Difference between revisions of "Team:NCTU Formosa/Design"

 
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            <li><a class="active" data-scroll-nav='0'>Core of APOllO E.Cotector: Customization</a></li>
 +
            <li><a data-scroll-nav="1">Single Chain Variable Fragment</a>
 +
                <ul>
 +
                <li><a data-scroll-nav="2">Probe: scFv from targeted drugs</a>
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                <li><a data-scroll-nav="3">Transmembrane Protein of scFv</a></li>
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                <li><a data-scroll-nav="4">Color Signal</a></li>
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                </ul>
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            </li>
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            <li><a data-scroll-nav="5">Gold Binding Polypeptide</a>
 +
                <ul>
 +
                <li><a data-scroll-nav="6">Transmembrane Protein of GBP</a>
 +
                <li><a data-scroll-nav="7">Application: Immobilize on Gold</a></li>
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                </ul>
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            </li>
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<div class="content" data-scroll-index="0"><h1>Core of APOllO E.Cotector: Customization</h1>
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Cotransforming Biobricks for creating Customized Detection Platform
+
<p>By utilizing the concept of <font color="#AC1F4A">co-transformation</font>, APOllO can offer various E.Cotectors with scFv, color signal or GBP and even any desired combination. Therefore, APOllO could <font color="#AC1F4A">customize the E.Cotector to satisfy the need of various detection platforms.</font></p>
 +
<div class="image">
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<img src="https://static.igem.org/mediawiki/2015/0/07/Nctu_formosa_design_newfig1.png" height="400px"><br><br>
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Figure 1. With the co-transform technique, we can insert any scFv or signal-related genetic sequences into the <i>E.coli</i>, and create a customized platform ─ the APOllO E.Cotector.
 
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    Cotransforming our various plasmids: probe of scFv, color signal and GBP, we created a customized detecting platform-The APOllO E.Cotector!
 
  
 
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<div class="contentitle">Single Chain Variable Fragment</div>
 
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  Tn the core design of customized E.Cotector, APOllO displayed scFv on the surface of E. coli as probes for detection
 
−
<br>
 
−
    ScFv is a fusion protein of the variable regions of heavy(VH) and light chain(VL) of immunoglobulins, and the heavy chain and light chain are connected with a short linker peptide of about 15 to 20 amino acids. The function of linker is to connect the heavy chain with light chain. With aid of a linker, scFv still reserve completely functional antigen-binding fragment and specificity of the original immunoglobulin; that is ,the property of specificity of antibody to antigen has being maintained.  Moreover, scFv is only 20 percent the size as antibody [4], therefore unlike monoclonal antibodies, which are often produced in mammalian cell cultures, scFv can be simply produced or displayed by bacteria such as E. coli.
 
  
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<div class="content" data-scroll-index="1"><h1>Single Chain Variable Fragment</h1>
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  <h2 data-scroll-index="2">Probe: scFv from targeted drugs</h2>
 +
<p>
 +
In order to provide doctors with new, direct, and innovative methods in determining the usage of <font color="#AC1F4A">monoclonal-antibody-targeted drugs</font>, we redesigned the <font color="#AC1F4A">FDA approved</font> monoclonal antibody targeted drugs, such as <font color="#AC1F4A">Bevacizumab (Avastin<sup>®</sup> anti-VEGF)<sup>[1]</sup></font>, <font color="#AC1F4A">Cetuximab (Erbitux<sup>®</sup> anti-EGFR)<sup>[2]</sup></font> and <font color="#AC1F4A">Trastuzumab (Herceptin<sup>®</sup> anti-HER2)<sup>[3]</sup></font> into scFv as probes.
 +
</p>
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<div class="image">
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<img src="https://static.igem.org/mediawiki/2015/e/ef/Nctu_Formosa_design_newfig2.png" height="300px"> <br><br>
 +
Figure 2. We design the platform to detect multimarkers as the reference for applying the combination therapy.
 
