Difference between revisions of "Team:Hong Kong-CUHK/Modeling"
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<center><div style="text-align:justify; text-justify:inter-ideograph; width:1000px"> | <center><div style="text-align:justify; text-justify:inter-ideograph; width:1000px"> | ||
− | + | <font face="Times New Roman" size="5pt"> | |
<h1> Modeling</h1> | <h1> Modeling</h1> | ||
− | <p> Magnetosome can be used in different perspective and it shows a good variety in different application. Three applications has been modelled in different perspective. Let me show the great variety of using magnetosome:</p> | + | <p><font face="Times New Roman" size="4pt"> Magnetosome can be used in different perspective and it shows a good variety in different application. Three applications has been modelled in different perspective. Let me show the great variety of using magnetosome:</p></font> |
<h2> 1) Protein extraction:</h2> | <h2> 1) Protein extraction:</h2> | ||
− | <p>Magnetosome can be used in microscopic point of view. We try to model his efficiency to bind with different proteins and use GFP-nanobody for immunoprecipitation. The main purpose of this modelling is to stimulate the binding dynamics of a fixed concentration of magnetosome and GFP-nanobody in different initial concentration of antigens.</p> | + | <p><font face="Times New Roman" size="4pt">Magnetosome can be used in microscopic point of view. We try to model his efficiency to bind with different proteins and use GFP-nanobody for immunoprecipitation. The main purpose of this modelling is to stimulate the binding dynamics of a fixed concentration of magnetosome and GFP-nanobody in different initial concentration of antigens.</p></font> |
− | <p>Various conditions and parameters:</p> | + | <p><font face="Times New Roman" size="4pt">Various conditions and parameters:</p></font> |
− | <table><tr> | + | <center><table><tr> |
<th>Fixed quantity</th> <th>quantity</th> | <th>Fixed quantity</th> <th>quantity</th> | ||
</tr><tr> | </tr><tr> | ||
<th>Volume of the mixture</th> <th>1000ul</th> | <th>Volume of the mixture</th> <th>1000ul</th> | ||
− | </tr></table> | + | </tr></table></center> |
− | <table><tr> | + | <center><table><tr> |
<th>Parameters</th> <th>quantity</th> | <th>Parameters</th> <th>quantity</th> | ||
</tr><tr> | </tr><tr> | ||
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<th>dissociation rate constant koff(Marta H. Kubala†, 2010)</th> | <th>dissociation rate constant koff(Marta H. Kubala†, 2010)</th> | ||
<th>1.24x10-4s-1</th> | <th>1.24x10-4s-1</th> | ||
− | </tr></table> | + | </tr></table></center> |
− | <table><tr> | + | <center><table><tr> |
<th>Condition</th> <th>quantity</th> | <th>Condition</th> <th>quantity</th> | ||
</tr><tr> | </tr><tr> | ||
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</tr><tr> | </tr><tr> | ||
<th>Initial amount of GFP:GFP-nanobody complex</th> <th>0</th> | <th>Initial amount of GFP:GFP-nanobody complex</th> <th>0</th> | ||
− | </tr></table> | + | </tr></table></center> |
− | <p>First, the molarity of the magnetosome is needed to calculate since the amount of magnetosome and its molecular weight are known,</p> | + | <p><font face="Times New Roman" size="4pt">First, the molarity of the magnetosome is needed to calculate since the amount of magnetosome and its molecular weight are known,</p></font> |
− | < | + | <Center>Molarity of Magnetosome=(1.5mg/6.89 x108 g)/(1ml)=2.18 x10-9M</center> |
− | <p>There are 362 GFP-nanobody per each magnetosome, the molarity of GFP-nanobody is:</p> | + | <p><font face="Times New Roman" size="4pt">There are 362 GFP-nanobody per each magnetosome, the molarity of GFP-nanobody is:</p></font> |
− | < | + | <Center>Molarity of GFP-nanobody = 2.18 x10-9M x 362 = 7.78 x10-7M</Center> |
− | <p>After that, a software called Simbiology is used in MATLAB and it help us to model and stimulate the dynamics of the association and dissociation between molecules. By constructing a model about the mathematics relationship between molecules. enmolecules,reaction process can be stimulated.</p> | + | <p><font face="Times New Roman" size="4pt">After that, a software called Simbiology is used in MATLAB and it help us to model and stimulate the dynamics of the association and dissociation between molecules. By constructing a model about the mathematics relationship between molecules. enmolecules,reaction process can be stimulated.</p></font> |
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− | <img src="https://static.igem.org/mediawiki/2015/6/6f/CUHK_Modeling_Binding_activity.jpg"> | + | <center><img src="https://static.igem.org/mediawiki/2015/6/6f/CUHK_Modeling_Binding_activity.jpg"></center> |
− | <p>Figure 1: Binding activity</p> | + | <p><font face="Times New Roman" size="4pt">Figure 1: Binding activity</p></font> |
− | <p>For Forward reaction (association) rate: </p> | + | <p><font face="Times New Roman" size="4pt">For Forward reaction (association) rate: </p> </font> |
− | kon *[GFP-nanobody]*[antigens]</ | + | <center>kon *[GFP-nanobody]*[antigens]</center> |
− | <p>For backward reaction (dissociation) rate: </p> | + | <p><font face="Times New Roman" size="4pt">For backward reaction (dissociation) rate: </p></font> |
− | koff *[GFP-nanobody-antigens-complex]</ | + | <center> koff *[GFP-nanobody-antigens-complex]</center> |
− | <p>Net reaction rate: </p> | + | <p><font face="Times New Roman" size="4pt">Net reaction rate: </p></font> |
− | kon *[GFP-nanobody]*[antigens] - koff *[GFP-nanobody-antigens-complex]</ | + | <center>kon *[GFP-nanobody]*[antigens] - koff *[GFP-nanobody-antigens-complex]</center> |
− | <p>Note: kon, koff are the reaction rate constant described in the parameters table.</p> | + | <p><font face="Times New Roman" size="4pt">Note: kon, koff are the reaction rate constant described in the parameters table.</p></font> |
− | <p>By using the function of SimBiology, we stimulate the dynamic of the system with the initial | + | <p><font face="Times New Roman" size="4pt">By using the function of SimBiology, we stimulate the dynamic of the system with the initial |
concentration of antigen from 0M to 1.6E-6M with an interval of 2E-7M. </p> | concentration of antigen from 0M to 1.6E-6M with an interval of 2E-7M. </p> | ||
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<img src="https://static.igem.org/mediawiki/2015/d/d7/CUHK_Modeling_Graph.jpg"> | <img src="https://static.igem.org/mediawiki/2015/d/d7/CUHK_Modeling_Graph.jpg"> | ||
+ | </font> | ||
Revision as of 08:51, 18 September 2015