2013 Fiscal Year Final Research Report
Theoretical elucidations of the reactions and the reaction-control mechanisms in enzymes
| Project/Area Number |
24750007
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Multi-year Fund |
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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, 数理物質系, 助教 (00593550)
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| Project Period (FY) |
2012-04-01 – 2014-03-31
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| Keywords | QM/MM / 酵素 / 反応機構 / トレオニン合成酵素 / 亜硝酸還元酵素 / 反応制御 / スーパーコンピュータ |
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| Research Abstract |
Enzymes catalyze important chemical reactions in living systems. The enzyme reactions for material formations and energy conversions are highly efficient. Simple reactions are clarified by theoretical analyses, however, complicated reactions in many important enzymes are still unclear. Therefore, reactions of threonine synthase (ThrS), nitrite reductase (NiR), nitric oxide reductase (NOR) and DNA topoisomerase (Topo) are investigated by a mixed quantum mechanical and molecular mechanical (QM/MM) method. We utilized supercomputers and massive parallel simulations were performed. We elucidated the reaction mechanism by investigations for the protonation states, hydrogen-bonding network, existence of waters and possible reaction pathways.
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Research Products
(66 results)
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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(12)
Pages: 4525-4533
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[Presentation] トレオニン合成酵素における反応特異性についての理論的解明2013
Author(s)
庄司光男, 氏家謙, 田中弥, 花岡恭平, 梅田宏明, 栢沼愛, 神谷克政, 白石賢二, 町田康博, 村川武志, 林秀行
Organizer
第86回日本生化学会大会
Place of Presentation
横浜(口頭+ポスター)
Year and Date
20130911-12
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[Presentation] Theoretical Investigation on the Substrate Specificity of Uridine-cytidine Kinase2013
Author(s)
W. Tanaka, Y. Ujiie, K. Hanaoka, M. Shoji, M. Kayanuma, K. Kamiya, T. Ishida, F. Tomoike, S. Kuramitsu, K. Shiraishi
Organizer
ISTCP-8
Place of Presentation
Budapest, Hungary(poster)
Year and Date
2013-08-25
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[Presentation] Molecular dynamics study on the substrate binding free energy of Threonine Synthase2013
Author(s)
Y. Ujiie, W. Tanaka, K. Hanaoka, M. Shoji, M. Kayanuma, K. Kamiya, T. Ishida, K. Shiraishi, Y. Machida, T. Murakawa, H. Hayashi
Organizer
ISTCP-8
Place of Presentation
Budapest, Hungary(poster)
Year and Date
2013-08-25
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[Presentation] トレオニン合成酵素における反応特異性決定過程の理論解明2013
Author(s)
庄司光男, 花岡恭平, 氏家謙, 田中弥, 梅田宏明, 栢沼愛, 神谷克政, 白石賢二, 町田康博, 村川武志, 林秀行
Organizer
蛋白質科学会年会
Place of Presentation
鳥取(口頭(若手奨励賞候補)+ポスター)
Year and Date
2013-06-13
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[Presentation]2013
Author(s)
M. Shoji, K. Hanaoka, Y. Ujiie, W. Tanaka, M. Kayanuma, H. Umeda,Y. Machida, T. Murakawa, H. Hayashi
Organizer
BIT's 4th Symposium on Enzymes and Biocatalysis 2013 (SEB-2013)
Place of Presentation
Nanjing, Chaina(oral)
Year and Date
2013-04-26
Invited
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[Presentation] トレオニン合成酵素におけるリン酸脱離以降の反応機構についての理論的解明2012
Author(s)
庄司光男, 花岡恭平, 近藤大生, 田口真彦, 栢沼愛, 梅田宏明, 鴨志田良和, 神谷克政, 白石賢二, 村川武志, 林秀行
Organizer
第85回日本生化学会大会
Place of Presentation
福岡国際会議場(ポスター)
Year and Date
2012-12-16
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[Presentation]2012
Author(s)
佐藤皓允, 田口真彦, 庄司光男
Organizer
第7回夏の学校宇宙ライフサイエンス若手の会
Place of Presentation
(ポスター発表)
Year and Date
2012-08-25
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