Inaba-Inoue Satomi

Faculty of Advanced Life ScienceAssistant Professor
Last Updated :2025/07/05

■Researcher basic information

Nickname etc.

  • Satomi Inoue

Degree

  • Ph.D.

Researchmap personal page

Home Page URL

Researcher number

  • 70785493

J-Global ID

Research Field

  • Life sciences, Structural biochemistry
  • Life sciences, Applied biochemistry
  • Life sciences, Biophysics

Educational Organization

■Career

Career

  • Feb. 2024 - Present
    Hokkaido University, Faculty of Advanced Life Science Division of Advanced Transdisciplinary Sciences, Assistant Professor
  • Oct. 2022 - Jan. 2024
    High Energy Accelerator Research Organization, Research Scientist
  • Mar. 2020 - Sep. 2022
    Japan Synchrotron Radiation Research Institute, Research Scientist, Japan
  • Oct. 2019 - Jun. 2022
    Research Complex at Harwell, Rutherford Appleton Laboratory, Visiting Researcher, United Kingdom
  • Oct. 2019 - Jun. 2022
    Imperial College London, Department of Life Sciences, Sponsored Researcher, United Kingdom
  • Oct. 2019 - Jun. 2022
    Japan Society for the Promotion of Science, Overseas Research Fellow, United Kingdom
  • Mar. 2017 - Feb. 2020
    Japan Synchrotron Radiation Research Institute, Postdoctoral Researcher
  • Feb. 2018 - Mar. 2018
    Diamond Light Source, Visiting Scientist, United Kingdom
  • Apr. 2016 - Feb. 2017
    Japan Society for the Promotion of Science, Research Fellow (PD)
  • Apr. 2015 - Mar. 2016
    Japan Society for the Promotion of Science, Research Fellow (DC)

Educational Background

  • Apr. 2011 - Mar. 2016, Kyoto Prefectural University, Graduate School of Life and Environmental Sciences
  • Apr. 2007 - Mar. 2011, Kyoto Prefectural University, School of Agriculture, Department of Agricultural chemistry

■Research activity information

Awards

  • Jun. 2025, The Protein Science Society of Japan, PSSJ Young Scientist Excellent Award
    Satomi Inaba-Inoue, 46051099
  • May 2023, United Japanese researchers Around the world (UJA), UJA Outstanding Paper Award 2023 [Disruptive innovation Basic Bioscience Award]
    Satomi Inaba-Inoue, 36800003
  • Dec. 2022, The Molecular Biology Society of Japan, MBSJ2022 Science Pitch Award
    Satomi Inaba-Inoue, 36800003
  • Apr. 2022, The British Crystallographic Association, BSG Group Poster Prize
    Satomi Inaba-Inoue, International society, United Kingdom, 36800003
  • Apr. 2022, The British Crystallographic Association, BSG David Blow Prize (1st Prize)
    Satomi Inaba-Inoue, International society, United Kingdom, 36800003
  • May 2021, ASG-Keio, The 2nd Scienc-ome XR Innovation Hub Hackathon Award (1st Prize)　　　　　　　　　　　　　　　
    Ryosuke Kojima;Tadayuki Akagi;Satomi Inaba-Inoue;Rina Ohnishi;Chiriro Goya;Davin HE Stetiamarga;Naoka Amari
  • Nov. 2017, 8th International and 10th Japan-China Joint Symposium on Calorimetry and Thermal Analysis, Best Poster Award　　　　　　　　　　　　　　　
    Satomi Inaba
  • Jul. 2017, The Japan Society for Bioscience, Biotechnology, and Agrochemistry, Young Scientist Award　　　　　　　　　　　　　　　
    Satomi Inaba
  • Mar. 2016, Kyoto Prefectural Public University Corporation, President Award　　　　　　　　　　　　　　　
    Satomi Inaba
  • Oct. 2015, The Japan Society of Calorimetry and Thermal Analysis, Poster Award　　　　　　　　　　　　　　　
    Satomi Inaba
  • Dec. 2012, GE healthcare Japan Corporation, Poster Award　　　　　　　　　　　　　　　
    Satomi Inaba

