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  1. B100 理学部/理学研究科
  2. B100a 雑誌掲載論文
  3. 学術雑誌

Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations

http://hdl.handle.net/2237/00029132
http://hdl.handle.net/2237/00029132
2ac88d00-530e-423c-9347-f339303c19b3
名前 / ファイル ライセンス アクション
1_5019209.pdf 1_5019209 (2.5 MB)
Item type 学術雑誌論文 / Journal Article(1)
公開日 2018-12-21
タイトル
タイトル Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations
言語 en
著者 Tsukamoto, Shuichiro

× Tsukamoto, Shuichiro

WEKO 88234

en Tsukamoto, Shuichiro

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Sakae, Yoshitake

× Sakae, Yoshitake

WEKO 88235

en Sakae, Yoshitake

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Itoh, Yukihiro

× Itoh, Yukihiro

WEKO 88236

en Itoh, Yukihiro

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Suzuki, Takayoshi

× Suzuki, Takayoshi

WEKO 88237

en Suzuki, Takayoshi

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Okamoto, Yuko

× Okamoto, Yuko

WEKO 88238

en Okamoto, Yuko

Search repository
アクセス権
アクセス権 open access
アクセス権URI http://purl.org/coar/access_right/c_abf2
権利
言語 en
権利情報 Copyright 2018 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing.The following article appeared in (The Journal of Chemical Physics. v.148, n.12, 2018, p.125102) and may be found at (http://dx.doi.org/10.1063/1.5019209).
抄録
内容記述 We performed protein-ligand docking simulations with a ligand T247, which has been reported as a selective inhibitor of a histone deacetylase HDAC3, by the replica-exchange umbrella sampling method in order to estimate the free energy profiles along ligand docking pathways of HDAC3-T247 and HDAC2-T247 systems. The simulation results showed that the docked state of the HDAC3-T247 system is more stable than that of the HDAC2-T247 system although the amino-acid sequences and structures of HDAC3 and HDAC2 are very similar. By comparing structures obtained from the simulations of both systems, we found the difference between structures of hydrophobic residues at the entrance of the catalytic site. Moreover, we performed conventional molecular dynamics simulations of HDAC3 and HDAC2 systems without T247, and the results also showed the same difference of the hydrophobic structures. Therefore, we consider that this hydrophobic structure contributes to the stabilization of the docked state of the HDAC3-T247 system. Furthermore, we show that Tyr209, which is one of the hydrophobic residues in HDAC2, plays a key role in the instability from the simulation results of a mutated-HDAC2 system.
言語 en
内容記述タイプ Abstract
出版者
言語 en
出版者 AIP Publishing
言語
言語 eng
資源タイプ
資源タイプresource http://purl.org/coar/resource_type/c_6501
タイプ journal article
出版タイプ
出版タイプ VoR
出版タイプResource http://purl.org/coar/version/c_970fb48d4fbd8a85
DOI
関連タイプ isVersionOf
識別子タイプ DOI
関連識別子 https://doi.org/10.1063/1.5019209
ISSN(print)
収録物識別子タイプ PISSN
収録物識別子 0021-9606
書誌情報 en : The Journal of Chemical Physics

巻 148, 号 12, p. 125102, 発行日 2018-03-28
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