Researchers Database

sato ayana

    PhysiologyMolecularPhysiology&Biophysics Assistant Professor
Last Updated :2021/12/04

Researcher Information


  • Doctor of Science(Tokyo Institute of Technology)


J-Global ID

Research Interests

  • 放射光   Dynamics   Structural Biology   Hemoglobin   Myoglobin   

Research Areas

  • Life sciences / Structural biochemistry

Academic & Professional Experience

  • 2018/01 - Today  Jichi Medical UniversityDivision of BiophysicsAssistant Professor
  • 2015/04 - Today  Jichi Medical UniversitySchool of MedicineResearch Associate
  • 2014/04 - 2015/03  High Energy Accelerator Research Organization(KEK)Institute of Materials Structure Science(IMSS)Assistant Professor
  • 2011/04 - 2014/03  High Energy Accelerator Research Organization(KEK)Institute of Materials Structure Science(IMSS)JSPS Research Fellow
  • 2009/10 - 2011/03  Tokyo Institute of TechnologyDepartment of Chemistry and Materials SciencePostdoctoral Fellow
  • 2009/04 - 2009/09  Tokyo Institute of TechnologyFrontier Research CenterPostdoctoral Fellow


  • 2004/04 - 2009/03  Tokyo Institute of Technology  理工学研究科  Department of Chemistry and Materials Science
  • 2000/04 - 2004/03  Chitose Institute of Science and Technology  光科学部  物質光科学科

