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

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, Satomi Inaba-Inoue
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）

Structural and thermodynamic analysis of co-stimulation receptor CD28 phosphopeptide interactions with Grb2, Gads, and PI3-kinese SH2 domains
Satomi Inaba, Nobutaka Numoto, Hisayuki Morii, Teikichi Ikura, Ryo Abe, Nobutoshi Ito, Masayuki Oda, PROTEIN SCIENCE, 24, 287, 287, 2015年10月
英語, 研究発表ペーパー・要旨（国際会議）

Generation of single-chain Fv antibody against (4-hydroxy-3-nitrophenyl)acetyl and analysis of its structural dynamics
Yusui Sato, Yusuke Tanaka, Hiroshi Sekiguchi, Satomi Inaba, Takahiro Maruno, Yuji C. Sasaki, Yuji Kobayashi, Takachika Azuma, Masayuki Oda, PROTEIN SCIENCE, 24, 163, 164, 2015年10月
英語, 研究発表ペーパー・要旨（国際会議）

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