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