Association Memberships


Published Papers

  • Tadayoshi Karasawa, Akira Kawashima, Fumitake Usui-Kawanishi, Sachiko Watanabe, Hiroaki Kimura, Ryo Kamata, Koumei Shirasuna, Yutaro Koyama, Ayana Sato-Tomita, Takashi Matsuzaka, Hiroshi Tomoda, Sam-Yong Park, Naoya Shibayama, Hitoshi Shimano, Tadashi Kasahara, Masafumi Takahashi
    Arteriosclerosis, Thrombosis, and Vascular Biology 38 (4) 744 - 756 1524-4636 2018/04 [Refereed][Not invited]
    Objective - Inflammation provoked by the imbalance of fatty acid composition, such as excess saturated fatty acids (SFAs), is implicated in the development of metabolic diseases. Recent investigations suggest the possible role of the NLRP3 (nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain containing 3) inflammasome, which regulates IL-1β (interleukin 1β) release and leads to inflammation, in this process. Therefore, we investigated the underlying mechanism by which SFAs trigger NLRP3 inflammasome activation. Approach and Results - The treatment with SFAs, such as palmitic acid and stearic acid, promoted IL-1β release in murine primary macrophages while treatment with oleic acid inhibited SFA-induced IL-1β release in a dose-dependent manner. Analyses using polarized light microscopy revealed that intracellular crystallization was provoked in SFA-treated macrophages. As well as IL-1β release, the intracellular crystallization and lysosomal dysfunction were inhibited in the presence of oleic acid. These results suggest that SFAs activate NLRP3 inflammasome through intracellular crystallization. Indeed, SFA-derived crystals activated NLRP3 inflammasome and subsequent IL-1β release via lysosomal dysfunction. Excess SFAs also induced crystallization and IL-1β release in vivo. Furthermore, SFA-derived crystals provoked acute inflammation, which was impaired in IL-1β-deficient mice. Conclusions - These findings demonstrate that excess SFAs cause intracellular crystallization and subsequent lysosomal dysfunction, leading to the activation of the NLRP3 inflammasome, and provide novel insights into the pathogenesis of metabolic diseases.
  • 佐藤文菜
    自治医科大学紀要 40 70‐71  1881-252X 2018/03 [Not refereed][Not invited]
  • Tomohiro Matsushita, Takayuki Muro, Fumihiko Matsui, Naohisa Happo, Shinya Hosokawa, Kenji Ohoyama, Ayana Sato-Tomita, Yuji C. Sasaki, Kouichi Hayashi
    Journal of the Physical Society of Japan 87 (6) 0031-9015 2018 [Refereed][Not invited]
    © 2018 The Physical Society of Japan. Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.
  • Ayana Sato-Tomita, Hiroshi Sekiguchi, Yuji C. Sasaki
    Journal of the Physical Society of Japan 87 (6) 1347-4073 2018 [Refereed][Not invited]
    New measurement methodologies have begun to be proposed with the recent progress in the life sciences. Here, we introduce two new methodologies, X-ray fluorescence holography for protein structural analysis and diffracted X-ray tracking (DXT), to observe the dynamic behaviors of individual single molecules.
  • Ayana Sato-Tomita, Naoya Shibayama
    CRYSTALS 7 (9) 2073-4352 2017/09 [Refereed][Not invited]
    While high-throughput screening for protein crystallization conditions have rapidly evolved in the last few decades, it is also becoming increasingly necessary for the control of crystal size and shape as increasing diversity of protein crystallographic experiments. For example, X-ray crystallography (XRC) combined with photoexcitation and/or spectrophotometry requires optically thin but well diffracting crystals. By contrast, large-volume crystals are needed for weak signal experiments, such as neutron crystallography (NC) or recently developed X-ray fluorescent holography (XFH). In this article, we present, using hemoglobin as an example protein, some techniques for obtaining the crystals of controlled size, shape, and adequate quality. Furthermore, we describe a few case studies of applications of the optimized hemoglobin crystals for implementing the above mentioned crystallographic experiments, providing some hints and tips for the further progress of advanced protein crystallography.
  • Satoru Fujiwara, Toshiyuki Chatake, Tatsuhito Matsuo, Fumiaki Kono, Taiki Tominaga, Kaoru Shibata, Ayana Sato-Tomita, Naoya Shibayama
    JOURNAL OF PHYSICAL CHEMISTRY B 121 (34) 8069 - 8077 1520-6106 2017/08 [Refereed][Not invited]
    Hemoglobin, the vital O-2 carrier in red blood cells, has long served as a classic example of an allosteric protein. Although high-resolution X-ray structural models are currently available for both the deoxy tense (T) and fully liganded relaxed (R) states of hemoglobin, much less is known about their dynamics, especially on the picosecond to subnanosecond time scales. Here, we investigate the picosecond dynamics of the deoxy and CO forms of human hemoglobin using quasielastic neutron scattering under near physiological conditions in order to extract the dynamics changes upon ligation. From the analysis of the global motions, we found that whereas the apparent diffusion coefficients of the deoxy form can be described by assuming translational and rotational diffusion of a rigid body, those of the CO form need to involve an additional contribution of internal large-scale motions. We also found that the local dynamics in the deoxy and CO forms are very similar in amplitude but are slightly lower in frequency in the former than in the latter. Our results reveal the presence of rapid large-scale motions in hemoglobin and further demonstrate that this internal mobility is governed allosterically by the ligation state of the heme group.
