稲葉　理美 (イナバ　サトミ)

先端生命科学研究院助教
Last Updated :2025/12/04

■研究者基本情報

通称等の別名

  • 井上 理美

学位

  • 博士（農学）

Researchmap個人ページ

ホームページURL

研究者番号

  • 70785493

J-Global ID

研究分野

  • ライフサイエンス, 構造生物化学
  • ライフサイエンス, 応用生物化学
  • ライフサイエンス, 生物物理学

担当教育組織

■経歴

経歴

  • 2024年02月 - 現在
    北海道大学, 大学院先端生命科学研究院 先端融合科学研究部門, 助教
  • 2022年10月 - 2024年01月
    高エネルギー加速器研究機構, 研究員
  • 2020年03月 - 2022年09月
    公益財団法人高輝度光科学研究センター, 研究員, 日本国
  • 2019年10月 - 2022年06月
    Research Complex at Harwell, Rutherford Appleton Laboratory, Visiting Researcher, グレートブリテン・北アイルランド連合王国(英国)
  • 2019年10月 - 2022年06月
    Imperial College London, Department of Life Sciences, Sponsored Researcher, グレートブリテン・北アイルランド連合王国(英国)
  • 2019年10月 - 2022年06月
    日本学術振興会, 海外特別研究員, グレートブリテン・北アイルランド連合王国(英国)
  • 2017年03月 - 2020年02月
    公益財団法人 高輝度光科学研究センター, テニュアトラック博士研究員
  • 2018年02月 - 2018年03月
    Diamond Light Source, Visiting Scientist, グレートブリテン・北アイルランド連合王国(英国)
  • 2016年04月 - 2017年02月
    日本学術振興会, 特別研究員PD
  • 2015年04月 - 2016年03月
    日本学術振興会, 特別研究員DC

学歴

  • 2011年04月 - 2016年03月, 京都府立大学大学院, 生命環境科学研究科
  • 2007年04月 - 2011年03月, 京都府立大学, 農学部, 生物資源化学科

委員歴

  • 2024年 - 現在
    クライオ電顕ネットワークユーザーグループ, 幹事
  • 2016年 - 2020年
    日本熱測定学会, 委員, 学協会

■研究活動情報

受賞

  • 2025年06月, 日本蛋白質科学会, 若手奨励賞優秀賞
    稲葉 (井上) 理美, 国内学会・会議・シンポジウム等の賞, 日本国, 46051099
  • 2023年05月, 海外日本人研究者ネットワーク, 2023年 UJA論文賞 (特別賞)
    稲葉理美, 36800003
  • 2022年12月, 日本分子生物学会, MBSJ2022 Science Pitch Award
    Satomi Inaba-Inoue, 36800003
  • 2022年04月, The British Crystallographic Association, BSG Group Poster Prize
    Satomi Inaba-Inoue, 国際学会・会議・シンポジウム等の賞, グレートブリテン・北アイルランド連合王国(英国), 36800003
  • 2022年04月, The British Crystallographic Association, BSG David Blow Prize (1st Prize)
    Satomi Inaba-Inoue, 国際学会・会議・シンポジウム等の賞, グレートブリテン・北アイルランド連合王国(英国), 36800003
  • 2021年05月, ASG-Keio, 第2回SXRハッカソン大賞 (1st Prize)　　　　　　　　　　　　　　　
    小嶋良輔;赤木紀之;井上(稲葉)理美;大西里奈;合屋智尋;Davin HE Stetiamarga;甘利直花
  • 2017年11月, 8th International and 10th Japan-China Joint Symposium on Calorimetry and Thermal Analysis, Best Poster Award　　　　　　　　　　　　　　　
    Satomi Inaba
  • 2017年07月, 日本農芸化学会 関西支部, 日本農芸化学会関西支部優秀発表賞　　　　　　　　　　　　　　　
    稲葉理美
  • 2016年03月, 京都府公立大学法人, 理事長表彰　　　　　　　　　　　　　　　
    稲葉理美
  • 2015年10月, 日本熱測定学会, 第51回 熱測定討論会 鳩山賞 (ポスター賞)　　　　　　　　　　　　　　　
    稲葉理美
  • 2012年12月, GEヘルスケアジャパン, Biasymposium 2012 優秀ポスター賞　　　　　　　　　　　　　　　
    稲葉理美

