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Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions
https://repository.lib.tottori-u.ac.jp/records/7265
https://repository.lib.tottori-u.ac.jp/records/7265e3104d9d-2eac-4361-a0b3-487c8b79a8ec
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
jmgm51_158.pdf (542.0 kB)
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| Item type | 学術雑誌論文 / Journal Article(1) | |||||
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| 公開日 | 2019-09-19 | |||||
| タイトル | ||||||
| タイトル | Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| キーワード | ||||||
| 主題 | Mononucleotide | |||||
| キーワード | ||||||
| 主題 | Molecular dynamics simulations | |||||
| キーワード | ||||||
| 主題 | 8-oxo-dGTP | |||||
| キーワード | ||||||
| 主題 | Divalent ion | |||||
| キーワード | ||||||
| 主題 | Nucleotide-sanitizing enzyme | |||||
| キーワード | ||||||
| 主題 | Conformation | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | Mononucleotide | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | Molecular dynamics simulations | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | 8-oxo-dGTP | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | Divalent ion | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | Nucleotide-sanitizing enzyme | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | Conformation | |||||
| 資源タイプ | ||||||
| 資源タイプ | journal article | |||||
| 著者 |
Fujiwara, Shin-ichi
× Fujiwara, Shin-ichi× Sawada, Kenichiro× Amisaki, Takashi |
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| 著者所属（英） | ||||||
| 言語 | en | |||||
| 値 | Department of Biological Regulation, Faculty of Medicine, Tottori University | |||||
| 著者所属（英） | ||||||
| 言語 | en | |||||
| 値 | Department of Biological Regulation, Faculty of Medicine, Tottori University | |||||
| 著者所属（英） | ||||||
| 言語 | en | |||||
| 値 | Department of Biological Regulation, Faculty of Medicine, Tottori University | |||||
| 抄録 | ||||||
| 内容記述タイプ | Other | |||||
| 内容記述 | The modified nucleotide base 7,8-dihydro-8-oxo-guanine (8-oxo-G) is one of the major sources of spontaneous mutagenesis. Nucleotide-sanitizing enzymes, such as the MutT homolog-1 (MTH1) and nudix-type motif 5 (NUDT5), selectively remove 8-oxo-G from the cellular pool of nucleotides. Previous studies showed that, although the syn conformation generally predominates in purine nucleotides with a bulky substituent at the 8-position, 8-oxo-dGMP binds to both MTH1 and NUDT5 in the anti conformation. This study was initiated to investigate the possibility that 8-oxo-dGMP itself may adopt the anti conformation. Molecular dynamics simulations of mononucleotides (dGMP, 8-oxo-dGMP) in aqueous solution were performed. 8-oxo-dGMP adopted the anti conformation as well as the syn conformation, and the proportion of adopting the anti conformation increased in the presence of metal ions. When 8-oxo-dGMP was in the anti conformation, a metal ion was located between the oxygen atom of phosphate and the oxygen atom at the 8-position of 8-oxo-G. The types of stable anti conformations of 8-oxo-dGMP differed, depending on the ionic radii and charges of coexisting ions. These data suggested a role for metal ions, other than as cofactors for the hydrolysis of the di- and tri-phosphate forms of mononucleotides; that the metal ions help retain the anti conformation of the N-glycosidic torsion angle of 8-oxo-dGMP to promote the binding between the 8-oxo-G deoxynucleotide and the nucleotide-sanitizing enzymes. | |||||
| 書誌情報 |
Journal of molecular graphics and modelling en : Journal of molecular graphics and modelling 巻 51, p. 158-167, 発行日 2014-06 |
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| 出版者 | ||||||
| 出版者 | Elsevier Inc. | |||||
| ISSN | ||||||
| 収録物識別子タイプ | ISSN | |||||
| 収録物識別子 | 10933263 | |||||
| 書誌レコードID | ||||||
| 収録物識別子タイプ | NCID | |||||
| 収録物識別子 | AA11533349 | |||||
| DOI | ||||||
| 関連タイプ | isVersionOf | |||||
| 識別子タイプ | DOI | |||||
| 関連識別子 | 10.1016/j.jmgm.2014.05.007 | |||||
| 権利 | ||||||
| 権利情報 | Copyright © 2014 Elsevier Inc. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/ | |||||
| 情報源 | ||||||
| 関連名称 | Shin-ichi Fujiwara, Kenichiro Sawada, Takashi Amisaki.. Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions. Journal of molecular graphics and modelling. 2014, 51, 158-167 | |||||
| 関連サイト | ||||||
| 識別子タイプ | URI | |||||
| 関連識別子 | https://www.sciencedirect.com/science/article/pii/S1093326314000801 | |||||
| 関連名称 | https://www.sciencedirect.com/science/article/pii/S1093326314000801 | |||||
| 著者版フラグ | ||||||
| 出版タイプ | AM | |||||
| 出版タイプResource | http://purl.org/coar/version/c_ab4af688f83e57aa | |||||
