Dynamics of hydrogen bond network among the side chains in the active site of enzyme revealed by NMR deuterium isotope shift

• Project/Area Number: 26650023
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: Hiroshima University
• Principal Investigator: Shin-ichi Tate 広島大学, 理学(系)研究科(研究院), 教授 (20216998)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: NMR / プロリン異性化酵素 / 重水素同位体シフト / 安定同位体 / タンパク質 / 酵素 / 水素結合 / タンパク質構造動態 / 同位体効果 / 化学シフト / 酵素活性部位

Outline of Final Research Achievements

NMR isotope shifts caused by the proton/deuteron change were exploited to reveal the relations between the proline isomerase activity of Pin1 and the hydrogen bond network formed in the active site. The isotope shift was used to quantitatively elucidate the changes in the strength of the hydrogen bonds in the network. We made three different mutants having amino acid changes to C113 in the active site of the isomerase domain of Pin1, PPIase. In addition, C138 mutation was applied to see the distal effect on the hydrogen bond network.
Combined the results from the analyses on the different mutants made the role of the hydrogen bond network in the PPIase active site clearer.

Research Products

• [Int'l Joint Research] Academia Sinica/清華大学(台湾)
• [Int'l Joint Research] Lyon1(フランス)
• [Journal Article] Sequential backbone resonance assignments of the E.coli dihydrofolate reductase Gly67Val mutant:folate complex (2016)
  • Author(s): Narayanan,S.P., Maeno,A., Wada,Y., Tate,S., Akasaka,K.
  • Journal Title: Biomol. NMR Assign. Volume: 10 Issue: 1 Pages: 125-129
  • DOI: 10.1007/s12104-015-9650-y
  • Peer Reviewed
• [Journal Article] Allosteric breakage to the hydrogen bond within the dual-histidine motif in the active site of human Pin1 PPIase (2015)
  • Author(s): Wang,J., Tochio,N., Kawasaki,R., Tamari,Y., Xu,N., Uewaki,J., Utsunomiya-Tate,N., Tate,S.
  • Journal Title: Biochemistry Volume: 54 Issue: 33 Pages: 5242-5253
  • DOI: 10.1021/acs.biochem.5b00606
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Coating the outer surface of glass nanopipette with chlorobenzene-terminated polysiloxane (2015)
  • Author(s): Takami,T., Ojiro,Y., Ogawa,S., Takaku,Y., Ogawa,Y., Saito,M., Matuoka,H., Tate,S.
  • Journal Title: e-J.Surf.Sci. Nanotech Volume: 13 Pages: 79-84
  • NAID: 130004933837
  • Peer Reviewed
• [Journal Article] Coating the Outer Surface of Glass Nanopipette with Chlorobenzene-Terminated Polysiloxane (2015)
  • Author(s): T. Takami, Y. Ojiro, Y. Ogawa, S. Ogawa, Y. Takakuwa, M. Saito, H. Matsuoka, S. Tate
  • Journal Title: e-Journal of Surface Science and Nanotechnology Volume: 13 Issue: 0 Pages: 79-84
  • DOI: 10.1380/ejssnt.2015.79
  • NAID: 130004933837
  • ISSN: 1348-0391
  • Peer Reviewed / Open Access
• [Journal Article] The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif (2014)
  • Author(s): Xu,N., Tochio,N., Wang,J., Tamari,Y., Uewaki,J., Utsunomiya-Tate,N., Igarashi,K., Shiraki,T, Kobayashi,N., Tate,S.
  • Journal Title: Biochemistry Volume: 53 Issue: 34 Pages: 5568-5578
  • DOI: 10.1021/bi5007817
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Structural dynamics and their functional implications of the intrinsically disordered regions (IDRs) in transcription regulatory proteins (2015)
  • Author(s): Shin-ichi Tate
  • Organizer: Pacifichem2016
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2015-12-16
  • Int'l Joint Research / Invited
• [Presentation] Structural dynamics and functions of folded and intrinsically disordered proteins (IDPs) (2015)
  • Author(s): Shin-ichi Tate
  • Organizer: Inst. Sciences Analytiques Seminar in Lyon1 Univ.