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<div class="contentitle">Transmembrane Protein of scFv</div>
 
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<div class="content">
 
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  To display scFv on the surface of E. coli, we use a transmembrane protein. The transmembrane protein is composed of lipoprotein(Lpp) and outer membrane protein(OmpA). <br>
 
−
  Lpp-OmpA was designed as a fusion protein consisting of the signal sequence and first 9 amino acid of Lpp, residue 46~159 of OmpA. The Lpp of the N-termini of this fusion protein targets the protein on the membrane while the trans-membrane domain of OmpA serves as an anchor. scFv is on the externally exposed loops of OmpA, which can be anchored to the outer membrane. Between the OmpA and scFv, there is a cut side of restriction enzyme called NcoI. With this cut side, the linked scFv can be easily changed just as a cassette.</div>
 
  
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<div class="contentitle">Color Signal</div>
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<p>Each distinct scFv of targeted drugs is displayed on the surfaces of <i>E.coli</i> allowing it to specifically detect target molecules. </p>
−
<div class="content">The color signals that we have selected are florescence proteins and chromoproteins. Comperating with iGEM, all of resources were from the Giant library of iGEM kit which is accessible to every iGEMer.  
+
<p>Furthermore, since APOllO E.Cotector expresses scFv and <font color="#AC1F4A">color signals</font> at the same time, the specific molecules that correspond to the scFv can be identified by different colors, which allows an accurate prescription of monoclonal antibody targeted drugs.</p>
−
APOllO utilized the red florescence protein BBa_E1010, the green fluorescent protein BBa_E0040, the blue fluorescent protein BBa_K592100 , and the blue chromoprotein BBa_K592009.
+
 
 +
<div class="image">
 +
<img src="https://static.igem.org/mediawiki/2015/thumb/a/a6/Figure_2_E.Cotector.png/800px-Figure_2_E.Cotector.png" height="250px"> <br><br>
 +
Figure 3. E.Cotector expresses scFv from targeted drugs.
 
</div>
 
</div>
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<div class="contentitle">Gold Binding Polypeptide</div>
 
−
<div class="content">Another plasmid we provide for customization is gold binding polypeptide, abbreviated as GBP. APOllO may display GBP on the surface of E.coli as glue for binding on gold surface.
 
−
<br>
 
−
  GBP was designed with the three-repeated of following 14 amino acid sequences: [MHGKTQATSGTIQS], which was developed in an E. coli cell-surface display system. The binding sequence of GBP does not contain cysteine which can form a covalent thiol linkage with gold, the linkage to the gold surface in Self-Assembled Monolayers (SAMs)[2].<br>
 
−
The mechanism of the connection between GBP and gold metal plane remains unknown. By using Molecular Dynamics (MD), it indicates that GBP, with an antiparallel β-sheet structure, can recognize gold surface via OH-binding. It is likely that the hydroxyl, together with amine, ligands on GBP recognize the atomic lattice of gold, aligning the molecule along the variants of a six-fold axis on the Au (111) surface [3].</div>
 
  
−
<div class="contentitle">Core of APOllO E.Cotector : Customization</div>
+
<h2 data-scroll-index="3">Transmembrane Protein of scFv</h2>
−
<div class="content">By utilizing the concept of Cotransformation , APOllO can offer various E. Cotectors with scFv ,color signal or GBP and even any desired combination. Therefore, APOllO could customize the E. Cotector to satisfy the need of various detection platforms.</div>
+
  <p>To display scFv on the surface of <i>E.coli</i>, we use a <font color="#AC1F4A">transmembrane protein</font>. The transmembrane protein is composed of <font color="#AC1F4A">lipoprotein (Lpp)</font> and <font color="#AC1F4A">outer membrane protein A (OmpA)</font>.</p>
 +
 
 +
<div class="image">
 +
  <img src="https://static.igem.org/mediawiki/2015/0/0b/Nctu_formosa_design_Lpp-Ompa123.png" height="200px"><br><br>
 +
  Figure 4. Transmembrane protein: Lpp-OmpA is composed of lipoprotein (Lpp) and outer membrane protein A (OmpA).
 +
  </div>
 +
 
 +
 
 +
  <p>Lpp-OmpA was designed as a fusion protein consisting of the signal sequence, first 9 amino acids of Lpp, and residue 46~159 amino acids of OmpA. The Lpp of the N-terminal of this fusion protein targets the protein on the membrane while the transmembrane domain of OmpA serves as an anchor. Owing to the fact that it is on the external exposed loops of the C-terminal of OmpA, scFv can be easily anchored to the outer membrane. Between the OmpA and scFv, there is <font color="#AC1F4A">a cut site of restriction enzyme</font> called <font color="#AC1F4A"><i>NcoI</i></font> allowing the linked scFv to be easily changed (like a cassette)<sup>[4]</sup>.</p>
 +
 
