ACHIEVEMENT

Research achievements

...

Original work(English)

2021-2024

  1. Rawiwan Wongnak, Subbaian Brindha, Takahiro Yoshizue, Sawaros Onchaiya, Kenji Mizutani, Yutaka Kuroda, “E. coli production of a multi-disulfide bonded SARS-CoV-2 Omicron BA.5 RBD exhibiting native-like biochemical and biophysical properties”. Biophysics and Physicobiology, Article ID e200036, Advance online publication September 21, 2023.
  2. Yoshizue Takehiro, Subbaian Brindha, Rawiwan Wongnak, Takemae Hitoshi, Oba Mami, Mizutani Tetsuya, Kuroda Yutaka , “Antisera Produced Using an E. coli-Expressed SARS-CoV-2 RBD and Complemented with a Minimal Dose of Mammalian-Cell-Expressed S1 Subunit of the Spike Protein Exhibits Improved Neutralization”Int J Mol Sci. 2023 Jun 24, 24(13):10583. doi: 10.3390/ijms241310583
  3. Kibria Md.Golam, Shiwaku Yukari, Subbaian Brindha, Kuroda Yutaka , “Biophysical and biochemical nature of amorphous protein oligomers determines the strength of Immune response and the generation of T-cell memory”FEBS J.2023 Oct, 290(19):4712-4725. doi: 10.1111/febs.16884.
  4. Islam Md.　Din, Sharmin Tahmina, Tipo Imrul Hasan, Saha Antara, Sanjida Yesmin, “Roy Moushumi Ghosh, Subbaian Brindha, Kuroda Yutaka, Islam Mnirul Mohammad. The Immunogenicity of DENV1–4 ED3s Strongly Differ despite Their Almost Identical Three-Dimensional Structures and High Sequence Similarities”. Int. J. Mol. Sci. 2023 Jan, 24(3), 2393. https://www.mdpi.com/1422-0067/24/3/2393
  5. Kohara Shin, Matsuzawa Yuki, Kuroda Yutaka , “Lattice-model analysis of the effect of protein surface charge distribution on amorphous aggregation and condensation”Chemical Physics lettersVolume 802, 2022 Sep, 139767
  6. Yutaka Kuroda , “Biophysical studies of amorphous protein aggregation and in vivo immunogenicity”. Biophysical Review. 2022;. doi: 10.1007/s12551-022-01011-y. PMID: 36465085; PMCID: PMC9684872.
  7. Nan Wu, Naohiro Kobayashi, Yutaka Kuroda, and Toshio Yamazaki , “Reflecting on mutational and biophysical analysis of Gaussia princeps Luciferase from a structural perspective: a unique bioluminescent enzyme”. Biophysical Review. 2022;.
  8. Subbaian Brindha , Takahiro Yoshizue, Rawiwan Wongnak, Hitoshi Takemae, Mami Oba, Tetsuya Mizutani and Yutaka Kuroda , “An E. coli Expressed Multi-Disulfide Bonded SARS-CoV2 RBD Shows Native-like Biophysical Properties and Elicits Neutralizing Antisera in a Mouse Model”. Int J Mol Sci. 2022, 23(3);. doi: 10.3390/ijms23031703. PMID: 35163624; PMCID: PMC8835783.
  9. Kyoko Takatsu, Naohiro Kobayashi, Nan Wu, Yves L. Janin, Toshio Yamazaki and Yutaka Kuroda , “Biophysical analysis of Gaussia Luciferase bioluminescence mechanisms using a non-oxidizable coelenterazine”. BBA Proteins and Proteomics. 2022 Oct 1;. doi: https://doi.org/10.1101/2022.10.01.510427.
  10. Onchaiya Sawaros, Tomonori Saotome, Kenji Mizutani, Martinez Jose C., Tame Jeremy RH., Shun-Ichi Kidokoro, Yutaka Kuroda, “Reverse Engineering Analysis of the High-Temperature Reversible Oligomerization and Amyloidogenicity of PSD95-PDZ3”. Molecules. 2022 Apr 28;27(9):2813. doi: 10.3390/molecules27092813. PMID: 35566161; PMCID: PMC9103278.
  11. Subbaian Brindha, Yutaka Kuroda, “A Multi-Disulfide Receptor-Binding Domain (RBD) of the SARS-CoV-2 Spike Protein Expressed in E. coli Using a SEP-Tag Produces Antisera Interacting with the Mammalian Cell Expressed Spike (S1) Protein". Int J Mol Sci. 2022 Feb 1;23(3):1703. doi: 10.3390/ijms23031703. PMID: 35163624; PMCID: PMC8835783.
  12. Tomonori Saotome, Onchaiya Sawaros, Subbaian Brindha, Taichi Mezaki, Satoru Unzai, Keiichi Noguchi, Martinez Jose C., Shun-Ichi Kidokoro, Yutaka Kuroda,“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.
  13. Huagn Janet Yuanpeng, Zhang Ning, Bersch Beate, Fidelis Krzysztof, Masayori Inoue, Yojiro Ishida, Kryshtafovych Andriy, Naohiro Kobayashi, Yutaka Kuroda, Liu Gaohua, LiWang Andy, Swapna G V T, Wu Nan, Toshio Yamazaki, Montelione Gaetano T, “Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2”. Proteins. 2021 Dec. 89(12):1959-1976. doi: 10.1002/prot.26246. Epub 2021 Oct 19. PMID: 34559429; PMCID: PMC8616817 (available on 2022-12-01).
  14. Rahman Nafsoon, Shiho Miura, Mami Okawa, Kibria Md.Golam, Islam Monirul Mohammad, Yutaka Kuroda,“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. doi: 10.3389/fimmu.2021.671590. PMID: 34177912; PMCID: PMC8226127.
  15. Kibria Md.Golam, Yoko Akazawa, Yoshihisa Hagihara, Yutaka Kuroda,”Immune response with long-term memory triggered by amorphous aggregates of misfolded anti-EGFR VHH-7D12 is directed against the native VHH-7D12 as well as the framework of the analogous VHH-9G8”. European Journal of Pharmaceutics and Biopharmaceutics. 2021 Aug 165:13-21. doi: 10.1016/j.ejpb.2021.05.004. Epub 2021 May 8.
  16. Kibria Md.Golam, Akari Fukutani, Yoko Akazawa, Yoshihisa Hagihara, Yutaka Kuroda,”Anti-EGFR VHH Antibody under Thermal Stress Is Better Solubilized with a Lysine than with an Arginine SEP Tag”. Biomolecules. 2021 May 29;11(6):810. doi: 10.3390/biom11060810. PMID: 34072518; PMCID: PMC8229009.
  17. Shiho Ando, Yuki Matsuzawa, Hiromichi Tsurui, Tetsuya Mizutani, Hall Damien, Yutaka Kuroda,”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. PMID: 33767233; PMCID: PMC7994631.
  18. Subbaian Brindha, Kibria Md. Golam, Tomonori Saotome, Satoru Unzai, Yutaka Kuroda,”EGFR extracellular domain III expressed in Escherichia coli with SEP tag shows improved biophysical and functional properties and generate anti-sera inhibiting cancer cell growth”. Biochem Biophys Res Commun. 2021 May 28;555:121-127. doi: 10.1016/j.bbrc.2021.03.102. Epub 2021 Apr 1. PMID: 33813270.

