャドウイング電子顕微鏡法によって、高等植物における光形態形成反応の初発反応を担う光受容蛋白質フィトクロムの低分解能四次構造モデルを提案した。本論文では、構造モデル構築に至る実験と解析の詳細を報告した。構造モデルでは、光受容ドメインが扁平な楕円体、相互作用ドメインが円盤で記述され、それらドメインのフィトクロム２量体内での相対配置が明らかにされた。

Structural study on M-intermediate of bacteriorhodopsin with X-ray diffraction technique at low temperature

M. Nakasako, M. Kataoka, F. Tokunaga and Y. Amemiya

“Molecular Physiology of retinal Proteins” (Hara. Ed.) (Academic Press) 1989.09

Joint Work, Accepted

Structural study on solubilized bacteriorhodopsin with small-angle X-ray scattering

M. Kataoka, M. Nakasako, F. Tokunaga and T. Ueki

“Molecular Physiology of retinal Proteins” (Hara. Ed.) (Academic Press) 1989.09

Joint Work, Accepted

Arginine remarkably prolongs the lifetime of the M-intermediate in the bacteriorhodopsin photocycle at room temperature

M. Nakasako, M. Kataoka and F. Tokunaga

FEBS Letters Vol. 254 211-214 1989.08

Research paper (scientific journal), Joint Work, Accepted

高度好塩菌の光駆動プロトンポンプであるバクテリオロドプシンにおいては、光反応中間体Ｍがその機能発現上最も重要であり、Ｍ中間体の構造解析のためにはその長寿命化が不可欠である。われわれは、室温下で数ミリ秒しかない同中間体の寿命を数秒まで延ばすことのできるアルギニンを用いた処理を発見した。論文ではその処理手順、分光学的およびＸ線回折実験によるアルギニン処理後の試料の特徴について報告し、アルギニンのグアニジウム基が寿命延長への寄与を示唆した。

A model for the dimeric molecular structure of phytochrome based on small-angle X-ray scattering

S. Tokutomi, M. Nakasako, J. Sakai, M. Kataoka, K.T. Yamamoto, M. Wada, F. Tokunaga and M. Furuya

FEBS Letters Vol. 247 139-142 1989.04

Research paper (scientific journal), Joint Work, Accepted

Sructural information on proteins obtainable from small-angle X-ray scattering with heavy atom labeling. application to solubilized bacteriorhodopsin

M. Kataoka, M. Nakasako and F. Tokunaga

Journal of Applied Crystallography Vol. 21 355-362 1988

Research paper (scientific journal), Joint Work, Accepted

放射光Ｘ線を利用した高精度の小角散乱実験における新たな解析手法として、従来のコントラスト変調と重原子修飾の併用法を定式化し、同併用法が蛋白質会合体の高次構造情報抽出に有効であることを見出した。さらに、同併用法を可溶化した膜蛋白質バクテリオロドプシンの溶液中での高次構造解析に適用し、同可溶化蛋白質が溶液中で３量体として存在することを示唆した。

Small-angle X-ray scattering studies on the macromolecular structure of the red-light-absorbing form of 121 kDa pea phytochrome and its 114 kDa chromopeptide

S. Tokutomi, M. Kataoka, J. Sakai, M. Nakasako, F. Tokunaga, M. Tasumi and M. Furuya

Biochimica et Biophysica Acta Vol. 953 297-305 1988

Research paper (scientific journal), Joint Work, Accepted

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