Papers

  • Plasticity and Co-Factor-Dependent Structural Changes in the RecA Nucleoprotein Filament Studied by Small-Angle X-Ray Scattering (SAXS) Measurements and Molecular Modeling
    Satomi Inaba-Inoue, Afra Sabei, Anne-Elisabeth Molza, Mara Prentiss, Tsutomu Mikawa, Hiroshi Sekiguchi, Chantal Prévost, Masayuki Takahashi
    Molecules, 16 Apr. 2025, [Lead author]
    Scientific journal
  • Structural analysis reveals how tetrameric tyrosine-phosphorylated STAT1 is targeted by the rabies virus P-protein
    Aoi Sugiyama, Miku Minami, Kaito Ugajin, Satomi Inaba-Inoue, Nana Yabuno, Yuichiro Takekawa, Sun Xiaomei, Shiho Takei, Mina Sasaki, Tomo Nomai, Xinxin Jiang, Shunsuke Kita, Katsumi Maenaka, Mika Hirose, Min Yao, Paul R. Gooley, Gregory W. Moseley, Yukihiko Sugita, Toyoyuki Ose
    Science Signaling, 18, 878, American Association for the Advancement of Science (AAAS), 18 Mar. 2025
    Scientific journal, Signal transducer and activator of transcription (STAT) family members mediate signaling in the Janus kinase (JAK)–STAT pathway and are activated by phosphorylation at a conserved tyrosine residue, resulting in dimerization through reciprocal interactions between the phosphotyrosine and a Src homology 2 (SH2) domain. Tyrosine-phosphorylated STAT (pY-STAT) then translocates to the nucleus to induce the expression of genes encoding antiviral proteins. Although the active and functional forms of STATs are conventionally considered to be dimers, STATs can undergo higher-order oligomerization, which is implicated in regulating transcriptional activity. We present the cryo–electron microscopy (cryo-EM) structure of the tetrameric form of intact pY-STAT1 in complex with DNA, which indicates that interactions between the amino-terminal domains (NTDs) of STAT1 induce oligomerization. The tetrameric structure revealed a compact conformation with a previously uncharacterized binding interface: Two DNA-bound dimers are twofold symmetrically aligned to transform into a tandem DNA-binding model without NTD dimer separation. Moreover, biochemical analyses indicated that the rabies virus P-protein selectively targeted tetrameric pY-STAT1. Combined with data showing which regions contribute to the interaction between pY-STAT1 and the P-protein, we constructed a binding model explaining how P recognizes the pY-STAT1 tetramer. These data provide insight into how pathogenic viruses target signaling pathways that mediate the host immune response.
  • Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters
    Thijs Ettema, Satomi Inaba-Inoue, Chancievan Thangaratnarajah, Leticia Alves da Silva, Amy Clarke, Piotr Stepien, Anokhi Shah, Yue Ma, Katie Hardman, Sophia David, Hassane El-Mkami, Jonathan Heddle, Norimichi Nomura, Satoshi Ogasawara, So Iwata, Dmitry Ghilarov, Christos Pliotas, Thomas Stockner, Dirk Slotboom, Konstantinos Beis
    03 Feb. 2025, [Lead author]
  • Ligand‐Mediated Quantum Yield Enhancement in 1‐D Silver Organothiolate Metal–Organic Chalcogenolates
    Mariya Aleksich, Yeongsu Cho, Daniel W. Paley, Maggie C. Willson, Hawi N. Nyiera, Patience A. Kotei, Vanessa Oklejas, David W. Mittan‐Moreau, Elyse A. Schriber, Kara Christensen, Ichiro Inoue, Shigeki Owada, Kensuke Tono, Michihiro Sugahara, Satomi Inaba‐Inoue, Mohammad Vakili, Christopher J. Milne, Fabio DallAntonia, Dmitry Khakhulin, Fernando Ardana‐Lamas, Frederico Lima, Joana Valerio, Huijong Han, Tamires Gallo, Hazem Yousef, Oleksii Turkot, Ivette J. Bermudez Macias, Thomas Kluyver, Philipp Schmidt, Luca Gelisio, Adam R. Round, Yifeng Jiang, Doriana Vinci, Yohei Uemura, Marco Kloos, Adrian P. Mancuso, Mark Warren, Nicholas K. Sauter, Jing Zhao, Tess Smidt, Heather J. Kulik, Sahar Sharifzadeh, Aaron S. Brewster, J. Nathan Hohman
    Advanced Functional Materials, Wiley, Dec. 2024
    Scientific journal, Abstract

