Articles ^*:Corresponding Author, Underline: Master/Ph.D student

1. Yospanya W., Matsumura A., Imasato Y., Itou T., Aoki Y., Nakazawa H., Matsui T., Yokoyama T., Ui M., Umetsu M., Nagatoishi S., Tsumoto K., Tanaka Y., Kinbara K.: Design of Cyborg Proteins by Loop Region Replacement with Oligo(ethylene glycol): Exploring Suitable Mutations for Cyborg Protein Construction Using Machine Learning. BCSJ, uoae090, 2024.
   DOI:10.1093/bulcsj/uoae090

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2. Takasawa T., Matsui T.*, Watanabe G., Kodera Y.: Molecular dynamics simulations reveal differences in the conformational stability of FtsZs derived from Staphylococcus aureus and Bacillus subtilis. Sci. Rep., 14:16043, 2024.
   DOI:10.1038/s41598-024-66763-x

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3. Okuda Y., Nakagawa Y., Matsui T.*, Konno R., Kawashima Y., Sato T., Itakura M., Kodera Y.: Data for peptidomic analysis of a single mouse hypothalamus. J. Proteome Data and Methods, 6:15, 2024.
   DOI:10.14889/jpdm.2024.0015

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4. Suto A., Kojitani E., Matsui T.*, Kodera Y.: Data for the solvent-accessible surfaces of protein observed by LC-MS. J. Proteome Data and Methods, 6:8, 2024.
   DOI:10.14889/jpdm.2024.0008

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5. Oshiro T., Ito H., Matsui T.*, Kodera Y.: Data for building LC-MS peak assignment algorithm based on machine learning. J. Proteome Data and Methods, 6:4, 2024.
   DOI:10.14889/jpdm.2024.0004

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6. Tsuchiya M., Ohashi Y., Fukushima K., Okuda Y., Suto A., Matsui T., Kodera Y., Sato M., Tsukada A., Inoue G., Takaso M., Uchida K.: Fibrocyte Phenotype of ENTPD1+CD55+ Cells and Its Association with Pain in Osteoarthritic Synovium. Int. J. Mol. Sci., 25:4085, 2024.
   DOI:10.3390/ijms25074085

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7. Tsuchiya M., Ohashi Y. Kodera Y., Satoh M., Matsui T., Fukushima K., Iwase D., Aikawa J., Mukai M., Inoue G., Takaso M., Uchida K.: CD39+CD55- Fb subset exhibits myofibroblast-like phenotype and is associated with pain in osteoarthritis of the knee. Biomedicines, 11:3047, 2023.
   DOI:10.3390/biomedicines11113047

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8. Nakazawa H., Katsuki T., Matsui T., Tsugita A., Yokoyama T., Ito T., Kawada S., Tanaka Y., Umetsu M.: Synthesis of epitope-targeting nanobody based on native protein–protein interactions for FtsZ filamentation suppressor. Biotechnol. J., 18:2300039, 2023.
   Outside Back Cover (Biotechnol. J., 11/2023)
   DOI:10.1002/biot.202300039

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9. Matsui T.*, Kojitani E., Takasawa T., Suto A., Tamari A., Watanabe G., Kodera Y.: Assessment of inconsistencies in the solvent-accessible surfaces of proteins between crystal structures and solution structures observed by LC-MS. Biochem. Biophys. Res. Commun., 640:97-104, 2023.
   DOI:10.1016/j.bbrc.2022.11.094

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10. Watari H., Kageyama H., Masubuchi N., Nakajima H., Onodera K., Focia P.J., Oshiro T., Matsui T., Kodera Y., Ogawa T., Yokoyama T., Hirayama M., Hori K., Freymann D.M., Imai M., Komatsu N., Araki M., Tanaka Y., Sakai R.: A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation. Nature Commun., 13:7262, 2022.
    DOI:10.1038/s41467-022-34921-2
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11. Hamdy S.A., Kodama T., Nakashima Y., Han X., Matsui T., Morita H.: Enzymatic formation of a prenyl β-carboline by a fungal indole prenyltransferase. J. Nat. Med., 76:873-879, 2022.
    DOI:10.1007/s11418-022-01635-0
12. Tsugita A., Uehara S., Matsui T., Yokoyama T., Ostash I., Deneka M., Yalamanachili S., Bennet C., Tanaka Y., Ostash B.: The carbohydrate tail of landomycin A is responsible for interaction of the antibiotic with repressor protein LanK. FEBS J., 289:6038-6057, 2022.
    DOI:10.1111/febs.16460
13. Ghanem N., Kanagami N., Matsui T., Takeda K., Kaneko J., Shiraishi Y., Choe C., Uchikubo-Kamo T., Shirouzu M., Hashimoto T., Ogawa T., Matsuura T., Po-Ssu H., Yokoyama T., Tanaka Y.: Chimeric mutants of staphylococcal hemolysin, which act as both one-component and two-component hemolysin, created by grafting the stem domain. FEBS J., 289:3505-3520, 2022.
    DOI:10.1111/febs.16354
14. Ito H.^#, Matsui T.^#, Konno R., Itakura M., Kodera Y.: LC-MS Peak Assignment Based on Unanimous Selection by Six Machine Learning Algorithms. Sci. Rep., 11:23411, 2021. ^#equal contribution
    DOI:10.1038/s41598-021-02899-4
15. Konno R., Matsui T., Ito H., Kawashima Y., Itakura M., Kodera Y.: Highly accurate and precise quantification strategy using stable isotope dimethyl labeling coupled with GeLC-MS/MS. Biochem. Biophys. Res. Commun., 550:37-42, 2021.
    DOI:10.1016/j.bbrc.2021.02.101