2016-2020

  1. Wu Nan, Naohiro Kobayashi, Kengo Tsuda, Satoru Unzai, Tomonori Saotome, Yutaka Kuroda, Toshio Yamazaki,”Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR. Sci Rep”. 2020 Nov 18;10(1):20069. doi: 10.1038/s41598-020-76486-4. PMID: 33208800; PMCID: PMC7674443.
  2. Rahman Nafsoon, slam Monirul Mohammad, Kibria Md. Golam, Satoru Unzai, Yutaka Kuroda,”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. 2020 Oct;10(10):1947-1956. doi: 10.1002/2211-5463.12941. Epub 2020 Aug 30. PMID: 33017095; PMCID: PMC7530378).
  3. Kibria Md. Golam, Yoko Akazawa, Rahman Nafsoon, Yoshihisa Hagihara, Yutaka Kuroda,”The immunogenicity of an anti-EGFR single domain antibody (VHH) is enhanced by misfolded amorphous aggregation but not by heat-induced aggregation”. Eur J Pharm Biopharm. 2020 Jul;152:164-174. doi: 10.1016/j.ejpb.2020.05.006. Epub 2020 May 19. PMID: 32416134.
  4. Rahman Nafsoon, Islam Monirul Mohhamad, Satoru Unzai, Shiho Miura, Yutaka Kuroda,”Nanometer-Sized Aggregates Generated Using Short Solubility Controlling Peptide Tags Do Increase the In Vivo Immunogenicity of a Nonimmunogenic Protein”. Mol Pharm. 2020 May 4;17(5):1629-1637. doi: 10.1021/acs.molpharmaceut.0c00071. Epub 2020 Apr 21. PMID: 32227965.
  5. Islam Monirul Mohhamad, Shiho Miura, Hasan Md Nazmul, Rahman Nafsoon, Yutaka Kuroda,”Anti-Dengue ED3 Long-Term Immune Response With T-Cell Memory Generated Using Solubility Controlling Peptide Tags”. Front Immunol. 2020 Mar 17;11:333. doi: 10.3389/fimmu.2020.00333. PMID: 32256488; PMCID: PMC7089932.
  6. Tomonori Saotome, Taichi Mezaki, Subbaian Brindha, Satoru Unzai, Martinez Jose C., Shun-Ichi Kidokoro, Yutaka Kuroda,”Thermodynamic Analysis of Point Mutations Inhibiting High-Temperature Reversible Oligomerization of PDZ3”. Biophys J. 2020 Oct 6;119(7):1391-1401. doi: 10.1016/j.bpj.2020.08.023. Epub 2020 Aug 28. PMID: 32961107; PMCID: PMC7567976.
  7. Shigeyoshi Nakamura, Kibria Md Golam, Satoru Unzai, Yutaka Kuroda, Shun-Ichi Kidokoro,”Reversible Oligomerization and Reverse Hydrophobic Effect Induced by Isoleucine Tags Attached at the C-Terminus of a Simplified BPTI Variant. Biochemistry”. 2020 Oct 6;59(39):3660-3668. doi: 10.1021/acs.biochem.0c00436. Epub 2020 Sep 22. PMID: 32924442.
  8. Yutaka Kuroda, Shigeru Endo, Haruki Nakamura,"How A Novel Scientific Concept Was Coined the "Molten Globule State"". Biomolecules. 2020 Feb 10;10(2):269. doi: 10.3390/biom10020269. PMID: 32050721; PMCID: PMC7072420.
  9. Masahiko Seki, Makoto Sato, Masaki Takiwaki, Koji Takahashi, Yoshikuni Kikutani, Mamoru Satoh, Fumio Nomura, Yutaka Kuroda, Seketsu Fukuzawa,”A novel caged Cookson-type reagent toward a practical vitamin D derivatization method for mass spectrometric analyses”. Rapid Commun Mass Spectrom. 2020 Apr 15;34(7):e8648. doi: 10.1002/rcm.8648. PMID: 31715032; PMCID: PMC7064983.
  10. Tomonori Saotome, Doret Maxime, Kulkarni Manjiri, Yang Yun-Shan, Barthe Philippe, Yutaka Kuroda, Roumestand Christian,”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):309. doi: 10.3390/biom9080309. PMID: 31357538; PMCID: PMC6723665.
  11. Tomonori Saotome, Toshio Yamazaki, Yutaka Kuroda,“Misfolding of a Single Disulfide Bonded Globular Protein into a Low-Solubility Species Conformationally and Biophysically Distinct from the Native One”. Biomolecules. 2019 Jun 25;9(6):250. doi: 10.3390/biom9060250. PMID: 31242697; PMCID: PMC6627273.
  12. Islam Monirul Mohhamad, Kei Kobayashi, Shun-Ichi Kidokoro, Yutaka Kuroda,”Hydrophobic surface residues can stabilize a protein through improved water-protein interactions”. FEBS J. 2019 Oct;286(20):4122-4134. doi: 10.1111/febs.14941. Epub 2019 Jun 17. PMID: 31175706.
  13. Tambi Richa, 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, 2019 Feb 21; 9(1):2530. doi: 10.1038/s41598-018-38401-w. PMID: 30792475 PMCID: PMC6384915richa
