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

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<td style="border-style: none;"><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:left"></td>  
+
<td style="border-style: none;" align="center"><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:left"></td>  
 
       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
<td style="border-style: none"; align="center"><h2>Fig. 1. The enzyme reaction by multiple complex<br>To connect different enzymes will<br>make continuous reaction efficiently. </h></td>
+
<td style="border-style: none"; align="center"><h2>Fig. 1. Enzyme reaction by multiple complex</h></td>
 
       </tr>
 
       </tr>
 
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</table>
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       <tr>
<td style="border-style: none"; align="center"><h2>Fig. 2. Huge complex using SAP<br>To connect same enzymes like fluorescent proteins will amplify thir effects.</h2></td>
+
<td style="border-style: none"; align="center"><h2>Fig. 2. Huge complex using SAP<br>We thought the intensity of fluorescent proteins, like GFP increased.</h2></td>
 
       </tr>
 
       </tr>
 
</table>
 
</table>
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<br>
 
<br>
<br>However, the ordinary method uses linkers to connect proteins. We think the new method using SAP is superior to the ordinary one for these reasons (Table. 1).</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>
 
<br>
 
<br>
 
<br>
 
<br>
 
<div>
 
<div>
 
   <table class="merit">
 
   <table class="merit">
  <h2>Table. 1. Comparison between linkers and SAPs</h2>
 
 
     <tr>
 
     <tr>
 
     <th width="50%">Linker Method</th>
 
     <th width="50%">Linker Method</th>
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     <tr>
 
     <tr>
 
     <td>Regulated by one promoter (Fig. 3)</td>
 
     <td>Regulated by one promoter (Fig. 3)</td>
     <td>Each protein can be produced individually (Fig. 4)</td>
+
     <td>Each protein can be expressed individually (Fig. 4)</td>
 
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<td style="border-style: none;"><h2>Fig. 3. Using linkers<br>Expressions of gene A, B and C which code protein A, B and C are regulated by one promoter. If you connect some huge proteins, the expression efficiency may be decreased because the coding sequence is too long. </h2></td>
+
<td style="border-style: none;"><h2>Fig. 3. Using linkers</h2></td>
<td style="border-style: none;"><h2>Fig. 4. Using SAPs<br>You can produce protein A, B and C individually. After expression, they gather by SAPs and form disufide bonds by SLs.</h2></td>
+
<td style="border-style: none;"><h2>Fig. 4. Using SAPs</h2></td>
 
       </tr>
 
       </tr>
 
</center>
 
</center>
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<td style="border-style:none; float:center"><img src="https://static.igem.org/mediawiki/2016/2/23/T--HokkaidoU_Japan--multimerization_image3.png" alt="steric hindrance" height="300px" width="auto">  </td> </tr>
 
<td style="border-style:none; float:center"><img src="https://static.igem.org/mediawiki/2016/2/23/T--HokkaidoU_Japan--multimerization_image3.png" alt="steric hindrance" height="300px" width="auto">  </td> </tr>
 
       <tr>
 
       <tr>
<td style="border-style: none"; align="center"><h2>Fig. 5. Demerit of using linkers<br>In linker method, you need to consider the linker length to avoid the steric hindrance.</h2></td>
+
<td style="border-style: none"; align="center"><h2>Fig. 5. Demerit of using linkers</h2></td>
 
       </tr>
 
       </tr>
 
</table>
 
</table>
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<span class="nomal2">
 
<span class="nomal2">
  
<br>We thought the SAP method was best one but it had also disadvantages. 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.
+
<br>There are also disadvantages to using SAP. Since the number of the possible combination of several  
<br>One solution to the problem is limiting the number of combination by using different SAP. That can reduce probability of incorrect connection a little.</br>
+
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.</br>
 
</span>
 
</span>
  
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<td style="border-style: none;"><h2>Fig. 6. Demerit of using SAP method<br>If some kinds of protein are expressed,<br>there are so many combination.<br>You may not be able to get the correct combination.</h2></td>
+
<td style="border-style: none;"><h2>Fig. 6. Demerit of using SAP method</h2></td>
<td style="border-style: none;"><h2>Fig. 7. Resolution for infinite combinations<br>When you use some kinds of SAP,<br>incorrect connections will decrease.</h2></td>
+
<td style="border-style: none;"><h2>Fig. 7. Resolution for miss connections</h2></td>
 
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       </tr>
  
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<span class="nomal2">
 
<span class="nomal2">
  
<br>Multimerization is very useful. As forming protein complex with different functions, this multimer let us create more functional units. When same kinds of protein are used, it’ll be a large block and its function is expected to be enhanced.
+
<br>As forming protein complex with different functions, this multimer forming method with SAP
<br>
+
let us create more functional units. When same kinds of proteins are used, it’ll be a large block and  
<br>We tried to establish novel uses of SAP in this yaer. We challenged multimerization using it and not only used it but also made firmly connection.
+
its function is expected to be enhanced.</br>
 +
 
