High pressure NMR study for conformational fluctuation of polyubiquitin

• Project/Area Number: 22770114
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: Ritsumeikan University
• Principal Investigator: KITAHARA Ryo 立命館大学, 薬学部, 准教授 (70512284)
• Project Period (FY): 2010 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2011: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2010: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: 蛋白質 / 圧力 / NMR / 高圧力 / ジユビキチン / 構造揺らぎ / ポリユビキチン / 高エネルギー構造 / 水和

Research Abstract

We investigated conformational fluctuation of Lys48-linked linear diubiquitin, as a minimum model of polyubiquitin chains, by using high-pressure NMR spectroscopy. Comparing pressure induced changes in chemical shifts between mono-ubiquitin and diubiquitin, we found that pressure stabilizes the "open" orientation of the two subunits for diubiquitin and the subunits have similar intrinsic motion to those of mono-ubiquitin. It is suggested that the intrinsic fluctuation of the subunits plays an essential role in the adaptation of global conformation of diubiquitin to the environment.

Research Products

• [Journal Article] A delicate interplay of structure, dynamics and thermodynamics for function. A high pressure NMR and fluorescence study of Outer surface protein A. (2012)
  • Author(s): Kitahara R., Simorellis A. K., Hata K., Maeno A., Yokoyama, S., Koide S. and Akasaka K.
  • Journal Title: Biophysical Journal Volume: 102 Pages: 916-926
  • Peer Reviewed
• [Journal Article] A delicate interplay of structure, dynamics and thermodynamics for function. A high pressure NMR and fluorescence study of Outer surface protein A (2012)
  • Author(s): Kitahara R., Simorellis A.K., Hata K., Maeno A., Yokoyama, S., Koide S., Akasaka K.
  • Journal Title: Biophysical Journal Volume: 102 Issue: 4 Pages: 916-926
  • DOI: 10.1016/j.bpj.2011.12.010
  • Peer Reviewed
• [Journal Article] Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH (2011)
  • Author(s): Ryo Kitahara, Kazumi Hata, Akihiro Maeno and Kazuyuki Akasaka, Michael Chimenti, Bertrand Garcia-Moreno, E. Martin A. Schroer, Christoph Jeworrek, Metin Tolan, Roland Winter, Julien Roche, Christian Roumestand, Karine Montet de Guillen and Catherine A. Ro
  • Journal Title: Proteins Volume: 79 Pages: 1293-1305
  • Peer Reviewed
• [Journal Article] Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH (2011)
  • Author(s): Kitahara R., Hata K.Maeno A., Akasaka K., Chimenti M.S., Garcia-Moreno B.E., Schroer M.A., Jeworrek C., Tolan M., Winter R., Roche J., Roumestand C., de Guillen K.M., Royer C.
  • Journal Title: Protein Science Volume: 79 Issue: 4 Pages: 1293-1305
  • DOI: 10.1002/prot.22966
  • Peer Reviewed
• [Presentation] 準安定構造に着目した構造-機能相関:ユビキチン、ジユビキチン (2012)
  • Author(s): 北原亮
  • Organizer: 第3回バイオ単分子研究会(招待講演)
  • Place of Presentation: 新世代研究所会議室(東京都)
  • Year and Date: 2012-03-09
• [Presentation] 準安定構造に着目した構造-機能相関:ユビキチン、ジユビキチン (2012)
  • Author(s): 北原亮
  • Organizer: 第3回バイオ単分子研究会
  • Place of Presentation: 新世代研究所会議室(東京都)(招待講演)
  • Year and Date: 2012-03-09
• [Presentation] ESIGN STRATEGY FOR HIGH FREE-ENERGY STATES OF PROTEINS BASED ON HIGH-PRESSURE NMR STUDY : ALTERNATIVELY FOLDED CONFORMATION OF UBIQUITIN (2012)
  • Author(s): Kitahara R., Kitazawa S., Yagi-Utsumi M., Ido A., Urushitani M., Sugase K., Kato K.
  • Organizer: Biophysical Society 56th Annual Meeting
  • Place of Presentation: サンディエゴUSA
  • Year and Date: 2012-02-26
• [Presentation] DESIGN STRATEGY FOR HIGH FREE-ENERGY STATES OF PROTEINS BASED ON HIGH-PRESSURE NMR STUDY : ALTERNATIVELY FOLDED CONFORMATION OF UBIQUITIN (2012)
  • Author(s): Kitahara R., Kitazawa S., Yagi-Utsumi M., Ido A., Urushitani M., Sugase K., Kato K.