  14. Nautiyal Kalpana, Kibria Md Golam, Yoko Akazawa, Yoshihisa Hagihara, Yutaka Kuroda,”Design and assessment of an active anti-epidermal growth factor receptor (EGFR) single chain variable fragment (ScFv) with improved solubility”. Biochem Biophys Res Commun. 2019 Jan 22;508(4):1043-1049. doi: 10.1016/j.bbrc.2018.11.170. Epub 2018 Dec 11. PMID: 30551882.
  15. Nautiyal Kalpana, Yutaka Kuroda,”A SEP tag enhances the expression, solubility and yield of recombinant TEV protease without altering its activity”. N Biotechnol. 2018 May 25;42:77-84. doi: 10.1016/j.nbt.2018.02.006. Epub 2018 Feb 12. PMID: 29448030. PubMed
  16. Yutaka Kuroda,”Biophysical studies of protein solubility and amorphous aggregation by systematic mutational analysis and a helical polymerization model”. Biophys Rev.2018 Apr;10(2):473-480. doi: 10.1007/s12551-017-0342-y. Epub 2018 Jan 4. PMID: 29302914; PMCID: PMC5899702. PubMed
  17. Kibria Md. Golam, Islam Monirul Mohhamad, Yutaka Kuroda ,“Reversible association of proteins into sub-visible amorphous aggregates using short solubility controlling peptide tags”. Biochim Biophys Acta Proteins Proteom, 2018 Feb;1866(2):366-372. doi: 10.1016/j.bbapap.2017.09.012. Epub 2017 Sep 22. PMID: 28951312. PubMed
  18. Islam Monirul Mohhamad, Yutaka Kuroda,“A hetero-micro-seeding strategy for readily crystallizing closely related protein variants”, Biochemical and Biophysical Research Communications, 2017 Nov 4;493(1):504-508. doi: 10.1016/j.bbrc.2017.08.161. Epub 2017 Sep 1. PMID: 28870811.
  19. Shigeyoshi Nakamura, Tomonori Saotome, Akiko Nakazawa, Masato Fukuda, Yutaka Kuroda, Shun-Ichi Kidokoro,”Thermodynamics of the Thermal Denaturation of Acid Molten Globule State of Cytochrome c Indicate a Reversible High-Temperature Oligomerization Process”. Biochemistry. 2017 May 9;56(18):2372-2378. doi: 10.1021/acs.biochem.6b01225. Epub 2017 May 1. PMID: 28429932. PubMed
  20. Islam Monirul Mohhamad, Masafumi Yohda, Shun-Ichi Kidokoro, Yutaka Kuroda,”Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy”. Sci Rep. 2017 Mar 7;7:41205. doi: 10.1038/srep41205. Erratum in: Sci Rep. 2017 May 09;7:46798. PMID: 28266637; PMCID: PMC5339861. PubMed
  21. Tambi Richa, Shoichi Ide, Ryosuke Suzuki, Teppei Ebina, Yutaka Kuroda ,”Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers”. J Comput Aided Mol Des. 2017 Feb;31(2):237-244. doi: 10.1007/s10822-016-9999-8. Epub 2016 Dec 27. PMID: 28028736. PubMed
  22. Hiroki Jozawa, Kabir Md Golam, Tamotsu Zako, Mizuo Maeda, Kazuhiro Chiba, Yutaka Kuroda,“Amorphous protein aggregation monitored using fluorescence self-quenching”. FEBS Lett., 5 2016 Oct;590(20):3501-3509. doi: 10.1002/1873-3468.12439. Epub 2016 Oct 18. PMID: 27685427 学長表彰論文 PubMed
  23. Tomonori Saotome, Shigeyoshi Nakamura, Islam Monirul Mohhamad, Akiko Nakazawa, Dellarole Mariano, Fumio Arisaka, Shun-Ichi Kidokoro, Yutaka Kuroda,”Unusual Reversible Oligomerization of Unfolded Dengue Envelope Protein Domain 3 at High Temperatures and Its Abolition by a Point Mutation. Biochemistry”. 2016 Aug 16;55(32):4469-75. doi: 10.1021/acs.biochem.6b00431. Epub 2016 Aug 4. PMID: 27433922. PubMed
  24. Kulkarni Manjiri Ravindra, Nobutaka Numoto, Nobutoshi Ito, Yutaka Kuroda,“Modeling and experimental assessment of a buried Leu-Ile mutation in dengue envelope domain III”. Biochem Biophys Res Commun. 2016 Feb 26;471(1):163-8. doi: 10.1016/j.bbrc.2016.01.159. Epub 2016 Jan 28. PMID: 26826384. PubMed
  25. Yutaka Kuroda, Atsushi Suenaga, Yuji Sato, Satoshi Kosuda, Makoto Taiji,”All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations”. Sci Rep. 2016 Jan 28;6:19479. doi: 10.1038/srep19479. PMID: 26817663; PMCID: PMC4730209. IF=5.58 PubMed
  26. Wu Nan, Tetsuya Kamioka, Yutaka Kuroda,”A novel screening system based on VanX-mediated autolysis-Application to Gaussia luciferase”. Biotechnol Bioeng. 2016 Jul;113(7):1413-20. doi: 10.1002/bit.25910. Epub 2016 Jan 28. PMID: 26694096. IF=4.13 PubMed

