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Sensitivity of Phage Lambda upon Variations of the Gibbs Free Energy
Author(s) -
Bakk Audun,
Metzler Ralf,
Sneppen Kim
Publication year - 2004
Publication title -
israel journal of chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.908
H-Index - 54
eISSN - 1869-5868
pISSN - 0021-2148
DOI - 10.1560/gb3t-2b64-pfwk-1q96
Subject(s) - repressor , chemistry , lambda , sensitivity (control systems) , operator (biology) , measure (data warehouse) , systematic error , bacteriophage , rna polymerase , dna , gibbs free energy , energy (signal processing) , lambda phage , quantum mechanics , rna , physics , statistics , gene , biochemistry , mathematics , escherichia coli , database , electronic engineering , computer science , transcription factor , engineering
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.