Theoretical Analysis of Enzymatic Functions based on Hybrid-Computational Modeling
| Project/Area Number |
19750021
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Single-year Grants |
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| Research Field |
Physical chemistry
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| Research Institution | National Institute of Advanced Industrial Science and Technology |
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Principal Investigator |
ISHIDA Toyokazu National Institute of Advanced Industrial Science and Technology, 計算科学研究部門, 研究員 (70443166)
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| Project Period (FY) |
2007 – 2009
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| Project Status |
Completed (Fiscal Year 2009)
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| Budget Amount *help |
¥4,000,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥300,000)
Fiscal Year 2009: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2008: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2007: ¥2,700,000 (Direct Cost: ¥2,700,000)
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| Keywords | 酵素反応 / 生体化学反応論 / 電子状態 / 分子動力学 / QM / MM計算 / 電子状態計算 / 分子動カ学計算 / 自由エネルギー計算 / FMO計算 / Chorismate Mutase / 糖鎖認識 / 分子動力学計算 / MM法 / FMO法 / 酸素反応 / 基質認識 / ODCase / FMO 法 |
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| Research Abstract |
Owing to the rapid progress of computational architecture and the advance of new chemical theories for treating large molecular systems, understanding complex chemical reactions in the condensed phase is becoming one of the important issues in modern theoretical chemistry. Before the mid 90's, mainly due to a lack of computational power, the major target of quantum chemistry was limited to simple chemical reactions in the gas phase. At present, however, various types of chemical reactions in the condensed phase (e.g.reactions in solutions, on surfaces, inside proteins, and so on) have become realistic targets for theoretical and computational studies.
In the field of biochemistry, understanding the nature of enzyme functions at atomistic level is one of the most important issues. Despite the intensive work over past decades, however, there is still no quantitative understanding of how enzymes work. Now, understanding the structure-function relationships of enzyme reactions is becoming a more and more important problem. In this research project, we developed a hybrid QM/MM modeling procedure combined with MD simulations and all-electron QM calculations for the entire protein matrix. By selecting typical protein systems, we then performed a systematic computational analyses based on QM/MM computations and discussed the major catalytic factors in typical enzyme reactions.
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Report
(4 results)
Research Products
(42 results)
