Difference between revisions of "Team:CCU Taiwan/Model"

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</section>
 
</section>
 
<nav class="section-nav">
 
<nav class="section-nav">
 
     <ul>
 
     <ul>
 
         <li>Rosetta</li>
 
         <li>Rosetta</li>
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         <li><a href="#ove">Overview</a></li>
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         <li onclick="display1('ros')"><a href="#ove">Overview</a></li>
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         <li>
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         <li onclick="display1('ros')">
 
             <a href="#pro">Protocols</a>
 
             <a href="#pro">Protocols</a>
 
             <ul>
 
             <ul>
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                 <li><a href="#cm">RosettaCM</a></li>
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                 <li onclick="display1('ros')"><a href="#cm">RosettaCM</a></li>
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                 <li><a href="#ab"><i>Ab initio</i></a></li>
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                 <li onclick="display1('ros')"><a href="#ab"><i>Ab initio</i></a></li>
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                 <li><a href="#clu">Clustering</a></li>
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                 <li onclick="display1('ros')"><a href="#clu">Clustering</a></li>
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                 <li><a href="#ppd">Protein-Protein Docking</a></li>
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                 <li onclick="display1('ros')"><a href="#ppd">Protein-Protein Docking</a></li>
 
             </ul>
 
             </ul>
 
         </li>
 
         </li>
 
         <li>DLVO theory</li>
 
         <li>DLVO theory</li>
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         <li><a href="#ove1">Overview</a></li>
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         <li onclick="display1('nano')"><a href="#ove1">Overview</a></li>
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         <li><a href="#rep">Repulsion between Gold Nanoparticles</a></li>
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         <li onclick="display1('nano')"><a href="#rep">Repulsion between Gold Nanoparticles</a></li>
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        <br>
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        <li id="abr"><b>Abbreviations</b></li>
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        <li id="abr">E protein: dengue virus envelope protein</li>
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        <li id="abr">PTRS: peptide of tandem-repeated sequence</li>
 
     </ul>
 
     </ul>
 
     <svg class="section-nav-marker" width="200" height="200"></svg>
 
     <svg class="section-nav-marker" width="200" height="200"></svg>
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<div class="contents s12 m6 l4" id="text" style="display:none">
 
<div class="contents s12 m6 l4" id="text" style="display:none">
 
     <article>
 
     <article>
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         <section id="ros">
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         <section id="ros" style="display:none">
 
             <section id="ove">
 
             <section id="ove">
 
                 <h2>Overview</h2>
 
                 <h2>Overview</h2>
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                 <p>Our goal is to design peptides to imitate CLEC5A docking with dengue virus. In order to ensure the peptides and the envelope protein (E protein) of dengue virus have an interaction, all the structure of peptides and proteins and their interactions were modeled using Rosetta. First, we utilized RosettaCM (Comparative modeling with Rosetta) to generate the structure of E protein from a local strain (PL046) based on the crystal structure (PDB: 1OAN). Second, we used the <i>ab initio</i> method to predict the peptide structures purely based on their sequences. Then, we utilized the clustering method to cluster the results and find the most probable structure of the peptide. Finally, we verified the interactions between these predicted peptides and the E protein based on the global protein-protein docking. Figure 1. shows the flow of our simulation.</p>
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                 <p>Our goal is to design the peptides of tandem-repeated sequence (PTRSs) to imitate C-type lectin domain, family 5, member A (CLEC5A) docking with dengue virus. In order to ensure the PTRs and the envelope protein (E protein) of dengue virus have an interaction, all the structure of PTRSs and proteins and their interactions were modeled using Rosetta. First, we utilized RosettaCM (Comparative modeling with Rosetta) to generate the structure of E protein from a local strain (PL046) based on the crystal structure (PDB: 1OAN). Second, we used the <i>ab initio</i> method to predict the PTRSs structures purely based on their sequences. Then, we utilized the clustering method to cluster the results and find the most probable structure of the PTRS. Finally, we verified the interactions between these predicted PTRSs and the E protein based on the global protein-protein docking. Figure 1 shows the flow of our simulation.</p>
 
                 <br>
 
                 <br>
 
                 <div id="imginfo2">
 
                 <div id="imginfo2">
 
                     <img id="imginfo1" src="https://static.igem.org/mediawiki/2020/8/89/T--CCU_Taiwan--Model_flow.png">
 
                     <img id="imginfo1" src="https://static.igem.org/mediawiki/2020/8/89/T--CCU_Taiwan--Model_flow.png">
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                     <p>Figure 1. The flow of our simulation</p>
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                     <p>Figure 1. The flow of our simulation procedures</p>
 
                 </div>
 
                 </div>
 
             </section>
 
             </section>
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                             <li>PDB files generated from step 2</li>
 
                             <li>PDB files generated from step 2</li>
 
                         </ul>
 
                         </ul>
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                         <p>Output: About 10,000 results. (Figure 2. shows one of the results.)</p>
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                         <p>Output: About 10,000 results. (The lowest Rosetta score of the structure is shown in Figure 2)</p>
 
                         <br>
 
                         <br>
 
                         <section id='slide-button3'>Commands and Flags</section>
 
                         <section id='slide-button3'>Commands and Flags</section>
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                 <div id="imginfo2">
 