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16. Nakagawa Y., Matsui T., Konno R., Kawashima Y., Sato T., Itakura M., Kodera Y.: A highly efficient method for extracting peptides from a single mouse hypothalamus. Biochem. Biophys. Res. Commun., 548(9):155-160, 2021.
    DOI:10.1016/j.bbrc.2021.02.041

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17. Nakamura M., Mizutani K., Kato R., Konno R., Matsumoto T., Matsui T., Itakura M., Ikeda K., Kodera Y., Nishiyama K., Sato T.: Quantitative proteomic analysis and single-protein-derived tryptic peptide profiling indicate qualitative alterations of annexin A6 in the brain of wobbler mice. Kitasato. Med. J., 51:76-83, 2021.
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18. Yano S., Suyotha W., Oguro N., Matsui T., Siga S., Itoh T., Hibi T., Tanaka Y., Wakayama M., Makabe K.: Crystal structure of the catalytic unit of GH 87 type α-1,3-glucanase Agl-KA from Bacillus circulans. Sci. Rep., 9:15295, 2019.
    DOI:10.1038/s41598-019-51822-5
19. Hashimoto T., Ye Y., Ui M., Ogawa T., Matsui T., Tanaka Y.: Protein encapsulation in the hollow space of hemocyanin crystals containing a covalently conjugated ligand. Biochem. Biophys. Res. Commun., 514(1):31-36, 2019.
    DOI:10.1016/j.bbrc.2019.04.062

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20. Tanaka Y., Kato S., Stabrin M., Raunser S., Matsui T., Gatsogiannis C.: CryoEM reveals the asymmetric assembly of squid hemocyanin. IUCrJ, 6(3):426-437, 2019.
    DOI:10.1107/S205225251900321X
21. Matsui T., Kamata S., Ishii K., Maruno T., Ghanem N., Uchiyama S., Kato K., Suzuki A., Oda-Ueda N., Ogawa T., Tanaka Y.: SDS-induced oligomerization of Lys49-phospholipase A₂ from snake venom. Sci. Rep., 9:2330, 2019.
    DOI:10.1038/s41598-019-38861-8
22. Hashimoto T., Ye Y., Matsuno A., Ohnishi Y., Kitamura A., Kinjo M., Abe S., Ueno T., Yao M., Ogawa T., Matsui T., Tanaka Y.: Encapsulation of biomacromolecules by soaking and co-crystallization into porous protein crystals of hemocyanin. Biochem. Biophys. Res. Commun., 509(2):577-584, 2019.
    DOI:10.1016/J.BBRC.2018.12.096

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23. Kato S., Matsui T., Gatsogiannis C., Tanaka, Y.: Molluscan Hemocyanin: Structure, Evolution, and Physiology, Biophys. Review, 10:191-202, 2018.
    DOI:10.1007/s12551-017-0349-4
24. Matsui T., Kodama T., Mori T., Tadakoshi T., Noguchi H., Abe I., Morita H.: 2-Alkylquinolone Alkaloid Biosynthesis in the Medicinal Plant Evodia rutaecarpa Involves Collaboration of Two Novel Type III Polyketide Synthases. J. Biol. Chem., 292(22):9117-9135, 2017.
    DOI:10.1074/jbc.M117.778977

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25. Matsui T., Lallo S., Nisa K., Morita H.: Filamenting temperature-sensitive mutant Z inhibitors from Glycyrrhiza glabra and their inhibitory mode of action. Bioorg. Med. Chem. Lett., 27:1420-1424, 2017.
    DOI:10.1016/j.bmcl.2017.01.095

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26. Nisa K., Ito T., Subehan, Matsui T., Kodama T., Morita H.: New acylphloroglucinol derivatives from the leaves of Baeckea frutescens. Phytochemistry Lett., 15:42-45, 2016.
    DOI:10.1016/j.phytol.2015.11.011

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27. Win N. N., Ito T., Matsui T., Aimaiti S., Kodama T., Ngwe H., Okamoto Y., Tanaka M., Asakawa Y., Abe I., Morita H.: Isopimarane diterpenoids from Kaempferia pulchra rhizomes collected in Myanmar and their Vpr inhibitory activity. Bioorg. Med. Chem. Lett., 26(7):1789-1793, 2016.
    DOI:10.1016/j.bmcl.2016.02.036