論文

  • Solution structure of the C-terminal domain of the measles virus V protein in its free form and mechanistic analysis of STAT2 targeting
    Morita, K., Goda, N., Kimoto, M., Inaba-Inoue, S., Yabuno, N., Sugiyama, A., Kumeta, H., Ose, T.
    Journal of Virology, 99, 10, American Society for Microbiology, 2025年10月23日
    英語, 研究論文（学術雑誌）, ABSTRACT



    Viruses commonly evade the host antiviral interferon (IFN) response by targeting key components of the Janus kinase–signal transducer and activator of transcription (JAK–STAT) pathway, typically STAT1 and STAT2. Among the well-characterized viral IFN antagonists, measles virus (MeV), a member of the
    Morbillivirus
    genus, encodes a multifunctional V protein (MeV-V) that directly interacts with STAT proteins. The C-terminal domain (CTD) of MeV-V selectively binds to STAT2, disrupting the formation of the IFN-stimulated gene factor 3 (ISGF3) complex by inhibiting the STAT2–interferon regulatory factor 9 (IRF9) association. Here, we report a solution structure covering the MeV-V
    CTD
    in its unbound form, as determined by nuclear magnetic resonance spectroscopy. While the overall architecture, including a distinctive zinc-finger motif, conforms to previously predicted features, our analysis reveals unexpected features, including distinct proline
    cis
    conformers that may have functional relevance. Molecular mapping analysis, combined with relaxation measurements, identified key residues implicated in STAT2 recognition and revealed substantial conformational flexibility within the domain. These findings suggest that MeV-V
    CTD
    employs a shared binding surface for STAT2 binding as for melanoma differentiation-associated protein 5 (MDA5) interaction, underscoring its structural adaptability. As V proteins across
    Morbillivirus
    species engage diverse host pathways, including immune signaling, cell cycle regulation, and apoptosis, by targeting multiple proteins, we propose that the dynamic yet folded nature of the V
    CTD
    underlies its ability to serve as a versatile interaction module in host–pathogen interplay.


    IMPORTANCE

    The measles virus V protein, encoded by the P gene, orchestrates the broad modulation of host responses, including immune evasion, by interacting with multiple host factors. With regard to structural studies of V
    CTD
    , to date, only one protein from parainfluenza virus 5 has been crystallographically analyzed in complex with host targets. Despite the conserved nature of the V
    CTD
    among paramyxoviruses, structural information on the unbound state of this domain is lacking, and current insights largely rely on computational predictions based on the structure of the bound form. Our nuclear magnetic resonance work provides the first structure of the V
    CTD
    from paramyxoviruses in its free form. In accordance with our previously presented data, we further confirmed that the MeV-V binding site of STAT2 overlaps that of IRF9. The conformational flexibility observed within the folded CTD provides the structural basis for its ability to engage with multiple host targets with high specificity.


  • Exploring the functions of JAKMIP1 in neuronal IL-6/STAT3 signaling and its relevance to chromosome 15q-duplication syndrome
    Josan Gandawijaya Martin, Emily-Rose Martin, Natsuki Takamura, Charli E Harlow, Rosemary A Bamford, Rebecca G Smith, Noel G Morgan, Satomi Inaba-Inoue, Jonathan Mill, Deepak P Srivastava, Helen R Dawe, John K Chilton, Mark A Russell, Asami Oguro-Ando
    Cold Spring Harbor Laboratory, 2025年10月22日
    Growing evidence supports neuroinflammation as a risk factor for neurodevelopmental and psychiatric disorders. Interleukin 6 (IL-6), a classical pro-inflammatory cytokine, has been associated with autism spectrum disorder (ASD)-related phenotypes. To better understand molecular factors that modify neuronal cytokine responses in ASD, we investigated potential roles for JAKMIP1, a gene linked to chromosome 15q-duplication syndrome (Dup15q; a form of syndromic ASD), in regulating IL-6/STAT3 signaling. We observe that JAKMIP1 deficiency impairs IL-6/STAT3 signaling and IL-6-induced neuritogenesis in SH-SY5Y cells; and discover that JAKMIP1 may regulate STAT3 expression via its C-terminus, which exhibits nucleoplasmic localization. Additionally, we find that IL-6/STAT3 signaling is altered in Dup15q hiPSCs-derived cortical neurons, which display heightened responsiveness to IL-6; though it is unclear whether and how JAKMIP1 contributes to this. Overall, our findings identify JAKMIP1 as a modulator of neuronal IL-6/STAT3 signaling and support that ASD-linked genetic variants can alter the inflammatory landscape of ASD.
  • Stabilization of multidrug efflux transporter MdfA and antibody fragments complex by cross-linking for Cryo-EM single-particle analysis
    Satomi Inaba-Inoue, Toshio Moriya, Norimichi Nomura, Mikio Tanabe
    Methods in Enzymology, Elsevier, 2025年10月, ［筆頭著者］
  • Barrel expansion of outer membrane protein G nanopore through β‐hairpin duplication
    Joshua C. Foster, Bach Pham, Ryan Pham, Patrick Ryan, Nhu Tong, Jacqueline Sharp, Satomi Inaba‐Inoue, Jie Liang, Konstantinos Beis, Min Chen
    Protein Science, 34, 8, Wiley, 2025年07月16日
    研究論文（学術雑誌）, Abstract