2011-2015

  1. Kulkarni Manjiri Ravindra, Islam Monirul Mohhamad, Nobutaka Numoto, Elahi Montasir, Mahib R Mamunur, Nobutoshi Ito, Yutaka Kuroda,”Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants”. Biochim Biophys Acta. 2015 Oct;1854(10 Pt A):1438-43. doi: 10.1016/j.bbapap.2015.07.004. Epub 2015 Jul 6. PMID: 26160751. CosmoBio Academic Paper Award IF=2.75 PubMed
  2. Islam Monirul Mohammad, Shigeyuki Nakamura, Keiichi Noguchi, Masafumi Yohda, Shun-ichi Kidokoro, Yutaka Kuroda,”Analysis and Control of Protein Crystallization Using Short Peptide Tags That Change Solubility without Affecting Structure”, Thermal Stability, and Function Crystal Growth & Design, 2015 May 8, 15 (6): 2703-2711 IF=4.89 ACS
  3. Wu Nan, Rathnayaka Tarangani, Yutaka Kuroda,”Bacterial expression and re-engineering of Gaussia princeps luciferase and its use as a reporter protein”. Biochim Biophys Acta. 2015 Oct;1854(10 Pt A):1392-9. doi: 10.1016/j.bbapap.2015.05.008. Epub 2015 May 27. PMID: 26025768. IF=2.75 PubMed
  4. Atsushi Kurotani, Yutaka Yamada, Kazuo Shinozaki, Yutaka Kuroda, Tetsuya Sakurai,”Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes”. Plant Cell Physiol. 2015 Jan;56(1):e11. doi: 10.1093/pcp/pcu176. Epub 2014 Nov 29. PMID: 25435546; PMCID: PMC4301743. IF=4.93 PubMed
  5. Sohya Shihori, Kamioka Tetsuya, Fujita Chisako, Maki Tei, Ohta Yoshihiro, Kuroda Yutaka,”Biochemical and biophysical characterization of an unexpected bacteriolytic activity of VanX, a member of the vancomycin-resistance vanA gene cluster”. J Biol Chem. 2014 Dec 26;289(52):35686-94. doi: 10.1074/jbc.M114.590265. Epub 2014 Oct 7. PMID: 25294880; PMCID: PMC4276839. IF=4.57 PubMed
  6. Ebina Teppei, Suzuki Ryosuke, Tsuji Ryotaro, Kuroda Yutaka,”H-DROP: an SVM based helical domain linker predictor trained with features optimized by combining random forest and stepwise selection”. J Comput Aided Mol Des. 2014 Aug;28(8):831-9. doi: 10.1007/s10822-014-9763-x. Epub 2014 Jun 26. PMID: 24965847. IF=2.99 PubMed
  7. Elahi Montasir, Islam Monirul Mohhamad, Keiichi Noguchi, Masfumi Yohda, Hiroyuki Toh, Yutaka Kuroda,”Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3)”. Biochim Biophys Acta. 2014 Mar;1844(3):585-92. doi: 10.1016/j.bbapap.2013.12.013. Epub 2013 Dec 27. PMID: 24373879. IF=2.75 PubMed
  8. Dellarole Mariano, Kei Kobayashi, Rouget Jean-Baptiste, Caro Alfredo, Roche Julien, Islam Monirul Mohammad, Garcia-Moreno E. Bertrand, Yutaka Kuroda, Royer A. Catherine,”Probing the physical determinants of thermal expansion of folded proteins”. J Phys Chem B. 2013 Oct 24;117(42):12742-9. doi: 10.1021/jp401113p. Epub 2013 May 21. PMID: 23646824. IF=3.3 PubMed
  9. Khan Monsur Alam, Islam Monirul Mohhamad, Yutaka Kuroda,”Analysis of protein aggregation kinetics using short amino acid peptide tags”. Biochim Biophys Acta Proteins and Proteomics, 2013 Oct;1834(10):2107-15. doi: 10.1016/j.bbapap.2013.06.013. Epub 2013 Jun 28. PMID: 2381147 IF=2.75 PubMed
  10. Teppei Ebina, Yuki Umezawa, Yutaka Kuroda,”IS-Dom: a dataset of independent structural domains automatically delineated from protein structures”. J Comput Aided Mol Des. 2013 May;27(5):419-26. doi: 10.1007/s10822-013-9654-6. Epub 2013 May 29. PMID: 23715893. IF=2.99 PubMed
  11. Tetsuya Kamioka, Shihori Sohya, Wu Nan, Tei Maki, Tomoki Matsuda, Takahisa Ikegami, Haruki Nakamura, Yutaka Kuroda,”Extraction of recombinant protein from Escherichia coli by using a novel cell autolysis activity of VanX. Anal Biochem”. 2013 Aug 15;439(2):212-7. doi: 10.1016/j.ab.2013.04.007. Epub 2013 Apr 25. PMID: 23624113. IF=2.2 PubMed
  12. Elahi Montasir, Islam Monirul Mohhamad, Keiichi Noguchi, Masfumi Yohda, Yutaka Kuroda,”High resolution crystal structure of dengue-3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition”. Proteins. 2013 Jun;81(6):1090-5. doi: 10.1002/prot.24237. Epub 2013 Apr 1. PMID: 23239402. IF=2.6 PubMed
  13. Saori Akiyama, Atsushi Suenaga, Takayuki Kobayashi, Tetsuya Kamioka, Makoto Taiji, Yutaka Kuroda,“Experimental identification and theoretical analysis of a thermally stabilized green fluorescent protein variant”. Biochemistry. 2012 Oct 9;51(40):7974-82. doi: 10.1021/bi300580j. Epub 2012 Sep 27. PMID: 22963334. IF=3.09 PubMed
  14. Islam Monirul Mohhamd, Khan Monsur Alam, Yutaka Kuroda,”Analysis of amino acid contributions to protein solubility using short peptide tags fused to a simplified BPTI variant”. Biochim Biophys Acta. 2012 Oct;1824(10):1144-50. doi: 10.1016/j.bbapap.2012.06.005. Epub 2012 Jun 20. PMID: 22728531. IF=2.75 PubMed
  15. Rathnayaka Tharangani, Minako Tawa, Takashi Nakamura, Shihori Sohya, Kunihiro Kuwajima, Masafumi Yohda, Yutaka Kuroda,”Solubilization and folding of a fully active recombinant Gaussia luciferase with native disulfide bonds by using a SEP-Tag”. Biochim Biophys Acta. 2011 Dec;1814(12):1775-8. doi: 10.1016/j.bbapap.2011.09.001. Epub 2011 Sep 14. PMID: 21945374. IF=2.75 PubMed
  16. Teppei Ebina, Toh Hiroyuki, Yutaka Kuroda,”DROP: an SVM domain linker predictor trained with optimal features selected by random forest”. Bioinformatics. 2011 Feb 15;27(4):487-94. doi: 10.1093/bioinformatics/btq700. Epub 2010 Dec 17. PMID: 21169376. PubMed

