Zabet, Nicolae Radu and Adryan, Boris (2012) Computational models for large-scale simulations of facilitated diffusion. Molecular BioSystems, 8 (11). p. 2815. DOI https://doi.org/10.1039/c2mb25201e
Zabet, Nicolae Radu and Adryan, Boris (2012) Computational models for large-scale simulations of facilitated diffusion. Molecular BioSystems, 8 (11). p. 2815. DOI https://doi.org/10.1039/c2mb25201e
Zabet, Nicolae Radu and Adryan, Boris (2012) Computational models for large-scale simulations of facilitated diffusion. Molecular BioSystems, 8 (11). p. 2815. DOI https://doi.org/10.1039/c2mb25201e
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: | Unnamed user with email elements@essex.ac.uk |
Depositing User: | Unnamed user with email elements@essex.ac.uk |
Date Deposited: | 03 Nov 2015 14:53 |
Last Modified: | 30 Oct 2024 16:10 |
URI: | http://repository.essex.ac.uk/id/eprint/15112 |
Available files
Filename: review_v3.pdf