| Project/Area Number |
14598001
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
ポストゲノムのナノサイエンス
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| Research Institution | Hirosaki University |
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Principal Investigator |
SAITO Minoru Hirosaki University, Faculty of Science and Technology, Professor, 理工学部, 教授 (60196011)
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| Project Period (FY) |
2002 – 2003
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| Project Status |
Completed (Fiscal Year 2003)
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| Budget Amount *help |
¥2,200,000 (Direct Cost: ¥2,200,000)
Fiscal Year 2003: ¥800,000 (Direct Cost: ¥800,000)
Fiscal Year 2002: ¥1,400,000 (Direct Cost: ¥1,400,000)
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| Keywords | computer experiment / DNA binding protein / binding affinity / free energy calculation / MD simulation / molecular substitution / DNA / 塩基配列 / 塩基置換 / 塩基配列の認識 / 蛋白質 / 結合自由エネルギー |
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| Research Abstract |
The purpose of this study was to calculate binding affinity between a DNA binding protein and a DNA by expanding my methodology(computational mutation→MD simulation→free energy calculation) which was developed to calculate unfolding free energy differences between a wild type protein and mutant proteins. Another purpose is to clarify the molecular mechanism of the base sequence recognition by DNA binding proteins using the developed method. To complete the purpose, I made it possible to substitute a DNA base to other bases for the simple case, i.e., thymine→uracil substitution. We calculated the binding free energy change due to the thymine→uracil substitution for the DNA-λ-repressor complex. The calculated value(1.5kcal/mol) was in good agreement with the respective experimental value(1.8kcal/mol). We clarified how the λ-repressor recognizes such small difference between thymine→uracil on the atomic level details.
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