Study of aromatic ring-flipping in protein interiors at high pressures

• Project/Area Number: 25440018
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Kumamoto University (2015); Nagoya University (2013-2014)
• Principal Investigator: TAKEDA MITSUHIRO 熊本大学, 生命科学研究部, 助教 (90508558)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000); Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2014: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2013: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: NMR / SAIL / ＮＭＲ / ＳＡＩＬ / タンパク質 / 構造ゆらぎ / 高圧実験 / 芳香環反転

Outline of Final Research Achievements

The side-chain aromatic rings of phenylalanine and tyrosine residues in the interior of protein frquenty rotate about their Cb-Cg axis, which is assumed to occur when the protein undergoes a large amplitude slow breathing motion. In this project, uder varied hydrotatic pressures, the ring flipping rates were evaluated by using the SAIL-NMR methds. This study expectedly provides new insight into the large amplitude motion of proteins.

Research Products

• [Journal Article] Nano-mole scale side-chain assignment by 1H-detected protein solid-state NMR by ultra-fast magic-angle spinning and stereo-array isotope labeling (2015)
  • Author(s): Songlin Wang, Sudhakar Parthasarathy, Yusuke Nishiyama, Yuki Endo, Takahiro Nemoto, Kazuo Yamauchi, Tetsuo Asakura, Mitsuhiro Takeda, Tsutomu Terauchi, Masatsune Kainosho, and Yoshitaka Ishii
  • Journal Title: PLoS One Volume: １０ Issue: 4 Pages: 1-12
  • DOI: 10.1371/journal.pone.0122714
  • Peer Reviewed / Open Access
• [Journal Article] Nano-mole scale sequential signal assignment by 1H-detected protein solid-state NMR (2015)
  • Author(s): Songlin Wang, Sudhakar Parthasarathy, Yiling Xiao, Yusuke Nishiyama, Fei Long, Isamu Matsuda, Yuki Endo, Takahiro Nemoto, Kazuo Yamauchi, Tetsuo Asakura, Mitsuhiro Takeda, Tsutomu Terauchi, Masatsune Kainosho, Yoshitaka Ishii
  • Journal Title: Chem. Commun. (Camb) Volume: ５１ Issue: 81 Pages: 15055-8
  • DOI: 10.1039/c5cc04618a
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Differential large-amplitude breathing motions in the interface of FKBP12-drug complexes (2015)
  • Author(s): Chun-Jiun Yang, Mitsuhiro Takeda, Tsutomu Terauchi, JunGoo Jee, Masatsune Kainosho
  • Journal Title: Biochemistry Volume: 54 Issue: 47 Pages: 6983-95
  • DOI: 10.1021/acs.biochem.5b00820
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Automated resonance assignment of the 21 kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA. (2014)
  • Author(s): Schmidt, E., Ikeya, T., Takeda, M., Loehr, F., Buchner, L., Ito, Y., Kainosho, M., Guentert, P.
  • Journal Title: J. Magn. Reson. Volume: 249 Pages: 88-93
  • DOI: 10.1016/j.jmr.2014.10.005
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Expression and purification of a GRAS domain of SLR1, the rice DELLAprotein (2014)
  • Author(s): Sato, T., Miyanoiri, Y., Takeda, M., Naoe, Y., Mitani, R., Hirano, K., Takehara, S., Kainosho, M., Matsuoka, M., Ueguchi-Tanaka, M., Kato, H.
  • Journal Title: Protein Expr. Purif. Volume: N/A Pages: 248-254
  • DOI: 10.1016/j.pep.2014.01.006
  • Peer Reviewed / Open Access
• [Journal Article] Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates (2014)
  • Author(s): Mitsuhiro Takeda, Yohei Miyanoiri, Tsutomu Terauchi, Chun-Jiun Yang, Masatsune Kainosho
  • Journal Title: J. Magn. Reson. Volume: 241 Pages: 148-154
  • DOI: 10.1016/j.jmr.2013.10.001
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Differential isotope-labeling for Leu and Val residues in a protein by E. coli cellular expression using stereo-specifically methyl labeled amino acids (2013)
  • Author(s): Yohei Miyanoiri, Mitsuhiro Takeda, Kosuke Okuma, Akira M. Ono, Tsutomu Terauchi, Masatsune Kainosho
  • Journal Title: J. Biomol. NMR Volume: 57 Issue: 3 Pages: 237-249
  • DOI: 10.1007/s10858-013-9784-0
  • Peer Reviewed
• [Journal Article] Molecular bases of multimodal regulation of a fungal transient receptor potential (TRP) channel (2013)
  • Author(s): Ihara M,Hamamoto S, Miyanoiri Y, Takeda M, Kainosho M, Yabe I, Uozumi N, Yamashita A
  • Journal Title: Journal of Biological Chemistry Volume: (in press) Issue: 21 Pages: 15303-17
  • DOI: 10.1074/jbc.m112.434795
  • Peer Reviewed
• [Presentation] NMR Hydrogen exchange study of polar side-chain groups in proteins (2015)
  • Author(s): Mitsuhiro Takeda, Yohei Miyanoiri, Chun-Jiun Yang, Sanae Kondo, Tsutomu Terauchi, Masatsune Kainosho
  • Organizer: ISMAR
  • Place of Presentation: Shanghai, China
  • Year and Date: 2015-08-17
  • Int'l Joint Research
• [Presentation] 13C NMR analyses using site-specific isotope labeling for studying hydrogen exchange and protonation states of polar side-chain groups in proteins (2015)
  • Author(s): Mitsuhiro Takeda, Yohei Miyanoiri, Chun-Jiun Yang, Sanae Kondo, Tsutomu Terauchi, Masatsune Kainosho
  • Organizer: Asia-Pacific NMR
  • Place of Presentation: Hong Kong, China
  • Year and Date: 2015-08-13
  • Int'l Joint Research / Invited
• [Presentation] SAIL法を利用したタンパク質構造揺らぎのＮＭＲ研究 (2014)
  • Author(s): 武田光広、甲斐荘正恒
  • Organizer: 第５３回NMR討論会
  • Place of Presentation: 大阪大学吹田キャンパス
  • Year and Date: 2014-11-04 – 2014-11-06
  • Invited
• [Presentation] NMR method for investigating hydrogen exchange rate of lysine side-chain amino group (2014)
  • Author(s): Mitsuhiro Takeda, Tsutomu Terauchi and Masatsune Kainosho
  • Organizer: International Conference of Magnetic Resonance in Biological System
  • Place of Presentation: USA, Dallas
  • Year and Date: 2014-08-24 – 2014-08-29
• [Presentation] 蛋白質リジン残基側鎖アミノ基の水素交換速度の解析 (2013)
  • Author(s): 武田光広、寺内勉、甲斐荘正恒
  • Organizer: 第５2回NMR討論会
  • Place of Presentation: 石川県金沢市石川県立音楽堂
• [Presentation] SAIL―ＮＭＲ法による蛋白質過渡的揺らぎの研究 (2013)
  • Author(s): 武田光広
  • Organizer: 平成25年度 日本分光学会ＮＭＲ分光部会 講習会
  • Place of Presentation: 愛知県名古屋市名古屋大学ES館会議室
  • Invited
• [Presentation] SAIL-NMR法による蛋白質の Large amplitude breathing motion の解析 (2013)
  • Author(s): 武田光広
  • Organizer: 大学院セミナー
  • Place of Presentation: 滋賀県草津市立命館大学びわこ・くさつキャンパス
  • Invited
• [Remarks] 名古屋大学理学研究科付属構造生物学研究センター
  • URL: http://str.bio.nagoya-u.ac.jp:8080/Plone