  • Mio Ohki, Ayana Sato-Tomita, Shigeru Matsunaga, Mineo Iseki, Jeremy R. H. Tame, Naoya Shibayama, Sam-Yong Park
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 (32) 8562 - 8567 0027-8424 2017/08 [Refereed][Not invited]
    The photoactivated adenylate cyclase (PAC) from the photosynthetic cyanobacterium Oscillatoria acuminata (OaPAC) detects light through a flavin chromophore within the N-terminal BLUF domain. BLUF domains have been found in a number of different light-activated proteins, but with different relative orientations. The two BLUF domains of OaPAC are found in close contact with each other, forming a coiled coil at their interface. Crystallization does not impede the activity switching of the enzyme, but flash cooling the crystals to cryogenic temperatures prevents the signature spectral changes that occur on photoactivation/deactivation. High-resolution crystallographic analysis of OaPAC in the fully activated state has been achieved by cryocooling the crystals immediately after light exposure. Comparison of the isomorphous light-and dark-state structures shows that the active site undergoes minimal changes, yet enzyme activity may increase up to 50-fold, depending on conditions. The OaPAC models will assist the development of simple, direct means to raise the cyclic AMP levels of living cells by light, and other tools for optogenetics.
  • Ayana Sato-Tomita, Naohisa Happo, Sam-Yong Park, Koichi Hayashi, Yuji C. Sasaki, Naoya Shibayama
    BIOPHYSICAL JOURNAL 112 (3) 579A - 579A 0006-3495 2017/02 [Not refereed][Not invited]
  • Nobuhisa Watanabe, Takayuki Nagae, Yusuke Yamada, Ayana Tomita, Naohiro Matsugaki, Masao Tabuchi
    JOURNAL OF SYNCHROTRON RADIATION 24 338 - 343 1600-5775 2017/01 [Refereed][Not invited]
    The protein crystallography beamline BL2S1, constructed at one of the 5 T superconducting bending-magnet ports of the Aichi synchrotron, is available to users associated with academic and industrial organizations. The beamline is mainly intended for use in X-ray diffraction measurements of single-crystals of macromolecules such as proteins and nucleic acids. Diffraction measurements for crystals of other materials are also possible, such as inorganic and organic compounds. BL2S1 covers the energy range 7-17 keV (1.8-0.7 angstrom) with an asymmetric-cut curved single-crystal monochromator [Ge(111) or Ge(220)], and a platinum-coated Si mirror is used for vertical focusing and as a higher-order cutoff filter. The beamline is equipped with a single-axis goniometer, a CCD detector, and an open-flow cryogenic sample cooler. High-pressure protein crystallography with a diamond anvil cell can also be performed using this beamline.
  • Ayana Sato-Tomita, Naoya Shibayama, Naohisa Happo, Koji Kimura, Takahiro Okabe, Tomohiro Matsushita, Sam-Yong Park, Yuji C. Sasaki, Kouichi Hayashi
    REVIEW OF SCIENTIFIC INSTRUMENTS 87 (6) 063707  0034-6748 2016/06 [Refereed][Not invited]
    Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metal-loprotein samples are described. Human hemoglobin, an alpha(2)beta(2) tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A chi-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 x 6 x 3 mm(3)) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0 degrees-70 degrees. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules. Published by AIP Publishing.
  • Ayana Sato-Tomita, Shin-ichi Adachi, Sam-Yong Park, Yuji C. Sasaki, Koichi Hayashi, Naoya Shibayama
    BIOPHYSICAL JOURNAL 110 (3) 160A - 160A 0006-3495 2016/02 [Not refereed][Not invited]
  • Kouhei Ichiyanagi, Hiroshi Sekiguchi, Tokushi Sato, Shunsuke Nozawa, Ayana Tomita, Manabu Hoshino, Shin-ichi Adachi, Yuji C. Sasaki
    JOURNAL OF SYNCHROTRON RADIATION 22 (Pt 1) 29 - 33 0909-0495 2015/01 [Refereed][Not invited]
    Picosecond time-resolved X-ray diffraction has been used to study the nanoscale thermal transportation dynamics of bare gold nanocrystals and thiol-based self-assembled monolayer (SAM)-coated integrated gold nanocrystals on a SiO2 glass substrate. A temporal lattice expansion of 0.30-0.33% was observed in the bare and SAM-coated nanocrystals on the glass substrate; the thermal energy inside the gold nanocrystals was transported to the contacted substrate through the gold-SiO2 interface. The interfacial thermal conductivity between the single-layered gold nanocrystal film and the SiO2 substrate is estimated to be 45 MW m(-2) K-1 from the decay of the Au 111 peak shift, which was linearly dependent on the transient temperature. For the SAM-coated gold nanocrystals, the thermal dissipation was faster than that of the bare gold nanocrystal film. The thermal flow from the nanocrystals to the SAM-coated molecules promotes heat dissipation from the laser-heated SAM-coated gold nanocrystals. The thermal transportation of the laser-heated SAM-coated gold nanocrystal film was analyzed using the bidirectional thermal dissipation model.
