top of page

Publicaion 研究業績

原著論文 Original Papers

​

  1. Saeko Yanaka, Atsuji Kodama, Shigetaka Nishiguchi, Rina Fujita, Jiana Shen, Pornthip Boonsri, Duckyong Sung, Yukiko Isono, Hirokazu Yagi, Yohei Miyanoiri, Takayuki Uchihashi, Koichi Kato, “Identification of potential C1-binding sites in the immunoglobulin CL domains”, Int. Immunol. dxae017 (2024).

  2. Satoshi Nakagawa, Hiroyuki Imachi, Shigeru Shimamura, Saeko Yanaka, Hirokazu Yagi, Maho Yagi-Utsumi, Hiroyuki Sakai, Shingo Kato, Moriya Ohkuma, Koichi Kato, Ken Takai, “Characterization of protein glycosylation in an Asgard archaeon.”, BBA Advance, 100118 (2024).

  3. Satoshi Nakagawa, Hiroyuki D Sakai, Shigeru Shimamura, Yoshiki Takamatsu, Shingo Kato, Hirokazu Yagi, Saeko Yanaka, Maho Yagi-Utsumi, Norio Kurosawa, Moriya Ohkuma, Koichi Kato, Ken Takai, “N-linked protein glycosylation in Nanobdellati (formerly DPANN) archaea and their hosts”, J. Bacteriol., 9 (2024).

  4. Methanee Hiranyakorn, Maho Yagi-Utsumi, Saeko Yanaka, Naoya Ohtsuka, Norie Momiyama, Tadashi Satoh, and Koichi Kato, “Mutational and environmental effects on the dynamic conformational distributions of Lys48-linked ubiquitin chains”, Int. J. Mol. Sci. 24, 6075 (2023).

  5. Saeko Yanaka, Rina Yogo, Hirokazu Yagi, Masayoshi Onitsuka, Natsumi Wakaizumi, Yuki Yamaguchi, Susumu Uchiyama, and Koichi Kato, “Negative interference with antibody-dependent cellular cytotoxicity mediated by rituximab from its interactions with human serum proteins”, Frontiers in Immunology. 14, (2023). 

  6. Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, and Kunihiro Kuwajima, “The B Domain of Protein A Retains Residual Structures in 6 M Guanidinium Chloride as Revealed by Hydrogen/Deuterium-Exchange NMR Spectroscopy”, Protein Science. e4569, (2023). 

  7. Saeko Yanaka, Hiroki Watanabe, Rina Yogo, Mesayamas Kongsema, Sachiko Kondo, Hirokazu Yagi, Takayuki Uchihashi, Koichi Kato, “Quantitative analysis of therapeutic antibody interactions with Fcγ receptors using high-speed atomic force microscopy”, Biological and Pharmaceutical Bulletin. b23-00751, (2023).

  8. Yuki Yamaguchi, Natsumi Wakaizumi, Mine Irisa, Takahiro Maruno, Mari Shimada, Koya Shintani, Haruka Nishiumi, Rina Yogo, Saeko Yanaka, Daisuke Higo, Tetsuo Torisu, Koichi Kato, and Susumu Uchiyama, “The Fab portion of immunoglobulin G has sites in the CL domain that interact with Fc gamma receptor IIIa”, mAbs. 14, e2038531 (2022). 

  9. Ryu Hashimoto, Masafumi Minoshima, Souhei Sakata, Fumihito Ono, Hirokazu Ishii, Yuki Watakabe, Tomomi Nemoto, Saeko Yanaka, Koichi Kato, and Kazuya Kikuchi, “Efficient Visible/NIR Light-driven Uncaging of Hydroxylated Thiazole Orange-based Caged Compounds in Aqueous Media”, Chemical Science. 13, 7462-7467 (2022). 

