Difference between revisions of "Team:TU-Eindhoven/Results/Model"
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<h1>Results description</h1> | <h1>Results description</h1> | ||
| − | In the <a href="#Figure_1">Figure 1</a> you can see that we used excess of the Inducers, as there is a decrease of the amount, but after a while stays at the same amount. This is because all the pockets of the scaffold construct are already filled with the inducer. Data supporting the inducer excess is also shown in the figure, as the amount of empty scaffold sites decreases as fast as the inducer. Furthermore, we see that the induced scaffold sites are very high in the beginning. Our initial state is defines as that the induced amount of scaffold sites starts at 0, this is also the case if you look closely to the data, but it increases so fast, that it isn’t visible in a logarithmic time axis. Another thing that stands out in the graph, is that the green graph (the one of the Binding Sites for the CenterPoint) isn’t visible in the figure, this is because these values are about the same as the ones of the CenterPoint Sites. They decrease with the same rate, because they both are used for the formation of a bond to create a complex and have about the same initial amount. Another thing that supports the graph is that the sum of the Induced Scaffold Sites and the Empty Scaffold sites is comparable with the dark blue graph (Binding Sites for Scaffold). The decrease of the dark blue graph means that there are bonds formed between the Scaffold and the Binding Partner. </br></br> | + | </h6>In the <a href="#Figure_1">Figure 1</a> you can see that we used excess of the Inducers, as there is a decrease of the amount, but after a while stays at the same amount. This is because all the pockets of the scaffold construct are already filled with the inducer. Data supporting the inducer excess is also shown in the figure, as the amount of empty scaffold sites decreases as fast as the inducer. Furthermore, we see that the induced scaffold sites are very high in the beginning. Our initial state is defines as that the induced amount of scaffold sites starts at 0, this is also the case if you look closely to the data, but it increases so fast, that it isn’t visible in a logarithmic time axis. Another thing that stands out in the graph, is that the green graph (the one of the Binding Sites for the CenterPoint) isn’t visible in the figure, this is because these values are about the same as the ones of the CenterPoint Sites. They decrease with the same rate, because they both are used for the formation of a bond to create a complex and have about the same initial amount. Another thing that supports the graph is that the sum of the Induced Scaffold Sites and the Empty Scaffold sites is comparable with the dark blue graph (Binding Sites for Scaffold). The decrease of the dark blue graph means that there are bonds formed between the Scaffold and the Binding Partner. </br></br> |
<div class="Figure_1"><img src="https://static.igem.org/mediawiki/2017/c/c8/T--TU-Eindhoven--Model_result_fig2.png" width="500" height="375" alt="Figure_2_of_model_part" /> | <div class="Figure_1"><img src="https://static.igem.org/mediawiki/2017/c/c8/T--TU-Eindhoven--Model_result_fig2.png" width="500" height="375" alt="Figure_2_of_model_part" /> | ||
Revision as of 09:15, 1 November 2017
Used Parameters
Before we could generate results with the model, we had to define some parameter, like concentrations and Kd-values. The Kd-values we could find in the paper of den Hamer (2017) and appeared to be 66 uM for the Inducer to the scaffold, 1 uM for the Binding Partner with the Center Point and 0.25 uM for the Binding Partner to the Scaffold. The Kd-value could then be used to calculate the association or dissociation rate, as long as you know the other. For the association rate, we used 10e5 as found in the paper of Schlosshauer [1] and is the average diffusion limited association rate they calculated for different proteins. In reality, our constructs probably are more diffusion limited than they calculated, as our construct are very large proteins and therefore will experience much more resistance.
Results description
In the Figure 1 you can see that we used excess of the Inducers, as there is a decrease of the amount, but after a while stays at the same amount. This is because all the pockets of the scaffold construct are already filled with the inducer. Data supporting the inducer excess is also shown in the figure, as the amount of empty scaffold sites decreases as fast as the inducer. Furthermore, we see that the induced scaffold sites are very high in the beginning. Our initial state is defines as that the induced amount of scaffold sites starts at 0, this is also the case if you look closely to the data, but it increases so fast, that it isn’t visible in a logarithmic time axis. Another thing that stands out in the graph, is that the green graph (the one of the Binding Sites for the CenterPoint) isn’t visible in the figure, this is because these values are about the same as the ones of the CenterPoint Sites. They decrease with the same rate, because they both are used for the formation of a bond to create a complex and have about the same initial amount. Another thing that supports the graph is that the sum of the Induced Scaffold Sites and the Empty Scaffold sites is comparable with the dark blue graph (Binding Sites for Scaffold). The decrease of the dark blue graph means that there are bonds formed between the Scaffold and the Binding Partner.
[1] Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Science (2004) 13:1660-1669