 
</span>
 
</span>
 
</div>
 
</div>
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width="270px" height="auto" alt="methods"></div>
 
width="270px" height="auto" alt="methods"></div>
  
 
+
<div>
 +
  <table  style="border-style: none; float: right;" height="350px" width="400px">
 +
<tr><td style="border-style: none;">
 +
<center><img src="https://static.igem.org/mediawiki/2016/0/0c/T--HokkaidoU_Japan--multimerization_image8.png" alt="methods" height="550px" width="auto"></center></td></tr>
 +
<tr><td style="border-style: none;"><h2>Fig. 8. Method for verifying whether proteins form multiple complex </h2></td></tr>
 +
</table>
  
 
<span class="nomal2">
 
<span class="nomal2">
  
 
<br>
 
<br>
<br>We tried forming multimers using the self-assembling peptide (SAP), P<span class="sitatuki">11</span>-4 (QQRFEWEFEQQ) and RADA16-I (RADARADARADARADA). And to make firmly bonds we designed short linker (GGCGG) called SL for short. We
+
<br>We tried forming multimers using the self-assembling peptide, P<sub>11</sub>-4 and RADA16-I. We
Connected SL and SAP to both ends of the protein. In this experiment, we used GFP as test (Fif. 8).  
+
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
 +
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 <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
 +
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.<br>
 +
</div>
 +
</span>
 +
<br>
 +
<br>
  
 
<table style="border-style: none">
 
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<td style="border-style: none;">  
 
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<td style="border-style:none; float:center"><img src="https://static.igem.org/mediawiki/2016/d/df/T--HokkaidoU_Japan--multimerization_construct.png
+
<td style="border-style:none; float:center"><img src="https://static.igem.org/mediawiki/2016/e/e9/T--HokkaidoU_Japan--Multimerization_unbrakablelinkages.png" alt="image" height="800px" width="auto"></td>  
" alt="construct" height="auto" width="900px"></td>  
+
 
       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
<td style="border-style: none"; align="center"><h2>Fig. 8. Design of the coding sequence</h2></td>
+
<td style="border-style: none"; align="center"><h2>Fig. 9. キャプション</h2></td>
 
       </tr>
 
       </tr>
 
</table>
 
</table>
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<h1>Assay</h1>
 
  
<div>
 
<table  style="border-style: none; float: right;" height="350px" width="400px">
 
<tr><td style="border-style: none;">
 
<center><img src="https://static.igem.org/mediawiki/2016/0/0c/T--HokkaidoU_Japan--multimerization_image8.png" alt="methods" height="550px" width="auto"></center></td></tr>
 
<tr><td style="border-style: none;"><h2>Fig. 9. Method for verifying whether proteins form multiple complex </h2></td></tr>
 
</table>
 
 
<br>GFP’s molecular mass is 26891Da. When fusing with P<span class="sitatuki">11</span>-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.
 
 
<br>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 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.<br>
 
</div>
 
</span>
 
<br clear="all">
 
 
<br>
 
<br>
 
<br>
 
<br>
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<span class="nomal2">
 
<span class="nomal2">
  
 
+
<br>ここに本文
<br>We put above CDS (Fig. 8) into pET15b and expressed (Fig. 10). As negative control we made a construction containing GFP without SAPs and SLs (Fig. 11). GFPs with SAPs and SLs was expected to become multiple complexs (Fig. 12).
+
  
 
</span>
 
</span>
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       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
<td style="border-style: none"; align="center"><h2>Fig. 10. The construction of multimerization using SAP<br>This is the construct for making multiple complex. We used RADA16-I and P<span class="sitatuki">11</span>-4 as SAP. <br>C is a cysteine residues in short linker.</h2></td>
+
<td style="border-style: none"; align="center"><h2>Fig. 9. Construct of multimerization using SAP<br>This is the construct for making multiple complex. We used RADA16-I and P<sub>11</sub>-4 as SAP. C is a cysteine residues in short linker.</h2></td>
 
       </tr>
 
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</table>
 
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       <tr>
 
       <tr>
<td style="border-style: none"; align="center"><h2>Fig. 11. The construction of a negative control<br>We made a negative control which had only GFP to test the effect of SAPs.</h2></td>
+
<td style="border-style: none"; align="center"><h2>Fig. 10. Construct of a negative control<br>We made a negative control which had only GFP to test the effect of SAPs.</h2></td>
 
