IGEM:Stanford/2009/Notebook/Marys iGEM Notebook/2009/08/20

Mary's SiGEM Project

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Entries Fitting of 5-methyl-trp and L-trp Binding with Wild Type Repressor <Val58> The reason why we do this fitting is because the set of fitting results for L-trp + wild type repressor doesn't fit in as well for other situations, including trp binding mutant repressor, 5MT binding with wild type or mutant repressor. As shown here:4 different situations of binding The following analysis is based the on assumption that k_R value for 5MT and trp, in each one of the three different models(1-step,2-step,3-step binding of repressor and operator), are the same. Since we're lacking of dissociation constant of a single 5MT binding with one single site of the repressor (R) dimer, the binding process of trp/5MT + R is considered as a one-step process in the following plotting and analysis. The value of k_T (dissociation constant of 2 molecules of trp or 5MT binding to aporepressor dimer) are from papers. The reason why I added in another "2-step binding" model is because, as discussed in some papers, and binding affinity of one of the three binding sites of the operator is really weak. And Reference [1] actually used the 2-step binding model. So I tried it out for comparison. Why none of the three models fit both trp and 5MT perfectly? It's probably due to the following reasons: Inaccurate models Inaccurate k_T values (Plus we're actually implying a one-step trp+repressor model here. It's inaccurate in itself.) Inaccurate k_c values (The k_coupling value is set as 15 in both 2-step and 3-step binding models. kc=40+_15, as shown in [1]. But we're not quite sure it fits with our model.) References 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 Daily Work Goals Project Accomplishments Problems Alternative Solutions Comments Weekly Goals