KURODA Yutaka

Professional Career

1990.04 - 1991.03 : Postdoctoral Research Fellow, Institute of Protein Engineering
1991.04 - 1995.08 : Researcher, Institute of Protein Engineering
1995.09 - 1997 : Human Frontier Science Program Fellow, Whitehead Fellow, Peter S Kim Laboratory, Whitehead Institute, Massachusetts Institute of Technology (U.S.A.)
1998.10 - 2003.12 : Senior Researcher, Genomic Sciences Research Complex, RIKEN
2004 - 2006 : Assistant Professor, Institute of Engineering, Tokyo University of Agriculture and Technology
2007 - 2016 : Associate Professor, Institute of Engineering, Tokyo University of Agriculture and Technology
2017 - present : Professor, Institute of Engineering, Tokyo University of Agriculture and Technology

Academic Degrees

1990　Ph.D. in Science, The University of Tokyo

Research Interests

protein folding, protein structure , NMR, CD , sedimentation equilibrum, thermodynamics, bioinformatics, sequence analysis, neural network, antibody engineering, Immunology

Publications

• 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
• 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
• 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)