       </tr>
 
       </tr>
 
</table>
 
</table>
 
<br clear="all">
 
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<td style="border-style:none; float:center"><img src="https://static.igem.org/mediawiki/2016/2/28/T--HokkaidoU_Japan--image21.png" alt="image" height="500px" width="auto"></td>  
+
<td style="border-style:none; float:center"><img src="https://static.igem.org/mediawiki/2016/7/7e/T--HokkaidoU_Japan--Multimerization_tool.png" alt="Tool" height="250px" width="auto"></td>  
 
       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
<td style="border-style: none"; align="center"><h2>Fig. 12. Expected forming multiple complex</h2></td>
+
<td style="border-style: none"; align="center"><h2>Fig. 11. Construct for making subunits of artificial multi-enzyme-complex<br>We designed this construct to had a cloning site. If you design the protein which ends are BamHI site, you can make the multimer easily.</h2></td>
 
       </tr>
 
       </tr>
 
</table>
 
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<span class="nomal2">
 
<span class="nomal2">
  
<br>As future work, anyone can make multi-enzyme-complex if the protein is designed to have BamHI restriction enzyme sites in both ends. Our construction have also BamHI site at GEP ends. So, you can cut out the GFP and put on any protein using cloning site (Fig. 13).
+
<br>ここに本文<br>
  
 
</span>
 
</span>
 
 
<table style="border-style: none">
 
<tr align="center">
 
<td style="border-style: none;">
 
      <tr>
 
<td style="border-style:none; float:center"><img src="https://static.igem.org/mediawiki/2016/7/7e/T--HokkaidoU_Japan--Multimerization_tool.png" alt="Tool" height="250px" width="auto"></td>
 
      </tr>
 
      <tr>
 
<td style="border-style: none"; align="center"><h2>Fig. 13. The construction for making subunits of artificial multi-enzyme-complex<br>We designed this construct to had a cloning site. If you design the protein which ends are BamHI site, you can make the multimer easily.</h2></td>
 
      </tr>
 
</table>
 
<br clear="all">
 
 
 
  
 
<br>
 
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<span class="nomal2">
 
<span class="nomal2">
<br>[1] Lee H, DeLoache WC, Dueber JE. Spatial organization of enzymes for metabolic engineering. Metab Eng. 2012;14:242?251.
+
<br>[1] Lee H, DeLoache WC, Dueber JE. Spatial organization of enzymes for metabolic engineering. Metab Eng. 2012;14:242–251.
 
<br>[2] Castellana M1, Wilson MZ2, Xu Y3, Joshi P2, Cristea IM2, Rabinowitz JD4, Gitai Z2, Wingreen NS3. Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol. 2014 Oct;32(10):1011-8.
 
<br>[2] Castellana M1, Wilson MZ2, Xu Y3, Joshi P2, Cristea IM2, Rabinowitz JD4, Gitai Z2, Wingreen NS3. Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol. 2014 Oct;32(10):1011-8.
 
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Revision as of 10:13, 19 October 2016

Team:HokkaidoU Japan - 2016.igem.org

 

Team:HokkaidoU Japan

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overview
enzymatic reaction

Fig. 1. 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

Fig. 2. 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 (Fig. 3) Each protein can be expressed individually (Fig. 4)
Difficult to produce several huge complex Possible to synthesize the proteins individually. Can also form a huge complex (Fig. 4)
The possibility of deformation of the 3D-structure (Fig. 5) Low possibility of deformation since they only connect with proteins which can condense

linker methods SAP methods

Fig. 3. Using linkers

Fig. 4. Using SAPs



steric hindrance

Fig. 5. 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 resolution

Fig. 6. Demerit of using SAP method

Fig. 7. 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

Fig. 8. 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.


image

Fig. 9. キャプション




results


ここに本文
construct

Fig. 9. Construct of multimerization using SAP
This is the construct for making multiple complex. We used RADA16-I and P11-4 as SAP. C is a cysteine residues in short linker.


Negative control

Fig. 10. Construct of a negative control
We made a negative control which had only GFP to test the effect of SAPs.


Tool

Fig. 11. Construct for making subunits of artificial multi-enzyme-complex
We designed this construct to had a cloning site. If you design the protein which ends are BamHI site, you can make the multimer easily.




conclusion

ここに本文


reference

[1] Lee H, DeLoache WC, Dueber JE. Spatial organization of enzymes for metabolic engineering. Metab Eng. 2012;14:242–251.
[2] Castellana M1, Wilson MZ2, Xu Y3, Joshi P2, Cristea IM2, Rabinowitz JD4, Gitai Z2, Wingreen NS3. Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol. 2014 Oct;32(10):1011-8.