  10. Takanori Matsumaru, Kasumi Sakuratani, Saeko Yanaka, Koichi Kato, Sho Yamasaki, and Yukari Fujimoto, “Fungal β‐Mannosyloxymannitol Glycolipids and Their Analogues: Synthesis and Mincle‐Mediated Signaling Activity”, European Journal of Organic Chemistry. 2022, e202200109 (2022). 

  11. Saeko Yanaka, Shigetaka Nishiguchi, Rina Yogo, Hiroki Watanabe, Jiana Shen, Hirokazu Yagi, Takayuki Uchihashi and Koichi Kato, “Quantitative Visualization of the Interaction between Complement Component C1 and Immunoglobulin G: The Effect of CH1 Domain Deletion”, Int. J. Mol. Sci. 76, 12-17 (2022). 

  12. Siriluk Ratanabunyong, Supaphorn Seetaha, Supa Hannongbua, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Atchara Paemanee, and Kiattawee Choowongkomon, “Biophysical Characterization of Novel DNA Aptamers against K103N/Y181C Double Mutant HIV-1 Reverse Transcriptase”, Molecules 27, 285 (2022). 

  13. Saeko Yanaka, Hirokazu Yagi, Rina Yogo, Masayoshi Onitsuka, and Koichi Kato, “Glutamine-free mammalian expression of recombinant glycoproteins with uniform isotope labeling: an application for NMR analysis of pharmaceutically relevant Fc glycoforms of human immunoglobulin G1”, J. Biomol. NMR. 76, 17-22 (2022). 

  14. Kazuhisa Miyazawa, Satoru G. Itoh, Hiroki Watanabe, Takayuki Uchihashi, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Kazuharu Arakawa, and Hisashi Okumura, “Tardigrade Secretory-Abundant Heat-Soluble Protein Has a Flexible β-Barrel Structure in Solution and Keeps This Structure in Dehydration”, J. Phys. Chem. 125, 9145-9154 (2022). 

  15. Maho Yagi‑Utsumi, Kazuhiro Aoki, Hiroki Watanabe, Chihong Song, Seiji Nishimura, Tadashi Satoh, Saeko Yanaka, Christian Ganser, Sae Tanaka,Vincent Schnapka, Ean Wai Goh, Yuji Furutani, Kazuyoshi Murata, Takayuki Uchihashi, Kazuharu Arakawa, and Koichi Kato, “Desiccation‑induced fbrous condensation of CAHS protein from an anhydrobiotic tardigrade”, Sci. Rep. 11, Article number: 21328 (2021). 

  16. Siriluk Ratanabunyong, Maho Yagi-Utsumi, Saeko Yanaka, Koichi Kato, Kiattawee Choowongkomon, and Supa Hannongbua, “Characterization of New DNA Aptamers for Anti-HIV-1 Reverse Transcriptase”, ChemBioChem. 22, 915-923 (2021). 

  17. Saeko Yanaka, Yoshiki Yamaguchi, Takeshi Takizawa, Yohei Miyanoiri, Rina Yogo, Ichio Shimada, and Koichi Kato, “NMR assignments of the N-glycans of the Fc fragment of mouse immunoglobulin G2b glycoprotein”, Biomol. NMR Assign. 15, 187–192 (2021). 

  18. Nobuhiro Sato, Rina Yogo, Saeko Yanaka, Anne Martel, Lionel Porcar, Ken Morishima, Rintaro Inoue, Taiki Tominaga, Takao Arimori, Junichi Takagi, Masaaki Sugiyama, and Koichi Kato, “A feasibility study of inverse contrast-matching small-angle neutron scattering method combined with size exclusion chromatography using antibody interactions as model systems”, J. Biochem. 169, 701-708 (2021). 

  19. Ryo Ohtani, Yuka Anegawa, Hikaru Watanabe, Yutaro Tajima, Masanao Kinoshita, Nobuaki Matsumori, Kenichi Kawano, Saeko Yanaka, Koichi Kato, Masaaki Nakamura, Masaaki Ohba, and Shinya Hayami, “Metal complex lipids for fluid-fluid phase separation in co-assembled phospholipid membranes”, Angew. Chem. Int. Ed. 60, 13603-13608 (2021). 

