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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
- 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?
References
- Dennis N. Arvidson,' Michael Shapiro and Philip Youderian. Mutant Tryptophan Aporepressors With Altered Specificities of Corepressor Recognition.Genetics Society of America,1991
- The OR Control System of Bacteriophage Lambda A Physical-Chemical Model for Gene Regulation. Madeline A. Shea and Gary K. Ackersf. J. Mol. Rid. (1985) 181, 211-230
- Mutant Trp Repressors with New DNA-Binding Specificities. STEVEN BASS,* VINCENZA SORRELLS,t PHILIP YOUDERLAN. SCIENCE, VOL. 242.
- In vivo and in vitro Studies of TrpR-DNA Interactions. Jie Yang, Angelo Gunasekera†, Teresa A. Lavoie, Lihua Jin, Dale E. A. Lewis and Jannette Carey. J. Mol. Biol. (1996) 258, 37–52.
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