  • TOMITA Ayana, NOZAWA Shunsuke, ADACHI Shin-ichi, SATO Tokushi, SHIBAYAMA Naoya
    X-RAYS The Crystallographic Society of Japan 56 (4) 253 - 258 0369-4585 2014/08 [Not refereed][Not invited]
    Today, we can determine the structural basis of a biological molecule by X-ray crystallography or X-ray solution scattering. However, static structures do not say a lot for the realtime transition of the functional dynamics. Here we introduce the pump-probe method using combined single bunch X-ray from synchrotron source and pulsed laser system in sub nanosecond time resolution. Time-resolved X-ray solution scattering measurement of dimeric hemoglobin revealed a spiral motion of two subunits and three intermediate states. The pump-probe method is even powerful technique in the other methods of measurement for the protein dynamics.
  • Manabu Hoshino, Emi Uchida, Yasuo Norikane, Reiko Azumi, Shunsuke Nozawa, Ayana Tomita, Tokushi Sato, Shin-ichi Adachi, Shin-ya Koshihara
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136 (25) 9158 - 9164 0002-7863 2014/06 [Refereed][Not invited]
    Trans-cis photoisomerization in an azo compound containing azobenzene chromophores and long alkyl chains leads to a photoinduced crystal-melt transition (PCMT). X-ray structure analysis of this crystal clarifies the characteristic coexistence of the structurally ordered chromophores through their pi center dot center dot center dot pi interactions and disordered alkyl chains around room temperature. These structural features reveal that the PCMT starts near the surface of the crystal and propagates into the depth, sacrificing the pi center dot center dot center dot pi interactions. A temporal change of the powder X-ray diffraction pattern under light irradiation and a two-component phase diagram allow qualitative analysis of the PCMT and the following reconstructive crystallization of the cis isomer as a function of product accumulation. This is the first structural characterization of a compound showing the PCMT, overcoming the low periodicity that makes X-ray crystal structure analysis difficult.
  • Ahmed F. Mabied, Shunsuke Nozawa, Manabu Hoshino, Ayana Tomita, Tokushi Sato, Shin-ichi Adachi
    JOURNAL OF SYNCHROTRON RADIATION 21 (Pt 3) 554 - 560 0909-0495 2014/05 [Refereed][Not invited]
    Singular value decomposition (SVD) analysis has important applications for time-dependent crystallographic data, extracting significant information. Herein, a successful application of SVD analysis of time-resolved powder diffraction data over the course of an in-situ photodimerization reaction of anthracene derivatives is introduced. SVD revealed significant results in the case of 9-methylanthracene and 1-chloroanthracene. The results support the formation of the 9-methylanthracene stable dimer phase and suggest the existence of an excimer state.
  • Kyung Hwan Kim, Jae Hyuk Lee, Joonghan Kim, Shunsuke Nozawa, Tokushi Sato, Ayana Tomita, Kouhei Ichiyanagi, Hosung Ki, Jeongho Kim, Shin-ichi Adachi, Hyotcherl Ihee
    PHYSICAL REVIEW LETTERS 110 (16) 165505  0031-9007 2013/04 [Refereed][Not invited]
    Ionic species often play important roles in chemical reactions occurring in water and other solvents, but it has been elusive to determine the solvent-dependent molecular structure with atomic resolution. The triiodide ion has a molecular structure that sensitively changes depending on the type of solvent and its symmetry can be broken by strong solute-solvent interaction. Here, by applying pump-probe x-ray solution scattering, we characterize the exact molecular structure of I-3(-) ion in water, methanol, and acetonitrile with subangstrom accuracy. The data reveal that I-3(-) ion has an asymmetric and bent structure in water. In contrast, the ion keeps its symmetry in acetonitrile, while the symmetry breaking occurs to a lesser extent in methanol than in water. The symmetry breaking of I-3(-) ion is reproduced by density functional theory calculations using 34 explicit water molecules, confirming that the origin of the symmetry breaking is the hydrogen-bonding interaction between the solute and solvent molecules. DOI: 10.1103/PhysRevLett.110.165505
  • Manabu Hoshino, Shunsuke Nozawa, Tokushi Sato, Ayana Tomita, Shin-ichi Adachi, Shin-ya Koshihara
    RSC ADVANCES 3 (37) 16313 - 16317 2046-2069 2013 [Refereed][Not invited]
    Photoinduced structural dynamics in tetrathiafulvalene-p-chloranil (TTF-CA) was directly observed by time-resolved X-ray crystal structure analysis. Temporal deformation corresponded to step-wise relaxation of intermolecular interactions and represented the generation of a more neutralized phase of TTF-CA than the initial one.
  • K. Ichiyanagi, N. Kawai, S. Nozawa, T. Sato, A. Tomita, M. Hoshino, K. G. Nakamura, S. Adachi, Y. C. Sasaki
    APPLIED PHYSICS LETTERS 101 (18) 181901  0003-6951 2012/10 [Refereed][Not invited]
    We study shock compressed fused quartz in the nonlinear elastic region using single-shot time-resolved x-ray scattering measurements. The first sharp diffraction peak (FSDP) of fused quartz shifts to the high Q region under shock compression. In contrast, the short-range order structure does not change around 3.5 GPa. The nanosecond FSDP shift provides clear evidence of intermediate-range order structural changes in the nonlinear elastic region. Because the intermediate-order structure is too short to produce the final structural state in the nonlinear elastic region, the FSDP shift is lower compared with hydrostatic experiments. (C) 2012 American Institute of Physics. []
