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Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex
http://hdl.handle.net/10458/0002001267
http://hdl.handle.net/10458/0002001267b45a03dc-80b8-473c-bf0b-8d837875fc11
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
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| アイテムタイプ | 学術雑誌論文 / Journal Article(1) | |||||||||||||||||
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| 公開日 | 2025-05-09 | |||||||||||||||||
| タイトル | ||||||||||||||||||
| タイトル | Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex | |||||||||||||||||
| 言語 | en | |||||||||||||||||
| 言語 | ||||||||||||||||||
| 言語 | eng | |||||||||||||||||
| キーワード | ||||||||||||||||||
| 言語 | en | |||||||||||||||||
| キーワード | Carbohydrate-binding protein | |||||||||||||||||
| キーワード | ||||||||||||||||||
| 言語 | en | |||||||||||||||||
| キーワード | Chito-oligosaccharide | |||||||||||||||||
| キーワード | ||||||||||||||||||
| 言語 | en | |||||||||||||||||
| キーワード | Molecular dynamics simulation | |||||||||||||||||
| キーワード | ||||||||||||||||||
| 言語 | en | |||||||||||||||||
| キーワード | Unbiased ligand docking | |||||||||||||||||
| 資源タイプ | ||||||||||||||||||
| 資源タイプ | journal article | |||||||||||||||||
| アクセス権 | ||||||||||||||||||
| アクセス権 | open access | |||||||||||||||||
| 著者 |
湯井, 敏文
× 湯井, 敏文
WEKO
25220
× 宇都, 卓也
WEKO
21867
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| 抄録 | ||||||||||||||||||
| 内容記述タイプ | Abstract | |||||||||||||||||
| 内容記述 | The ligand-docking behavior of hevein, the major latex protein from the rubber tree Hevea brasiliensis (Euphorbiaceae), has been investigated by the unguided molecular dynamics (MD) simulation method. An oligosaccharide molecule, initially placed in an arbitrary position, was allowed to move around hevein for a prolonged simulation time, on the order of microseconds, with the expectation of spontaneous ligand docking of the oligosaccharide molecule to the binding site of hevein. In the binary solution system consisting of a hevein molecule and a chito-trisaccharide (GlcNAc3) molecule, three out of the six separate simulation runs successfully reproduced the complex structure of the observed binding from. It appeared that the surface topology formed by two aromatic side chains of the hevein molecule played a role in orienting the GlcNAc3 molecule in the correct direction. We also performed MD simulations of the ternary solution system containing a cello-hexasaccharide (Glc6) molecule in addition to hevein and a chito-hexasaccharide (GlcNAc6) molecule. Formation of hevein–GlcNAc6 complex structures was exclusively observed, while the Glc6 molecule remained in the solvent phase throughout the simulations. Obviously, the acetamide groups of GlcNAc play a role in detecting the binding site and its vicinity on the protein surface. | |||||||||||||||||
| 言語 | en | |||||||||||||||||
| 内容記述 | ||||||||||||||||||
| 内容記述タイプ | Other | |||||||||||||||||
| 内容記述 | Citation: Toshifumi Yui, Takuya Uto, Unbiased picture of the ligand docking process for the hevein protein–oligosaccharide complex, Scientific Reports, 15(1), 2025-01-27, https://doi.org/10.1038/s41598-025-87407-8 | |||||||||||||||||
| 言語 | en | |||||||||||||||||
| bibliographic_information |
en : Scientific Reports 巻 15, 号 1, 発行日 2025-01-27 |
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| 出版者 | ||||||||||||||||||
| 出版者 | Springer Science and Business Media LLC | |||||||||||||||||
| 言語 | en | |||||||||||||||||
| ISSN | ||||||||||||||||||
| 収録物識別子タイプ | EISSN | |||||||||||||||||
| 収録物識別子 | 2045-2322 | |||||||||||||||||
| item_10001_relation_14 | ||||||||||||||||||
| 関連タイプ | isVersionOf | |||||||||||||||||
| 識別子タイプ | DOI | |||||||||||||||||
| 関連識別子 | https://doi.org/10.1038/s41598-025-87407-8 | |||||||||||||||||
| 権利 | ||||||||||||||||||
| 権利情報 | © The Author(s) 2025 | |||||||||||||||||
| 言語 | en | |||||||||||||||||
| 出版タイプ | ||||||||||||||||||
| 出版タイプ | VoR | |||||||||||||||||