    X‐ray free electron laser (XFEL) microcrystallography and synchrotron single‐crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X‐ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0‐1%), the methyl ester in the ortho position yields a high quantum yield of 22%. The proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2‐ and 3‐ positions, resulting in needle‐like crystals. Further analysis using density functional theory (DFT) and many‐body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.
  • Cyclic Ion Mobility for Hydrogen/Deuterium Exchange-Mass Spectrometry Applications
    Damon Griffiths, Malcolm Anderson, Keith Richardson, Satomi Inaba-Inoue, William J. Allen, Ian Collinson, Konstantinos Beis, Michael Morris, Kevin Giles, Argyris Politis
    Analytical Chemistry, American Chemical Society (ACS), 01 Apr. 2024
    English, Scientific journal, Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localisation of dynamic changes. Consequently, HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase data quality by providing an orthogonal mode of peptide ion separation in the gas-phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage and/or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multi-pass IM separations. Using 1-pass and multi-pass cIM routines, we use the recently commercialised SELECT SERIES™ Cyclic™ IM spectrometer for HDX-MS analyses of 4 detergent solubilised IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multi-pass cIM data. Interestingly, use of 1-pass and multi-pass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM which has the potential to enable the analysis of more complex systems with greater accuracy and speed.
  • Cyclic ion mobility for hydrogen/deuterium exchange-mass spectrometry applications
    Damon Griffiths, Malcolm Anderson, Keith Richardson, Satomi Inaba-Inoue, William J. Allen, Ian Collinson, Konstantinos Beis, Michael Morris, Kevin Giles, Argyris Politis
    20 Dec. 2023
    Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localisation of dynamic changes. Consequently, HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase data quality by providing an orthogonal mode of peptide ion separation in the gas-phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage and/or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multi-pass IM separations. Using 1-pass and multi-pass cIM routines, we use the recently commercialised SELECT SERIES™ Cyclic™ IM spectrometer for HDX-MS analyses of 4 detergent solubilised IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multi-pass cIM data. Interestingly, use of 1-pass and multi-pass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM which has the potential to enable the analysis of more complex systems with greater accuracy and speed.
  • Engineering Supramolecular Hybrid Architectures with Directional Organofluorine Bonds
    Patience A. Kotei, Daniel W. Paley, Vanessa Oklejas, David W. Mittan-Moreau, Elyse A. Schriber, Mariya Aleksich, Maggie C. Willson, Ichiro Inoue, Shigeki Owada, Kensuke Tono, Michihiro Sugahara, Satomi Inaba-Inoue, Andrew Aquila, Frédéric Poitevin, Johannes P. Blaschke, Stella Lisova, Mark S. Hunter, Raymond G. Sierra, José A. Gascón, Nicholas K. Sauter, Aaron S. Brewster, J. Nathan Hohman
    Small Science, 4, 1, Wiley, 13 Dec. 2023
    English, Scientific journal, Understanding how chemical modifications alter the atomic‐scale organization of materials is of fundamental importance in materials engineering and the target of considerable efforts in computational prediction. Incorporating covalent and noncovalent interactions in designing crystals while “piggybacking” on the driving force of molecular self‐assembly has augmented efforts to understand the emergence of complex structures using directed synthesis. In this work, microcrystalline powders of the silver 2‐, 3‐, and 4‐fluorobenzenethiolates are prepared and their structures are resolved by small‐molecule serial femtosecond X‐ray crystallography. These three compounds enable the emergence and role of supramolecular synthons in the crystal structures of 3D metal‐organic chalcogenolates to be examined. The unique divergence in their optoelectronic, morphological, and structural behaviors is assessed. The extent of CHF interactions and their influence on the structure and the observed trends in the thermal stability of the crystals are quantified through theoretical calculations and thermogravimetric analysis.
  • CRAFTing Delivery of Membrane Proteins into Protocells using Nanodiscs
    Piotr Stępień, Sylwia Świątek, Manuel Yamil Yusef Robles, Joanna Markiewicz-Mizera, Dhanasekaran Balakrishnan, Satomi Inaba-Inoue, Alex H. De Vries, Konstantinos Beis, Siewert J. Marrink, Jonathan G. Heddle