2006-2010

  1. Shuichi Hirose, Kiyonobu Yokota, Yutaka Kuroda, Hiroshi Wako, Shigeru Endo, Satoru Kanai, Tamotsu Noguchi, “Prediction of protein motions from amino acid sequence and its application to protein-protein interaction”, BMC Structural Biology, 13:10:20（2010） IF=1.2 PubMed
  2. Tharangani Rathnayaka, Minako Tawa, Shihori Sohya, Masafumi Yohda, Yutaka Kuroda, “Biophysical characterization of highly active recombinant Gaussia luciferase expressed in Escherichia coli”. Biochim Biophys Acta. Proteins and Proteomics, 1804(9):1902-7 (2010)IF=2.75 PubMed
  3. Eisuke Chikayama, Atsushi Kurotani, Takanori Tanaka, Takashi Yabuki, Satoshi Miyazaki, Shigeyuki Yokoyama, Yutaka Kuroda, “Mathematical Model for Empirically Optimizing Large Scale Production of Soluble Protein Domains”, BMC Bioinformatics, 11:113(2010) IF=2.57 PubMed
  4. Mohammed M. Islam, Sohya Shihori, Keiichi Noguchi, Shun-Ichi Kidokoro, Masafumi Yohda, Yutaka Kuroda, “Thermodynamic and structural analysis of highly stabilizing single and double mutations in BPTI variants”, PROTEINS, 77(4), 962 -970 (2009) IF=2.6 PubMed
  5. Kamioka Tetsuya, Tawa Mikako, Shihori Sohya, Toshio Yamazaki, Yutaka Kuroda, ”Improved protein splicing reaction for low solubility protein fragments without insertion of native extein residues (NERs) Biopolymers (Peptide Science)”, 92(5):465-70 (2009) IF=2.39 PubMed
  6. Teppei Ebina, Hiroyuki Toh, Yutaka Kuroda, ”Loop-length dependent SVM prediction of domain linkers for high-throughput structural proteomics”, Biopolymers (Peptide Science), 92(1):1-8 (2009) IF=2.39 PubMed
  7. Mohammed M. Islam, Shihori Sohya, Noguchi Keiichi, Masafumi Yohda, Yutaka Kuroda, “Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines”, Proc. Natl. Acad. Sci. USA, 105:15334 - 39 (2008) IF=9.7 PubMed
  8. Atsushi Kato, Munetaka Yamada, Shigeyoshi Nakamura, Shun-Ichi Kidokoro, Yutaka Kuroda, “Thermodynamic properties of BPTI variants with highly simplified amino acid sequences”, J. Mol. Biol. 372(3):737-746 (2007) IF=4.33 PubMed
  9. Hirose Shuichi, Kana Shimizu, Satoru Kanai, Yutaka Kuroda, and Tamotsu Noguchi, “POODLE-L: A two-level SVM prediction system for reliably predicting long disordered regions”. Bioinformatics 23(16):2046-2053 (2007). IF=4.9 PubMed
  10. Kato, Atsushi, Maki Kosuke, Ebina Teppei, Kuwajima Kunihiro, Soda Kunitsugu, Kuroda Yutaka, “Mutational analysis of protein solubility enhancement using short peptide tags”, Biopolymers, 85:12-18. (2007). IF=2.39 PubMed
  11. Takayuki Hondoh, Kato Atsushi, Shigeyuki Yokoyama, Yutaka Kuroda, ”Computer-aided NMR assay for detecting natively folded structural domains”, Protein Science, 15(4), 871-883 (2006). IF=2.85 PubMed
  12. Takanori Tanaka, Shigeyuki Yokoyama, Yutaka Kuroda, ”Improvement of domain linker prediction by incorporating loop length-dependent characteristics”, Biopolymers (Peptide Science) 84(2):161-168 (2006). IF=2.39 PubMed
  13. Satoshi Miyazaki, Yutaka Kuroda, Yokoyama Satoshi, ”Identification of putative domain linkers by a neural network - application to a large sequence database“, BMC Bioinformatics, 7:323, (2006). PubMed
  14. Elmi M. Maryam, Amininasab Mehriar, Takayuki Hondo, Jun Kikuchi, Yutaka Kuroda, Hossein Naderi-Manesh, Mohammad N. Sarbolouki, “Structural and functional characterization of a mutant of Pseudocerastes persicus natriuretic peptide”, Protein and Peptide Letters, 13(3):295-300(2006). PubMed

