2004 Fiscal Year Final Research Report Summary
Molecular Recognition of Binding Site for the Geometrical Flexibility of Bioactive Ligands
| Project/Area Number |
15590043
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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 pharmacy
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| Research Institution | The University of Tokushima |
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Principal Investigator |
GOTO Satoru University of Tokushima, Institute of Health Bioscience (HBS), Research Associate, 大学院・ヘルスバイオサイエンス研究部, 助手 (50253232)
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| Co-Investigator(Kenkyū-buntansha) |
MUNAKATA Tatsuo Tohwa University, Faculty of Engineerings, Lecturer, 工学部, 講師 (30320261)
TERADA Hiroshi Tokyo University of Science, Faculty of Pharmaceutical Sciences, Professor, 薬学部, 教授 (00035544)
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| Project Period (FY) |
2003 – 2004
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| Keywords | Puckering Coordinates / Manifold / Principle Component Analysis / cyclic compound / cycloalkane / erythromycin / ciguatoxins / conformation analysis |
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| Research Abstract |
The structure changes through the process of the ligand bindings to the binding site of the receptor proteins and the structure of ligand induced a three-dimensional complementarity mutually. The computation of the significant frequency in the statistical thermodynamics when this is analyzed by using the simulation technique of the molecular dynamics method etc. is required.
However, though the equivalent large memory capacity is needed when the network structure data approved by calculating the snap shot of the space covering it when the moment of the space momentarily is caught at 4th Dimension of the combination of an affiliated change at that time with the protein structure, and analyzing those interrelations is analyzed, the calculation load decreases rapidly compared with the repetition of the simulation because the calculation frequency of each route like becoming statistically effective it is finished by the calculation frequency once. A dynamic space in the protein structure of
… More
the protein molecule and the ligand is calculated in the generation of the snap shot of the space covering it at the particular 4th Dimension, and the technique for verifying the spatial combination can be applied.
Then, Conformation of the molecule was generated covering it by calculating Monte Carlo to clarify what one dynamic spaced about a molecular structure, the internal coordinates were constructed, and the system that generated an independent solution space was constructed with the principal ingredient analysis at time. When this calculation result was examined in detail, it was clarified to the compound with the ring structure that the solution space corresponding to the characteristic of the ring structure appeared. Then, a mathematical principle that estimated the topology of the solution space of the material that had a more complex protein structure was clarified by catching the relation between the structure and the solution space as the phase geometrical in three dimension figure. Less
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Author(s)
Nagao, Y., Iimori, H., Honjo, T., Goto, S., Ooi, T., Sano, S., Shiro, M.
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Journal Title
Tetrahedron Letters 45
Pages: 8757-8761
Description
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[Journal Article] New ring-expansion reactions of hydroxy propenoyl cyclic compounds under palladium(0)/phosphine-catalyzed conditions2004
Author(s)
Nagao, Y., Tanaka, S., Ueki, A., Kumazawa, M., Goto, S., Ooi, T., Sano, S., Shiro, M.
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Journal Title
Org.Lett. 24
Pages: 2133-2136
Description
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[Journal Article] Mechanistic considerations for the consecutive cyclization of 2,3-dibromopropylarmine hydrobromide giving a strained molecule, 1-azabicyclo[1.1.0]butane2004
Author(s)
Hayashi, K., Ikee, Y., Goto, S., Shiro, M., Nagao, Y.
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Journal Title
Chem.Pharm.Bull. 52
Pages: 89-94
Description
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[Journal Article] α-Tocopheryl succinate activates protein kinase C in cellular and cell-free systems2003
Author(s)
Kogure, K., Hama, S., Goto, S., Munakata, T., Tokumura, A., Fukuzawa, K.
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Journal Title
J.Nutr.Sci.Vitaminol. 49
Pages: 310-314
Description
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[Journal Article] Synthesis, structure, and reaction of 1-alkynyl(aryl)-λ^3-bromanes2003
Author(s)
Ochiai, M., Nishi, Y., Goto, S., Shiro, M., Frohn, H.J.
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Journal Title
J.Am.Chem.Soc. 125
Pages: 15304-15305
Description
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[Journal Article] Two lignan dimmers from bamboo stems (Phyllostachys edulis).2003
Author(s)
Suga, A., Takaishi, Y., Goto, S., Munakata, T., Yamauchi, I., Kogure, K.
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Journal Title
Phytochemistry 64
Pages: 991-996
Description
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[Journal Article] Secondary hypervalent I (III)【triple bond】O interactions : Synthesis and structure of hypervalent complexes of diphenyl-λ^3-iodanes with 18-crown-62003
Author(s)
Ochiai, M., Suefuji, T., Miyamoto, K., Tada, N., Goto, S., Shiro, M., Sakamoto, S., Yamaguchi, K.
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Journal Title
J.Am.Chem.Soc. 125
Pages: 769-773
Description
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