A02-2 津本 浩平（東京大学大学院 工学系研究科）

A02-2 津本 浩平（東京大学大学院 工学系研究科）

  1. H. Akiba, H. Tamura, M. Kiyoshi, S. Yanaka, K. Sugase, J. M. M. Caaveiro, K. 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, 15481 (2019) DOI: https://doi.org/10.1038/s41598-019-50722-y
  2. T. Chigira, S. Nagatoishi, H. Takeda, T. Yoshimaru, T. Katagiri, K. Tsumoto: “Biophysical Characterization of the Breast Cancer-related BIG3-PHB2 Interaction: Effect of Non-conserved Loop Region of BIG3 on the Structure and the Interaction” Biochem. Biophys. Res. Commun., 518, 183-189 (2019) DOI: https://doi.org/10.1016/j.bbrc.2019.08.028
  3. N. Katagiri, S. Nagatoishi, K. Tsumoto, H. Endo: “Structural Features of Methionine Aminopeptidase2-active Core Peptide Essential for Binding with S100A4” Biochem. Biophys. Res. Commun., 516, 1123-1129 (2019) DOI: https://doi.org/10.1016/j.bbrc.2019.07.006
  4. H. Kosuge, S. Nagatoishi, M. Kiyoshi, A. Ishii-Watabe, T. Tanaka, Y. Terao, S. Oe, T. Ide, K. Tsumoto: “Highly Sensitive HPLC Analysis and Biophysical Characterization of N-glycans of IgG-Fc Domain in Comparison between CHO and 293 Cells Using FcγRIIIa Ligand” Biotechnol. Prog., 36, e3016 (2020) DOI: https://doi.org/10.1002/btpr.3016
  5. H. Akiba, H. Tamura, J. M. M. Caaveiro, K. Tsumoto: “Computer-guided Library Generation Applied to the Optimization of Single-domain Antibodies” Protein Eng. Des. Sel., 32, 423-431 (2019) DOI: https://doi.org/10.1093/protein/gzaa006
  6. H. Akiba, K. Takayanagi, O. Kusano-Arai, H. Iwanari, T. Hamakubo, K. Tsumoto: “Generation of Biparatopic Antibody through Two-step Targeting of Fragment Antibodies on Antigen Using SpyTag and SpyCatcher” Biotechnol. Rep. (Amst)., 25:e00418 (2020) DOI: https://doi.org/10.1016/j.btre.2020.e00418
  7. R. Kawade, D. Kuroda, K. Tsumoto: “How the Protonation State of a Phosphorylated Amino Acid Governs Molecular Recognition: Insights from Classical Molecular Dynamics Simulations” FEBS Lett., 594, 903-912 (2020) DOI: https://doi.org/10.1002/1873-3468.13674
  8. C. Yoshimura, S. Nagatoishi, D. Kuroda, Y. Kodama, T. Uno, M. Kitade, K.  Chong-Takata, H. Oshiumi, H. Muraoka, S. Yamashita, Y. Kawai, S. Ohkubo, K.  Tsumoto: “Thermodynamic Dissection of Potency and Selectivity of Cytosolic Hsp90 Inhibitors.” J. Med. Chem.,64, 2669-2677(2021) DOI: https://doi.org/10.1021/acs.jmedchem.0c01715
  9. H. Kosuge, M. Nakakido, S. Nagatoishi, T. Fukuda, Y. Bando, S. I. Ohnuma, K. Tsumoto: “Proteomic Identification and Validation of Novel Interactions of the Putative Tumor Suppressor PRELP with Membrane Proteins Including IGFI-R and p75NTR” J. Biol. Chem., 296, 100278 (2021) DOI: https://doi.org/10.1016/j.jbc.2021.100278
  10. M. Ishii, M. Nakakido, J. M. M. Caaveiro, D. Kuroda, C. J. Okumura, T. Maruyama, K. Entzminger, K. Tsumoto: “Structural Basis for Antigen Recognition by Methylated Lysine Specific Antibodies” J. Biol. Chem., 296, 100176 (2021) DOI: https://doi.org/10.1074/jbc.RA120.015996
