Abstract
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].
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Barnes, D.J., Chu, D.F.: An efficient model for investigating specific site binding of transcription factors. In: 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE), June 18-20, pp. 1–4. IEEE Xplore, Chengdu (2010)
Benichou, O., Loverdo, C., Moreau, M., Voituriez, R.: Optimizing intermittent reaction paths. Physical Chemistry Chemical Physics 10(47), 7059–7072 (2008)
Berg, O.G., Winter, R.B., von Hippel, P.H.: Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. models and theory. Biochemistry 20(24), 6929–6948 (1981)
Chu, D., Zabet, N.R., Mitavskiy, B.: Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology 257(3), 419–429 (2009)
Halford, S.E.: An end to 40 years of mistakes in dnaprotein association kinetics? Biochemical Society Transactions 37, 343–348 (2009)
Mirny, L., Slutsky, M., Wunderlich, Z., Tafvizi, A., Leith, J., Kosmrlj, A.: How a protein searches for its site on dna: the mechanism of facilitated diffusion. Journal of Physics A: Mathematical and Theoretical 42, 434013 (2009)
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© 2012 Springer-Verlag Berlin Heidelberg
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Zabet, N.R., Adryan, B. (2012). A Comprehensive Computational Model to Simulate Transcription Factor Binding in Prokaryotes. In: Lones, M.A., Smith, S.L., Teichmann, S., Naef, F., Walker, J.A., Trefzer, M.A. (eds) Information Processign in Cells and Tissues. IPCAT 2012. Lecture Notes in Computer Science, vol 7223. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28792-3_6
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DOI: https://doi.org/10.1007/978-3-642-28792-3_6
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