    ACS Applied Materials & Interfaces, American Chemical Society (ACS), 28 Nov. 2023, [Peer-reviewed]
    Scientific journal
  • Functional Structure Analysis of DNA-binding Protein by SAXS
    Satomi Inaba, Satomi Inaba-Inoue
    SPring-8/SACLA Research Report, SPring-8/SACLA Research Report, 31 Oct. 2023
    Japanese, Scientific journal
  • Cryogenic electron microscope facility at KEK-SBRC
    Akihito Ikeda, Masato Kawasaki, Takayuki Kubota, Misato Yamamoto, Yusuke Yamada, Satomi Inaba-Inoue, Akira Takasu, Shinji Aramaki, Chiho Masuda, Naruhiko Adachi, Toshio Moriya, Toshiya Senda
    Acta Crystallographica Section A Foundations and Advances, 07 Jul. 2023
    Scientific journal
  • Dual-Uptake Mode of the Antibiotic Phazolicin Prevents Resistance Acquisition by Gram-Negative Bacteria
    Dmitrii Y. Travin, Romain Jouan, Armelle Vigouroux, Satomi Inaba-Inoue, Joy Lachat, Fazal Haq, Tatiana Timchenko, Dmitry Sutormin, Svetlana Dubiley, Konstantinos Beis, Solange Moréra, Konstantin Severinov, Peter Mergaert
    mBio, American Society for Microbiology, 21 Feb. 2023
    Scientific journal, Many bacteria produce antimicrobial peptides to eliminate competitors and create an exclusive niche. These peptides act either by membrane disruption or by inhibiting essential intracellular processes.
  • The antibiotic phazolicin displays a dual mode of uptake in Gram-negative bacteria
    Dmitrii Y. Travin, Armelle Vigouroux, Satomi Inaba-Inoue, Feng Qu, Romain Jouan, Joy Lacha, Dmitry Sutormin, Svetlana Dubiley, Konstantinos Beis, Solange Mor{\'{e } }ra, Konstantin Severinov, Peter Mergaer
    Cold Spring Harbor Laboratory, 28 Apr. 2022
    Scientific journal, ABSTRACTPhazolicin (PHZ) is a peptide antibiotic exhibiting narrow-spectrum activity against rhizobia closely related to its producer Rhizobium sp. Pop5. Using genetic and biochemical techniques, we here identified BacA and YejABEF as two importers of PHZ in a sensitive model strain Sinorhizobium meliloti Sm1021. BacA and YejABEF are members of SLiPT and ABC transporter families of non-specific peptide importers, respectively. The uptake of PHZ by two distinct families of transporters dramatically decreases the naturally occurring rate of resistance. Moreover, since both BacA and YejABEF are essential for the development of functional symbiosis of rhizobia with leguminous plants, the acquisition of PHZ resistance via the inactivation of transporters is further disfavoured since single bacA or yejABEF mutants are unable to propagate in root nodules. Crystal structures of the periplasmic subunit YejA from S. meliloti and Escherichia coli revealed fortuitous bound peptides, suggesting a non-specific peptide-binding mechanism that facilitates the uptake of PHZ and other antimicrobial peptides.SIGNIFICANCEMany bacteria produce antimicrobial peptides to eliminate competitors and create an exclusive niche. These peptides kill bacteria by either membrane disruption or inhibiting essential intracellular processes. The Achilles heel of the latter type of antimicrobials is their dependence on transporters to enter the susceptible bacteria since mutations in such transporters result in resistance. We describe here how the ribosome-targeting peptide phazolicin, produced by Rhizobium sp. Pop5, uses two different transporters, BacA and YejABEF, to get into the cells of the symbiotic bacterium Sinorhizobium meliloti. This dramatically reduces the probability of resistance acquisition. Both transporters need to be inactivated for phazolicin resistance acquisition. Since these transporters are also crucial in S. meliloti for its symbiotic association with host plants, their inactivation in biological settings is highly unlikely. This makes PHZ an attractive lead for the development of a biocontrol agent with potential for use in agriculture.
  • Letters from Abroad
    Satomi Inaba-Inoue
    Seibutsu Butsuri, 62, 2, 148, 149, Biophysical Society of Japan, 2022
    English, Scientific journal
  • Molecular mechanism of SbmA, a promiscuous transporter exploited by antimicrobial peptides
    Dmitry Ghilarov, Satomi Inaba-Inoue, Piotr Stepien, Feng Qu, Elizabeth Michalczyk, Zuzanna Pakosz, Norimichi Nomura, Satoshi Ogasawara, Graham Charles Walker, Sylvie Rebuffat, So Iwata, Jonathan Gardiner Heddle, Konstantinos Beis
    Science Advances, 7, 37, American Association for the Advancement of Science (AAAS), 10 Sep. 2021, [Peer-reviewed], [Lead author]
    Scientific journal, 36800003
  • Crystal and solution structures of SH2 domain of signaling molecule in complex with the co-stimulatory receptor CD28
    Satomi Inaba-Inoue, Katsuaki Inoue, Takaaki Hikima, Hiroshi Sekiguchi, Robert Rambo
    Acta Crystallographica Section A Foundations and Advances, 75, a2, e69, e69, 18 Aug. 2019, [Lead author]
    Scientific journal