  • Organizer: Biophysical Society 56th Annual Meeting
  • Place of Presentation: サンディエゴUSA
  • Year and Date: 2012-02-26
• [Presentation] Structure and Function of NMR "invisible" states of proteins (2012)
  • Author(s): 北原亮
  • Organizer: よこはま構造生物学研究会第43回ワークショップ
  • Place of Presentation: 理化学研究所横浜研究所交流棟ホール(神奈川県)(招待講演)
  • Year and Date: 2012-02-06
• [Presentation] High pressure NMR reveals a delicate interplay of protein's structure, dynamics, and thermodynamics for function (2012)
  • Author(s): 北原亮
  • Organizer: RRR国際シンポジウム
  • Place of Presentation: 首都大学東京秋葉原サテライトキャンパス(東京都)
  • Year and Date: 2012-01-25
• [Presentation] Structure, dynamics and function of high-energy statemutant of ubiquitin : Structure, dynamics and function of high-energy state mutant of ubiquitin (2012)
  • Author(s): Soichiro Kitazawa, Maho Yagi-Utsumi, Kenji Sugase, Koichi Kato, Ryo Kitahara
  • Organizer: The 5th International Symposium for Molecular Science of Fluctuations toward Biological Functions
  • Place of Presentation: 東大寺総合文化センター(奈良県)
  • Year and Date: 2012-01-07
• [Presentation] Two natively folded conformations of folate-bound forms of E.coli DHFR-D27E mutant (2012)
  • Author(s): Tomoko Kunihara, Soichiro Kitazawa, Naohiro Kobayashi, Eiji Ohmae, Ryo Kitahara
  • Organizer: The 5th International Symposium for Molecular Science of Fluctuations toward Biological Functions
  • Place of Presentation: 東大寺総合文化センター(奈良県)
  • Year and Date: 2012-01-07
• [Presentation] Two natively folded conformations of folate-bound form of E.Coli DHFR-D27E mutant (2011)
  • Author(s): Tomoko Kunihara, Soichiro Kitazawa, Naohiro Kobayashi, Eiji Ohmae, Ryo Kitahara
  • Organizer: ISNMR
  • Place of Presentation: 大さん橋ホール(神奈川県)
  • Year and Date: 2011-11-15
• [Presentation] Conformational fluctuation of Lys48-linked diubiquitin studied by high pressure NMR spectroscopy (2011)
  • Author(s): Ryo Kitahara, Takashi Hirano, Maho Yagi, Kazumi Hata, Kazuyuki Akasaka, Koichi Kato
  • Organizer: ISNMR
  • Place of Presentation: 大さん橋ホール(神奈川県)
  • Year and Date: 2011-11-15
• [Presentation] 高圧力NMRによる構造生物学の新展開 (2011)
  • Author(s): 北原亮
  • Organizer: NEDO特別講演会(招待講演)
  • Place of Presentation: 東京大学薬学部講堂(東京都)
  • Year and Date: 2011-10-13
• [Presentation] 高圧力NMRによる構造生物学の新展開 (2011)
  • Author(s): 北原亮
  • Organizer: NEDO特別講演会
  • Place of Presentation: 東京大学薬学部講堂(東京都)(招待講演)
  • Year and Date: 2011-10-13
• [Presentation] Cavity hydration and the dynamics of a protein (2011)
  • Author(s): 前野覚大、北原亮、鎌足雄司、Sunilkumar PN、赤坂一之
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学(兵庫県)
  • Year and Date: 2011-09-17
• [Presentation] High pressure NMR discloses a rich world of high-energy structures of proteins (2011)
  • Author(s): 北原亮
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学(兵庫県)
  • Year and Date: 2011-09-16
• [Presentation] Cavity hydration as a gatewayto internal movility : A high pressure 13C and 15N NMR study of T4 lysozyme (2011)
  • Author(s): Akihiro Maeno, Ryo Kitahara, Fredelrick Dahlquist, Shegeyuki Yokoyama, Frans Mulder, Kazuyuki Akasaka
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学(兵庫県)
  • Year and Date: 2011-09-16
• [Presentation] A design strategy of high-energy states of proteins based on high pressure NMR study (2011)
  • Author(s): Soichiro Kitazawa, Maho Yagi, Kenji Sugase, Koichi Kato, Ryo Kitahara