  • Place of Presentation: Lyon, France
  • Year and Date: 2015-11-29
  • Invited
• [Presentation] Functional significance of the transient folding of intrinsically disordered proteins (IDPs) (2015)
  • Author(s): Shin-ichi Tate
  • Organizer: 第５３回 日本生物物理学会年会
  • Place of Presentation: 金沢
  • Year and Date: 2015-09-13
  • Invited
• [Presentation] How life can be understood by physics and mathematics (2015)
  • Author(s): Shin-ichi Tate
  • Organizer: Inst. Mathematics in Univ. Science and Technology of China
  • Place of Presentation: Shanghai, China
  • Year and Date: 2015-09-03
  • Invited
• [Presentation] Functional significance of the transient folding of intrinsically disordered proteins (IDPs) (2015)
  • Author(s): Shin-ichi Tate
  • Organizer: 第１５回 日本蛋白質科学会年会
  • Place of Presentation: 徳島
  • Year and Date: 2015-06-25
  • Invited
• [Presentation] Functional significance of the transient folding of intrinsically disordered proteins (IDPs) revealed by combinatorial approaches including high-speed AFM, SAXS, molecular dynamics and NMR (2015)
  • Author(s): Shin-ichi Tate
  • Organizer: Gorodn Research Seminar
  • Place of Presentation: Lucca, Italy
  • Year and Date: 2015-06-04
  • Int'l Joint Research / Invited
• [Presentation] Functional significance of the transient folding of intrinsically disordered proteins (IDPs) revealed by the combinatorial approaches (2015)
  • Author(s): Shin-ichi Tate
  • Organizer: Academia Sinica Inviting Seminar
  • Place of Presentation: Taipei, Taiwan
  • Year and Date: 2015-04-11
  • Invited
• [Presentation] 酵素活性部位水素結合ネットワーク中にあるHisの'tug-of-war'による構造安定性変化 (2014)
  • Author(s): 栃尾直哉，Xu Ning，玉利佑，津田亮，楯 真一
  • Organizer: 第５３回NMR討論会
  • Place of Presentation: 大阪
  • Year and Date: 2014-11-04 – 2014-11-06
• [Presentation] プロリン異性化酵素Pin1のドメイン間接触頻度による機能制御 (2014)
  • Author(s): Tochio,N., Kawasaki,R., Tamari,Y., Tate,S.
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2014-09-25 – 2014-09-27
• [Presentation] Transient folding and functional roles of the intrinsically disordered proteins in gene regulatory proteins (2014)
  • Author(s): Shin-ichi Tate
  • Organizer: Gordon Research Conference
  • Place of Presentation: Boston, USA
  • Year and Date: 2014-07-06 – 2014-07-11
  • Invited
• [Presentation] Functional significance of transient folding in the intrinsically disordered proteins (IDPs) (2014)
  • Author(s): Shin-ichi Tate
  • Organizer: Euromar2014
  • Place of Presentation: Zurich, Switzerland
  • Year and Date: 2014-06-29 – 2014-07-03
  • Invited
• [Presentation] ヒストンシャペロンタンパク質HMGB1の酸化型構造のNMR解析 (2014)
  • Author(s): Wang,J., Tochio,N., Takeuchi,A., Uewaki,J., Tate,S.
  • Organizer: 日本生物物理学会 中国四国支部大会
  • Place of Presentation: 鳥取
  • Year and Date: 2014-05-17 – 2014-05-18
• [Presentation] プロリン異性化酵素PIN1と二価型リガンドとの結合様式の解析 (2014)
  • Author(s): 栃尾直哉，玉利佑，楯 真一
  • Organizer: 日本生物物理学会 中国四国支部大会
  • Place of Presentation: 鳥取
  • Year and Date: 2014-05-17 – 2014-05-18
• [Presentation] Structural dynamics intrinsically detuning enzyme action revealed by NMR (2014)
  • Author(s): Shin-ichi Tate
  • Organizer: AnalytiX
  • Place of Presentation: Dalian, China
  • Year and Date: 2014-04-25 – 2014-04-28
  • Invited
• [Remarks] TaleLab Home
  • URL: http://www.mls.sci.hiroshima-u.ac.jp/biophys/index.html
• [Remarks] TateLab Home
  • URL: http://www.mls.sci.hiroshima-u.ac.jp/biophys/index.html
• [Patent(Industrial Property Rights)] ナノピペット及びその作製方法 (2014)
  • Inventor(s): 高見知秀, 楯 真一 他
  • Industrial Property Rights Holder: 高見知秀, 楯 真一 他
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2014-220411
  • Filing Date: 2014-10-29