  • Site-specific observation of the conformational change of a protein with 15N-labeled Tyr residues using NMR
    Satomi Inaba, Ayako Shiota, Takuya Yoshida, Masayuki Oda
    Analytical Biochemistry, 574, 34, 38, 01 Jun. 2019, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Binding thermodynamics of metal ions to HIV-1 ribonuclease H domain
    Masayuki Oda, Zhaoyong Xi, Satomi Inaba, Ryan L. Slack, Rieko Ishima
    Journal of Thermal Analysis and Calorimetry, 135, 5, 2647, 2653, Mar. 2019
    English, Scientific journal
  • Folding thermodynamics of PET-hydrolyzing enzyme Cut190 depending on Ca2+ concentration
    Satomi Inaba, Narutoshi Kamiya, Gert-Jan Bekker, Fusako Kawai, Masayuki Oda
    Journal of Thermal Analysis and Calorimetry, 135, 5, 2655, 2663, Mar. 2019, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Structural and functional properties of Grb2 SH2 dimer in CD28 binding
    Yuhi Hosoe, Nobutaka Numoto, Satomi Inaba, Shuhei Ogawa, Hisayuki Morii, Ryo Abe, Nobutoshi Ito, Masayuki Oda
    Biophysics and Physicobiology, 16, 80, 88, Biophysical Society of Japan, 2019, [Domestic magazines]
    English, Scientific journal, Growth factor receptor-bound protein 2 (Grb2) is an adaptor protein that plays a critical role in cellular signal transduction. It contains a central Src homology 2 (SH2) domain flanked by two Src homology 3 (SH3) domains. Binding of Grb2 SH2 to the cytoplasmic region of CD28, phosphorylated Tyr (pY) containing the peptide motif pY-X-N-X, is required for costimulatory signaling in T cells. In this study, we purified the dimer and monomer forms of Grb2 SH2, respectively, and analyzed their structural and functional properties. Size exclusion chromatography analysis showed that both dimer and monomer exist as stable states. Thermal stability analysis using circular dichroism showed that the dimer mostly dissociates into the monomer around 50°C. CD28 binding experiments showed that the affinity of the dimer to the phosphopeptide was about three fold higher than that of the monomer, possibly due to the avidity effect. The present crystal structure analysis of Grb2 SH2 showed two forms; one is monomer at 1.15 Å resolution, which is currently the highest resolution analysis, and another is dimer at 2.00 Å resolution. In the dimer structure, the C-terminal region, comprising residues 123-152, was extended towards the adjacent molecule, in which Trp121 was the hinge residue. The stable dimer purified using size exclusion chromatography would be due to the C-terminal helix "swapping". In cases where a mutation caused Trp121 to be replaced by Ser in Grb2 SH2, this protein still formed dimers, but lost the ability to bind CD28.
  • Enzymatic hydrolysis of PET: functional roles of three Ca2+ ions bound to a cutinase-like enzyme, Cut190*, and its engineering for improved activity
    Masayuki Oda, Yuri Yamagami, Satomi Inaba, Tatsuo Oida, Masaki Yamamoto, Sakihito Kitajima, Fusako Kawai
    Applied Microbiology and Biotechnology, 102, 23, 10067, 10077, Springer Science and Business Media {LLC}, Dec. 2018
    English, Scientific journal
  • Effects of active site residues of 3α-hydroxysteroid dehydrogenase from pseudomonas sp. b-0831 on its catalysis and cofactor binding
    Ayako Shiota, Satomi Inaba, Masayuki Oda
    Bioscience, Biotechnology, and Biochemistry, 82, 10, 1702, 1707, 03 Oct. 2018
    English, Scientific journal
  • Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle
    Nobutaka Numoto, Narutoshi Kamiya, Gert-Jan Bekker, Yuri Yamagami, Satomi Inaba, Kentaro Ishii, Susumu Uchiyama, Fusako Kawai, Nobutoshi Ito, Masayuki Oda
    Biochemistry, 57, 36, 5289, 5300, American Chemical Society ({ACS}), 11 Sep. 2018
    English, Scientific journal
  • DNA-binding induced conformational change of c-Myb R2R3 analyzed using diffracted X-ray tracking
    Yuhi Hosoe, Satomi Inaba, Hiroshi Sekiguchi, Yuji C. Sasaki, Masayuki Oda
    Biochemical and Biophysical Research Communications, 503, 1, 338, 343, Elsevier {BV}, Sep. 2018, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, Previous structural analyses have shown that R2R3, the minimum unit of the DNA-binding domain of the transcriptional factor c-Myb, is largely flexible in solution, and changes to a more rigid structure upon DNA binding. In this study, we evaluated the structural dynamics using the diffracted X-ray tracking method, in correlation with DNA-binding abilities under different salt conditions, and compared them with the previous results. The resultant curve of the mean square angular displacements (MSD) clearly showed that the flexibility of R2R3 was decreased upon DNA binding, and the DNA-binding energies determined using the angular diffusion coefficients were in good agreement with those determined using isothermal titration calorimetry. The results of the MSD curves also indicate that the translational length reduces by approximately half upon DNA binding.