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28. Yang X., Matsui T., Kodama T., Mori T., Zhou X., Taura F., Noguchi H., Abe I., Morita H.: Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa. FEBS J., 283(6):1088-1106, 2016.
    DOI:10.1111/febs.13654
29. Yang X., Matsui T., Mori T., Taura F., Noguchi H., Abe I., Morita H.: Expression, purification, and crystallization of a plant polyketide cyclase from Cannabis sativa. Acta Crystallogr F Struct Biol Commun., 71:1470-1474, 2015.
    DOI:10.1107/S2053230X15020385
30. Mori T., Hoshino S., Sahashi S., Wakimoto T., Matsui T., Morita H., Abe I.: Structural basis for the β-carboline alkaloids production by the microbial homodimeric enzyme McbB. Chem&Biol., 22:898-906, 2015.
    DOI:10.1016/j.chembiol.2015.06.006

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31. Mori T., Yang D., Matsui T., Hashimoto M., Morita H., Fujii I., Abe I.: Structural basis for the formation of acylalkylpyrones from two β-ketoacyl units by the fungal type III polyketide synthase CsyB. J. Biol. Chem., 290(8):5214-5225, 2015.
    DOI:10.1074/jbc.M114.626416

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32. Noike M., Matsui T., Ooya K., Sasaki I., Ohtaki S., Hamano Y., Maruyama C., Ishikawa J., Satoh Y., Ito H., Morita H., Dairi T.: A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin. Nature Chem. Biol., 11:71-76, 2015.
    DOI:10.1038/nchembio.1697
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33. Yang D., Mori T., Matsui T., Hashimoto M., Morita H., Fujii I., Abe I.: Expression, purification, and crystallization of a fungal type III polyketide synthase that produces the csypyrones. Acta Crystallogr F Struct Biol Commun., 70:730-733, 2014.
    DOI:10.1107/S2053230X15020385
34. Matsui T., Han X., Yu J., Yao M., Tanaka I.: Structural change in FtsZ induced by intermolecular interactions between bound GTP and the T7 Loop. J. Biol. Chem., 289:3501-3509, 2014.
    DOI:10.1074/jbc.M113.514901
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35. Mori T., Shimokawa Y., Matsui T., Kinjo K., Kato R., Noguchi H., Sugio S., Morita H., Abe I.: Cloning and structure-function analyses of quinolone- and acridone-producing novel type III polyketide synthases from Citrus microcarpa. J. Biol. Chem., 288:28845-28858, 2013.
    DOI:10.1074/jbc.M113.493155

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36. Saito T., Kawashima Y., Minamida S., Matsumoto K., Araki K., Matsui T., Satoh M., Nomura F., Iwamura M., Maeda T., Baba S., Kodera Y.: Establishment and application of a high-quality comparative analysis strategy for the discovery and small-scale validation of low-abundance biomarker peptides in serum based on an optimized novel peptide extraction method. J Electrophoresis, 57:1-9, 2013.
    DOI:10.2198/jelectroph.57.1
37. Kawashima Y., Satoh M., Saito T., Matsui T., Nomura F., Matsumoto H., Kodera Y.: Cyclic sample pooling using two-dimensional liquid chromatography system enhances coverage in shotgun proteomics. Biomed. Chromatogr., 27:691-4, 2013.
    DOI:10.1002/bmc.2864
38. Matsui T., Yamane J., Mogi N., Yamaguchi H., Takemoto H., Yao M., Tanaka I.: Structural reorganization of the bacterial cell division protein FtsZ from Staphylococcus aureus. Acta Crystallographica Section D, 68:1175-1188, 2012.
    DOI:10.1107/S0907444912022640
39. Matsui T., Tanaka T., Endoh H., Sato K., Tanaka H., Miyauchi E., Kawashima Y., Nagai-Makabe M., Komatsu H., Kohno T., Maeda T., Kodera Y.: The RNA recognition mechanism of human immunodeficiency virus (HIV) type 2 NCp8 is different from that of HIV-1 NCp7. Biochemistry, 48:4314-4323, 2009.
    DOI:10.1021/bi802364b
40. Kawashima Y., Fukuno T., Satoh M., Takahashi H., Matsui T., Maeda T., Kodera Y.: A simple and highly reproducible method for discovering potential disease markers in low abundance serum proteins. J. Electrophoresis, 53:13-18, 2009.
    DOI:10.2198/jelectroph.53.13
41. Matsui T., Kodera Y., Miyauchi E., Tanaka H., Endoh H., Komatsu H., Tanaka T., Kohno T., Maeda T.: Structural role of the secondary active domain of HIV-2 NCp8 in multi-functionality. Biochem. Biophys. Res. Commun., 358:673-678, 2007.
    DOI:10.1016/j.bbrc.2007.04.141

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42. Matsui T., Kodera Y., Endoh H., Miyauchi E., Komatsu H., Sato K., Tanaka T., Kohno T., Maeda T.: RNA recognition mechanism of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein. J. Biochem., 141:269-277, 2007.
    DOI:10.1093/jb/mvm037