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A Comprehensive Computational Model to Simulate Transcription Factor Binding in Prokaryotes

  • Nicolae Radu Zabet
  • Boris Adryan
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7223)

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].

Keywords

Search Process Specific Target Site Downing Street Physical Chemistry Chemical Physic Ideal Entry Point 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    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)CrossRefGoogle Scholar
  2. 2.
    Benichou, O., Loverdo, C., Moreau, M., Voituriez, R.: Optimizing intermittent reaction paths. Physical Chemistry Chemical Physics 10(47), 7059–7072 (2008)CrossRefGoogle Scholar
  3. 3.
    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)CrossRefGoogle Scholar
  4. 4.
    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)CrossRefGoogle Scholar
  5. 5.
    Halford, S.E.: An end to 40 years of mistakes in dnaprotein association kinetics? Biochemical Society Transactions 37, 343–348 (2009)CrossRefGoogle Scholar
  6. 6.
    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)MathSciNetCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Nicolae Radu Zabet
    • 1
    • 2
  • Boris Adryan
    • 1
    • 2
  1. 1.Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
  2. 2.Department of GeneticsUniversity of CambridgeCambridgeUK

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