Entries
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 Ltryptophan (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 cooperative 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, cooperative 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 trprepressor model
 Data needed for the trprepressor binding trp operator cooperativity model
 Gibbs free energy (ΔG) or dissociation constant of every single binding site bound with wtrepressor 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 PhysicalChemical Model for Gene Regulation. Madeline A. Shea and Gary K. Ackersf. J. Mol. Rid. (1985) 181, 211230
 Mutant Trp Repressors with New DNABinding Specificities. STEVEN BASS,* VINCENZA SORRELLS,t PHILIP YOUDERLAN. SCIENCE, VOL. 242.
 In vivo and in vitro Studies of TrpRDNA Interactions. Jie Yang, Angelo Gunasekera†, Teresa A. Lavoie, Lihua Jin, Dale E. A. Lewis and Jannette Carey. J. Mol. Biol. (1996) 258, 37–52.
Daily Work
Goals
Project
Accomplishments
Problems
Alternative Solutions
Weekly Goals
