An application of computational geometry to solution theory of biomolecule association
| Project/Area Number |
14540473
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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 |
Physical chemistry
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| Research Institution | Kyushu Institute of Technology |
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Principal Investigator |
IRISA Masayuki Kyushu Institute of Technology, Faculty of Computer Science and Systems Engineering, associate professor, 情報工学部, 助教授 (60284600)
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| Project Period (FY) |
2002 – 2005
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| Project Status |
Completed (Fiscal Year 2005)
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| Budget Amount *help |
¥3,000,000 (Direct Cost: ¥3,000,000)
Fiscal Year 2005: ¥600,000 (Direct Cost: ¥600,000)
Fiscal Year 2004: ¥600,000 (Direct Cost: ¥600,000)
Fiscal Year 2003: ¥900,000 (Direct Cost: ¥900,000)
Fiscal Year 2002: ¥900,000 (Direct Cost: ¥900,000)
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| Keywords | macromolecular crowding / protein / actin / SPT / FMT / alpha shape / excluded volume effect / dimmer / 水和 / エントロピー / 熱容量 / ボロノイ図 / ドロネー図 / αシェイプ / scaled particle theory / 溶液理論 / 排除体積 / 会合 / モーター蛋白質 / フィラメント形成 / アルファシェイプ / 凸包 / ボロノイ図形 / 生体高分子 / 溶液 / 計算幾何学 / 浸透圧 / fused spheres / 剛体球 |
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| Research Abstract |
Actin molecules, which have functions in cell movement, spontaneously associates to form actin filament at high salt concentration in aquerous solution. Potential of mean force originated from macromolecular crowding was calculated by using extended scaled particle theory (XSPT), which is one of the solution theories. Calculated results show that the most stable configuration of actin dimmer is the one believed from small angle X-ray scattering. At high concentration (packing fraction >0.6) of crowding agents, actin monomers, the most stable configuration of actin dimmer in calculation was the same as that of longitudinal adjacent two molecules in actin filaments and different from that in aquerous solution. Therefore, we cannot distinguish the effect of macromolecular crowding effect by the order of excluded volumes at various configurations. In our methods, alpha shape method in computational geometry was used in analytical derivation of a excluded volume function of scaling parameter. The alpha shape method enabled XSPT to incorporate difference of both configuration of a dimmer and 3-D structure of an actin molecule. In this work, we found Fundamental measure theory (FMT), which is one of the density functional theories, and XSPT differ only one term in the analytical expression of the potential of mean force. Potentials of mean force originated from macromolecular crowding effect by using two methods, FMT and XSPT, sandwiches the true value when the alpha shape method is also applied to FMT.
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Report
(5 results)
Research Products
(12 results)
