2012 | OriginalPaper | Buchkapitel
A Comprehensive Computational Model to Simulate Transcription Factor Binding in Prokaryotes
verfasst von : Nicolae Radu Zabet, Boris Adryan
Erschienen in: Information Processign in Cells and Tissues
Verlag: Springer Berlin Heidelberg
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Site specific transcription factors (TF) are proteins that orchestrate transcription by binding to specific target sites on the DNA. This binding can be both sequence- and conformation-specific. However, also non-specific binding with lower affinity can be observed [3]. The number of specific target sites is significantly smaller compared to the number of non-specific sites and, consequently, TF molecules bind, in a first instance, non-specifically to the DNA. Once bound to the DNA the TF molecules perform an one dimensional random walk on the DNA until they either find a target site or unbind from the DNA template. In particular, during the one dimensional random walk on the DNA, a molecule will perform one of the three types of movements: (
i
) sliding , (
ii
) hopping and (
iii
) jumping [6]. This combination of one and three dimensional diffusion is called
facilitated diffusion
and it is hypothesised that this speeds up the search process [3,2,5].