ACHIEVEMENT

研究業績

...

原著(英文)

2021-2022

  1. 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.

  2. 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.

  3. 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.

  4. 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).

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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. コスモバイオ学術論文賞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
...

総説論文
(和文学術誌)

タイトル 掲載雑誌 著者 出版社 年月日
"溶解性制御ペプチドタグを用いた蛋白質のアモルファス凝集の物理化学的解析とその免疫原性増強効果" 月刊「細胞」,2021年8月号:53(9):P74(586)-78(590) 黒田裕,田口英樹 ニューサイエンス社 2021-7/26
"タンパク質表面電荷が溶解性に及ぼす影響の格子モデル解析" 化学と工業,2019年10月号:72(10):P35-41 小原真,黒田裕 日本化学会 2019
"蛍光セルフクエンチを用いたアモルファス凝集形成機構の解析" 月刊「バイオインダストリー(特集:タンパク質生産と溶解度制御)」,2015年9月号 如澤浩樹,座古保,前田瑞夫,千葉一裕,黒田裕 シーエムシー出版 2015-9/11
"短いテトラペプチドの全原子シミュレーションによるアミノ酸のアモルファスな凝集性の洞察" 情報処理学会研究報告 BIO,バイオ情報学(2014年5号):2014(5):p1-2 佐藤雄士,末永敦,泰地真弘人,黒田裕 情報処理学会 2014-12/11
"ペプチド系溶解度向上タグ"SEPタグ"によるタンパク質の溶解性の解析と制御" 月刊「バイオインダストリー」,2013年7月号 黒田裕 シーエムシー出版 2013-7/12
"共同利用研究ハイライト:最小レポータータンパク質の構築を目指した組換えガウシアルシフェラーゼの解析と改変" 分子研レターズ,67:p.26-27 黒田裕,Wu Nan 分子科学研究所 2013-3
"海外研究室訪問:大学院生によるフランス・モンペリエ大学・構造生化学研究センターへ短期訪問" 生物物理,2012年8月号:52(4):P.206-207 小林慶,Catherine Royer,黒田裕 日本生物物理学会 2012
"VanXの溶菌活性の解明と菌体内生産物の精製工程の簡略化" 未来材料,2011年8月号:11(7)p32-36 黒田裕,上岡哲也,惣谷志保里 (株)エヌ・ティー・エス 2011-7/10
"東日本大震災:東京の会員からのご報告" 生物物理,2011年10月号:51(5):P238-239 黒田裕 日本生物物理学会 2011
"ジュネーブ・Swiss-Protグループの紹介" 生物物理,2010年10月号:50(5):P252-253 黒田裕,Damien Lieberherr 日本生物物理学会 2010
"蛋白質構造形成に必要な最小情報とは?~単純化ウシ膵臓トリプシン阻害蛋白質(BPTI)変異体の構造と熱力学~" 蛋白質核酸酵素,2009年4月号:54(5):p643-648 加藤淳,モハメド モニール イスラム,黒田裕 共立出版 2009-3/23
"タンパク質溶解性向上技術~SEP-tagについて~" 生物物理,2008年6月号:48(3):P185-189 加藤淳,泉川直重,黒田裕 日本生物物理学会 2008-5/28
"大腸菌由来DNA水溶液の動的粘弾性測定" 高分子論文集,64(7):P458-463 木下太郎,惣谷志保里,黒田裕,増渕雄一 高分子学会 2007-7
"プロテインスプライシングの工学的応用と技術" 実用産業情報,39:p24-27 上岡哲矢,田輪みな子,惣谷志保里,黒田裕 ㈱ニューマチック 2006
"編集後記" 日本物理学会誌,60(10):P.835-836 黒田裕 日本物理学会 2005
"単純化したアミノ酸配列でタンパク質の折りたたみを調べる" パリティ,3月号:18(3):P57-61 黒田裕 丸善出版 2003-2/25
"構造ゲノム科学と蛋白質の立体構造研究についての考察" 生体分子解析研究センターだより,23:p10-14 黒田裕 大阪大学蛋白質研究所附属生体分子解析研究センター 2002
"構造解析のターゲット選択:迅速な構造決定が可能な蛋白質ドメインの同定システム" 蛋白質核酸酵素,46(14):p2066-2072 黒田裕,近山英輔,横山茂之 共立出版 2001
"アミノ酸配列に含まれる情報量の実験的検証:蛋白質立体構造構築原理と分子進化の観点からの考察" 生物物理,41(5):p224-230 赤沼哲,黒田裕 日本生物物理学会 2001
"構造ゲノム科学のためのバイオインフォマティクス" 実験医学,19(8):p934-940 松尾洋,黒田裕,木下賢吾,中村春木 羊土社 2001-5/18
...

特許
表彰等(国外)

特許

特許名 発明者 登録日 出願人
特許第698626号 : "組換ポリペプチドの発現量及び収量の向上方法" 黒田裕,NAUTIYAL Kalpana 2021-12/1 国立大学法人東京農工大学
特許第5521236号 : "発現予測装置及び発現予測法" 廣瀬修一,野口保,五島直樹,河村義史,黒田裕 2014-4/8 独)産業技術総合研究所,バイオ産業情報化コンソーシアム,国立大学法人東京農工大学
特許第5509421号 : "可溶性予測装置及び可溶性予測法" 廣瀬修一,野口保,五島直樹,河村義史,黒田裕 2014-4/4 独)産業技術総合研究所,バイオ産業情報化コンソーシアム,国立大学法人東京農工大学
特許第5273438号 : "ペプチドの溶解度計算方法" 黒田裕,泉川直重,加藤淳,惣谷志保里 2013-5/24 国立大学法人東京農工大学
特許第4213034号 : "タンパク質のドメインリンカーを予測する方法" 黒田裕,宮崎哲,田中隆則,横山茂之 2001-9/25(出願日) 理化学研究所
特許第2895594号 : "NMRにおける溶媒信号除去方法" 永山国昭,山崎俊夫,黒田裕 1999-5/24 日本電子株式会社

表彰等(国外)

論文名 表彰名 受賞者 受賞日
"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