Difference between revisions of "Team:HokkaidoU Japan/Multimerization"

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<div>
 
<div>
 
<img src="https://static.igem.org/mediawiki/2016/3/3b/T--HokkaidoU_Japan--multimerization_image6.png" alt="enzymatic reaction" height="300px" width="auto" style="float:right">  
 
<img src="https://static.igem.org/mediawiki/2016/3/3b/T--HokkaidoU_Japan--multimerization_image6.png" alt="enzymatic reaction" height="300px" width="auto" style="float:right">  
<br>We advocate the new method to create multimer using the self-assembling ability of SAP. By fusing SAP to the end of a protein, it will condense with other proteins’ SAP domains and form the complex. By using this method, we’ll be able to connect several enzymes and allow huge complexed proteins to be formed. It’ll improve the efficiency of a continuous reaction.
+
<p>Fig1. Enzyme reaction by multiple complex</p>
The ordinary method uses linkers to connect proteins. The new method that we suggest which uses SAP is superior to the ordinary one for these reasons.
+
 
 +
<br>We made a platform of technology for constructing covalently linked multi-enzyme-complex through disulfide bonds recruited by self-assembling peptide (SAP). By fusing SAP to the end of a protein, it will condense with other proteins’ SAP domains and form the complex. The SAP domains is pinched by short linkers (SL) that have cysteine residues. When the SAPs gather and SLs get close, disulfide bonds are formed between other SLs. So, we will make unbreakable complex. By using this method, we’ll be able to connect several enzymes and allow huge complexed proteins to be formed. It’ll improve the efficiency of a continuous reaction.</br>
 +
 
 
<br>
 
<br>
 
<center><img src="https://static.igem.org/mediawiki/2016/0/08/T--HokkaidoU_Japan--multimerization_image7.png" alt="large block" height="300px" width="auto"></center>
 
<center><img src="https://static.igem.org/mediawiki/2016/0/08/T--HokkaidoU_Japan--multimerization_image7.png" alt="large block" height="300px" width="auto"></center>
 +
<p>Fig2. Huge complex using SAP</p>
 +
<p>We thought the intensity of fluorescent proteins, like GFP increased.</p>
 +
 +
 +
 
</div>
 
</div>
 
<br>
 
<br>
 
+
<br>The ordinary method uses linkers to connect proteins. We think the new method using SAP is superior to the ordinary one for these reasons.</br>
 
<div>
 
<div>
 
   <table class="merit">
 
   <table class="merit">
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     <th width="50%">SAP Method</th>
 
     <th width="50%">SAP Method</th>
 
     </tr>
 
     </tr>
 +
  
 
     <tr>
 
     <tr>
     <td>Difficult to connect several huge proteins</td>
+
     <td>Regulated by one promoter (Fig3)</td>
     <td>Possible to synthesize the proteins individually. Can also form a huge complex</td>
+
     <td>Each protein can be expressed individually (Fig4)</td>
 
     </tr>
 
     </tr>
 
+
 
 
     <tr>
 
     <tr>
     <td>Regulated by one promoter</td>
+
     <td>Difficult to produce several huge complex</td>
     <td>Each protein can be expressed individually</td>
+
     <td>Possible to synthesize the proteins individually. Can also form a huge complex (Fig4)</td>
 
     </tr>
 
     </tr>
 +
  
 
     <tr>
 
     <tr>
     <td>The possibility of deformation of the 3D-structure</td>
+
     <td>The possibility of deformation of the 3D-structure (Fig5)</td>
 
     <td>Low possibility of deformation since they only connect with proteins which can condense</td>
 
     <td>Low possibility of deformation since they only connect with proteins which can condense</td>
 
     </tr>
 
     </tr>
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<div style="float:left; margin: 0px;">
 
<div style="float:left; margin: 0px;">
 
<img src="https://static.igem.org/mediawiki/2016/e/e0/T--HokkaidoU_Japan--multimerization_image1.png" alt="linker methods" height="260px" width="auto">
 
<img src="https://static.igem.org/mediawiki/2016/e/e0/T--HokkaidoU_Japan--multimerization_image1.png" alt="linker methods" height="260px" width="auto">
 +
<p>Fig3. Using linkers</p>
 
</div>
 
</div>
 +
 
<div style="float:left; margin: 30px;">
 
<div style="float:left; margin: 30px;">
 
<img src="https://static.igem.org/mediawiki/2016/7/72/T--HokkaidoU_Japan--multimerization_image2.png" alt="SAP methods" height="400px" width="auto">
 