    Outer membrane β‐barrel proteins (OMPs) are channels found in the outer membranes of Gram‐negative bacteria characterized by a stable and diverse barrel architecture, which has made them attractive for nanopore sensing applications. Here, we systematically investigated the feasibility of expanding outer membrane protein G (OmpG) from its native 14‐stranded β‐barrel to an enhanced conductance variant by independently duplicating each of its seven hairpin units and inserting them downstream of their endogenous positions. Most combinations did not increase pore diameter, but duplication of the terminal seventh hairpin exhibited a rare population of pores with enhanced conductance, suggesting barrel enlargement. Further engineering efforts to optimize the terminal β‐turn sequence have resulted in up to 50% of pores with increased conductance. Importantly, the enlarged pores retained the sensing functionality of the original scaffold, highlighting the potential of this approach for developing β‐barrel OMP sensors with tunable dimensions.
  • 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, 2025年04月16日, ［筆頭著者］
    研究論文（学術雑誌）
  • 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), 2025年03月18日
    研究論文（学術雑誌）, 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
    2025年02月03日, ［筆頭著者］
  • 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, 2024年12月
    研究論文（学術雑誌）, 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), 2024年04月01日
    英語, 研究論文（学術雑誌）, 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
    2023年12月20日
    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, 2023年12月13日
    英語, 研究論文（学術雑誌）, 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), 2023年11月28日, ［査読有り］
    研究論文（学術雑誌）
  • Functional Structure Analysis of DNA-binding Protein by SAXS
    Satomi Inaba-Inoue, Hiroshi Sekiguchi
    SPring-8/SACLA Research Report, SPring-8/SACLA Research Report, 2023年10月31日
    日本語, 研究論文（学術雑誌）
  • 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, 2023年07月07日
    研究論文（学術雑誌）
  • 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, 2023年02月21日
    研究論文（学術雑誌）, 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, 2022年04月28日
    研究論文（学術雑誌）, 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年
    英語, 研究論文（学術雑誌）
  • 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), 2021年09月10日, ［査読有り］, ［筆頭著者］
    研究論文（学術雑誌）, 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, 2019年08月18日, ［筆頭著者］
    研究論文（学術雑誌）
  • 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, 2019年06月01日, ［査読有り］, ［筆頭著者］
    英語, 研究論文（学術雑誌）
  • 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, 2019年03月
    英語, 研究論文（学術雑誌）
  • 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, 2019年03月, ［査読有り］, ［筆頭著者］
    英語, 研究論文（学術雑誌）
  • 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年, ［国内誌］
    英語, 研究論文（学術雑誌）, 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}, 2018年12月
    英語, 研究論文（学術雑誌）
  • 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, 2018年10月03日
    英語, 研究論文（学術雑誌）
  • 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}), 2018年09月11日
    英語, 研究論文（学術雑誌）
  • 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}, 2018年09月, ［査読有り］, ［筆頭著者］, ［国際誌］
    英語, 研究論文（学術雑誌）, 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, 2018年03月
    英語, 研究論文（学術雑誌）
  • 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, 2018年01月, ［査読有り］, ［筆頭著者］
    英語, 研究論文（学術雑誌）
  • 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, 2017年09月02日
    英語, 研究論文（学術雑誌）
  • 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}, 2017年09月, ［国際誌］
    英語, 研究論文（学術雑誌）, 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, 2017年05月04日
    英語, 研究論文（学術雑誌）
  • 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, 2017年05月
    英語, 研究論文（学術雑誌）
  • 生理的条件下で揺らぎの大きなDNA結合タンパク質の機能構造解析
    稲葉 理美
    生物物理, 57, 5, 257, 258, 一般社団法人 日本生物物理学会, 2017年, ［査読有り］, ［招待有り］, ［筆頭著者, 責任著者］
    英語, 研究論文（学術雑誌）
  • 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}, 2017年01月, ［査読有り］, ［筆頭著者］, ［国際誌］
    英語, 研究論文（学術雑誌）, 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}, 2016年10月, ［国際誌］
    英語, 研究論文（学術雑誌）, 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}, 2016年08月
    英語, 研究論文（学術雑誌）
  • 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, 2016年03月, ［査読有り］, ［筆頭著者］
    英語, 研究論文（学術雑誌）
  • 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, 2016年01月, ［査読有り］, ［筆頭著者］
    英語, 研究論文（学術雑誌）
  • 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, 2015年12月, ［査読有り］, ［筆頭著者］, ［国際誌］
    英語, 研究論文（学術雑誌）, 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, 2015年10月03日, ［査読有り］, ［筆頭著者］
    英語, 研究論文（学術雑誌）
  • 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, 2013年09月15日, ［査読有り］, ［筆頭著者］
    英語, 研究論文（学術雑誌）
  • 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}), 2013年09月12日
    英語, 研究論文（学術雑誌）