2000-2004

  1. Eisuke Chikayama, Atsushi Kurotani, Yutaka Kuroda, Shigeyuki Yokoyama, “ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences”, Bioinformatics, 20, 2836-2838(2004). IF=4.9 PubMed
  2. Takayuki Tanaka, Yutaka Kuroda, Shigeyuki Yokoyama, “Characterization and prediction of domain linkers in multi-domain proteins”, J. Struct. Funct. Genomics, 4, 79-85 (2003). PubMed
  3. Kay Fukushima, Jun Kikuchi, Seizo Koshiba, Takanori Kigawa, Yutaka Kuroda, Shigeyuki Yokoyama, “Solution structure of the C-terminal domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation”, J. Mol. Biol., 321, 317-327 (2002). IF=4.9 PubMed
  4. Satoshi Miyazaki, Yutaka Kuroda, Shigeyuki Yokoyama, “Characterization and prediction of linker sequences of multi-domain proteins by a neural networks”, J. Struct Funct. Genomics 2, 37-51 (2002). PubMed
  5. Yutaka Kuroda, Peter S Kim, ”Folding of bovine pancreatic trypsin inhibitor (BPTI) variants in which almost half the residues are alanine”, J. Mol. Biol., 298, 493-501 (2000) IF=4.9 PubMed
  6. Yutaka Kuroda, Yo Matsuo, Tani, Kazutoshi, Shigeyuki Yokoyama, “Automated search of folded protein fragments for high-throughput structure determination in structural genomics”, Protein Science, 9, 2313-2321 (2000). IF=2.85 PubMed
  7. Shigeyuki Yokoyama, Hiroshi Hirota, Takanori Kigawa, Takashi Yabuki, Mikako Shirouzu, Takako Terada, Yutaka Ito, Yo Matsuo, Yutaka Kuroda, Yoshifumi Nishimura, Yoshimasa Kyogoku, Kunio Miki, Ryoji Masui, Seiki Kuramitsu, “Structural genomics projects in Japan”, Nature Struct. Biol, 7, 943-945 (2000). IF=13.3 PubMed
  8. Shigeyuki Yokoyama, Yo Matsuo, Hiroshi Hirota, Takanori Kigawa, Mikako Shirouzu, Yutaka Kuroda, Hitoshi Kurumizaka, Shinichi Kawaguchi, Yutaka Ito, Takehiko Shibata, Masatsune Kainosho, Yoshifumi Nishimura, Yorinao Inoue, Seiki Kuramitsu, “Structural genomics projects in Japan”, Prog. Biophys. Mol. Biol, 73(5), 363-376 (2000). IF=2.3 PubMed