  • Structural and thermodynamic characterization of endo-1,3-β-glucanase: Insights into the substrate recognition mechanism
    Masayuki Oda, Satomi Inaba, Narutoshi Kamiya, Gert-Jan Bekker, Bunzo Mikami
    Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1866, 3, 415, 425, Mar. 2018
    English, Scientific journal
  • Effect of a salt-bridge between inter-repeats on the 3D structure of the c-Myb DNA-binding domain revealed by thermodynamic analysis
    Satomi Inaba, Harumi Fukada, Masayuki Oda
    Journal of Thermal Analysis and Calorimetry, 131, 1, 335, 341, Jan. 2018, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Light-chain residue 95 is critical for antigen binding and multispecificity of monoclonal antibody G2
    Daiki Usui, Satomi Inaba, Yuji O. Kamatari, Naotaka Ishiguro, Masayuki Oda
    Biochemical and Biophysical Research Communications, 490, 4, 1205, 1209, 02 Sep. 2017
    English, Scientific journal
  • First observation of metal ion-induced structural fluctuations of α-helical peptides by using diffracted X-ray tracking
    Daiki Usui, Satomi Inaba, Hiroshi Sekiguchi, Yuji C. Sasaki, Toshiki Tanaka, Masayuki Oda
    Biophysical Chemistry, 228, 81, 86, Elsevier {BV}, Sep. 2017, [International Magazine]
    English, Scientific journal, In order to analyze protein structural dynamics, we designed simple model peptides whose structures changed from random-coil to helix-bundle structures by forming stable hydrophobic core in the presence of metal ions. The strategy involved destabilizing a de novo designed three helix-bundle protein by substituting the residues present in its hydrophobic core with histidine and small amino acids. The conformational changes of peptides induced upon binding of Zn2+ to histidine were analyzed using circular dichroism spectroscopy, which revealed peptides, HA and HG, to be good candidates for further analyses. The diffracted X-ray tracking experiments showed that the structural fluctuations of both HA and HG were suppressed upon binding of Zn2+. We succeeded in observing the differences in fluctuations of HA and HG in solution between random-coil like and helix-bundle structures. The metal-binding energies determined using the angular diffusion coefficients were in good agreement with those determined using isothermal titration calorimetry.
  • Tryptophan introduction can change β-glucan binding ability of the carbohydrate-binding module of endo-1,3-β-glucanase
    Ayako Miki, Satomi Inaba, Takahiro Maruno, Yuji Kobayashi, Masayuki Oda
    Bioscience, Biotechnology, and Biochemistry, 81, 5, 951, 957, 04 May 2017
    English, Scientific journal
  • Pronounced effect of hapten binding on thermal stability of an anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain
    Yusui Sato, Satomi Inaba, Harumi Fukada, Takachika Azuma, Masayuki Oda
    Molecular Immunology, 85, 130, 136, May 2017
    English, Scientific journal
  • Structural and Functional Analysis of DNA-binding Protein under Physiological Conditions
    Satomi INABA
    Seibutsu Butsuri, 57, 5, 257, 258, Biophysical Society of Japan, 2017, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
    English, Scientific journal
  • Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
    Satomi Inaba, Nobutaka Numoto, Shuhei Ogawa, Hisayuki Morii, Teikichi Ikura, Ryo Abe, Nobutoshi Ito, Masayuki Oda
    Journal of Biological Chemistry, 292, 3, 1052, 1060, Elsevier {BV}, Jan. 2017, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases.
  • Structural dynamics of a single-chain Fv antibody against (4-hydroxy-3-nitrophenyl)acetyl
    Yusui Sato, Yusuke Tanaka, Satomi Inaba, Hiroshi Sekiguchi, Takahiro Maruno, Yuji C. Sasaki, Harumi Fukada, Yuji Kobayashi, Takachika Azuma, Masayuki Oda
    International Journal of Biological Macromolecules, 91, 151, 157, Elsevier {BV}, Oct. 2016, [International Magazine]
    English, Scientific journal, Protein structure dynamics are critical for understanding structure-function relationships. An antibody can recognize its antigen, and can evolve toward the immunogen to increase binding strength, in a process referred to as affinity maturation. In this study, a single-chain Fv (scFv) antibody against (4-hydroxy-3-nitrophenyl)acetyl, derived from affinity matured type, C6, was designed to comprise the variable regions of light and heavy chains connected by a (GGGGS)3 linker peptide. This scFv was expressed in Escherichia coli in the insoluble fraction, solubilized in the presence of urea, and refolded by stepwise dialysis. The correctly refolded scFv was purified, and its structural, physical, and functional properties were analyzed using analytical ultracentrifugation, circular dichroism spectrometry, differential scanning calorimetry, and surface plasmon resonance biosensor. Thermal stability of C6 scFv increased greatly upon antigen binding, due to favorable enthalpic contributions. Antigen binding kinetics were comparable to those of the intact C6 antibody. Structural dynamics were analyzed using the diffracted X-ray tracking method, showing that fluctuations were suppressed upon antigen binding. The antigen binding energy determined from the angular diffusion coefficients was in good agreement with that calculated from the kinetics analysis, indicating that the fluctuations detected at single-molecule level are well reflected by antigen binding events.
