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

From OpenWetWare
Jump to: navigation, search
Owwnotebook icon.png Mary's SiGEM Project <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>      </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>


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.

L-trp(and 5MT)with WT Repressor.jpg
5MT (and L-trp)with WT Repressor.jpg
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:
  1. Inaccurate models
  2. Inaccurate k_T values (Plus we're actually implying a one-step trp+repressor model here. It's inaccurate in itself.)
  3. 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.)


  1. 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





Alternative Solutions


Weekly Goals