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Energetic funnel facilitates facilitated diffusion
https://oist.repo.nii.ac.jp/records/351
https://oist.repo.nii.ac.jp/records/3517db3efe0-3e2a-4c10-90ca-9d8b65f284d5
名前 / ファイル | ライセンス | アクション |
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gkx1220 (489.3 kB)
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Creative Commons Attribution-Non-Commercial 4.0 International
(http://creativecommons.org/licenses/by-nc/4.0/) |
Item type | 学術雑誌論文 / Journal Article(1) | |||||
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公開日 | 2018-04-06 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Energetic funnel facilitates facilitated diffusion | |||||
言語 | ||||||
言語 | eng | |||||
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 | journal article | |||||
著者(英) |
Cencini, Massimo
× Cencini, Massimo× Pigolotti, Simone |
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書誌情報 |
en : Nucleic Acids Research 巻 46, 号 2, p. 558-567, 発行日 2017-12-04 |
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抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | Transcription factors (TFs) are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional sliding along the DNA chain, a mechanism-dubbed facilitated diffusion. By studying a collection of TF binding sites of Escherichia coli from the RegulonDB database and of Bacillus subtilis from DBTBS, we reveal a funnel in the binding energy landscape around the target sequences. We show that such a funnel is linked to the presence of gradients of AT in the base composition of the DNA region around the binding sites. An extensive computational study of the stochastic sliding process along the energetic landscapes obtained from the database shows that the funnel can significantly enhance the probability of TFs to find their target sequences when sliding in their proximity. We demonstrate that this enhancement leads to a speed-up of the association process. | |||||
出版者 | ||||||
出版者 | Oxford University Press | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 0305-1048 | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/29216364 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1093/nar/gkx1220 | |||||
権利 | ||||||
権利情報 | ©2017 Authors | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://academic.oup.com/nar/article/46/2/558/4690584 | |||||
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 |