  11. E. Ikeuchi, D. Kuroda, M. Nakakido, A. Murakami, K. Tsumoto: “Delicate Balance among Thermal Stability, Binding Affinity, and Conformational Space Explored by Single-domain VHH Antibodies.” Sci. Rep., 11, 20624 (2021) DOI: https://doi.org/10.1038/s41598-021-98977-8
  12. T. Ten, S. Nagatoishi, R. Maeda, M. Hoshino, Y. Nakayama, M. Seiki, T. Sakamoto, K. Tsumoto: “Structural and Thermodynamical Insights into the Binding and Inhibition of FIH-1 by the N-terminal Disordered Region of Mint3.” J. Biol. Chem., 297, 101304 (2021) DOI: https://doi.org/10.1016/j.jbc.2021.101304
  13. D. Kuroda, K. Tsumoto: “Microsecond Molecular Dynamics Suggest That a Non-synonymous Mutation, Frequently Observed in Patients with Mild Symptoms in Tokyo, alters Dynamics of the SARS-CoV-2 Main Protease.” Biphys. Physicobiol., 18, 215-222 (2021) DOI: https://doi.org/10.2142/biophysico.bppb-v18.022
  14. K. Murakami, S. Nagatoishi, K. Kasahara, H. Nagai, Y. Sasajima, R. Sasaki, K. Tsumoto: “Electrostatic-triggered Exothermic Antibody Adsorption to the Cellulose Nanoparticles.” Anal. Biochem., 632, 114337 (2021) DOI: https://doi.org/10.1016/j.ab.2021.114337
  15. 【領域内連携】T. Yamawaki, M. Nakakido, K. Ujiie, C. Aikawa, I. Nakagawa, K. Tsumoto: “Characterization of a putative maltodextrin-binding protein of Streptococcus pyogenes, SPs0871 and the development of a VHH inhibitor” Biochem. Biophys. Res. Commun., 565, 1-7 (2021) DOI: https://doi.org/10.1016/j.bbrc.2021.05.056
  16. K. Kasahara, D. Kuroda, A. Tanabe, R. Kawade, S. Nagatoishi, K. Tsumoto: “Anion solvation enhanced by positive supercharging mutations preserves thermal stability of an antibody in a wide pH range” Biochem. Biophys. Res. Commun., 563, 54-59 (2021) DOI: https://doi.org/10.1016/j.bbrc.2021.05.053
  17. Y. Watanabe, A. Tanabe, T. Hamakubo, S. Nagatoishi, K. Tsumoto: “Development of Biparatopic Bispecific Antibody Possessing Tetravalent scFv-Fc Capable of Binding to ROBO1 Expressed in Hepatocellular Carcinoma Cells.” J. Biochem.,170, 307-315(2021) DOI: https://doi.org/10.1093/jb/mvab049
  18. A. Senoo, S. Ito, S. Nagatoishi, Y. Saito, G. Ueno, D. Kuroda, K. Yoshida, T. Tashima, S. Kudo, S. Sando, K. Tsumoto: “Regulation of Cadherin Dimerization by Chemical Fragments as a Trigger to Inhibit Cell Adhesion” Commun. Biol., 4, 1041 (2021) DOI: https://doi.org/10.1038/s 42003-021-02575-3
  19. A. Yui, J. M. M. Caaveiro, D. Kuroda, M. Nakakido, S. Nagatoishi, S. Goda, T. Maruno, S. Uchiyama, K. Tsumoto: “Mechanism of Dimerization and Structural Features of Human LI-Cadherin” J. Biol. Chem., 297, 101054 (2021) DOI: https://doi.org/10.1016/j.jbc.2021.101054
