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Computational models for large-scale simulations of facilitated diffusion

Zabet, Nicolae Radu and Adryan, Boris (2012) 'Computational models for large-scale simulations of facilitated diffusion.' Molecular BioSystems, 8 (11). p. 2815. ISSN 1742-206X

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Abstract

The binding of site-specific transcription factors to their genomic target sites is a key step in gene regulation. While the genome is huge, transcription factors belong to the least abundant protein classes in the cell. It is therefore fascinating how short the time frame is that they require to home in on their target sites. The underlying search mechanism is called facilitated diffusion and assumes a combination of three-dimensional diffusion in the space around the DNA combined with one-dimensional random walk on it. In this review, we present the current understanding of the facilitated diffusion mechanism and identify questions that lack a clear or detailed answer. One way to investigate these questions is through stochastic simulation and, in this manuscript, we support the idea that such simulations are able to address them. Finally, we review which biological parameters need to be included in such computational models in order to obtain a detailed representation of the actual process. © 2012 The Royal Society of Chemistry.

Item Type: Article
Uncontrolled Keywords: Animals; Humans; Transcription Factors; Binding Sites; Protein Binding; Computer Simulation; Facilitated Diffusion
Subjects: Q Science > QC Physics
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health
Faculty of Science and Health > Life Sciences, School of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 03 Nov 2015 14:53
Last Modified: 18 Aug 2022 12:10
URI: http://repository.essex.ac.uk/id/eprint/15112

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