    Optronics (368) 113 - 117 0286-9659 2012/08 [Not refereed][Not invited]
    Photon Factory News 30 (2) 24 - 28 0916-0604 2012/08 [Not refereed][Not invited]
  • Ahmed F. Mabied, Melanie Mueller, Robert E. Dinnebier, Shunsuke Nozawa, Manabu Hoshino, Ayana Tomita, Tokushi Sato, Shin-ichi Adachi
    ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE 68 (Pt 4) 424 - 430 0108-7681 2012/08 [Refereed][Not invited]
    The [4 pi + 4 pi] photodimerization process of the 9-substituted anthracene derivative crystalline 9-methylanthracene (9-MA) was investigated using time-resolved X-ray powder diffraction. The study was carried out in-situ using a CCD area detector. Sequential and parametric Rietveld refinement was applied for quantitative phase analysis. The results of traditional sequential Rietveld refinement showed that the evolution of the dimerization process can be described using the Johnson-Mehl-Avrami-Kolmogorov (JMAK) model. The parameters of the JMAK equation were obtained successfully by parametric Rietveld refinement and suggest that the reaction follows heterogeneous nucleation and one-dimensional growth with a decreasing nucleation rate.
  • Tokushi Sato, Shunsuke Nozawa, Ayana Tomita, Manabu Hoshino, Shin-ya Koshihara, Hiroshi Fujii, Shin-ichi Adachi
    JOURNAL OF PHYSICAL CHEMISTRY C 116 (27) 14232 - 14236 1932-7447 2012/07 [Not refereed][Not invited]
    Time-resolved X-ray absorption spectra of photoexcited nithenium(H)-tris-2,2'-bipyridine ([Ru-II(bpy)(3)](2+) in the triplet metal-to-ligand charge transfer ((MLCT)-M-3) state are measured and analyzed to investigate transient structural changes directly related to the photophysical properties of the complex. The results from visible (400 rim) and UV (267 nm) excitation indicate that electrostatic interaction between the oxidized Ru atom and the reduced bipyridine ligand is the dominant factor affecting the Ru-N bond contraction. This thus leads to two groups of Ru ligand distances, one exhibiting the ground-state Ru-N distance and another yielding a slightly decreased Ru-N distance due to the localized MLCT excited state. The EXAFS analysis of the photoexcited complex was analyzed toward one single Ru-N distance., yielding a contraction of 0.04 (0.01) angstrom with an increased DW factor (corresponding to a 0.05 angstrom mean increase).
  • Takayuki Tsuduki, Ayana Tomita, Shin-ya Koshihara, Shin-ichi Adachi, Takahisa Yamato
    JOURNAL OF CHEMICAL PHYSICS 136 (16) 165101  0021-9606 2012/04 [Refereed][Not invited]
    A ligand-migration mechanism of myoglobin was studied by a multidisciplinary approach that used x-ray crystallography and molecular dynamics simulation. The former revealed the structural changes of the protein along with the ligand migration, and the latter provided the statistical ensemble of protein conformations around the thermal average. We developed a novel computational method, homogeneous ensemble displacement, and generated the conformational ensemble of ligand-detached species from that of ligand-bound species. The thermally averaged ligand-protein interaction was illustrated in terms of the potential of mean force. Although the structural changes were small, the presence of the ligand molecule in the protein matrix significantly affected the 3D scalar field of the potential of mean force, in accordance with the self-opening model proposed in the previous x-ray study. (C) 2012 American Institute of Physics. []
  • Manabu Hoshino, Hidehiro Uekusa, Ayana Tomita, Shin-ya Koshihara, Tokushi Sato, Shunsuke Nozawa, Shin-ichi Adachi, Kei Ohkubo, Hiroaki Kotani, Shunichi Fukuzumi
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 (10) 4569 - 4572 0002-7863 2012/03 [Refereed][Not invited]
    Extensive efforts have been devoted to developing electron donor acceptor systems that mimic the utilization of solar energy that occurs in photosynthesis. X-ray crystallographic analysis shows how absorbed photon energy is stabilized in those compounds by structural changes upon photoinduced electron transfer (ET). In this study, structural changes of a simple electron donor acceptor dyad, 9-mesityl-10-methylacridinium cation (Acr(+)-Mes), upon photoinduced ET were directly observed by laser pump and X-ray probe crystallographic analysis. The N-methyl group in Acr(+) was bent, and a weak electrostatic interaction between Mes and a counteranion in the crystal (ClO4) was generated by photoinduced ET. These structural changes correspond to reduction and oxidation due to photoinduced ET and directly elucidate the mechanism in Acr(+)-Mes for mimicking photosynthesis efficiently.
  • Hirohiko Ichikawa, Shunsuke Nozawa, Tokushi Sato, Ayana Tomita, Kouhei Ichiyanagi, Matthieu Chollet, Laurent Guerin, Nicky Dean, Andrea Cavalleri, Shin-ichi Adachi, Taka-hisa Arima, Hiroshi Sawa, Yasushi Ogimoto, Masao Nakamura, Ryo Tamaki, Kenjiro Miyano, Shin-ya Koshihara
    NATURE MATERIALS 10 (2) 101 - 105 1476-1122 2011/02 [Refereed][Not invited]