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学(兵庫県)
  • Year and Date: 2011-09-16
• [Presentation] 蛋白質の準安定状態に着目した新しい構造生物学の展開 (2011)
  • Author(s): 北原亮
  • Organizer: 蛋白質研究所セミナー(招待講演)
  • Place of Presentation: 大阪大学蛋白研究所(大阪府)
  • Year and Date: 2011-07-29
• [Presentation] 蛋白質の準安定状態に着目した新しい構造生物学の展開 (2011)
  • Author(s): 北原亮
  • Organizer: 蛋白質研究所セミナー
  • Place of Presentation: 大阪大学蛋白研究所(大阪府)(招待講演)
  • Year and Date: 2011-07-29
• [Presentation] 高圧力NMRで観る蛋白質の高エネルギー構造と水和 (2011)
  • Author(s): 北原亮、前野覚大、赤坂一之
  • Organizer: 第11回日本蛋白質科学会年会
  • Place of Presentation: ホテル阪急エキスポワーク(大阪府)
  • Year and Date: 2011-06-09
• [Presentation] ユビキチンの高エネルギー構造安定化変異体 (2011)
  • Author(s): 北沢創一郎、矢木真穂、菅瀬謙治、加藤晃一
  • Organizer: 第11回日本蛋白質科学会年会
  • Place of Presentation: ホテル阪急エキスポワーク(大阪府)
  • Year and Date: 2011-06-08
• [Presentation] タンパク質の高エネルギー構造に注目した新しい構造生物学の展開 (2011)
  • Author(s): 北原亮
  • Organizer: 第2回若手育成講習会(招待講演)
  • Place of Presentation: 大阪大学蛋白研究所(大阪府)
  • Year and Date: 2011-04-26
• [Presentation] タンパク質の高エネルギー構造に注目した新しい構造生物学の展開 (2011)
  • Author(s): 北原亮
  • Organizer: 第2回若手育成講習会
  • Place of Presentation: 大阪大学蛋白研究所(大阪府)(招待講演)
  • Year and Date: 2011-04-26
• [Presentation] 高圧力NMRで見る蛋白質の高エネルギー構造の世界 (2011)
  • Author(s): 北原亮
  • Organizer: よこはまNMR構造生物学研究会 第41回ワークショップ
  • Place of Presentation: 理化学研究所横浜研究所(神奈川県)
  • Year and Date: 2011-03-02
• [Presentation] The Functional Importance of Locally Disordered Structures of Proteins (2011)
  • Author(s): Ryo Kitahara
  • Organizer: Intrinsically disordered regions in proteins and related topics
  • Place of Presentation: 立命館大学(滋賀県)
  • Year and Date: 2011-01-31
• [Presentation] High pressure NMR reveals a locally disordered conformation of insulin (2010)
  • Author(s): Ryo Kitahara, Akiko Tanji, Souichirou Kitazawa, Yoshihiro Taniguchi
  • Organizer: Pacifichem 2010
  • Place of Presentation: ハワイ・アメリカ
  • Year and Date: 2010-12-19
• [Presentation] High-Energy State Mutant of Ubiquitin (2010)
  • Author(s): Soichiro Kitazawa, Maho Yagi, Kenji Sugase, Koichi Kato, Ryo Kitahara
  • Organizer: The 4th International Symposium, Molecular Science of Fluctuations toward Biological Functions
  • Place of Presentation: 近江ピアザ(滋賀県)
  • Year and Date: 2010-11-30
• [Presentation] NMR Characterization of High-Energy state of ubiquitin and poly-ubiquitin (2010)
  • Author(s): Ryo Kitahara
  • Organizer: The 4th International Symposium, Molecular Science of Fluctuations toward Biological Functions
  • Place of Presentation: 近江ピアザ(滋賀県)
  • Year and Date: 2010-11-30
• [Presentation] 準安定状態が安定化されたユビキチン変異体 (2010)
  • Author(s): 北沢創一郎、矢木真穂、菅瀬謙治、加藤晃一、北原亮
  • Organizer: 第49回NMR討論会
  • Place of Presentation: タワーホール船堀(東京都)
  • Year and Date: 2010-11-15
• [Presentation] 高圧力NMR法によるLys48結合型ジユビキチンの構造揺らぎ (2010)
  • Author(s): 北原亮、平野貴志、矢木真穂、秦和澄、赤坂一之、加藤晃一
  • Organizer: 第49回NMR討論会
  • Place of Presentation: タワーホール船堀(東京都)
  • Year and Date: 2010-11-15
• [Presentation] 準安定構造が安定化したユビキチン変異体のNMR解析 (2010)
  • Author(s): 北沢創一郎, 矢木真穂, 菅瀬謙治, 加藤晃一, 北原亮
  • Organizer: 第60回日本薬学会近畿支部総会・大会
  • Place of Presentation: 摂南大学(大阪府)
  • Year and Date: 2010-10-30
• [Presentation] Conformational fluctuation of highly stable form of staphylococcal nuclease delta +PHS and its V66K variant studied by high pressure NMR spectroscopy (2010)