  20. Tokio Watanabe, Hirokazu Yagi, Saeko Yanaka, Takumi Yamaguchi, and Koichi Kato, “Comprehensive characterization of oligosaccharide conformational ensembles with conformer classification by free-energy landscape via reproductive kernel Hilbert space”, Phys. Chem. Chem. Phys. 23, 9753-9760 (2021). 

  21. ​Hirokazu Yagi, Saeko Yanaka, Rina Yogo, Akari Ikeda, Masayoshi Onitsuka, Toshio Yamazaki, Ttsuya Kato, Enoch Y. Park, Jun Yokoyama, Koichi Kato, “Silkworm pupae function as efficient producers of recombinant glycoproteins with stable-isotope labeling”, Biomolecules. 10, 1482 (2020). 

  22. Maho Yagi-Utsumi, Mahesh Chandak, Saeko Yanaka, Methanee Hiranyakorn, Takashi Nakamura, Koichi Kato, and Kunihiro Kuwajima, “Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR”, Biophys. J. 119, 2029-2038 (2020). 

  23. Ryo Ohtani, Kenichi Kawano, Masanao Kinoshita, Saeko Yanaka, Hikaru Watanabe,Kenji Hirai, Shiroh Futaki, Nobuaki Matsumori, Hiroshi Uji-i, Masaaki Ohba, Koichi Kato, Shinya Hayami, “Pseudo-membrane jackets: Two-dimensional coordination polymers achieving visible phase separation in cell membrane”, Angew. Chem. Int. Ed. 59, 17931-17937 (2020). 

  24. Tatsuya Suzuki, Saeko Yanaka, Tokio Watanabe, Gengwei Yan, Tadashi Satoh, Hirokazu Yagi, Takumi Yamaguchi, Koichi Kato, “Remodeling of the oligosaccharide conformational space in the prebound state to improve lectin-binding affinity”, Biochemistry 59, 3180-3185 (2020). 

  25. ​Methanee Hiranyakorn, Saeko Yanaka, Tadashi Satoh, Thunchanok Wilasri, Benchawan Jityuti, Maho Yagi-Utsumi, Koichi Kato, “NMR characterization of conformational interconversions of Lys48-linked ubiquitin chains”, Int. J. Mol. Sci. 21, 5351 (2020). 

  26. Maho Yagi-Utsumi, Saeko Yanaka, Chihong Song, Tadashi Satoh, Chiaki Yamazaki, Haruo Kasahara, Toru Shimazu, Kazuyoshi Murata, Koichi Kato, “Characterization of amyloid β fibril formation under microgravity conditions”, NPJ Microgravity 6, 17 (2020). 

  27. Saeko Yanaka, Rina Yogo, Hiroki Watanabe, Yuki Taniguchi, Tadashi Satoh, Naoko Komura, Hiromune Ando, Hirokazu Yagi, Nobuhiro Yuki, Takayuki Uchihashi, and Koichi Kato, “On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q” , Int. J. Mol. Sci. 21, 147 (2020).

  28. ​Hiroki Akiba, Hiroko Tamura, Masato Kiyoshi, Saeko Yanaka, Kenji Sugase, Jose M. M. Caaveiro, Kouhei Tsumoto, “Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody”, Sci. Rep. 9, Article number: 15481 (2019). 

  29. Rintarou Inoue, Tatsuo Nakagawa, Ken Morishima, Nobuhiro Sato, Aya Okuda, Rieko Urade, Rina Yogo, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Kazuki Omoto, Kazuki Ito, Masaaki Sugiyama, “Newly developed Laboratory-based Size exclusion chromatography Small-angle x-ray scattering System (La-SSS)” , Sci. Rep. 9, Article number: 12610 (2019). 