    Photoinduced phase transitions are of special interest in condensed matter physics(1,2) because they can be used to change complex macroscopic material properties on the ultrafast timescale. Cooperative interactions between microscopic degrees of freedom greatly enhance the number and nature of accessible states, making it possible to switch electronic, magnetic or structural properties in new ways(2-9). Photons with high energies, of the order of electron volts, in particular are able to access electronic states that may differ greatly from states produced with stimuli close to equilibrium(10). In this study we report the photoinduced change in the lattice structure of a charge and orbitally ordered Nd(0.5)Sr(0.5)MnO(3) thin film using picosecond time-resolved X-ray diffraction. The photoinduced state is structurally ordered, homogeneous, metastable and has crystallographic parameters different from any thermodynamically accessible state. A femtosecond time-resolved spectroscopic study shows the formation of an electronic gap in this state. In addition, the threshold-like behaviour and high efficiency in photo-generation yield of this gapped state highlight the important role of cooperative interactions in the formation process. These combined observations point towards a 'hidden insulating phase' distinct from that found in the hitherto known phase diagram.
  • Ayana Tomita, Ulrike Kreutzer, Shin-ichi Adachi, Shin-ya Koshihara, Thomas Jue
    JOURNAL OF EXPERIMENTAL BIOLOGY 213 (16) 2748 - 2754 0022-0949 2010/08 [Refereed][Not invited]
    Despite a century of research, the cellular function of myoglobin (Mb), the mechanism regulating oxygen (O(2)) transport in the cell and the structure-function relationship of Mb remain incompletely understood. In particular, the presence and function of pores within Mb have attracted much recent attention. These pores can bind to Xe as well as to other ligands. Indeed, recent cryogenic X-ray crystallographic studies using novel techniques have captured snapshots of carbon monoxide (CO) migrating through these pores. The observed movement of the CO molecule from the heme iron site to the internal cavities and the associated structural changes of the amino acid residues around the cavities confirm the integral role of the pores in forming a ligand migration pathway from the protein surface to the heme. These observations resolve a long-standing controversy - but how these pores affect the physiological function of Mb poses a striking question at the frontier of biology.
    有機結晶部会ニュースレター (26) 12  2010/03 [Not refereed][Not invited]
  • Ayana Tomita, Tokushi Sato, Shunsuke Nozawa, Shin-ya Koshihara, Shin-ichi Adachi
    ACTA CRYSTALLOGRAPHICA SECTION A 66 (Pt 2) 220 - 228 0108-7673 2010/03 [Refereed][Not invited]
    In order to explore the ligand-migration dynamics in myoglobin induced by photodissociation, cryogenic X-ray crystallographic investigations of carbonmonoxy myoglobin crystals illuminated by continuous wave and pulsed lasers at 1-15 kHz repetition rate have been carried out. Here it is shown that this novel method, extended pulsed-laser pumping of carbonmonoxy myoglobin, promotes ligand migration in the protein matrix by crossing the glass transition temperature repeatedly, and enables the visualization of the migration pathway of the photodissociated ligands in native Mb at cryogenic temperatures. It has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino-acid residues around the cavity which result in the expansion of the cavity. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand-migration channel arising by induced fit.
    放射光 日本放射光学会 23 (1) 7 - 19 0914-9287 2010/01 [Not refereed][Not invited]
  • Shunsuke Nozawa, Tokushi Sato, Matthieu Chollet, Kouhei Ichiyanagi, Ayana Tomita, Hiroshi Fujii, Shin-ichi Adachi, Shin-ya Koshihara
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 132 (1) 61 - + 0002-7863 2010/01 [Refereed][Not invited]
    The first direct observation of the transient spin-state in a disordered magnetic system with time-resolved XAFS is reported. By observing the evolution of the Fe(II) 1s -3d transition, the spin crossover transition from the (1)A(1) low spin state to (5)T(2) high spin state has been directly observed on a picosecond time scale. Moreover, observation of the transient spin state with time-resolved XAFS allows for the investigation of the variations in the electronic state and molecular structure. This unique experimental technique probes the excited states involved in the ultrafast photoinduced reactions in disordered magnetic systems.
    蛋白質 核酸 酵素 54 (11) 1395 - 1401 0039-9450 2009/09 [Not refereed][Not invited]
    日本結晶学会誌 The Crystallographic Society of Japan 51 (4) 258 - 264 0369-4585 2009/08 [Not refereed][Not invited]
    Experimental strategy and setup for the 100 ps time-resolved X-ray absorption spectroscopy (TR-XAS) is presented. X-ray positional active feedback combined with a figure-of-merit scan of the laser beam position was employed as a key technique. It is shown that the pump-probe TR-XAS technique using the X-ray pulse structure of synchrotron radiation sources is a powerful tool to investigate dynamics of the electronic state and molecular structure of non-crystalline samples. A TR-XAS measurement of a photo-induced spin crossover reaction of the tris(1,10-phenanthrorine)iron(II) complex in water is presented.