 +
<div class="image">
 +
 
 +
<img src="https://static.igem.org/mediawiki/2015/b/b4/Figure_4_NocI_scFv.png" height="200px">
 +
<img src="https://static.igem.org/mediawiki/2015/8/84/Nctu_formosa_design_figure4-2.png" height="250px"><br> <br> <br> <br>
 +
<img src="https://static.igem.org/mediawiki/2015/b/b4/Lpp-OmpA_NcoI.png" height="70px">
 +
<img src="https://static.igem.org/mediawiki/2015/a/ab/Ncol_scFv.png" height="85px"> <br><br>
 +
  Figure 5. To change the scFv sequence easily, we designed the <I>Nco</I>I restriction site between Lpp-OmpA and scFv. When designing <i>XbaI</i>-<i>Spe</i>I restriction site between Lpp-OmpA and scFv, it can cause a mixed site. Therefore, the <i>NcoI</i> restriction site rather than the EX-SP restriction site was designed.
 +
 
 +
 
 +
  </div>
 +
   
 +
  <h2 data-scroll-index="4">Color Signal</h2>
 +
<p>The color signals that we have selected are <font color="#AC1F4A">fluorescent proteins</font> and <font color="#AC1F4A">chromoproteins</font>. Cooperating with iGEM, all of the resources that were from the giant registry of iGEM is accessible to every iGEMer.  
 +
APOllO utilized red flourescent protein <a href="http://parts.igem.org/Part:BBa_E1010">BBa_E1010</a>, green fluorescent protein <a href="http://parts.igem.org/Part:BBa_E0040">BBa_E0040</a>, and blue chromoprotein <a href="http://parts.igem.org/Part:BBa_K592009">BBa_K592009</a>.</p><br>
 +
 
 +
<div class="image">
 +
<img src="https://static.igem.org/mediawiki/2015/4/48/Design_Figure_5-1.png" height="100px"> 
 +
<img src="https://static.igem.org/mediawiki/2015/2/26/Design_Figure_5.png" height="100px">
 +
<img src="https://static.igem.org/mediawiki/2015/d/d3/Design_Figure_5-3.png" height="100px"> <br><br>
 +
    Figure 6. Different Color Signal
 +
  </div>
 +
 
 +
<h2><a href="https://2015.igem.org/Team:NCTU_Formosa/Results">Jump to results to check the scFv function.</a></h2>
 
</div>
 
</div>
  
  
 +
<div class="content" data-scroll-index="5"><h1>Gold Binding Polypeptide</h1>
 +
<p>Another plasmid is <font color="#AC1F4A">gold binding polypeptide</font>, abbreviated as GBP. APOllO may display GBP on the surface of <i>E.coli</i> for <font color="#AC1F4A">binding on gold surface</font>.</p>
 +
 
 +
<p>GBP was designed with the three-repeated following 14 amino acids sequences: [MHGKTQATSGTIQS]. The binding sequence of GBP does not contain cysteine which can form a covalent thiol linkage with gold, the linkage to the gold surface in Self-Assembled Monolayers (SAMs)<sup>[5]</sup>.</P>
 +
<p>The mechanism of the connection between GBP and gold metal plane remains unknown. By using Molecular Dynamics (MD), it indicates that GBP, with an antiparallel β-sheet structure, can recognize gold surface via OH-binding. It is likely that the hydroxyl, together with amine, ligands on GBP recognize the atomic lattice of gold, aligning the molecule along the variants of a six-fold axis on the Au (111) surface<sup>[6]</sup>.</p>
 +
 +
<div class="image">
 +
<img src="https://static.igem.org/mediawiki/2015/thumb/3/36/Design_Figure_6.png/800px-Design_Figure_6.png" height="200px">  <br><br>
 +
  Figure 7. GBP can recognize and bind on the gold surface.
 +
  </div>
 +
</div>
 +
<div class="content" data-scroll-index="6"><h2>Transmembrane Protein of GBP</h2>
 +
<p>To display the GBP to the outer membrane of E.Cotector, we use a transmembrane protein called <font color="#AC1F4A">Long-chain fatty acid</font> short as FadL. We selected the first 384 amino acids sequence from the FadL for the transmembrane protein of GBP<sup>[7]</sup>.</p>
 +
<div class="image">
 +
<img src="https://static.igem.org/mediawiki/2015/thumb/1/1a/Design_Figure_7.png/800px-Design_Figure_7.png" height="200px">  <br><br>
 +
  Figure 8. Transmembrane Protein FadL transports GBP out of the surface of <i>E.coli</i>.
 +
  </div>   
 +
 +
<h2 data-scroll-index="7">Application: Immobilize on Gold</h2>
 +
 
