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- W2775698833 abstract "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." @default.
- W2775698833 created "2017-12-22" @default.
- W2775698833 creator A5050455964 @default.
- W2775698833 creator A5077871434 @default.
- W2775698833 date "2017-12-04" @default.
- W2775698833 modified "2023-10-16" @default.
- W2775698833 title "Energetic funnel facilitates facilitated diffusion" @default.
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- W2775698833 doi "https://doi.org/10.1093/nar/gkx1220" @default.
- W2775698833 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/29216364" @default.
- W2775698833 hasPublicationYear "2017" @default.
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