Difference between revisions of "Team:TU-Eindhoven/Results/Model"
| Line 24: | Line 24: | ||
In the first figure 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, actually, the induced amount of scaffold sites starts at 0, but 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 Scaffold) isn’t visible in the figure, this is because these values are about the same as the ones of the induced scaffold sites. They decrease with the same rate, because they both are used for the formation of a bond to create a complex. </br></br> | In the first figure 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, actually, the induced amount of scaffold sites starts at 0, but 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 Scaffold) isn’t visible in the figure, this is because these values are about the same as the ones of the induced scaffold sites. They decrease with the same rate, because they both are used for the formation of a bond to create a complex. </br></br> | ||
| − | <div id=" | + | <div id="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> </br> |
In the second graph, we can see how many complexes are formed. With the programs provided by NFsim, we could extract the total amount of molecules and the average complex size. They also provided us with a method to determine the amount of single molecules (they call it complexes with size one) and we used that to determine the amount of formed complexes and the average complex size, where the single molecules aren’t taken into account. Just as we mentioned as comment for the first figure, also here the initial values of Complexes and Average Complex size >1 start at zero, but isn’t visible in the figure because of the logarithmic scale. </br></br> | In the second graph, we can see how many complexes are formed. With the programs provided by NFsim, we could extract the total amount of molecules and the average complex size. They also provided us with a method to determine the amount of single molecules (they call it complexes with size one) and we used that to determine the amount of formed complexes and the average complex size, where the single molecules aren’t taken into account. Just as we mentioned as comment for the first figure, also here the initial values of Complexes and Average Complex size >1 start at zero, but isn’t visible in the figure because of the logarithmic scale. </br></br> | ||
| − | <div id="Figure_2"><img src="https://static.igem.org/mediawiki/2017/ | + | <div id="Figure_2"><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> </br> |
| Line 34: | Line 34: | ||
<div class="sources"> | <div class="sources"> | ||
| − | <sub>[1]</sub>Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model | + | <sub>[1]</sub>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 </br> |
</div> | </div> | ||
</html> | </html> | ||
{{TU-Eindhoven_footer}} | {{TU-Eindhoven_footer}} | ||
Revision as of 08:37, 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.
In the first figure 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, actually, the induced amount of scaffold sites starts at 0, but 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 Scaffold) isn’t visible in the figure, this is because these values are about the same as the ones of the induced scaffold sites. They decrease with the same rate, because they both are used for the formation of a bond to create a complex.
In the second graph, we can see how many complexes are formed. With the programs provided by NFsim, we could extract the total amount of molecules and the average complex size. They also provided us with a method to determine the amount of single molecules (they call it complexes with size one) and we used that to determine the amount of formed complexes and the average complex size, where the single molecules aren’t taken into account. Just as we mentioned as comment for the first figure, also here the initial values of Complexes and Average Complex size >1 start at zero, but isn’t visible in the figure because of the logarithmic scale.
Furthermore, we also simplified our system a little and simulated a system based on two large constructs. This is the case if we first let the Scaffold construct incubate with excess Inducer and let the Binding Partner and the Center Point incubate. These interactions are high enough that they barely dissociate. We did this because this is computationally much easier and gave us similar outputs.
[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
Footer
