Theoretical elucidation on the full reaction mechanisms of threonine synthase
| Project/Area Number |
26410002
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Physical chemistry
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| Research Institution | University of Tsukuba |
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Principal Investigator |
SHOJI MITSUO 筑波大学, 計算科学研究センター, 助教 (00593550)
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| Co-Investigator(Renkei-kenkyūsha) |
HAYASHI HIDEYUKI 大阪医科大学, 医学部, 教授 (00183913)
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| Research Collaborator |
UJIIE YUZURU 筑波大学, 数理物質系
TANAKA WATARU 筑波大学, 数理物質系
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| Project Period (FY) |
2014-04-01 – 2017-03-31
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| Project Status |
Completed (Fiscal Year 2016)
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| Budget Amount *help |
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2016: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2015: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2014: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
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| Keywords | トレオニン合成酵素 / 反応機構 / 生成物支援機構 / QM/MM / molecular dynamics / 自由エネルギー / スパコン / 反応制御 / 反応制御機構 / 副反応経路 / molecular dynamics (MD) / スーパーコンピュータ / 量子古典混合計算 / 酵素反応 |
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| Outline of Final Research Achievements |
Reaction mechanisms of the threonine synthase (ThrS) were theoretically investigated by using the mixed quantum mechanics/molecular mechanics (QM/MM) and classical molecular dynamics methods. By utilizing the supercomputers, long time scale CMD (total 3 micro sec) were performed and important protein-substrate interactions and free energy changes were elucidated. Significantly, conformational changes on the active site molecules (PLP, water and amino acid residues) were observed depending on the intermediate states. It was also shown that the anion important for the product assisted mechanism plays important role to construct active site conformations. These results clearly indicate that precise structural controls optimized for the reactions are performed in ThrS. This reaction control mechanism provides valuable insights for other reaction mechanisms and functional modifications.
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Report
(4 results)
Research Products
(54 results)
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[Journal Article] Molecular mechanisms of substrate specificities of uridine-cytidine kinase2016
Author(s)
W. Tanaka, M. Shoji, F. Tomoike, Y. Ujiie, K. Hanaoka, R. Harada, M. Kayanuma, K. Kamiya, T. Ishida, R. Masui, S. Kuramitsu, Y. Shigeta
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Journal Title
BIOPHYSICS
Volume: 13
Issue: 0
Pages: 77-84
DOI
NAID
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Peer Reviewed
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[Journal Article] A QM/MM Study of the l-Threonine Formation Reaction of Threonine Synthase: Implications into the Mechanism of the Reaction Specificity2014
Author(s)
M.Shoji, K.Hanaoka, Y.Ujiie, W.Tanaka, D.Kondo, H.Umeda, Y.Kamoshida, M.Kayanuma, K.Kamiya, K.Shiraishi,Y.Machida, T.Murakawa, H.Hayashi
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Journal Title
Journal of the American Chemical Society
Volume: 136
Related Report
Peer Reviewed
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[Presentation] QM/MM study on the L-threonine formation reaction of threonine synthase2014
Author(s)
Mitsuo Shoji, Yuzuru Ujiie, Wataru Tanaka, Megumi Kayanuma, Ryuhei Harada, Hiroaki Umeda, Yasuteru Shigeta, Takeshi Murakawa, Hideyuki Hayashi
Organizer
QSCP XIX
Place of Presentation
Tamkang University, Taipei, Taiwan
Year and Date
2014-11-11 – 2014-11-17
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