IGEM:Stanford/2009/Notebook/Marys iGEM Notebook/2009/08/13

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Mary's SiGEM Project
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Stuffs we need to find out for the new trp model
'''If you know anything about these, please put it right after the list, or in "comments". Thanks^^''' Let's start with wild type system--
 * kt or ΔG :dissociation constant/Gibbs free energy of WT aporepressor binding with one single L-tryptophan (there are two binding sites in all).
 * Alternative solutions: find out through fitting with equations based on plots in [1], but need to build out the whole system model first.
 * On WT repressor and WT operator binding, I borrowed several assumptions in [2], and need to check out whether it's the same situation for the trp system:
 * (1) The three binding sites are specific, nonoverlapping, DNA sequences; each site binds one repressor at a time.
 * (2) Repressors are bound at the operator sites in their dimeric forms only. Repressor monomers are in equilibrium with dimers.
 * (3) There are no co-operative interactions between WT repressor dimers and any other mutant repressors, including adjacent operator bound mutant repressors. (Is it true???)
 * (4) At an operator with three bound repressor dimers, co-operative interactions only happens between two of them. (Is it true???)
 * (5) What effect does RNA polymerase binding promoter have on WT repressor binding operator? (Need to find out...)
 * (6) Occupancy of operator sites is determined by equilibrium statistical thermodynamic probabilities. (This is the basis of our model, especially on cooperativity.)
 * Thus, it's important to find out the follow values:
 * Gibbs free energy (ΔG) or dissociation constant of every single operator binding site bound with WT repressor.(ΔG_1, ΔG_2, ΔG_3)
 * Coupling free energy between adjacent bound repressors.(ΔG_12, ΔG_23)

As for the mutant system, it's much the same--
 * Data needed for the 5MT binding Leu58 trp-repressor model
 * kt value or ΔG
 * Data needed for the trp-repressor binding trp operator cooperativity model
 * Gibbs free energy (ΔG) or dissociation constant of every single binding site bound with wt-repressor and Lys79 repressor
 * Alternative solutions: estimation based on data in [3], but need to build out the whole system model first.
 * For instance, ΔG of 7C(one of the mutant operator binding sites) bound with Lys79(mutant repressor binding site)
 * Already know the coupling free energy between adjacent Lys79 repressors, which is ~−2 kcal/mol ([4]). Is there cooperativity between adjacent WT and mutant repressor?

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