その他活動・業績

書籍等出版物

講演・口頭発表等

  • Molecular Mechanisms of Antimicrobial Resistance: Structural Insights from Bacterial Membrane Transporters
    Satomi Inaba-Inoue
    LSI external seminar, University of Exeter, 2025年09月24日, 英語
    36800003, ［招待講演］
  • 抗菌ペプチドを取り込む膜輸送体の構造基盤と輸送機構の解明　　　　　　　　　　　　　　　
    Inaba-Inoue S, Beis K
    第25回日本蛋白質科学会年会・若手奨励賞シンポジウム, 2025年06月19日, 英語, シンポジウム・ワークショップパネル（指名）
    ［招待講演］
  • Capturing MdfA Dynamics: A Cryo-EM Study of Outward-Facing States Stabilized by Antibody Fragment　　　　　　　　　　　　　　　
    Inaba-Inoue S, Moriya T, Terada T, Tanabe M
    Gordon Research Conference 2025 Multi-Drug Efflux System, 2025年04月28日, 英語
  • 新規輸送体ファミリーSbmAの立体構造と基質取り込み機構の解明　　　　　　　　　　　　　　　
    稲葉(井上)理美
    第61 回 日本生化学会北海道支部例会, 2024年07月
    ［招待講演］
  • KEKクライオ電顕施設における解析プラットフォーム⾼度化の現状　　　　　　　　　　　　　　　
    稲葉 理美
    第46回日本分子生物学会年会・フォーラム：クライオ電顕ネットワーク・ユーザーグループミーティング, 2023年12月
    ［招待講演］
  • 留学中に築いたネットワークを活かしてキャリアアップ！　　　　　　　　　　　　　　　
    稲葉 理美
    第96回日本生化学会年会・シンポジウム：UJA留学のすゝめ2023 日本の科学技術を推進するネットワーク構築, 2023年11月, シンポジウム・ワークショップパネル（指名）
    ［招待講演］
  • Molecular mechanism of antibacterial peptide uptake by SLiPTs
    Inaba-Inoue S., Ghilarov D., Beis K.
    Biochemical Society meeting on Molecular Mechanism of Membrane Proteins, 2023年04月, 英語, シンポジウム・ワークショップパネル（公募）
    46051099
  • 抗菌ペプチドはどのようにして細胞膜タンパク質をハイジャックするのか?　　　　　　　　　　　　　　　
    稲葉 理美
    第9回 タタバイオ分子クラブ, 2023年03月
    ［招待講演］
  • How to optimize the purification methods of membrane protein for structural and functional analysis?　　　　　　　　　　　　　　　
    Satomi Inaba-Inoue
    第6回つくば精製フォーラム, 2023年03月
    ［招待講演］
  • Molecular mechanism of SbmA, a promiscuous transporter exploited by antibacterial peptides　　　　　　　　　　　　　　　
    Inaba-Inoue S.
    University of Oxford Structural Biology & Molecular Biophysics (SBMB) theme weekly seminar, 2022年06月, 英語
    ［招待講演］
  • Molecular mechanism of antibacterial peptide uptake by SLiPT transporters　　　　　　　　　　　　　　　
    Inaba-Inoue S., Beis K.
    Centre for Structural Biology (CSB) Open days 2022, 2022年05月, 英語
