RESEARCH
生命物理学
キーワード:#質量分析 #X線・中性子回折 #タンパク質
物理的な観点で生命・生物のシステムの解明を目指す
本講座では、質量分析技術とバイオインフォマティクスの融合や、X線・クライオ電子顕微鏡を用いて、生物システムの担い手であるタンパク質間ネットワークの解析と、各タンパク質の機能解明を目指し研究を進めています。
業績
jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data
Okuda S., Yoshizawa C. A., Kobayashi D., Takahashi Y., Watanabe Y., Moriya Y., Hatano A., Takami T., Matsumoto M., Araki N., Tabata T., Iwasaki M., Sugiyama N., Kodera Y., Tanaka S., Goto S., Kawano S., Ishihama Y.
Nucl. Acids Res., gkae1032, (2024)
https://doi.org/10.1093/nar/gkae1032
Design of Cyborg Proteins by Loop Region Replacement with Oligo(ethylene glycol): Exploring Suitable Mutations for Cyborg Protein Construction Using Machine Learning.
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.
BCSJ, uoae090, (2024)
https://doi.org/10.1093/bulcsj/uoae090
Reducing Offsite Modification using 2-mercaptoethanol for Proteome Analysis
Suto A., Matsui T., Kodera Y.
bioRxiv, (2024)
https://doi.org/10.1101/2024.08.09.607156
Molecular dynamics simulations reveal differences in the conformational stability of FtsZs derived from Staphylococcus aureus and Bacillus subtilis
Takasawa T., Matsui T., Watanabe G., Kodera Y.
Sci. Rep., 14: 16043, (2024)
https://doi.org/10.1038/s41598-024-66763-x
Data for peptidomic analysis of a single mouse hypothalamus
Okuda Y., Nakagawa Y., Matsui T., Konno R., Kawashima Y., Sato T., Itakura M., Kodera Y.
J. Proteome Data and Methods, 6: 15, (2024)
https://doi.org/10.14889/jpdm.2024.0015
Data for the solvent-accessible surfaces of protein observed by LC-MS
Suto A., Kojitani E., Matsui T., Kodera Y.
J. Proteome Data and Methods, 6: 8, (2024)
https://doi.org/10.14889/jpdm.2024.0008
Data for building LC-MS peak assignment algorithm based on machine learning
Oshiro T., Ito H., Matsui T., Kodera Y.
J. Proteome Data and Methods, 6: 4, (2024)
https://doi.org/10.14889/jpdm.2024.0004
Fibrocyte Phenotype of ENTPD1+CD55+ Cells and Its Association with Pain in Osteoarthritic Synovium
Tsuchiya M., Ohashi Y., Fukushima K., Okuda Y., Suto A., Matsui T., Kodera Y., Sato M., Tsukada A., Inoue G., Takaso M., Uchida K.
Int. J. Mol. Sci., 25(7): 4085, (2024)
https://doi.org/10.3390/ijms25074085
CD39+CD55− Fb Subset Exhibits Myofibroblast-Like Phenotype and Is Associated with Pain in Osteoarthritis of the Knee
Tsuchiya M., Ohashi Y., Kodera Y., Satoh M., Matsui T., Fukushima K., Iwase D., Aikawa J., Mukai M., Inoue G., Takaso M., Uchida K.
Biomedicines, 11(11): 3047, (2023)
https://doi.org/10.3390/biomedicines11113047
Interaction between membranous EBP50 and myosin 9 as a favorable prognostic factor in ovarian clear cell carcinoma.
Nakagawa M., Matsumoto T., Yokoi A., Hashimura M., Oguri Y., Konno R., Ishibashi Y., Ito T., Ohhigata K., Harada Y., Fukagawa N., Kodera Y., Saegusa M.
Mol. Oncol., (2023)
https://doi.org/10.1002/1878-0261.13503
Nucleobindin-2 Mediates Transforming Growth Factor-β1 -Driven Phenotypes in Zinc Finger E-Box Binding Homeobox 1-High Uterine Carcinosarcoma.
Kobayashi Y., Yokoi A., Hashimura M., Oguri Y., Konno R., Matsumoto T., Tochimoto M., Nakagawa M., Ishibashi Y., Ito T., Ohhigata K., Harada Y., Fukagawa N., Kodera Y., Saegusa M..
Am. J. Pathol., 193 (8) :1116-1128 (2023)
https://doi.org/10.1016/j.ajpath.2023.04.011
Synthesis of epitope-targeting nanobody based on native protein-protein interactions for FtsZ filamentation suppressor.
Nakazawa H., Katsuki T., Matsui T., Tsugita A., Yokoyama T., Ito T., Kawada S., Tanaka Y., Umetsu M.
Biotechnol. J., :e2300039 (2023)
https://doi.org/10.1002/biot.202300039
Assessment of inconsistencies in the solvent-accessible surfaces of proteins between crystal structures and solution structures observed by LC-MS
Matsui T.,Kojitani E.,Takasawa T., Suto A., Tamari A., Watanabe G., Kodera Y.
Biochem. Biophys. Res. Commun., 640 :97-104 (2022)
https://doi.org/10.1016/j.bbrc.2022.11.094
A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation.
