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Sensitivity of Phage Lambda upon Variations of the Gibbs Free Energy

Audun Bakk·Ralf Metzler·Kim Sneppen
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Abstract

We investigate the sensitivity of production rates (activities) of the regulatory proteins CI (repressor) and Cro at the right operator (O_R}) of bacteriophage lambda. The DNA binding energies of CI, Cro, and RNA polymerase are perturbed to check the uncertainty of the activity, due to the experimental error, by means of a computational scattering method according to which the binding energies are simultaneously chosen at random around the literature values, with a width corresponding to the experimental error. In a grand canonical ensemble, with the randomly drawn protein-DNA binding energies as input, we calculate the corresponding activities of the promoters P_RM and P_R. By repeating this procedure we obtain a mean value of the activity that roughly corresponds to wild-type (unperturbed) activity. The standard deviation emerging from this scheme, a measure of the sensitivity due to experimental error, is significant (typically > 20% relative to wild-type activity), but still the promoter activities are sufficiently separated to make the switch feasible. We also suggest a new compact way of presenting repressor and Cro data.

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Audun Bakk, Ralf Metzler, Kim Sneppen. 2003-10-28. Sensitivity of Phage Lambda upon Variations of the Gibbs Free Energy. https://arxiv.org/abs/cond-mat/0310656

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