  20. 【領域内連携】M. Nishinaga, H. Sugimoto, Y. Nishitani, S. Nagai, S. Nagatoishi, N. Muraki, T. Tosha, K. Tsumoto, S. Aono, Y. Shiro, H. Sawai: “Heme Controls the Structural Rearrangement of Its Sensor Protein Mediating the Hemolytic Bacterial Survival” Commun. Biol., 4, 467 (2021) DOI: https://doi.org/10.1038/s42003-021-01987-5
  21. S. Valenciano-Bellido, J. M. M. Caaveiro, K. Morante, T. Sushko, M. Nakakido, S.  Nagatoishi, K. Tsumoto: “Structure and Role of the Linker Domain of the Iron Surface-determinant Protein IsdH in Heme Transportation in Staphylococcus aureus” J. Biol. Chem., 298, 101995 (2022) DOI: https://doi.org/10.1016/j.jbc.2022.101995
  22. R. Matsunaga, K. Tsumoto: “Addition of Arginine Hydrochloride and Proline to the Culture Medium Enhances Recombinant Protein Expression in Brevibacillus choshinensis: The Case of RBD of SARS-CoV-2 Spike Protein and Its Antibody.” Protein Expr. Purif.,194, 106075 (2022) DOI: https://doi.org/10.1016/j.pep.2022.106075
  23. M. Nakakido, N. Tanaka, A. Shimojo, N. Miyamae, K. Tsumoto: “Development of a High-throughput Method to Screen Novel Antiviral Materials.” PLoS ONE,17, e0266474 (2022) DOI: https://doi.org/10.1371/journal.pone.0266474
  24. T. Yokoo, A. Tanabe, Y. Yoshida, J. M. M. Caaveiro, M. Nakakido, Y. Ikeda, Y. Fujimura, M. Matsumoto, K. Entzminger, T. Maruyama, C. J. Okumura, M. Nangaku, K. Tsumoto: “Antibody Recognition of Complement Factor H Reveals a Flexible Loop Involved in Atypical Hemolytic Uremic Syndrome Pathogenesis” J. Biol. Chem.,298, 101962 (2022) DOI: https://doi.org/10.1016/j.jbc.2022.101962
  25. K. Yonesato, M. Nakakido, K. Tsumoto, Y. Egami, N. Miyamae, T. Wakihara, K. Suzuki, K. Yamaguchi: “Investigating the Antiviral Properties of Copper- and Silver-containing Polyoxometalates Using a High-throughput Screening Method” Chem. Lett., 52, 678-681 (2023) DOI: https://doi.org/10.1246/cl.230264
  26. T. Tatsuma, M. Nakakido, T. Ichinohe, Y. Kuroiwa, K. Tomioka, C. Liu, N. Miyamae, T. Onuki, K. Tsumoto, K. Hashimoto, T. Wakihara: “Inactivation and Spike Protein Denaturation of Novel Coronavirus Variants by CuxO/TiO2 Nano-photocatalysts” Sci. Rep., 13, 4033 (2023) DOI: https://doi.org/10.1038/s41598-023-30690-0
  27. A. Yui, D. Kuroda, T. Maruno, M. Nakakido, S. Nagatoishi, S. Uchiyama, K. Tsumoto: “Molecular Mechanism Underlying the Increased Risk of Colorectal Cancer Metastasis Caused by Single Nucleotide Polymorphisms in LI-cadherin Gene” Sci. Rep., 13, 6493 (2023) DOI: https://doi.org/10.1038/s41598-023-32444-4
  28. 【領域内連携】D. Tang, Y. Kato, D. Zhang, L. Negishi, H. Kurumizaka, T. Hirata, M. Nakakido, K. Tsumoto, F. Shuji, S. Tsuguyuki, T. Okumura, K. Nagata, M. Suzuki: “Dispersion Function of a Protein, DP-1, Identified in Collimonas sp. D-25, for the Synthesis of Gold Nanoparticles” Chembiochem, 24, e202300221 (2023) DOI: https://doi.org/10.1002/cbic.202300221