  30. Rina Yogo, Yuki Yamaguchi, Hiroki Watanabe, Hirokazu Yagi, Tadashi Satoh, Mahito Nakanishi, Masayoshi Onitsuka, Takeshi Omasa, Mari Shimada, Takahiro Maruno, Tetsuo Torisu, Shio Watanabe, Daisuke Higo, Takayuki Uchihashi, Saeko Yanaka, Susumu Uchiyama, Koichi Kato, “The Fab portion of immunoglobulin G contributes to its binding to Fcγ receptor III”, Sci. Rep. 9, Article number: 11957 (2019). 

  31. Saeko Yanaka, Rina Yogo, Rintaro Inoue, Masaaki Sugiyama, Satoru G. Itoh, Hisashi Okumura, Yohei Miyanoiri, Hirokazu Yagi, Tadashi Satoh, Takumi Yamaguchi, Koichi Kato, “Dynamic Views of the Fc Region of Immunoglobulin G Provided by Experimental and Computational Observations”, Antibodies 8, 39 (2019). 

  32. Robert G. Brinson, (中略) Saeko Yanaka, Koichi Kato et al., “Enabling adoption of 2D-NMR for the higher order structure assessment of monoclonal antibody therapeutics”, MAbs 11, 94-105 (2019). 

  33. Taichiro Sekiguchi, Tadashi Satoh, Eiji Kurimoto, Chihong Song, Toshiya Kozai, Hiroki Watanabe, Kentaro Ishii, Hirokazu Yagi, Saeko Yanaka, Susumu Uchiyama, Takayuki Uchihashi, Kazuyoshi Murata, Koichi Kato, “Mutational and combinatorial control of self-assembling and disassembling of human proteasome α subunits” , Int. J. Mol. Sci. 20, 2308 (2019). 

  34. ​Saeko Yanaka, Hirokazu Yagi, Rina Yogo, Maho Yagi-Utsumi, and Koichi Kato, “Stable isotope labeling approaches for NMR characterization of glycoproteins using eukaryotic expression systems”, J. Biomol. NMR. 71, 193-202 (2018). 

  35. Rina Yogo, Saeko Yanaka, and Koichi Kato, “Backbone 1H, 13C, and 15N assignments of the extracellular region of human Fcγ receptor IIIb”, Biomol. NMR Assign., 12, 201-204 (2018). 

  36. Jintawee Kicuntod, Kanyani Sangpheak, Monika Mueller, Peter Wolschann, Helmut Viernstein, Saeko Yanaka, Koichi Kato, Warinthorn Chavasiri, Piamsook Pongsawasdi, Nawee Kungwan, and Thanyada Rungrotmongkol, “Theoretical and Experimental Studies on Inclusion Complexes of Pinostrobin and β-Cyclodextrins”, Sci. Pharm. 86, 5 (2018). 

  37. ​Saeko Yanaka, Toshio Yamazaki, Rina Yogo, Hirokazu Yagi, and Koichi Kato, “NMR Detection of Semi-Specific Antibody Interactions in Serum Environments.”, Molecules 22, 1619 (2017). 

  38. Yoshitake Sakae, Tadashi Satoh, Hirokazu Yagi, Saeko Yanaka, Takumi Yamaguchi, Yuya Isoda, Shigeru Iida, Yuko Okamoto, and Koichi Kato, “Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa”, Sci. Rep. 7, article number: 13789 (2017).

  39. Toshio Takenaka, Takashi Nakamura, Saeko Yanaka, Maho Yagi-Utsumi, Mahesh S. Chandak, Kazunobu Takahashi, Subhankar Paul, Koki Makabe, Munehito Arai, Koichi Kato, and Kunihiro Kuwajima, “Formation of the chaperonin complex studied by 2D NMR spectroscopy”, Plos One. 12, article number: e0187022 (2017). 

  40. Saeko Yanaka, Yoshitaka Moriwaki, Tsumoto Kouhei, and Kenji sugase, “Elucidation of potential sites for antibody engineering by fluctuation editing”, Sci. Rep. 7, article number: 9597 (2017). 