    固体物理 44 (5) 293 - 305 0454-4544 2009/05 [Not refereed][Not invited]
  • K. Ichiyanagi, T. Sato, S. Nozawa, K. H. Kim, J. H. Lee, J. Choi, A. Tomita, H. Ichikawa, S. Adachi, H. Ihee, S. Koshihara
    JOURNAL OF SYNCHROTRON RADIATION 16 391 - 394 0909-0495 2009/05 [Refereed][Not invited]
    100 ps time-resolved X-ray solution-scattering capabilities have been developed using multilayer optics at the beamline NW14A, Photon Factory Advanced Ring, KEK. X-ray pulses with an energy bandwidth of Delta E/E = 1-5% are generated by reflecting X-ray pulses (Delta E/E = 15%) through multilayer optics, made of W/B(4)C or depth-graded Ru/C on silicon substrate. This tailor-made wide-bandwidth X-ray pulse provides high-quality solution-scattering data for obtaining photo-induced molecular reaction dynamics. The time-resolved solution scattering of CH(2)I(2) in methanol is demonstrated as a typical example.
  • Ayana Tomita, Tokushi Sato, Kouhei Ichiyanagi, Shunsuke Nozawa, Hirohiko Ichikawa, Matthieu Chollet, Fumihiro Kawai, Sam-Yong Park, Takayuki Tsuduki, Takahisa Yamato, Shin-ya Koshihara, Shin-ichi Adachi
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 106 (8) 2612 - 2616 0027-8424 2009/02 [Refereed][Not invited]
    Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e. g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.
  • S. Adachi, S. Nozawa, K. Ichiyanagi, H. Ichikawa, M. Chollet, L. Guerin, R. Tazaki, T. Sato, A. Tomita, H. Sawa, T. Arima, H. Kawata, S. Koshihara
    Time-resolved X-ray techniques utilizing pulsed nature of synchrotron radiation are becoming general and powerful tools to explore structural dynamics in materials and biological systems. The time-resolved technique enables to produce structural movies at 100-picosecond temporal and sub-nanometer spatial resolution. It will be fascinating to apply such capabilities to capture ultrafast cooperative phenomena in strongly-correlated electron systems, photochemical catalytic reaction dynamics in liquid or on solid surface, light-induced response of photosensitive protein molecules, etc. The time-resolved X-ray studies conducted at NW14, PF-AR, KEK will be presented.
  • Hirohiko Ichikawa, Shunsuke Nozawa, Tokushi Sato, Ayana Tomita, Kouhei Ichiyanagi, Matthieu Chollet, Laurent Guerin, Shin-ichi Adachi, Kenjiro Miyano, Shin-ya Koshihara
    We report the lattice dynamics in the photoinduced phase of Nd0.5Sr0.5MnO3 thin film by means of time-resolved x-ray diffraction measurements at the NW14A beamline in the Photon Factory Advanced Ring. We observed the decrease of intensity after the photoirradiation for a superlattice reflection which is associated with Jahn-Teller distortion.
  • Tokushi Sato, Shunsuke Nozawa, Kouhei Ichiyanagi, Ayana Tomita, Hirohiko Ichikawa, Matthieu Chollet, Hiroshi Fujii, Shin-ichi Adachi, Shin-ya Koshihara
    Studying photo-induced molecular dynamics in liquid with sub-nanosecond time-resolution and sub-Angstrom spatial resolution gives information for understanding fundamental chemical process in the photo-induced cooperative phenomena of molecular systems and also for developing new materials and devices. Here, we present time-resolved Xray absorption fine structure on the spin-crossover complex Fe-II tris-(1,10-phenanthroline) dissolved in aqueous solution. We utilized femtosecond laser at 400nm pulse for excitation and 100ps X-ray pulse for probe.
  • A. Tomita, S. Koshihara, S. Adachi, J. Itatani, K. Onda, S. Ogihara, Y. Nakano, H. Yamochi
    The study of photo-controled nature of materials, including their optical, magnetic, and conducting properties, is a fascinating research field. The finding of photo-induced phase transition (PIPT) has triggered the search for inorganic and organic systems with highly efficient and ultrafast photo-responses. As a result of the recent progress in quantum-beam technologies, the time-resolved study of PIPT dynamics on the femto-second time scale, which is comparable with the single-cycle of phonon vibration, has become feasible. In contrast, ultra-slow dynamics on the time scales of a few seconds to several minutes play an important role in the cooperative phenomena in complex systems. Here, we review both the ultra-fast and ultra-slow dynamics of the photo-induced cooperative effects in a typical organic CT crystal (EDO-TTF)(2)PF6 and a protein molecule, myoglobin (Mb). In the case of Mb, we discuss the results from the viewpoint of a unique photo-functionality, i.e., the photo-induced transportation of a small molecule in the "super-structure" of a protein molecule.
  • Tokushi Sato, Shunsuke Nozawa, Kohei Ichiyanagi, Ayana Tomita, Matthieu Chollet, Hirohiko Ichikawa, Hiroshi Fujii, Shin-ichi Adachi, Shin-ya Koshihara
    JOURNAL OF SYNCHROTRON RADIATION 16 (Pt 1) 110 - 115 0909-0495 2009/01 [Refereed][Not invited]
    An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented. The X-ray positional active feedback to crystals in a monochromator combined with a figure-of-merit scan of the laser beam position has been utilized as an essential tool to stabilize the spatial overlap of the X-ray and laser beams at the sample position. As a typical example, a time-resolved XAFS measurement of a photo-induced spin crossover reaction of the tris(1,10-phenanthrorine)iron(II) complex in water is presented.
