Theoretical Studies on reactions in biological molecules
| Project/Area Number |
11166247
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas (A)
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| Allocation Type | Single-year Grants |
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| Review Section |
Science and Engineering
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| Research Institution | Hiroshima University |
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Principal Investigator |
AIDA Misako Graduate School of Science, Professor, 大学院・理学研究科, 教授 (90175159)
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| Co-Investigator(Kenkyū-buntansha) |
青木 百合子 広島大学, 理学部, 助教授 (10211690)
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| Project Period (FY) |
1999 – 2001
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| Project Status |
Completed (Fiscal Year 2001)
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| Budget Amount *help |
¥11,500,000 (Direct Cost: ¥11,500,000)
Fiscal Year 2001: ¥1,000,000 (Direct Cost: ¥1,000,000)
Fiscal Year 2000: ¥4,000,000 (Direct Cost: ¥4,000,000)
Fiscal Year 1999: ¥6,500,000 (Direct Cost: ¥6,500,000)
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| Keywords | ab initio MD method / OM / MM method / hydration energy / ab initio MO method / hydrogen bonding interaction / specific interaction / nucleic acid bases / 蛋白質 / 水和エネルギー / 加水分解反応 / 分子動力学法 / MM-vib法 / 生体高分子 / 特異的相互作用 / 水クラスター / 溶液内反応 |
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| Research Abstract |
Structural data of protein-DNA complex show redundancy and flexibility in base-amino acid interactions. To understand the origin of the specificity in protein-DNA recognition, we calculated the interaction free-energy, enthalpy, entropy and minimum energy maps for AT-Asn, GC-Asn, AF-Ser and GC-Ser by means of a set of ab initio force field with extensive conformational sampling. We found that the most preferable interactions in these pairs are stabilized by hydrogen bonding, and are mainly enthalpy-driven. However, minima in the free energy maps are not necessarily the same as minimum energy map or enthalpy maps, doe to the entrppic effect The effect of entropy is important in the case of GC-Asn. Experimentally observed structures of base-amino acid within preferable regions in the calculated free energy maps, where there are many different configurations with similar energy. The full geometry optimization procedure using ab initio molecular orbital method was applied to get the optimal interaction geometries for AT-Asn, GC-Asn, AF-Ser and GC-Ser. We found that mere are various base-amino acid combinations with similar interaction energies. These results suggest that the redundancy and conformational flexibility in the base-amino acid interactions play an important role in the protein-DNA recognition.
Using QM/MM method, we showed that the stable structures (local minima) of molecules in the gas phase are different from those in aqueous solution : a local minimum in the gas phase is not minimum structure in the aqueous solution. It is very important to take account of the solvent explicitly in the calculations. We analyzed how molecules change their conformations by initio MD method.
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Report
(4 results)
Research Products
(11 results)
