Analysis of protein folding and conformational change based on the characterization of the transition state

• Project/Area Number: 24657103
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Biophysics
• Research Institution: Kyoto University
• Principal Investigator: IMAMOTO Yasushi 京都大学, 理学(系)研究科(研究院), 准教授 (80263200)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2013: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: 光生物学 / 構造変化 / 異性化 / 折りたたみ / 中間体 / 吸収スペクトル / 光センサー / イエロープロテイン / 平衡 / 遷移状態 / 光反応サイクル / アイリング・プロット / 遷移状体

Outline of Final Research Achievements

Photoactivation of photoactive yellow protein yields the physiologically active state called PYPM. In PYPM, the structure is partially unfolded, and photocycle of PYP is a good model to study the protein folding. Here we analyzed the photocycle of PYP based on the characterization of the transition state between the intermediates.

Research Products

• [Journal Article] Intramolecular interactions that induce helical rearrangement upon rhodopsin activation: Light-induced structural changes in metarhodopsin IIa probed by cysteine S-H stretching vibrations (2014)
  • Author(s): Y. Yamazaki, T. Nagata, A. Terakita, H. Kandori, Y. Shichida, Y. Imamoto*
  • Journal Title: J. Biol. Chem Volume: 289 Issue: 20 Pages: 13792-13800
  • DOI: 10.1074/jbc.m113.527606
  • NAID: 120005741087
  • Peer Reviewed
• [Journal Article] Mapping of the local environmental changes in proteins by cysteine scanning (2014)
  • Author(s): Y. Yamazaki, T. Nagata, A. Terakita, H. Kandori, Y. Shichida, Y. Imamoto
  • Journal Title: BIOPHYSICS Volume: 10 Issue: 0 Pages: 1-7
  • DOI: 10.2142/biophysics.10.1
  • NAID: 130003392785
  • ISSN: 1349-2942
  • Peer Reviewed
• [Journal Article] Evolution of mammalian opn5 as a specialized UV-absorbing pigment by a single amino acid mutation (2014)
  • Author(s): Yamashita, T., Ono, K., Ohuchi, H., Yumoto, A., Gotoh, H., Tomonari, S., Sakai, K., Fujita, H., Imamoto, Y., Noji, S., Nakamura, K., and Shichida, Y.
  • Journal Title: J. Biol. Chem. Volume: 289 Issue: 7 Pages: 3991-4000
  • DOI: 10.1074/jbc.m113.514075
  • NAID: 120005690203
  • Peer Reviewed
• [Journal Article] Rod visual pigment optimizes active state to achieve efficient G protein activation as compared to cone visual pigments (2014)
  • Author(s): Kojima, K., Imamoto, Y., Maeda, R., Yamashita, T., and Shichida, Y
  • Journal Title: J. Biol. Chem Volume: 289 (8) Issue: 8 Pages: 5061-5073
  • DOI: 10.1074/jbc.m113.508507
  • Peer Reviewed
• [Journal Article] Ligand-induced population shift leads to the activation of rhodopsin, a G-protein coupled receptor (2014)
  • Author(s): Maeda, R., Hiroshima, M., Yamashita, T., Wada, A., Nishimura, S., Sako, Y., Shichida, Y., and Imamoto, Y
  • Journal Title: Biophys. J Volume: 106 (4) Issue: 4 Pages: 915-924
  • DOI: 10.1016/j.bpj.2014.01.020
  • Peer Reviewed
• [Journal Article] Efficiencies of activation of transducin by cone and rod visual pigments (2013)
  • Author(s): Imamoto, Y., Seki, I., Yamashita, T., and Shichida, Y
  • Journal Title: Biochemistry Volume: 52 (17) Issue: 17 Pages: 3010-3018
  • DOI: 10.1021/bi3015967
  • Peer Reviewed
• [Journal Article] Ultrafast carbonyl motion of the photoactive yellow protein chromophore probed by femtosecond circular dichroism (2013)
  • Author(s): Mendonca, L., Hache, F., Changenet-Barret, P., Plaza, P., Chosrowjan, H., Taniguchi, S., and Imamoto, Y.