 +
<p> According to the concept of biosensor, APOllO’s customers may deem the E.Cotector to play the role of biological recognition part and the gold chip to <font color="#AC1F4A">act as the signal transducer part</font>. Combining with multiple physicochemical nanoscale detectors in various fields, such as optical, electrochemistry, microbalance and etcetera, greater precision and accuracy will be achieved.</p>
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<div class="image">
 +
<img src="https://static.igem.org/mediawiki/2015/7/79/Nctu_formosa_design_figure12.png" height="300px"> <br><br>
 +
Figure 9. Concept of Biosensor via E.Cotector
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</div>
 +
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<h2><a href="https://2015.igem.org/Team:NCTU_Formosa/Results">Jump to results to check GBP function.</a></h2>
 +
</div>
 +
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<div class="content">
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<div class="reference">
 +
<b>Reference<br></b>
 +
[1] <a href="http://www.ncbi.nlm.nih.gov/pubmed/15961063">Bevacimab(Avastin)</a><br>
 +
[2] <a href="http://www.drugbank.ca/drugs/DB00002">Cetuximab(Erbitux)</a><br>
 +
[3] <a href="http://www.drugbank.ca/drugs/DB00072">Trastuzumab(Herceptin)</a><br>
 +
[4] <a href="http://www.uniprot.org/uniprot/P0A910">UniProtKB - P0A910 (OMPA_ECOLI)</a><br>
 +
[5] <a href="http://onlinelibrary.wiley.com/doi/10.1002/sia.2536/abstract">Adsorption of genetically engineered proteins studied by time-of-flight secondary ion mass spectrometry (TOF-SIMS). Part A: data acquisition and principal component analysis (PCA), Noriaki Suzuki,1 Lara Gamble,2 Candan Tamerler,3 Mehmet Sarikaya,1 David G. Castner2,4 (2007)</a><br>
 +
[6] <a href="http://austinpublishinggroup.com/biosensors-bioelectronics/fulltext/ajbb-v1-id1005.php">Assembly of Gold-Binding Proteins for Biomolecular Recognition, Zareie HM1,2* and Sarikaya M3, Austin Journal of Biosensors & Bioelectronics (2015)</a><br>
 +
[7] <a href="http://www.ncbi.nlm.nih.gov/pubmed/19228193">Tae Jung Park et al. (2009) Development of a whole-cell biosensor by cell surface display of a gold-binding polypeptide on the gold surface </a><br>
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Latest revision as of 03:28, 19 September 2015

Design

Core of APOllO E.Cotector: Customization

By utilizing the concept of co-transformation, APOllO can offer various E.Cotectors with scFv, color signal or GBP and even any desired combination. Therefore, APOllO could customize the E.Cotector to satisfy the need of various detection platforms.



Figure 1. With the co-transform technique, we can insert any scFv or signal-related genetic sequences into the E.coli, and create a customized platform ─ the APOllO E.Cotector.

Single Chain Variable Fragment

Probe: scFv from targeted drugs

In order to provide doctors with new, direct, and innovative methods in determining the usage of monoclonal-antibody-targeted drugs, we redesigned the FDA approved monoclonal antibody targeted drugs, such as Bevacizumab (Avastin® anti-VEGF)[1], Cetuximab (Erbitux® anti-EGFR)[2] and Trastuzumab (Herceptin® anti-HER2)[3] into scFv as probes.



Figure 2. We design the platform to detect multimarkers as the reference for applying the combination therapy.

Each distinct scFv of targeted drugs is displayed on the surfaces of E.coli allowing it to specifically detect target molecules.

Furthermore, since APOllO E.Cotector expresses scFv and color signals at the same time, the specific molecules that correspond to the scFv can be identified by different colors, which allows an accurate prescription of monoclonal antibody targeted drugs.



