2012 Fiscal Year Final Research Report
Development of computational method of solvation dynaics and the application to ATP hydrolysys
| Project Area | Water plays a key role in ATP hydrolysis and ATP-driven functions of proteins |
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| Project/Area Number |
20118003
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| Research Category |
Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
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| Allocation Type | Single-year Grants |
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| Review Section |
Complex systems
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| Research Institution | Ritsumeikan University |
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Principal Investigator |
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| Project Period (FY) |
2008 – 2012
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| Keywords | 水和 / MD / QM / ハイパーモバイル水 / ダイナミクス / 水モデル / ATP 加水分解 / イオン |
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| Research Abstract |
Various functions that describe the dynamics change of the system in each step of the ATP hydrolysis (rotational relaxation time and self-diffusion coefficient) were calculated and in some case faster movement of water than bulk water was found. Around monoatomic ions, we confirmed that the combination of conventional ion and water model parameters could not reproduce faster movement of water than bulk. Therefore, we developed a new water model based on the TIP5P water model, and reproduced the faster movement of water around monoatomic ions. We also performed xhaustive calculations for polyphosphate molecules including the study of electronic states for the force field improvements. We developed computational techniques for high-speed calculation of solvent effects on macromolecules such as proteins, and quantitative evaluation of the molecular interactions was achieved.
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