  • Molecular mechanism of antimicrobial peptide transporter SbmA　　　　　　　　　　　　　　　
    Inaba-Inoue S., Ghilarov D., Stepien P., Heddle JG, Beis K.
    Spring meetings of the British Crystallographic Association 2022, 2022年04月, 英語, シンポジウム・ワークショップパネル（公募）
    ［招待講演］
  • Molecular mechanism of SbmA, a promiscuous transporter exploited by antimicrobial peptides　　　　　　　　　　　　　　　
    Inaba-Inoue S., Ghilarov D., Stepien P., Iwata S., Heddle JG, Beis K.
    Next generations of Harwell 2021, 2021年11月, 英語
  • ハイジャックの正体を暴く　　　　　　　　　　　　　　　
    稲葉(井上)理美
    The 71st Scienc-ome, 2021年10月
    ［招待講演］
  • Structural changes of RecA protein/DNA complex filament promoted by ATP/Mg2+ analyzed using small-angle X-ray scattering and compared with its models　　　　　　　　　　　　　　　
    Inaba-Inoue S.
    FilaVisu Workshop 2021, 2021年09月
    ［招待講演］
  • Structure and function of a bacterial transporter　　　　　　　　　　　　　　　
    Inaba-Inoue S., Beis K.
    Centre for Structural Biology (CSB) Open days 2021, 2021年06月
  • Crystal and solution structures of SH2 domain of signaling molecule in complex with the co-stimulatory receptor CD28
    Inaba-Inoue S., Inoue K., Hikima T., Sekiguchi H., Rambo RP
    32nd European Crystallographic Meeting (ECM32), 2019年08月
    36799834, ［招待講演］
  • 免疫系シグナル伝達分子 SH2 と補助刺激受容体との分子間相互作用解析　　　　　　　　　　　　　　　
    稲葉 理美
    第18回日本蛋白質科学会年会・ワークショップ: 抗体医薬を含む免疫関連タンパク質の熱測定による研究, 2018年06月
    ［招待講演］
  • Thermodynamic studies on protein conformational fluctuations　　　　　　　　　　　　　　　
    Inaba S., Oda M.
    16th International Confederation on Thermal Analysis and Calorimetry (ICTAC2016), 2016年08月, 英語, シンポジウム・ワークショップパネル（公募）
  • 高圧力を利用した転写因子 c-Myb DNA 結合ドメインの準安定励起構造解析　　　　　　　　　　　　　　　
    稲葉 理美
    第15回日本蛋白質科学会年会・ワークショップ：圧力軸から見えてくる生体高分子の研究, 2015年06月
    ［招待講演］
  • Entropic contributions to stability and DNA-binding in multiple conformations of a protein　　　　　　　　　　　　　　　
    Inaba S., Fukada H., Maruno T., Kobayashi Y., Oda M.
    15th International Confederation on Thermal Analysis and Calorimetry (ICTAC2012), 2012年08月, 英語, シンポジウム・ワークショップパネル（公募）