  • Structural and binding properties of laminarin revealed by analytical ultracentrifugation and calorimetric analyses
    Masayuki Oda, Yoichi Tanabe, Masanori Noda, Satomi Inaba, Elena Krayukhina, Harumi Fukada, Susumu Uchiyama
    Carbohydrate Research, 431, 33, 38, Elsevier {BV}, Aug. 2016
    English, Scientific journal
  • Thermodynamic effects of a linker region between two repeats of a protein, c-Myb R2R3, on its stability and structural dynamics
    Satomi Inaba, Harumi Fukada, Masayuki Oda
    Journal of Thermal Analysis and Calorimetry, 123, 3, 1763, 1767, Mar. 2016, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Folding thermodynamics of c-Myb DNA-binding domain in correlation with its α-helical contents
    Satomi Inaba, Harumi Fukada, Masayuki Oda
    International Journal of Biological Macromolecules, 82, 725, 732, Jan. 2016, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Functional conformer of c-Myb DNA-binding domain revealed by variable temperature studies
    Satomi Inaba, Akihiro Maeno, Kazumasa Sakurai, Sunilkumar Puthenpurackal Narayanan, Takahisa Ikegami, Kazuyuki Akasaka, Masayuki Oda
    FEBS Journal, 282, 23, 4497, 4514, Wiley, Dec. 2015, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, The conformational fluctuation in the minimum DNA-binding domain of c-Myb, repeats 2 and 3 (R2R3), was studied under closely physiological conditions. A global unfolding transition, involving both the main chain and the side chains, was found to take place at the approximate temperature range 30-70 °C, with a transition temperature of approximately 50 °C. In addition, the observation of simultaneous shift change and broadening of NMR signals in both (1)H one-dimensional and (15)N/(1)H two-dimensional NMR spectra indicated the occurrence of locally fluctuating state at physiological temperature. In the wild-type protein containing a cavity in R2, the local fluctuation of R2 is more prominent than that of R3, whereas it is suppressed in the cavity-filled mutant, V103L. This indicates that the cavity in R2 contributes significantly to the conformational instability and the transition into the locally fluctuating state. For the wild-type R2R3 protein, the more dynamic conformer is estimated to be present to some extent at 37 °C and is likely beneficial for its biological function: DNA-binding. This result is in agreement with the concept of an excited-state conformer that exists in equilibrium with the dominant ground-state conformer and acts as the functional conformer of the protein. From the findings of the present study, it appears that the tandem repeats of two small domains with no disulfide bonds and with a destabilizing cavity function as the evolutionary strategy of the wide-type c-Myb DNA-binding domain to produce an appropriate fraction of the locally fluctuating state at 37 °C, which is more amenable to DNA-binding. Database: Chemical shifts and peak lists have been deposited in the Biological Magnetic Resonance Bank under entries 11584 and 11585.
  • Structural and physical properties of collagen extracted from moon jellyfish under neutral pH conditions
    Ayako Miki, Satomi Inaba, Takayuki Baba, Koji Kihira, Harumi Fukada, Masayuki Oda
    Bioscience, Biotechnology, and Biochemistry, 79, 10, 1603, 1607, 03 Oct. 2015, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Thermodynamic effects of multiple protein conformations on stability and DNA binding
    Satomi Inaba, Harumi Fukada, Takahisa Ikegami, Masayuki Oda
    Archives of Biochemistry and Biophysics, 537, 2, 225, 232, 15 Sep. 2013, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Crystal Structures of Hereditary Vitamin D-Resistant Rickets-Associated Vitamin D Receptor Mutants R270L and W282R Bound to 1,25-Dihydroxyvitamin D3and Synthetic Ligands
    Makoto Nakabayashi, Yoshito Tsukahara, Yukiko Iwasaki-Miyamoto, Mika Mihori-Shimazaki, Sachiko Yamada, Satomi Inaba, Masayuki Oda, Masato Shimizu, Makoto Makishima, Hiroaki Tokiwa, Teikichi Ikura, Nobutoshi Ito
    Journal of Medicinal Chemistry, 56, 17, 6745, 6760, American Chemical Society ({ACS}), 12 Sep. 2013
    English, Scientific journal