  29. 【領域内連携】S. Valenciano-Bellido, JMM. Caaveiro, M. Nakakido, D. Kuroda, C. Aikawa, I. Nakagawa, K. Tsumoto: “Targeting Hemoglobin Receptors IsdH and IsdB of Staphylococcus aureus with a Single VHH Antibody Inhibits Bacterial Growth” J. Biol. Chem., 299, 104927 (2023) DOI: https://doi.org/10.1016/j.jbc.2023.104927
  30. 【領域内連携】C. Aikawa, A. Shimizu, M. Nakakido, K. Murase, T. Nozawa, K. Tsumoto, I. Nakagawa: “Group A Streptococcus Cation Diffusion Facilitator Proteins Contribute to Immune Evasion by Regulating Intracellular Metal Concentrations” Biochem. Biophys. Res. Commun., 676, 141-148. (2023) DOI: https://doi.org/10.1016/j.bbrc.2023.07.052
  31. A. Senoo, S. Nagatoishi, D. Kuroda, S. Ito, G. Ueno, J. M. M. Caaveiro, K. Tsumoto: “Modulation of a Conformational Ensemble by a Small Molecule that Inhibits Key Protein-protein Interactions Involved in Cell Adhesion” Protein Sci., 32, e4744 (2023) DOI: https://doi.org/10.1002/pro.4744
  32. A. Tanabe, K. Tsumoto: “Analytical Method for Experimental Validation of Computer-Designed Antibody” Methods Mol. Biol., 2552, 409-433 (2023) DOI: https://doi.org/10.1007/978-1-0716-2609-2_23
  33. D. Kuroda, K. Tsumoto: “Structural Classification of CDR-H3 in Single-Domain VHH Antibodies.” Methods Mol. Biol.,2552, 61-79 (2023) DOI: https://doi.org/10.1007/978-1-0716-2609-2_2
  34. S. Kinoshita, M. Nakakido, C. Mori, D. Kuroda, J. M. M. Caaveiro, K. Tsumoto: “Molecular Basis for Thermal Stability and Affinity in a VHH: Contribution of the Framework Region and Its Influence in the Conformation of the CDR3” Protein Sci., 31, e4450 (2022) DOI: https://doi.org/10.1002/pro.4450
  35. H. Kosuge, S. Nagatoishi, M. Kiyoshi, A. Ishii-Watabe, Y. Terao, T. Ide, K. Tsumoto: “Biophysical Characterization of the Contribution of the Fab Region to the IgG-FcγRIIIa Interaction” Biochemistry, 62, 262-269 (2023) DOI: https://doi.org/10.1021/acs.biochem.1c00832
  36. A. Hirao, S. Nagatoishi, E. Ikeuchi, T. Yamawaki, C. Mori, M. Nakakido, K. Tsumoto: “Design of Single-domain VHH Antibodies to Increase the Binding Activity in SPR Amine Coupling” Biochem. Biophys. Res. Commun., 663, 54-60 (2023) DOI: https://doi.org/10.1016/j.bbrc.2023.04.048
  37. S. Maeta, M. Nakakido, H. Matsuura, N. Sakai, K. Hirata, D. Kuroda, A. Fukunaga, K. Tsumoto: “Arginine Cluster Introduction on Framework Region in Anti-lysozyme Antibody Improved Association Rate Constant by Changing Conformational Diversity of CDR Loops” Protein Sci., 32, e4745 (2023) DOI: https://doi.org/10.1002/pro.4745
  38. T. Yamazaki, S. Nagatoishi, T. Yamawaki, T. Nozawa, R. Matsunaga, M. Nakakido, JMM. Caaveiro, I. Nakagawa, K. Tsumoto: “Anti-InlA Single-domain Antibodies that Inhibit the Cell Invasion of Listeria monocytogenes” J. Biol. Chem., in press DOI: https://doi.org/10.1016/j.jbc.2023.105254
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