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We analyze protein dynamics in multicomponent system, using mass spectrometry and H/D exchange. 　　　 Ribosome dynamics [P4],[P6],[P7],[Rj2],[Rj3] Structural dynamics of other multicomponent systems [P4] Protein dynamics for Medical study [P1],[P2],[P3],[P8],[P9] Development of new tool, software, and experiments for protein dynamics [P1],[P4],[P7],[Rj1],[S1]

Papers

1. Tatsuya Yamamoto, Shunsuke Izumi, and Kunihiko Gekko*
   “Mass Spectrometry on Segment-Specific Hydrogen Exchange of Dihydrofolate Reductase”
   The Journal of Biochemistry, 135(1), 17-24 (2004)


2. Tatsuya Yamamoto, Shunsuke Izumi, Eiji Ohmae, and Kunihiko Gekko*
   “Mass Spectrometry of Hydrogen/Deuterium Exchange of Escherichia coli Dihydrofolate Reductase: Effects of Loop Mutations”
   The Journal of Biochemistry, 135(4), 487-494 (2004)


3. Tatsuya Yamamoto, Shunsuke Izumi, and Kunihiko Gekko*
   “Mass Spectrometry on Hydrogen/Deuterium Exchange of Dihydrofolate Reductase: Effects of Ligand Binding”
   The Journal of Biochemistry, 135(6), 663-671 (2004)


4. Tatsuya Yamamoto*, Shunsuke Izumi, and Kunihiko Gekko
   “Mass spectrometry of hydrogen/deuterium exchange in 70S ribosomal proteins from E. coli”
   FEBS Letters, 580, 3638-3642 (2006)


5. Tatsuya Yamamoto*, Toshifumi Takao, Shunsuke Izumi, and Kunihiko Gekko
   “Site-Specific H/D Exchange Analysis of a Protein by Mass Spectrometry Coupled with Carboxypeptidase Digestion”
   Journal of the Mass Spectrometry Society of Japan, 55, 333-338 (2007)


6. Tatsuya Yamamoto*, Yoshihiro Shimizu, Takuya Ueda, and Yoshitsugu Shiro
   “Mg²⁺ Dependence of 70 S Ribosomal Protein Flexibility Revealed by Hydrogen/Deuterium Exchange and Mass Spectrometry”
   The Journal of Biological Chemistry, 285, 5646-5652 (2010)


7. Tatsuya Yamamoto, Yoshihiro Shimizu, Takuya Ueda, Yoshitsugu Shiro*, and Makoto Suematsu*
   “Application of micro-reactor chip technique for millisecond quenching of deuterium incorporation into 70S ribosomal protein complex”
   International Journal of Mass Spectrometry, 302, 132-138 (2011)


8. Tatsuya Yamamoto, Hitoshi Iino, Kwang Kim, Seiki Kuramitsu, and Kenji Fukui*
   “Evidence for the ATP-dependent structural rearrangement of the nuclease catalytic site in the DNA mismatch repair endonuclease MutL”
   The Journal of Biological Chemistry, 286, 42339-42348 (2011)


9. Yasuaki Kabe, Takanori Nakane, Ikko Koike, Tatsuya Yamamoto, Yuki Sugiura, Erisa Harada, Kenji Sugase, Tatsuro Shimamura, Mitsuyo Ohmura, Kazumi Muraoka, Ayumi Yamamoto, Takeshi Uchida, So Iwata, Yuki Yamaguchi, Elena Krayukhina, Masanori Noda, Hiroshi Handa, Koichiro Ishimori, Susumu Uchiyama, Takuya Kobayashi*, Makoto Suematsu*
   “Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance”
   Nature Communications, 7, 11030 (2016)


10. Tatsuya Yamamoto, Tohru Yamagaki., Honoo Satake*.
    “Development of Software for the In-Depth Analysis of Protein Dynamics as Determined by MALDI Mass Spectrometry-Based Hydrogen/Deuterium Exchange”
    Mass Spectrom (Tokyo) , 8, S0082 (2019)

Reviews (in japanese)

1. Tatsuya Yamamoto and Kunihiko Gekko
   「質量分析法を用いた蛋白質の揺らぎの研究《(Study on Flexibility of Protein by Mass Spectrometry）
   Journal of the Mass Spectrometry Society of Japan, 51(3), 412-414 (2003)


2. Tatsuya Yamamoto and Kunihiko Gekko
   「質量分析法を用いた巨大タンパク質複合体のH/D交換の研究《 (H/D Exchange Study of Macro-Protein Complexes by Mass Spectrometry）
   Journal of the Mass Spectrometry Society of Japan, 55(3), 217-219 (2007)


3. Tatsuya Yamamoto
   「質量分析法による巨大タンパク質複合体ダイナミクスの研究《 (Mass Spectrometry of Protein Dynamics in Macro Complexes）
   生物物理, 48(6), 345-346 (2008)


4. Tatsuya Yamamoto
   「タンパク質の構造変化を量る《(Measuring structural changes of protein）
   実験医学別冊　質量分析実験ガイド, 160-169(2013)

Software

　　
1. The software development for the fragment identification and analysis of post-translation modification (JAVA)　[free]
2. The software development for the H/D exchange analysis of proteins using MALDI-MS coupled with pepsin digestion. (JAVA)　[semi-free]

Please access [] for this project.