<img src="https://static.igem.org/mediawiki/2016/7/72/T--HokkaidoU_Japan--multimerization_image2.png" alt="SAP methods" height="400px" width="auto">
 +
<p>Fig4. Using SAPs</p>
 
</div>
 
</div>
 
<br clear="both"/>
 
<br clear="both"/>
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<br>
 
<br>
 
<center><img src="https://static.igem.org/mediawiki/2016/2/23/T--HokkaidoU_Japan--multimerization_image3.png" alt="steric hindrance" height="300px" width="auto"></center>
 
<center><img src="https://static.igem.org/mediawiki/2016/2/23/T--HokkaidoU_Japan--multimerization_image3.png" alt="steric hindrance" height="300px" width="auto"></center>
 +
<p>Fig5. Demerit of using linkers </p>
  
  
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different proteins is infinite, there is no guarantee that we can always obtain the expected combination  
 
different proteins is infinite, there is no guarantee that we can always obtain the expected combination  
 
when we form the protein complex.
 
when we form the protein complex.
One solution to the problem is limiting the number of combination by using different SAP.  
+
One solution to the problem is limiting the number of combination by using different SAP. That can reduce probability of miss connection a little.</br>
As forming protein complex with different functions, this multimer forming method with SAP
+
 
let us create more functional units. When same kinds of proteins are used, it’ll be a large block and
+
its function is expected to be enhanced.
+
  
 
<div style="float:left; margin: 80px;">
 
<div style="float:left; margin: 80px;">
 
<img src="https://static.igem.org/mediawiki/2016/d/d8/T--HokkaidoU_Japan--multimerization_image5.png" alt="demerit" height="220px" width="auto">
 
<img src="https://static.igem.org/mediawiki/2016/d/d8/T--HokkaidoU_Japan--multimerization_image5.png" alt="demerit" height="220px" width="auto">
 +
<p>Fig6. Demerit of using SAP method</p>
 
</div>
 
</div>
 
<div style="float:left; margin: 30px;">
 
<div style="float:left; margin: 30px;">
 
<img src="https://static.igem.org/mediawiki/2016/c/cf/T--HokkaidoU_Japan--multimerization_image4.png" alt="resolution"  height="380px" width="auto" style="float:right">
 
<img src="https://static.igem.org/mediawiki/2016/c/cf/T--HokkaidoU_Japan--multimerization_image4.png" alt="resolution"  height="380px" width="auto" style="float:right">
 +
<p>Fig7. Resolution for miss connections</p>
 
</div>
 
</div>
 
<br clear="both"/>
 
<br clear="both"/>
 +
 +
 +
<br>As forming protein complex with different functions, this multimer forming method with SAP
 +
let us create more functional units. When same kinds of proteins are used, it’ll be a large block and
 +
its function is expected to be enhanced.</br>
  
 
</div>
 
</div>
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<div>
 
<div>
 
<img src="https://static.igem.org/mediawiki/2016/0/0c/T--HokkaidoU_Japan--multimerization_image8.png" alt="methods" height="500px" width="auto"style="float:right">
 
<img src="https://static.igem.org/mediawiki/2016/0/0c/T--HokkaidoU_Japan--multimerization_image8.png" alt="methods" height="500px" width="auto"style="float:right">
<br><br>We tried forming multimers using the self-assembling peptide, P<sub>11</sub>-4 and RADA16-I. We
+
<p>Fig8. Method for verifying whether proteins form multiple complex </p>
 +
 
 +
<br>
 +
<br>We tried forming multimers using the self-assembling peptide, P<sub>11</sub>-4 and RADA16-I. We
 
Connected short linker(GGCGG) and SAP to both ends of the protein. In this experiment, we  
 
Connected short linker(GGCGG) and SAP to both ends of the protein. In this experiment, we  
 
formed the multimers of GFP. GFP’s molecular mass is 26891Da. When fusing with P<sub>11</sub>-4, it’s  
 
formed the multimers of GFP. GFP’s molecular mass is 26891Da. When fusing with P<sub>11</sub>-4, it’s  
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than 60kDa. Consequently, we used the filter which filters out the proteins with mass of more than 50KDa.
 
than 60kDa. Consequently, we used the filter which filters out the proteins with mass of more than 50KDa.
 
