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Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site
https://doi.org/10.24517/00055867
https://doi.org/10.24517/000558676ada1667-6e15-4013-b5de-c93b7d9ab6e5
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
Sci_Rep63-002.pdf (1.9 MB)
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| Item type | 紀要論文 / Departmental Bulletin Paper(1) | |||||
|---|---|---|---|---|---|---|
| 公開日 | 2019-10-21 | |||||
| タイトル | ||||||
| タイトル | Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site | |||||
| 言語 | en | |||||
| タイトル | ||||||
| タイトル | Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題Scheme | Other | |||||
| 主題 | CA I active site | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題Scheme | Other | |||||
| 主題 | ligand molecule | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題Scheme | Other | |||||
| 主題 | force field parameters | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題Scheme | Other | |||||
| 主題 | free energy profile | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題Scheme | Other | |||||
| 主題 | free energy surface | |||||
| 資源タイプ | ||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
| 資源タイプ | departmental bulletin paper | |||||
| ID登録 | ||||||
| ID登録 | 10.24517/00055867 | |||||
| ID登録タイプ | JaLC | |||||
| 著者 |
Arwansyah, MS
× Arwansyah, MS× Kodama, Koichi× Kurniawan, Isman× Kataoka, Tatsuki× Kawaguchi, Kazutomo× Nagao, Hidemi |
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| 著者別表示 |
川口, 一朋
× 川口, 一朋× 長尾, 秀実 |
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| 書誌情報 |
The Science Reports of Kanazawa University en : The Science Reports of Kanazawa University 巻 63, p. 15-28, 発行日 2019 |
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| ISSN | ||||||
| 収録物識別子タイプ | ISSN | |||||
| 収録物識別子 | 2433-040X | |||||
| 出版者 | ||||||
| 出版者 | Institute of Science and Engineering, Kanazawa University | |||||
| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | We investigate the binding/dissociation process of ligand molecule from carbonic anhydrase (CA) I carbonic anhydrase (CA) I enzyme by using all-atom molecular dynamics simulation. The force field parameters of zinc ion in the CA I active site are estimated by quantum chemical calculations and are summarized in this paper. The free energy profile for binding/dissociation process of ligand from CA I active site is calculated by the thermodynamic integration combined with the all-atom molecular dynamics simulation. The binding free energy as a function of the distance between the center of mass positions of CA I active site and the ligand molecule is estimated. The radial distribution function of the CA I-ligand complex is calculated from the trajectory of all-atom molecular dynamics (MD) simulation. We estimate the free energy surface from the radial distribution function. We can obtain the bond constant of the equilibrium state from the value of the free energy surface. We discuss the binding/dissociation process of ligand molecule by calculating the free energy profile to know the stability of the CA I-ligand complex with some thermodynamic properties such as the binding free energy, the equilibrium state of the free energy surface and so on. |
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| 著者版フラグ | ||||||
| 出版タイプ | VoR | |||||
| 出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |||||
| 関連URI | ||||||
| 識別子タイプ | URI | |||||
| 関連識別子 | http://scirep.w3.kanazawa-u.ac.jp/ | |||||
| 関連名称 | http://scirep.w3.kanazawa-u.ac.jp/ | |||||