  41. Rina Yogo, Saeko Yanaka, Hirokazu Yagi, Rintaro Inoue, Nobuhiro Sato, Masaaki Sugiyama, and Koichi Kato, “Characterization of conformational deformation-coupled interaction between immunoglobulin G1 Fc glycoprotein and a low-affinity Fcγ receptor by deuteration-assisted small-angle neutron scattering”, Biochem. Biophys. Rep. 12, 1-4 (2017).

  42. Tatsuya Suzuki, Megumi Kajino，Saeko Yanaka，Tong Zhu，Hirokazu Yagi，Tadashi Satoh，Takumi Yamaguchi，and Koichi Kato, “Conformational analysis of a high-mannose-type oligosaccharide displaying glucosyl determinant recognised by molecular chaperones using NMR-validated molecular dynamics simulation”, ChemBioChem. 18, 396-410 (2017).

  43. Gengwei Yan, Takumi Yamaguchi, Tatsuya Suzuki, Saeko Yanaka, Sota Sato, Makoto Fujita, and Koichi Kato, “Hyper-assembly of self-assembled glycoclusters mediated by specific carbohydrate–carbohydrate interactions”, Chem. Asian J. 12, 968-972 (2017).

  44. ​Saeko Yanaka, Takamasa Ueno, Yi Shi, Jianxun Gi, George F. Gao, Kouhei Tsumoto, and Kenji Sugase, “Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class Ⅰ complex” , J. Biol. Chem. 268, 24680-90 (2014).

  45. Ryo Matsunaga, Saeko Yanaka, Satoru Nagatoishi, Kouhei Tsumoto, “Hyperthin nanochain composed of self-polimerizing protein shackles”, Nature Commun. 4, 2211 (2013).

  46. Takashi Nishina, Sachiko Komazawa-Sakon, Saeko Yanaka, Xyehua Piao, Dong-Mei Zheng, Jiang-Hu Paio, Yuko Kojima, Shunhei Yamashina, Sano E, Tracy Putoczki, Takahiro Doi, Takashi Ueno, Junji Ezaki, Hiroko Ushio, Matthias Ernst, Tsumoto Kouhei, Ko Okamura, and Hiroyasu Nakano, “Interleukin-11 Links Oxidative Stress and Compensatory Proliferation”, Science Signal. 207 (2012).

  47. ​Saeko Yanaka, Emiko Sano, Norio Naruse, Kin-ichiro Miura, Mutsumi Futatsumori-Sugai, Jose M. M. Caaveiro, and Kouhei Tsumoto, “Non-core region modulates interleukin-11 signaling activity: Generation of agonist and antagonist variants”, J Biol Chem. 286, 8085-93 (2011).

  48. Saeko Yanaka, Motonori Kudou, Yoshikazu Tanaka, Takumi Sasaki, Sumiyo Takemoto, Atsuko Sakata, Yukio Hattori, Tomoyuki Koshi, Shiro Futaki, Kouhei Tsumoto, and Toshihiko Nakashima, “Contribution of the flexible loop region to the function of staphylococcal enterotoxin B”, Protein Eng Des Sel. 23, 415-21 (2010).

  49. Chihiro Motozono, Saeko Yanaka, Kouhei Tsumoto, Masafumi Takiguchi, Takamasa Ueno, “Impact of intrinsic cooperative thermodynamics of peptide-MHC complexes on antiviral activity of HIV-specific cytotoxic T lymphocytes”, J. Immunol. 182, 5528-36 (2009).

  50. Regina Ragasa, Eiji Nakamura, Lisa Marrone, Saeko Yanaka, Shusaku Hayashi, Koji Takeuchi, and Susan J. Hagen, “Isothiocyanate inhibits restitution and wound repair after injury in the stomach: ex vivo and in vitro studies”, J Pharmacol Exp Ther. 323, 1-9 (2007).​

Reviews 総説

​英文​

  1. Koichi Kato, Hirokazu Yagi, and Saeko Yanaka, “Four-dimensional Structures and Molecular Designs of Glycans”, Trends in Glycosci. and Glycotech. 34, E85-E90 (2022).