For the evaluation, we ordered IDT the designed constructions and put them on the vectors. Then,  
 
For the evaluation, we ordered IDT the designed constructions and put them on the vectors. Then,  
we introduced them to <span style="font-style: italic">E.coli</span>. Using IPTG induction , the proteins were expressed. Causing  
+
we introduced them to <span style="font-style: italic">E.coli</span>. Using IPTG induction , the proteins were expressed. Causing bacteriolysis with freeze-thaw, we acquired the supernatant contains the proteins by centrifugal  
bacteriolysis with freeze-thaw, we acquired the supernatant contains the proteins by centrifugal  
+
 
separation. Purifying the protein with Ni-affinity chromatography, we filtrated the solution
 
separation. Purifying the protein with Ni-affinity chromatography, we filtrated the solution
 
to separate the proteins with mass of less than 50KDa. We irradiated 480nm light to filtrate and observed  
 
to separate the proteins with mass of less than 50KDa. We irradiated 480nm light to filtrate and observed  
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<img src="https://static.igem.org/mediawiki/2016/d/df/T--HokkaidoU_Japan--multimerization_construct.png" alt="construct"
 
<img src="https://static.igem.org/mediawiki/2016/d/df/T--HokkaidoU_Japan--multimerization_construct.png" alt="construct"
 
" height="250px" width="auto">
 
" height="250px" width="auto">
 +
<p>Fig9. Construct of multimerization using SAP</p>
  
 
<br>
 
<br>

Revision as of 18:34, 16 October 2016

Team:HokkaidoU Japan - 2016.igem.org

 

Team:HokkaidoU Japan

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overview

enzymatic reaction

Fig1. Enzyme reaction by multiple complex


We made a platform of technology for constructing covalently linked multi-enzyme-complex through disulfide bonds recruited by self-assembling peptide (SAP). By fusing SAP to the end of a protein, it will condense with other proteins’ SAP domains and form the complex. The SAP domains is pinched by short linkers (SL) that have cysteine residues. When the SAPs gather and SLs get close, disulfide bonds are formed between other SLs. So, we will make unbreakable complex. By using this method, we’ll be able to connect several enzymes and allow huge complexed proteins to be formed. It’ll improve the efficiency of a continuous reaction.

large block

Fig2. Huge complex using SAP

We thought the intensity of fluorescent proteins, like GFP increased.



The ordinary method uses linkers to connect proteins. We think the new method using SAP is superior to the ordinary one for these reasons.
Linker Method SAP Method
Regulated by one promoter (Fig3) Each protein can be expressed individually (Fig4)
Difficult to produce several huge complex Possible to synthesize the proteins individually. Can also form a huge complex (Fig4)
The possibility of deformation of the 3D-structure (Fig5) Low possibility of deformation since they only connect with proteins which can condense

linker methods

Fig3. Using linkers

SAP methods

Fig4. Using SAPs



steric hindrance

Fig5. Demerit of using linkers


There are also disadvantages to using SAP. Since the number of the possible combination of several different proteins is infinite, there is no guarantee that we can always obtain the expected combination when we form the protein complex. One solution to the problem is limiting the number of combination by using different SAP. That can reduce probability of miss connection a little.
demerit

Fig6. Demerit of using SAP method

resolution

Fig7. Resolution for miss connections



As forming protein complex with different functions, this multimer forming method with SAP let us create more functional units. When same kinds of proteins are used, it’ll be a large block and its function is expected to be enhanced.
methods
methods

Fig8. Method for verifying whether proteins form multiple complex



We tried forming multimers using the self-assembling peptide, P11-4 and RADA16-I. We Connected short linker(GGCGG) and SAP to both ends of the protein. In this experiment, we formed the multimers of GFP. GFP’s molecular mass is 26891Da. When fusing with P11-4, it’s 31709Da. With RADA16-I, it’s 31943Da. When they form multimer, the molecular mass will be more than 60kDa. Consequently, we used the filter which filters out the proteins with mass of more than 50KDa. For the evaluation, we ordered IDT the designed constructions and put them on the vectors. Then, we introduced them to E.coli. Using IPTG induction , the proteins were expressed. Causing bacteriolysis with freeze-thaw, we acquired the supernatant contains the proteins by centrifugal separation. Purifying the protein with Ni-affinity chromatography, we filtrated the solution to separate the proteins with mass of less than 50KDa. We irradiated 480nm light to filtrate and observed whether 580nm wave-length light was emitted.
construct

Fig9. Construct of multimerization using SAP





results


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conclusion


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reference


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