担当経験のある科目_授業

  • 細胞構造科学Ⅰ　　　　　　　　　　　　　　　
    北海道大学
  • 生体高分子学実験Ⅰ　　　　　　　　　　　　　　　
    北海道大学
  • 高分子機能学基礎実験　　　　　　　　　　　　　　　
    北海道大学
  • 一般教育演習 (フレッシュマンセミナー) 北大バイオ研究への招待　　　　　　　　　　　　　　　
    北海道大学
  • 生命分子化学実験 IV　　　　　　　　　　　　　　　
    京都府立大学
  • 生物物理化学　　　　　　　　　　　　　　　
    京都府立大学
  • 情報処理基礎演習　　　　　　　　　　　　　　　
    京都府立大学

所属学協会

  • 日本分子生物学会　　　　　　　　　　　　　　　
  • 日本蛋白質科学会　　　　　　　　　　　　　　　

共同研究・競争的資金等の研究課題

  • 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
    2024年04月 - 2027年03月
    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, 研究代表者, 24K08708
  • ナノ集光X線自由電子レーザーを利用した構造解析法の開発
    科学研究費助成事業
    2022年04月01日 - 2025年03月31日
    井上 伊知郎, 稲葉 理美
    X線を用いたタンパク質の構造解析では、これまで数10マイクロメートル程度の大型で良質な結晶を作ることが不可欠であった。本研究では、X線自由電子レーザーをナノメートル(nm)サイズにまで極限的に集光した超高強度X線パルスを利用することでnmサイズの極微小タンパク質結晶試料の構造解析を実現する。具体的には、(i) X線自由電子レーザーから出射された波長 1 AのX線をナノ集光する光学系(Advanced KBミラー)の開発、および(ii) ダメージの影響を組み込んだX線構造解析法の開発とタンパク質のナノ結晶への応用、を行う。超高強度X線を利用した新しい構造解析技術を確立することで、将来のX線1分子構造解析への第一歩を踏み出す。
    2023年度は、X線集光ミラー作製の最終仕上げとしてミラーのコーティングを行った。完成したミラーの性能をX線自由電子レーザー施設SACLAにおいて確認し、100 nm x 200 nmの微小スポットにX線を集光できていることが確認できた。
    また、ミラーの作製と並行して、高強度X線照射下における物質の原子散乱因子の変化を実験及び理論によって検証した。その結果、X線照射中に電子励起によって原子散乱因子が減少することや、その現象の程度が理論の予測とよく一致することが確認できた。この結果は、X線自由電子レーザーのような強いX線を用いた場合にはダメージの影響を組み込んだX線構造解析法の開発が必要であることを意味している。
    日本学術振興会, 基盤研究(B), 国立研究開発法人理化学研究所, 23K25131
  • 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
    2018年04月 - 2024年03月
    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
  • 抗菌ペプチドを取り込む膜タンパク質SbmAの立体構造と輸送機構の解明
    海外特別研究員
    2019年10月 - 2022年06月
    井上(稲葉) 理美
    日本学術振興会, インペリアルカレッジロンドン, 研究代表者
  • 補助刺激受容体を介する免疫系シグナル伝達分子の構造基盤の解明　　　　　　　　　　　　　　　
    学術研究助成
    2018年06月 - 2019年03月
    稲葉理美
    公益財団法人ひょうご科学技術協会
  • 高付加価値機能性素材創製を目指したクラゲ由来コラーゲンの物性解析　　　　　　　　　　　　　　　
    若手研究者育成支援費
    2016年04月 - 2017年03月
    稲葉理美
    京都府公立大学法人
  • 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
    2015年04月 - 2017年03月
    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, 研究代表者, 15J03576
  • 免疫系シグナル伝達分子と受容体CD28ファミリー細胞内領域との分子間相互作用解析　　　　　　　　　　　　　　　
    大学院生研究奨励事業
    2014年06月 - 2015年03月
    稲葉理美
    植田安也子学術振興基金, 研究代表者
  • 高圧NMR法および蛍光スペクトル法によるタンパク質の準安定構造と分子間相互作用の解析　　　　　　　　　　　　　　　
    植田安也子基金大学院生研究奨励事業
    2012年06月 - 2013年03月
    稲葉理美
    財団法人京都府立大学学術振興会, 研究代表者
  • 転写因子c-Myb DNA結合ドメインの準安定構造の検出と機能構造との相関解明　　　　　　　　　　　　　　　
    若手研究者育成支援費
    2011年06月 - 2012年03月
    稲葉理美
    京都府公立大学法人, 研究代表者