黒田　裕

Professional Career

経歴

1990年4月 - 1991年3月 : 蛋白質工学研究所 ポスドク研究員
1991年4月 - 1995年8月 : 蛋白質工学研究所 研究員
1995年9月 - 1997年 : 米国、マサチューセッツ工科大学(MIT)、Whitehead研究所、Peter S Kim研究室留学 (95/96年 Human Frontier Science Program Fellow、97年Whitehead Fellow)
1998年10月 - 2003年12月 : 理化学研究所・ゲノム科学総合研究センター・タンパク質構造・機能研究グループ研究員及び上級研究員
2004年 - 2006年: 東京農工大学　共生科学技術研究院　助教授
2007年 - 2009年: 東京農工大学　共生科学技術研究院　准教授
2010年 - 2016年 : 東京農工大学　工学研究院　准教授
2017年 - 現在 : 東京農工大学　工学研究院　教授

Academic Degrees

学位

1990年　博士（理学）東京大学

Research Interests

キーワード

蛋白質の物性、特にフォールディング、蛋白質工学、溶液NMR,二色性分光（CD）、沈降平行、熱力学的解、配列解析、構造、遺伝子組み換え、バイオインフォマティクス、抗体工学、免疫工学

Publications

論文

• Wongnak R, Brindha S, Oba M, Yoshizue T, Islam MD, Islam MM, Takemae H, Mizutani T, Kuroda Y. Non-Glycosylated SARS-CoV-2 Omicron BA.5 Receptor Binding Domain (RBD) with a Native-like Conformation Induces a Robust Immune Response with Potent Neutralization in a Mouse Model. MOLECULES. 2024 Jun 5;29(11):2676. doi: 10.3390/molecules29112676. PMID: 38893549; PMCID: PMC11173568.

• Islam, M.D. Sharmin, T.; Tipo, I.H.; Saha, A.; Yesmin, S.; Roy, M.G.; Brindha, S.; Kuroda, Y.; Islam, M.M. The Immunogenicity of DENV1–4 ED3s Strongly Differ despite Their Almost Identical Three-Dimensional Structures and High Sequence Similarities. Int. J. Mol. Sci. 2023, 24, 2393.

• Aklima J, Onchaiya S, Saotome T, Velmurugan P, Motoichi T, Naima J, Kuroda Y, Ohta Y. Direct Analysis of Mitochondrial Damage Caused by Misfolded/Destabilized Proteins. International Journal of Molecular Science (Int J Mol Sci.) 2022 Aug 31;23(17):9881. doi: 10.3390/ijms23179881. PMID: 36077279; PMCID: PMC9456338.

• Yuanpeng Janet Huang, Ning Zhang, Beate Bersch, Krzysztof Fidelis, Masayori Inouye, Yojiro Ishida, Andriy Kryshtafovych, Naohiro Kobayashi, Yutaka Kuroda, Gaohua Liu, Andy LiWang , G V T Swapna, Nan Wu, Toshio Yamazaki, Gaetano T Montelione, Assessment of Prediction Methods for Protein Structures Determined by NMR in CASP14: Impact of AlphaFold2. Proteins 2021 Sep 24. doi: 10.1002/prot.26246

• Saotome T, Onchaiya S, Brindha S, Mezaki T, Unzai S, Noguchi K, Martinez JC, Kidokoro SI, Kuroda Y. Blocking PSD95-PDZ3’s amyloidogenesis through point mutations that inhibit high-temperature reversible oligomerization (RO). FEBS J. 2021 Dec 30. doi: 10.1111/febs.16339. Epub ahead of print. PMID: 34967499.

• Rahman N, Miura S, Okawa M, Kibria MG, Islam MM, Kuroda Y. Solubility Controlling Peptide Tags of Opposite Charges Generate a Bivalent Immune Response Against Dengue ED3 Serotypes 3 and 4. Front Immunol. 2021 Jun 11;12:671590.
• Ando S, Matsuzawa Y, Tsurui H, Mizutani T, Hall D, Kuroda Y.　 Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19. Sci Rep. 2021 Mar 25;11(1):6856. doi: 10.1038/s41598-021-86027-2
• Wu nan, Tomonori Saotome, Satoru Unzai, Yutaka Kuroda and Toshio Yamazaki, Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR, Scientific Reports volume 10, Article number: 20069 (2020)
• Saotome T, Mezaki T, Brindha S, Unzai S, Martinez JC, Kidokoro SI, Kuroda Y.　Thermodynamic Analysis of Point Mutations Inhibiting High-Temperature Reversible Oligomerization of PDZ3.　Biophysical Journal. 2020. 119.7, 1391-1401
• Rahman N, Islam MM, Kibria MG, Unzai S, Kuroda Y.　A systematic mutational analysis identifies a 5-residue proline tag that enhances the in vivo immunogenicity of a non-immunogenic model protein.　FEBS Open Bio. 10(10):1947-1956, 2020.
• Rahman N, Islam MM, Unzai S, Miura S, Kuroda Y.　Nanometer-Sized Aggregates Generated Using Short Solubility Controlling Peptide Tags Do Increase the In Vivo Immunogenicity of a Nonimmunogenic Protein.  Mol Pharm. 17(5):1629-1637, 2020.
• Mohammad M. Islam, Shiho Miura, Mohammad. N. Hasan, Nafsoon Rahman, Yutaka Kuroda,  Anti-Dengue ED3 long-term immune response with T-cell memory generated using Solubility Controlling Peptide tags , Frontiers in Immunology, Published online 2020 Mar 17. doi: 10.3389/fimmu.2020.00333
• Mohammad, M Islam, Kei Kobayashi, Shun Ichi Kidokoro, Yutaka Kuroda, Hydrophobic surface residues can stabilize a protein through improved water-protein interactions., FEBS J. 2019 Jun 7. doi.org/10.1111/febs.14941.　286.20. 4122-4134
• Tomonori Saotome, Maxime Doret, Manjiri Kulkarni, Yin-Shan Yang, Philippe Barthe, Yutaka Kuroda and Christian Roumestand.Folding of the Ig-Like Domain of the Dengue Virus Envelope Protein Analyzed by High-Hydrostatic-Pressure NMR at a Residue-Level Resolution Biomolecules. 2019 Jul 26;9(8). pii: E309. doi: 10.3390/biom9080309.
• Richa Tambi, Gentaro Morimoto, Satoshi Kosuda, Makoto Taiji, Yutaka Kuroda, Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity, Scientific Reports, 9.2530 2019
• Golam M Kabir, Mohammad M Islam, Yutaka Kuroda.　Reversible association of proteins into sub-visible amorphous aggregates using short solubility controlling peptide tags. Biochim Biophys Acta.1866(2): 366- 372(2018)
• Mohammad M. Islam and Yutaka Kuroda. A hetero-micro-seeding strategy for readily crystallizing closely related protein variants, Biochemical and Biophysical Research Communications, 493(1):504-508 (2017)