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.
Nature Commun., 13 (1) :7262 (2022)
https://doi.org/10.1038/s41467-022-34921-2
Enzymatic formation of a prenyl β-carboline by a fungal indole prenyltransferase.
Hamdy S.A., Kodama T., Nakashima Y., Han X., Matsui T., Morita H..
J. Nat. Med., 76 (4) :873-879 (2022)
https://doi.org/10.1007/s11418-022-01635-0
Importance of the Q/N-rich segment for protein stability of endogenous mouse TDP-43.
Sato T., Oda K., Sakai S., Kato R., Yamamori S., Itakura M., Kodera Y., Nishizawa M., Sasaoka T., Onodera O., Yokoyama M..
Sci. Rep., 12 (1) :14923 (2022)
https://doi.org/10.1038/s41598-022-19153-0
ANGT_HUMAN[448-462], an Anorexigenic Peptide Identified Using Plasma Peptidomics.
Sasaki S., ObaK, Kodera Y., Itakura M., Shichiri M.
J. Endocr. Soc., 6 (7) :bvac082 (2022)
https://doi.org/10.1210/jendso/bvac082
The carbohydrate tail of landomycin A is responsible for its interaction with the repressor protein LanK
Tsugita A.,Uehara S., Matsui T., Yokoyama T., Ostash I., Deneka M., Yalamanchili S., Bennett C.S., Tanaka Y., Ostash B.
FEBS J., 289 (19) :6038-6057 (2022)
https://doi.org/10.1111/febs.16460
Chimeric mutants of staphylococcal hemolysin, which act as both one-component and two-component hemolysin, created by grafting the stem domain.
Ghanem N., Kanagami N., Matsui T., Takeda K., Kaneko J., Shiraishi Y., Choe C.A., Uchikubo-Kamo T., Shirouzu M., Hashimoto T., Ogawa T., Matsuura T., Po-Ssu H., Yokoyama T., Tanaka Y.
FEBS J., 289 (12) :3505-3520 (2022)
https://doi.org/10.1111/febs.16354
A novel peptide identified from visceral ganglia induces oocyte maturation, spermatozoa active motility, and spawning in the pen shell Atrinapectinata.
Funayama S., Matsumoto T., Kodera Y., Awaji M.
Biochem. Biophys. Res. Commun., 598 :9-14 (2022)
https://doi.org/10.1016/j.bbrc.2022.02.006
LC-MS peak assignment based on unanimous selection by six machine learning algorithms.
Ito H., Matsui T., Konno R., Itakura M., Kodera Y.
Sci. Rep., 11 (1) :23411 (2021)
https://doi.org/10.1038/s41598-021-02899-4
AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation.
Sekita Y., Sugiura Y., Matsumoto A., Kawasaki Y., Akasaka K., Konno R., Shimizu M., Ito T., Sugiyama E., Yamazaki T., Kanai E., Nakamura T., Suematsu M., Ishino F., Kodera Y., Kohda T., Kimura T..
Stem Cell Res. Ther., 12 (1) :510 (2021)
https://doi.org/10.1186/s13287-021-02578-1
Cytoplasmic EBP50 and elevated PARP1 are unfavorable prognostic factors in ovarian clear cell carcinoma.
Matsumoto T., Yoki A., Konno R., Oguri Y., Hashimura M., Tochimoto M., Nakagawa M., Jiang Z., Ishibashi Y., Ito T., Kodera Y., Saegusa M.
Carcinogenesis, 42 (9) :1162-1170 (2021)
https://doi.org/10.1093/carcin/bgab070
GIP_HUMAN[22-51] is a new proatherogenic peptide identified by native plasma peptidomics.
Masaki T., Kodera Y., Terasaki M., Fujimoto K., Hirano T., Shichiri M.
Sci. Rep., 11 (1) :14470 (2021)
https://doi.org/10.1038/s41598-021-93862-w
Circulating prorenin: its molecular forms and plasma concentrations
Fujimoto K., Kawamura S., Bando S., Kamata Y., Kodera Y., Shichiri M.
Hypertens. Res., 44 (6) :674-684 (2021)
https://doi.org/10.1038/s41440-020-00610-0
A highly efficient method for extracting peptides from a single mouse hypothalamus
Nakagawa Y., Matsui T., Konno R., Kawashima Y., Sato T., Itakura M., Kodera Y..
Biochem. Biophys. Res. Commun., 548 :155-160 (2021)
https://doi.org/10.1016/j.bbrc.2021.02.041
Highly accurate and precise quantification strategy using stable isotope dimethyl labeling coupled with GeLC-MS/MS
Konno R., Matsui T., Ito H., Kawashima Y., Itakura M., Kodera Y..
Biochem. Biophys. Res. Commun., 550 :37-42 (2021)
https://doi.org/10.1016/j.bbrc.2021.02.101
Suprabasin-derived bioactive peptides identified by plasma peptidomics
Taguchi T., Kodera Y., Oba K., Saito T., Nakagawa Y., Kawashima Y., Shichiri M.
Sci. Rep., 11 (1) :1047 (2021)
https://doi.org/10.1038/s41598-020-79353-4