    Photon Factory News 26 (3) 20 - 23 0916-0604 2008/11 [Not refereed][Not invited]
  • Kouhei Ichiyanagia, Shin-Ichi Adachi, Shunsuke Nozawa, Yoichiro Hironaka, Kazutaka G. Nakamura, Tokushi Sato, Ayana Tomita, Shin-Ya Koshihara
    APPLIED PHYSICS LETTERS 91 (23) 231918-231918-3  0003-6951 2007/12 [Refereed][Not invited]
    We report a single-shot nanosecond time-resolved Laue diffraction measurement of cadmium sulfide (CdS) single crystal under laser-induced shock compression. The observed Laue diffraction pattern maintains sixfolding axis of the wurtzite structure for 10 ns at a shock pressure of 3.92 GPa, which is above the threshold pressure of phase transition to a rocksalt structure. This result shows that a transient wurtzite structure is observed above its threshold pressure to a rocksalt structure on a nanosecond time scale. Uniaxial compression was confirmed by the c/a value of the transient structure obtained from the (201) and (302) peaks. (c) 2007 American Institute of Physics.
  • Shunsuke Nozawa, Shin-ichi Adachi, Jun-ichi Takahashi, Ryoko Tazaki, Laurent Guerin, Masahiro Daimon, Ayana Tomita, Tokushi Sato, Matthieu Chollet, Eric Collet, Herve Cailleau, Shigeru Yamamoto, Kimichika Tsuchiya, Tatsuro Shioya, Hiroyuki Sasaki, Takeharu Mori, Kohei Ichiyanagi, Hiroshi Sawa, Hiroshi Kawata, Shin-ya Koshihara
    JOURNAL OF SYNCHROTRON RADIATION 14 (Pt 4) 313 - 319 0909-0495 2007/07 [Refereed][Not invited]
    NW14A is a newly constructed undulator beamline for 100 ps time-resolved X-ray experiments at the Photon Factory Advanced Ring. This beamline was designed to conduct a wide variety of time- esolved X-ray measurements, such as time-resolved diffraction, scattering and X-ray absorption fine structure. Its versatility is allowed by various instruments, including two undulators, three diffractometers, two pulse laser systems and an X-ray chopper. The potential for the detection of structural changes on the 100 ps time scale at NW14A is demonstrated by two examples of photo-induced structural changes in an organic crystal and photodissociation in solution.
  • S Adachi, S Nozawa, R Tazaki, J Takahashi, J Itatani, M Daimon, T Mori, H Sawa, H Kawata, T Sato, A Tomita, M Chollet, L Guerin, E Collet, H Cailleau, S Koshihara
    Second International Conference on Photo-Induced Phase Transitions: Cooperative, Nonlinear and Functional Properties 21 101 - 105 1742-6588 2005 [Refereed][Not invited]
    Ultra-fast time-resolved X-ray crystallography using electron-accelerator-based Xray sources has been becoming a general and powerful tool to explore structural dynamics of crystalline state in material and biological sciences. Photon Factory Advanced Ring (PF-AR) is a full-time single-bunch synchrotron radiation source operated for such time-resolved X-ray studies using pulsed X-rays. Here we report instrumentation, feasibility, and applications of time-resolved X-ray diffraction at PF-AR. The time-resolved X-ray diffraction equipment consists of an X-ray pulse selector, an X-ray diffractometer, a femtosecond laser system and their timing modules which provide synchronized X-ray pulses with 50-picosecond duration (rms) and 150-femtosecond laser pulses for laser-pump-X-ray-probe experiment. The current status of the beam lines NW2 and NW14, and their applications are described.
  • A Tomita, T Sato, K Tanaka, Y Kawabe, M Shirai, K Tanaka, E Hanamura
    JOURNAL OF LUMINESCENCE 109 (1) 19 - 24 0022-2313 2004/07 [Refereed][Not invited]
    Two independent luminescence channels are observed from manganese-doped spinel Mn:MgAl2O4. The luminescence around 520 nm is assigned to transition from the lowest electronic excited state T-4(1) to the ground state (6)A(1) of Mn2+ (3d)(5) ion by analyzing the excitation spectrum and electron spin resonance measurement. The emission at 650 nm is triggered by the band edge excitation and is assigned similarly to the charge-transfer process associated with the manganese ion. (C) 2004 Elsevier B.V. All rights reserved.
  • E Hanamura, Y Kawabe, H Takashima, T Sato, A Tomita
    JOURNAL OF NONLINEAR OPTICAL PHYSICS & MATERIALS 12 (4) 467 - 473 0218-8635 2003/12 [Refereed][Invited]
    Strong blue emission is observed from Ti-doped MgAl2O4, yellow emission from a Mn-doped one and white light emission from a V-doped one. The optimum condition to obtain the strongest emission was studied by changing the doping density and growing atmosphere. The microscopic models for these emission processes are proposed from observation of other optical responses and electron spin resonance spectra both in the electronic ground and excited states.

Conference Activities & Talks

Awards & Honors

  • 2015/09 3D Active Site Science Daimon Award
    受賞者: Ayana Sato
  • 2014/11 Poster Award 2014, The Crystallographic Society of Japan
    受賞者: Ayana Tomita
  • 2009/09 L'Oréal-UNESCO for Women in Science Japan Fellowships 2009
    受賞者: Ayana Tomita

Research Grants & Projects

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