Molecular Dynamics Study of the Hydrogen-Bond Kinetics of Protein Hydration Water
| Project/Area Number |
23740321
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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 |
Biophysics/Chemical physics
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| Research Institution | Japan Atomic Energy Agency |
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Principal Investigator |
YONETANI Yoshiteru 独立行政法人日本原子力研究開発機構, 量子ビーム応用研究部門, 研究副主幹 (80399419)
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| Project Period (FY) |
2011 – 2012
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| Project Status |
Completed (Fiscal Year 2012)
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| Budget Amount *help |
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2011: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
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| Keywords | 水 / 水素結合 / 生体分子 / 蛋白質 / 核酸 / 分子動力学 / タンパク質 / 分子動力学計算 |
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| Research Abstract |
The lifetime during which a water molecule resides at the surface of a biomolecule varies according to the hydration site. What determines this variety of lifetimes? Despite many previous studies, there is still no uniform picture quantitatively explaining this phenomenon. Here we calculate the lifetime for a particular hydration pattern, the water bridge, to show that the water-bridge lifetime varies from 1 to ~300 ps. We find that it follows 1/k(V_<step>)Pm, where Pm and V_<step> are two crucial factors, namely the probability of forming a specific hydrogen bond in which more than one donor atom participates, and the structural fluctuation of the hydration site, respectively. This relationship provides a picture of the hydrogen bond kinetics with atomistic detail and shows that hydrogen bond switching occurs when a particular hydrogen-bonding pattern appears. The rate constant of hydrogen bond switching k can be described as a function of the structural fluctuations of the hydration site.
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Report
(3 results)
Research Products
(11 results)