-2000

  1. Daizo Hamada, Yutaka Kuroda, Mikio Kataoka, Saburo Aimoto, Tetsuo Yoshimura, Yuji Goto, ”Role of heme axial ligands in the conformational stability of the native and molten globule states of horse cytochrome c”, J. Mol. Biol., 256, 172-186 (1996). IF=4.9 PubMed
  2. Yutaka Kuroda, Daizo Hamada, Toshiki Tanaka, Yuji Goto, “Unexpected high helicity of peptide fragments corresponding to β-strand regions of β-lactoglobulin”, Folding and Design , 1, 255-263 (1996). PubMed
  3. Yutaka Kuroda, “A Strategy for the de novo design of helical proteins with stable folds”, Prot. Eng., 18, 97-101 (1995). IF=2.53 PubMed
  4. Daizo Hamada, Yutaka Kuroda, Toshiki Tanaka, Yuji Goto, “High helical propensity of the peptide fragments derived from β-lactoglobulin, a predominantly β-sheet protein: Implication for non-hierarchical protein folding”, J. Mol. Biol., 254, 737-746 (1995). IF=4.9 PubMed
  5. Yutaka Kuroda, Shigeru Endo, Kuniaki Nagayama, Akiyoshi Wada, “Stability of α-helices in a molten globule state of cytochrome c by hydrogen-deuterium exchange and two-dimensional NMR spectroscopy”, J. Mol. Biol., 247, 682-688 (1995). IF=4.9 PubMed
  6. Eiichi Kitakuni, Yutaka Kuroda, Motohisa Oobatake, Toshiki Tanaka, Haruki Nakamura, “Thermodynamic characterization of an artificially designed α-helical peptide containing periodic prolines: Observation of high thermal stability and cold denaturation”, Protein Science, 3, 831-837 (1994). IF=2.85 PubMed
  7. Yasushi Oda, Toshio Yamazaki, Nagayama Kuniaki, Shigenori Kanaya, Yutaka Kuroda, Haruki Nakamura, “Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR”, Biochemistry, 33, 5275-5284 (1994). IF=3.09 PubMed
  8. Yutaka Kuroda, Takahisa Nakai, Tadayasu Ohkubo, “Solution structure of a de novo helical protein by 2D-NMR spectroscopy”, J. Mol. Biol., 236, 862-868 (1994). IF=4.9 PubMed
  9. Toshiki Tanaka, Yutaka Kuroda, Hiromi Kimura, Shun-Ichi Kidokoro, Haruki Nakamura, “Cooperative deformation of a de novo designed protein”, Prot. Eng., 7, 969-976 (1994). IF=2.53 PubMed
  10. Yutaka Kuroda, “Residual helical structure in the C-terminal fragment of cytochrome c”, Biochemistry, 32, 1219-1224 (1993). IF=3.09 PubMed
  11. Yutaka Kuroda, Shun-Ichi Kidokoro, Akiyoshi Wada, “Thermodynamic characterization of cytochrome c at low pH; Observation of the molten globule state and of the cold denaturation process”, J. Mol. Biol., 223, 1139-1153 (1992). IF=4.9 PubMed
  12. Yutaka Kuroda, Akiyoshi Wada, Toshio Yamazaki, Kuniaki Nagayama, “Postaquisition data processing method for suppression of the solvent signal II: The weighted derivative”, J. Magn. Res., 88, 141-145 (1990). IF=2.51
  13. Yutaka Kuroda, Akiyoshi Wada, Toshio Yamazaki, Kuniaki Nagayama, “Postaquisition data processing method for suppression of the solvent signal”, J. Magn. Res., 84, 604-610 (1989). IF=2.51
...

Review Papers
(Japanese Academic Journal)