  • Author(s): Ryo Kitahara, Kazumi Hata, Akihiro Maeno, Michael Chimenti, Bertrand Garcia-Moreno, E.Julien Roche, Christian Roumestand, Karine Montet de Guillen, Catherine A.Royer, Kazuyuki Akasaka
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学(宮城県)
  • Year and Date: 2010-09-21
• [Presentation] Dynamics of Lys48-linked di-ubiquitin as studied by NMR spectroscopy (2010)
  • Author(s): Takashi Hirano, Olivier Serve, Maho Yagi, Tsunehiro Mizushima, Ryo Kitahara, Koichi Kato
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学(宮城県)
  • Year and Date: 2010-09-21
• [Presentation] High pressure NMR reveals significant shifts in populations of higher-energy conformers in ubiquitin variants (2010)
  • Author(s): Souichirou Kitazawa, Maho Yagi, Koichi Kato, Kazuyuki Akasaka, Ryo Kitahara
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学(宮城県)
  • Year and Date: 2010-09-21
• [Presentation] The Functional Importance of Locally Disordered Structures of Proteins (2010)
  • Author(s): Ryo Kitahara, Kazuyuki Akasaka
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学(宮城県)
  • Year and Date: 2010-09-21
• [Presentation] Conformational fluctuation of Lys48-linked diubiquitin characterized by high-pressure NMR spectroscopy (2010)
  • Author(s): Ryo Kitahara, Takashi Hirano, Maho Yagi, Kazumi Hata, Yoshihiro Taniguchi, Kazuyuki Akasaka, Koichi Kato
  • Organizer: 第48回日本生物物理学会年会
  • Place of Presentation: 東北大学(宮城県)
  • Year and Date: 2010-09-20
• [Presentation] High pressure NMR reveals evolutinally conserved intermediates between ubiquitin and NEDD8 (2010)
  • Author(s): Ryo Kitahara
  • Organizer: 13th international symposium at MNRC
  • Place of Presentation: 滋賀医科大学(滋賀県)
  • Year and Date: 2010-09-01
• [Presentation] High-pressure NMR characterizes conformational fluctuation of Lys48-linked diubiquitin (2010)
  • Author(s): Ryo Kitahara, Takashi Hirano, Maho Yagi, Kazumi Hata, Yoshihiro Taniguchi, Kazuyuki Akasaka, Koichi Kato
  • Organizer: 24th International Conference on Magnetic Resonance in Biological Systems
  • Place of Presentation: ケアンズ オーストラリア
  • Year and Date: 2010-08-23
• [Presentation] Conformational fluctuation of highly stable form of staphylococcal nuclease ・+PHS and its V66K variant studied by high pressure NMR spectroscopy (2010)
  • Author(s): Ryo Kitahara, Kazumi Hata, Akihiro Maeno, Michael Chimenti, Bertrand Garcia-Moreno, E.Julien Roche, Christian Roumestand, Karine Montet de Guillen, Catherine A.Royer, Kazuyuki Akasaka
  • Organizer: 24th International Conference on Magnetic Resonance in Biological Systems
  • Place of Presentation: ケアンズ オーストラリア
  • Year and Date: 2010-08-23
• [Presentation] 高圧力NMR法によるユビキチンの高エネルギー構造に基づく構造-機能相関研究 (2010)
  • Author(s): 北原亮、北沢創一郎、坂田絵理、平野貴志、矢木内海真穂、谷口吉弘、水島恒裕、赤坂一之、加藤晃一
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター(北海道)
  • Year and Date: 2010-06-18
• [Book] 広がるNMRの世界 (2011)
  • Author(s): 朝倉哲郎
  • Publisher: コロナ社
• [Book] 広がるNMRの世界 (2011)
  • Author(s): 朝倉哲郎編著
  • Publisher: コロナ社
• [Book] 広がるNMRの世界-40人の研究者からの熱いメッセージ- (2011)
  • Author(s): 朝倉哲郎(編著), 北原亮, ら
  • Total Pages: 182
  • Publisher: コロナ社
• [Remarks]
  • URL: http://www.ritsumei.ac.jp/pharmacy/kitahara/kitahara_lab.html
• [Remarks]
  • URL: http://www.ritsumei.ac.jp/pharmacy/kitahara/kitahara_lab.html
• [Remarks]
  • URL: http://www.ritsumei.ac.jp/pharmacy/kitahara/kitahara_lab.html