Figure 3. E.Cotector expresses scFv from targeted drugs.

Transmembrane Protein of scFv

To display scFv on the surface of E.coli, we use a transmembrane protein. The transmembrane protein is composed of lipoprotein (Lpp) and outer membrane protein A (OmpA).



Figure 4. Transmembrane protein: Lpp-OmpA is composed of lipoprotein (Lpp) and outer membrane protein A (OmpA).

Lpp-OmpA was designed as a fusion protein consisting of the signal sequence, first 9 amino acids of Lpp, and residue 46~159 amino acids of OmpA. The Lpp of the N-terminal of this fusion protein targets the protein on the membrane while the transmembrane domain of OmpA serves as an anchor. Owing to the fact that it is on the external exposed loops of the C-terminal of OmpA, scFv can be easily anchored to the outer membrane. Between the OmpA and scFv, there is a cut site of restriction enzyme called NcoI allowing the linked scFv to be easily changed (like a cassette)[4].







Figure 5. To change the scFv sequence easily, we designed the NcoI restriction site between Lpp-OmpA and scFv. When designing XbaI-SpeI restriction site between Lpp-OmpA and scFv, it can cause a mixed site. Therefore, the NcoI restriction site rather than the EX-SP restriction site was designed.

Color Signal

The color signals that we have selected are fluorescent proteins and chromoproteins. Cooperating with iGEM, all of the resources that were from the giant registry of iGEM is accessible to every iGEMer. APOllO utilized red flourescent protein BBa_E1010, green fluorescent protein BBa_E0040, and blue chromoprotein BBa_K592009.




Figure 6. Different Color Signal

Jump to results to check the scFv function.

Gold Binding Polypeptide

Another plasmid is gold binding polypeptide, abbreviated as GBP. APOllO may display GBP on the surface of E.coli for binding on gold surface.

GBP was designed with the three-repeated following 14 amino acids sequences: [MHGKTQATSGTIQS]. The binding sequence of GBP does not contain cysteine which can form a covalent thiol linkage with gold, the linkage to the gold surface in Self-Assembled Monolayers (SAMs)[5].

The mechanism of the connection between GBP and gold metal plane remains unknown. By using Molecular Dynamics (MD), it indicates that GBP, with an antiparallel β-sheet structure, can recognize gold surface via OH-binding. It is likely that the hydroxyl, together with amine, ligands on GBP recognize the atomic lattice of gold, aligning the molecule along the variants of a six-fold axis on the Au (111) surface[6].



Figure 7. GBP can recognize and bind on the gold surface.

Transmembrane Protein of GBP

To display the GBP to the outer membrane of E.Cotector, we use a transmembrane protein called Long-chain fatty acid short as FadL. We selected the first 384 amino acids sequence from the FadL for the transmembrane protein of GBP[7].



Figure 8. Transmembrane Protein FadL transports GBP out of the surface of E.coli.

Application: Immobilize on Gold

According to the concept of biosensor, APOllO’s customers may deem the E.Cotector to play the role of biological recognition part and the gold chip to act as the signal transducer part. Combining with multiple physicochemical nanoscale detectors in various fields, such as optical, electrochemistry, microbalance and etcetera, greater precision and accuracy will be achieved.



Figure 9. Concept of Biosensor via E.Cotector

Jump to results to check GBP function.

Reference
 [1] Bevacimab(Avastin)
[2] Cetuximab(Erbitux)
[3] Trastuzumab(Herceptin)
[4] UniProtKB - P0A910 (OMPA_ECOLI)
[5] Adsorption of genetically engineered proteins studied by time-of-flight secondary ion mass spectrometry (TOF-SIMS). Part A: data acquisition and principal component analysis (PCA), Noriaki Suzuki,1 Lara Gamble,2 Candan Tamerler,3 Mehmet Sarikaya,1 David G. Castner2,4 (2007)
[6] Assembly of Gold-Binding Proteins for Biomolecular Recognition, Zareie HM1,2* and Sarikaya M3, Austin Journal of Biosensors & Bioelectronics (2015)
[7] Tae Jung Park et al. (2009) Development of a whole-cell biosensor by cell surface display of a gold-binding polypeptide on the gold surface


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