  • Journal Title: J. Am. Chem. Soc. 135, Volume: 135 Issue: 39 Pages: 14637-14643
  • DOI: 10.1021/ja404503q
  • Peer Reviewed
• [Journal Article] Ultrafast time-resolved pump-probe spectroscopy of PYP by a sub-8fs pulse laser at 400 nm (2013)
  • Author(s): Liu, J., Yabushita, A., Taniguchi, S., Chosrowjan, H., Imamoto, Y., Sueda, K., Miyanaga, N., and Kobayashi, T.
  • Journal Title: J. Phys. Chem. B Volume: 117 Issue: 17 Pages: 4818-4826
  • DOI: 10.1021/jp4001016
  • Peer Reviewed
• [Journal Article] Photochemical nature of parietopsin. (2012)
  • Author(s): K. Sakai, Y. Imamoto, C.Y. Su, H. Tsukamoto, T. Yamashita, A. Terakita, K.W. Yau and Y. Shichida
  • Journal Title: Biochemistry Volume: 51 Issue: 9 Pages: 1933-41
  • DOI: 10.1021/bi2018283
  • Peer Reviewed
• [Journal Article] The C-Terminus of the G Protein α Subunit Controls the Affinity of Nucleotides (2012)
  • Author(s): Naoki Kimata, Takahiro Yamashita, Take Matsuyama, Yasushi Imamoto, Yoshinori Shichida
  • Journal Title: Biochemistry Volume: 51 Issue: 13 Pages: 2768-2774
  • DOI: 10.1021/bi201702d
  • Peer Reviewed
• [Journal Article] Comparative studies on the late bleaching processes of four kinds of cone visual pigments and rod visual pigment (2012)
  • Author(s): K. Sato, T. Yamashita, Y. Imamoto and Y. Shichida
  • Journal Title: Biochemistry Volume: 51 Issue: 21 Pages: 4300-8
  • DOI: 10.1021/bi3000885
  • Peer Reviewed
• [Journal Article] Photochemical properties of mammalian melanopsin. (2012)
  • Author(s): T. Matsuyama, T. Yamashita, Y. Imamoto and Y. Shichida
  • Journal Title: Biochemistry Volume: 51 Issue: 27 Pages: 5454-62
  • DOI: 10.1021/bi3004999
  • Peer Reviewed
• [Presentation] Single-molecule observation of the ligand-induced population shift of rhodopsin, a G-protein coupled receptor (2014)
  • Author(s): Imamoto, Y.
  • Organizer: 16th International Conference on Retinal Proteins
  • Place of Presentation: 長浜ロイヤルホテル
  • Year and Date: 2014-10-07
  • Invited
• [Presentation] イエロープロテイン光反応中間体の熱平衡の解析 (2014)
  • Author(s): 今元 泰、七田 芳則
  • Organizer: 第52 回日本生物物理学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 2014-09-27
• [Presentation] Photoactive yellow proteinの光反応サイクルと構造ダイナミクス (2014)
  • Author(s): 今元 泰、松山 武、七田 芳則
  • Organizer: 第18回 日本光生物学協会年会
  • Place of Presentation: 大阪市立大学学術情報総合センター
  • Year and Date: 2014-08-22
• [Presentation] Light-induced structural changes of rhodopsin probed by cysteine S-H stretching vibrations (2012)
  • Author(s): Imamoto, Y.
  • Organizer: 15th International Conference on Retinal Proteins
  • Place of Presentation: Ascona, Switzerland
  • Invited
• [Presentation] Helical rearrangement of photoactivated rhodopsin probed by high-angle X-ray scattering
  • Author(s): Imamoto, Y., Oka, T., Kojima, K., Maeda, R., Shichida, Y.
  • Organizer: 日本生物物理学会第51回年会
  • Place of Presentation: 国立京都国際会館
• [Presentation] Characterization of visual pigments in membrane environment using nanodiscs
  • Author(s): Imamoto, Y., Kojima, K., Maeda, R., Oka, T., Yamashita, T., and Shichida, Y.
  • Organizer: The 6th Asia & Oceania Conference on Photobiology
  • Place of Presentation: Novotel Sydney Central, Australia
  • Invited
• [Presentation] 構造ダイナミクスからみたロドプシンの活性化機構
  • Author(s): 今元 泰、前田 亮、廣島通夫、佐甲靖志、七田芳則
  • Organizer: 分子研研究会「ロドプシン研究の故きを温ねて新しきを知る」
  • Place of Presentation: 岡崎コンファレンスセンター大会議室
  • Invited