  2. Kunihiro Kuwajima, Maho Yagi-Utsumi, Saeko Yanaka, Koichi Kato, “DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science”, Molecules. 27, (2022).

  3. Hirokazu Yagi, Saeko Yanaka, and Koichi Kato, “Four-dimensional Structures and Molecular Designs of Glycans”, Comprehensive Glycosci. Second Edition, 534-542 (2021).

  4. Saeko Yanaka, Susumu Uchiyama, “Current status and issues of protein solution biophysics—Session 1SDP”, Biophysical Reviews. 12, 263-264 (2020).

  5. Saeko Yanaka, Rina Yogo, and Koichi Kato, “Biophysical characterization of dynamic structures of immunoglobulin G” , Biophysical Reviews. 12, 637-645 (2020).

  6. Koichi Kato, Saeko Yanaka, and Hirokazu Yagi, “Technical basis for nuclear magnetic resonance approach for glycoproteins”, Experimental Approaches of NMR Spectroscopy (The Nuclear Magnetic Resonance Society of Japan ed.), Springer Nature Songapore, 415-438 (2018).

  7. Hirokazu Yagi, Saeko Yanaka, and Koichi Kato, “Structure and dynamics of immunoglobulin G glycoproteins”
    Glycobiophysics (Y.Yamaguchi and K.Kato ed.), Springer Nature Singapore, 219-235 (2018).

  8. Koichi Kato, Saeko Yanaka, Hirokazu Yagi, “Structural Biological Approach to Biopharmaceuticals”
    Yakugaku Zasshi. 138, 12, 1495-1502 (2018).

  9. Saeko Yanaka(corresponding author), and Kenji Sugase, “Exploration of the conformational dynamics of MHC molecules”, Front. Immunol. 8, 632 (2017).

  10. Ayako Furukawa, Tsuyoshi Konuma, Saeko Yanaka, Kenji Sugase, “Quantitative analysis of protein–ligand interactions by NMR”, Progress in Nuclear Magnetic Resonance Spectroscopy 96, 47 (2016). 

  11. Saeko Yanaka, Takamasa Ueno, Kouhei Tsumoto, and Kenji Sugase, “Revealing the peptide presenting process of the human leukocyte antigen through the analysis of fluctuation”, BIOPHYSICS. 11, 103-106 (2015).

和文​​

  1. 谷中冴子, 加藤晃一, 抗体医薬の作動メカニズムの分子基盤,生物工学会誌, 101, 347-349 (2023)

  2. 山口拓実, 谷中冴子, 加藤晃一, 分子シミュレーションによる糖鎖の​3次元構造の動態予測, In silicoスクリーニングへの応用事例, 技術情報協会, pp.237-245（2023）

  3. 谷中冴子, 加藤晃一, 複雑な糖鎖のコンフォメーション空間の探査と改変―計算と実験の統合によるアプローチ, 化学, 75, 30-71 (2020)

  4. 矢木宏和，鈴木達哉，谷中冴子，山口拓実，加藤晃一, 核磁気共鳴分光法と分子動力学計算を通じて観る糖鎖の動的構造とレクチンの糖鎖認識の理解, 医学のあゆみ, 269, 761-767（2019）

  5. 加藤晃一, 谷中冴子, 矢木宏和, バイオ医薬品への構造生物学的アプローチ, 薬学雑誌, 138, 1495-1502 (2018)

  6. 加藤晃一, 谷中冴子, 抗体のNMR研究の趨向と展望, SAR News, 35, 1-7 (2018)

  7. 加藤晃一, 谷中冴子, 矢木-内海真穂, NMR構造生物学がもたらす新たな創薬研究のツール, MEDCHEM NEWS, 26, 195-200 (2016)

  8. 谷中冴子, 動的構造解析による人主要組織適合複合体の安定化機構の解明, 生物物理, 55, 101-102 (2015)

bottom of page