Other Activities and Achievements

Courses

  • Cell Structural Science I　　　　　　　　　　　　　　　
    Hokkaido University
  • Laboratory Work on Bio-macromolecular Science I　　　　　　　　　　　　　　　
    Hokkaido University
  • Fundamental Laboratory Work on Bio-macromolecular Science　　　　　　　　　　　　　　　
    Hokkaido University
  • Freshman Seminar Introduction to the bio-labs in Hokkaido University　　　　　　　　　　　　　　　
    Hokkaido University
  • Laboratory Work in Biomolecular Chemistry IV　　　　　　　　　　　　　　　
    Kyoto Prefectural University
  • Biophysical Chemistry　　　　　　　　　　　　　　　
    Kyoto Prefectural University
  • Basic Seminar of Information Processing　　　　　　　　　　　　　　　
    Kyoto Prefectural University

Affiliated academic society

  • The Molecular Biology Society of Japan　　　　　　　　　　　　　　　
  • The Japan Society for Bioscience, Biotechnology, and Agrochemistry　　　　　　　　　　　　　　　
  • The Biophysical Society of Japan　　　　　　　　　　　　　　　
  • Protein Science Society of Japan　　　　　　　　　　　　　　　

Research Themes

  • 複数の抗菌ペプチドを輸送する膜タンパク質の基質認識特性と輸送過程の解明
    科学研究費助成事業
    Apr. 2024 - Mar. 2027
    稲葉 理美
    日本学術振興会, 基盤研究(C), 大学共同利用機関法人高エネルギー加速器研究機構, Principal investigator, 24K08708
  • Developments of structure determination techniques with nanofocused X-ray free-electron laser pulses
    Grants-in-Aid for Scientific Research
    Apr. 2022 - Mar. 2025
    井上 伊知郎, 稲葉 理美
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Institute of Physical and Chemical Research, 22H03877
  • 創薬を指向した補助刺激受容体CD28ファミリーとシグナル伝達分子の構造基盤解明
    科学研究費助成事業
    Apr. 2018 - Mar. 2024
    稲葉 理美
    2022年6月より、海外渡航に伴って一時中断していた本課題を再開した。2022年度はSAXSなどで得られた実験データを元に、構造情報との相関づけを試みた。具体的には、SAXSなどで得られた溶液情報は、結晶構造を支持する結果となっているが、一部の(分解能)領域においては一致しないことが分かっていた。その原因としては、構造解析で用いたリガンドと溶液物性解析で用いるリガンドの鎖長が異なっていることが考えられた。そのため、比較する分子モデルを既存の構造情報をもとに新たに構築して比較することにした。さらに、溶媒条件(pHやイオン強度)を変えることでもSAXSの特性が変わることもわかった。以上のことより、よりダイナミクスにフォーカスした解析が必要であることが明らかとなり、次年度に向けてどのような解析を進めるべきかなどの指針を立てることができた。
    日本学術振興会, 若手研究, 18K14395
  • Structural and functional analysis of the antibacterial peptide membrane transporter SbmA
    Overseas Research Fellowship
    Oct. 2019 - Jun. 2022
    Satomi Inaba-Inoue
    Japan Society for the Promotion of Science, Imperial College London, Principal investigator
  • Elucidation of the structural basis for signalling molecules mediated by the co-stimulation receptors using X-ray　　　　　　　　　　　　　　　
    Research Grant
    Jun. 2018 - Mar. 2019
    Satomi Inaba
    Hyogo Science and Technology Association
  • Physical properties of jellyfish-derived collagen for the creation of high value-added functional materials　　　　　　　　　　　　　　　
    Research Grant for Young Scientist
    Apr. 2016 - Mar. 2017
    Satomi Inaba
    Kyoto Prefectural Public University Corporation
  • ｃ－Ｍｙｂ ＤＮＡ結合ドメインの機能に着目した生物学的揺らぎの多角的解析
    科学研究費助成事業
    Apr. 2015 - Mar. 2017
    稲葉 理美
    2016年度は、前年度にNMRや熱測定で得られたc-Myb DNA結合ドメインに関する知見をさらに多角的に評価するべく、1分子解析や高圧下での研究を進めた。1分子解析は、SPring-8の高輝度X線を用いた時分割測定（DXT）を適用し、DNA結合に伴う運動性変化をミリ秒～マイクロ秒で追跡した。測定にあたり、変異体の作製やプローブのラベル部位などの検討も進め、1分子系のアンサンブル量の運動性変化と多分子系での揺らぎの情報がよく相関することを明らかにした。加えて、DNA結合状態での揺らぎの減少が認められ、これはITCやDSCで得られたエントロピー変化量の結果と相関することも明らかとなった。
    高圧解析では、ダイアモンドアンビルセルを用いて、1 GPaを超える圧力まで測定することで、圧力軸での安定性の差異を明らかにすることに成功した。対象タンパク質の変性圧力中間点は約800 MPaであり、蛍光やNMR測定条件下においてはフォールド構造内の揺らぎを検出可能であることも示した。また、変異体を用いた実験により、タンパク質内部のキャビティと部分モル体積変化（ΔV）との間に良い相関を見出した。これらの結果は、これまでの温度変化やpH変化により得られた揺らぎの情報とも一致する。現在、双方ともに論文執筆中である。
    さらに、リピート間の構造安定性に着目した研究も進め、c-MybがDNA結合に2つのリピートが必須である裏付けをフォールディングに関わる熱力学量により実証した。
    日本学術振興会, 特別研究員奨励費, 京都府立大学, Principal investigator, 15J03576
  • Molecular interactions between signalling molecules and CD28 family intracellular regions　　　　　　　　　　　　　　　
    Research Grant for Graduate Student
    Jun. 2014 - Mar. 2015
    Satomi Inaba
    UEDA AYAKO Foundation, Principal investigator
  • Low-lying excited states and molecular interactions of proteins analyzed by high-pressure NMR and fluorescence spectroscopy　　　　　　　　　　　　　　　
    Research Grant for Graduate Student
    Jun. 2012 - Mar. 2013
    Satomi Inaba
    UEDA AYAKO Foundation, Principal investigator
  • Probing low-lying excited states of the transcription factor, c-Myb DNA-binding domain, and its correlation with the functional structure　　　　　　　　　　　　　　　
    Research Grant for Young Scientist
    Jun. 2011 - Mar. 2012
    Satomi Inaba
    Kyoto Prefectural Public University Corporatio, Principal investigator