Title Journal Author Publisher Date
"Physicochemical analysis of amorphous aggregation of proteins with solubility-controlling peptide tags and their immunogenicity-enhancing effects" Monthly "Cell", 2021-8:53(9):P74(586)-78(590) Yutaka Kuroda,Hideki Taguchi New Science Inc 2021-7/26
"Lattice Model Analysis of the Effect of Protein Surface Charge on Solubility" Chemistry and Industry, 2019-10:72(10):P35-41 Makoto Obara,Yutaka Kuroda The Chemical Society of Japan 2019
"Analysis of amorphous aggregate formation mechanism using fluorescence self-quenching" Monthly Bioindustry (Special Issue: Protein Production and Solubility Control) ,2015-9 Hiroki Kisarasawa,Yasushi Zamitsu,Mizuo Maeda,Kazuhiro Chiba,Yutaka Kuroda CMC Publishing 2015-9/11
"Insights into amorphous aggregation of amino acids by all-atom simulation of short-chain tetrapeptides" IPSJ Research Report BIO, Bioinformatics (2014, Issue 5):2014(5):p1-2 Yushi Sato,Atsushi Suenaga,Mahiroto Taiji,Yutaka Kuroda IPSJ 2014-12/11
"Analysis and Control of Protein Solubility by Peptide-Based Solubility Enhancement Tag "SEP Tag" " Bioindustry, 2013-7 Yutaka Kuroda CMC Publishing 2013-7/12
"Joint Research Highlight: Analysis and modification of recombinant Gaussian luciferase for construction of minimal reporter protein" Molecular Science Letters, 67:p.26-27 Yutaka Kuroda,Wu Nan Institute for Molecular Science 2013-3
"Overseas laboratory visit: Short-term visit by graduate students to the Research Center for Structural Biochemistry, University of Montpellier, France" Biophysics, 2012-8:52(4):P.206-207 Kei Kobayashi,Catherine Royer,Yutaka Kuroda Japanese Biophysical Society 2012
"Elucidation of the bacteriolytic activity of VanX and simplification of the purification process of its intracellular products" Future Materials, 2011-8:11(7)p32-36 Yutaka Kuroda,Tetsuya Ueoka,Shihori Soya NTS Inc. 2011-7/10
"The Great East Japan Earthquake: A report from a member in Tokyo" Biophysics, 2011-10:51(5):P238-239 Yutaka Kuroda The Japanese Society of Biophysics 2011
"Introduction of Swiss-Prot group in Geneva" Biophysics,2010-10:50(5):P252-253 Yutaka Kuroda,Damien Lieberherr Japanese Biophysical Society 2010
"What is the Minimum Information Required for Protein Structure Formation? -Structure and thermodynamics of a simplified bovine pancreatic trypsin inhibitor protein (BPTI) mutant-" Protein Nucleic Acid Enzymes, 2009-4:54(5):p643-648 Jun Kato,Mohamed Monir Islam,Yutaka Kuroda Kyoritsu Shuppan 2009-3/23
"Protein Solubility Enhancement Technique -About SEP-tag-" Biophysics, 2008-6:48(3):P185-189 Jun Kato,Naoshige Izumikawa,Yutaka Kuroda The Japanese Society for Biophysics 2008-5/28
"Dynamic viscoelasticity measurement of aqueous DNA solution from Escherichia coli" Collection of Papers on Macromolecules,　64(7):P458-463 Taro Kinoshita,Shihori Soya,Yutaka Kuroda,Yuichi Masubuchi SPSJ 2007-7
"Engineering Application and Technology of Protein Splicing" Practical Industrial Information, 39:p24-27 Tetsuya Ueoka,Minako Tawa,Shihori Soya,Yutaka Kuroda Pneumatic Inc. 2006
"Editor's Postscript" Journal of the Physical Society of Japan, 60(10):P.835-836 Yutaka Kuroda The Physical Society of Japan 2005
"Protein Folding with Simplified Amino Acid Sequences" Parity,2003-3:18(3):P57-61 Yutaka Kuroda Maruzen Shuppan 2003-2/25
"Consideration of structural genomics and protein conformational studies" Biomolecular Analysis Research Center, 23:p10-14 Yutaka Kuroda Biomolecular Analysis Research Center,Institute for Protein Research,Osaka University 2002
"Target Selection for Structural Analysis: A Rapid Structure Determination System for Protein Domain Identification" Protein Nucleic Acid Enzyme, 46(14):p2066-2072 Yutaka Kuroda, Eisuke Chikayama, Shigeyuki Yokoyama Kyoritsu Shuppan 2001
"Experimental verification of the amount of information contained in amino acid sequences: A consideration from the viewpoint of protein three-dimensional structure construction principles and molecular evolution" Biophysics, 41(5):p224-230 Tetsu Akanuma,Yutaka Kuroda The Japanese Society for Biophysics 2001
"Bioinformatics for Structural Genomics" Experimental Medicine, 19(8):p934-940 Hiroshi Matsuo,Yutaka Kuroda,Kengo Kinoshita,Haruki Nakamura/td> Yodosha 2001-5/18
...

Patents
Awards (Overseas)

Patents

Patent Name Inventor Registration Date Applicant
Patent No.7194442 : "Antigen composition抗原組成物" Yutaka Kuroda,ISLAM M.Monirul,Shiho Miura,RAHMAN Nafsoon,Tetsuya Kamioka 2022-12/14 Tokyo University of Agriculture and Technology
Patent No.6986261 : "Method for improving expression and yield of recombinant polypeptide" Yutaka Kuroda,NAUTIYAL Kalpana 2021-12/1 Tokyo University of Agriculture and Technology
Patent No.5521236 : "Expression Prediction Device and Method" Shuichi Hirose,Tamotsu Noguchi,Naoki Goto,Yoshifumi Kawamura,Yutaka Kuroda 2014-4/8 National Institute of Advanced Industrial Science and Technology (AIST), Bio-industry Informatics Consortium, Tokyo University of Agriculture and Technology
Patent No.5509421 : "Solubility Prediction Device and Solubility Prediction Method" Shuichi Hirose,Tamotsu Noguchi,Naoki Goto,Yoshifumi Kawamura,Yutaka Kuroda 2014-4/4 National Institute of Advanced Industrial Science and Technology (AIST), Consortium for Bioindustrial Informatics, Tokyo University of Agriculture and Technology
Patent No.5273438 : "Solubility calculation method for peptides" Yutaka Kuroda,Naoshige Izumikawa,Jun Kato,Shihori Soya 2013-5/24 Tokyo University of Agriculture and Technology
Patent No.4213034 : "Method for predicting domain linkers of proteins" Yutaka Kuroda,Satoshi Miyazaki,Takanori Tanaka,Shigeyuki Yokoyama 2001-9/25(Application date) RIKEN
Patent No. 2895594 : "Method of Solvent Signal Removal in NMR" Kuniaki Nagayama,Toshio Yamazaki,Yutaka Kuroda 1999-5/24 JEOL Ltd.

Awards (Overseas)

Title of paper Name of Award Awardee Award Date
"Epitope grafted mutants provide molecular insights into sero-specific interactions of Dengue's ED3 with its monoclonal antibody" Best Poster Award (MRK) Manjiri R. Kulkarni, Montasir Elahi, Mohamad M. Islam, Nobutaka Numoto, Nobutoshi Ito, Yutaka Kuroda 2014-6/27
Certificate of Appreciation (ACS Publications) Yutaka Kuroda 2011-11
"Effect of short peptide tagson protein solubility,function, and structure" Best Poster Award (MMI) Mohammed M Islam, Keiichi Noguchi, Masafumi Yohda, Yutaka Kuroda 2010-5/21
"Loop-length dependent SVM prediction of domain linkers" Travel Award (to T.E.) Teppei Ebina, Hiroyuki Toh, Yutaka Kuroda 2008-6