                 <div id="imginfo2">
 
                     <video width="90%" height="auto" muted src="https://static.igem.org/mediawiki/2020/0/04/T--CCU_Taiwan--Model_Rosetta3.mp4" loop autoplay="autoplay"></video>
 
                     <video width="90%" height="auto" muted src="https://static.igem.org/mediawiki/2020/0/04/T--CCU_Taiwan--Model_Rosetta3.mp4" loop autoplay="autoplay"></video>
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                     <p>Figure 2. E protein PL046 (cyan) based on homology (magenta)</p>
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                     <p>Figure 2. The homology structure of PL046 E protein in cyan based on the deposited structure (PDB: 1OAN) in magenta</p>
 
                 </div>
 
                 </div>
 
                 <br>
 
                 <br>
 
                 <div id="ab">
 
                 <div id="ab">
 
                     <h3><i>Ab initio</i></h3>
 
                     <h3><i>Ab initio</i></h3>
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                     <p>Purpose: To generate the structure of the peptides</p>
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                     <p>Purpose: To generate the structure of the PTRSs</p>
 
                     <p>Input: </p>
 
                     <p>Input: </p>
 
                     <ul>
 
                     <ul>
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                         <p>The last two inputs were generated from <a href="https://robetta.bakerlab.org/fragmentsubmit.jsp" target="_blank">Robetta</a> Fragment</p>
 
                         <p>The last two inputs were generated from <a href="https://robetta.bakerlab.org/fragmentsubmit.jsp" target="_blank">Robetta</a> Fragment</p>
 
                     </ul>
 
                     </ul>
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                     <p>Output: About 20,000 results. (Figure 3. shows two of the results.)</p>
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                     <p>Output: About 20,000 results. (Two of the representative structures are shown in Figure 3)</p>
 
                     <br>
 
                     <br>
 
                     <section id='slide-button4'>Commands and Flags</section>
 
                     <section id='slide-button4'>Commands and Flags</section>
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                 <div id="ppd">
 
                 <div id="ppd">
 
                     <h3>Protein-Protein Docking (global docking)</h3>
 
                     <h3>Protein-Protein Docking (global docking)</h3>
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                     <p>Purpose: To find the interaction between peptides and E Protein</p>
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                     <p>Purpose: To find the interaction between PTRSs and E Protein</p>
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                     <p>Input: The structures of ligand (peptide or CLEC5A) and receptor (E protein) in the same input file.</p>
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                     <p>Input: The structures of ligand (PTRS or CLEC5A) and receptor (E protein) in the same input file.</p>
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                     <p>Output: About 10,000 results. (Figure 4. shows the the most frequent sites among the results.)</p>
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                     <p>Output: About 10,000 results. (The most 100 frequent docking sites are shown in Figure 4)</p>
 
                     <br>
 
                     <br>
 
                     <section id='slide-button8'>Commands and Flags</section>
 
                     <section id='slide-button8'>Commands and Flags</section>
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                     <div id="imginfo2">
 
                     <div id="imginfo2">
 
                         <video width="90%" height="auto" muted src="https://static.igem.org/mediawiki/2020/6/62/T--CCU_Taiwan--Model_Rosetta4.mp4" loop autoplay="autoplay"></video>
 
                         <video width="90%" height="auto" muted src="https://static.igem.org/mediawiki/2020/6/62/T--CCU_Taiwan--Model_Rosetta4.mp4" loop autoplay="autoplay"></video>
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                         <p>Figure 4. 100 results of PTRS-1, PTRS-2 and E protein (PL046) docking respectively</p>
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                         <p>Figure 4. The best 100 results (based on the Rosetta score) of PTRS-1 or PTRS-2 docking to PL046 E protein (in red). The space above the plane (in grey) indicates the external surface of the virions, where the interactions occur.</p>
 
                     </div>
 
                     </div>
 
                     <br>
 
                     <br>
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         </section>
 
         </section>
 
         <br>
 
         <br>
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         <section id="nano" style="display:none">
 
             <section id="ove1">
 
             <section id="ove1">
 
                 <h2>Overview</h2>
 
                 <h2>Overview</h2>
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                 <p>The weakness of our design is that the peptides from the gold nanoparticles and the ones from the glass fiber compete for the same binding sites on the E protein. Moreover, if the E proteins on the virus particles are fully covered by the gold nanoparticles, there are no sites available to interact the peptides from the glass fiber.</p>
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                 <p>The weakness of our design is that the PTRSs from the gold nanoparticles and the ones from the glass fiber compete for the same binding sites on the E protein. Moreover, if the E proteins on the virus particles are fully covered by the gold nanoparticles, there are no sites available to interact the PTRSs from the glass fiber.</p>
 
             </section>
 
             </section>
 
             <br>
 
             <br>
 
             <section id="rep">
 
             <section id="rep">
 
                 <h2>Repulsion between gold nanoparticles</h2>
 
                 <h2>Repulsion between gold nanoparticles</h2>
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                 <p>To assess this potential problem, we used DLVO theory to calculate the repulsion between gold nanoparticles to estimate the number of gold nanoparticles that would bind to a virus particle. The structure of dengue virus is icosahedral, and there are nine E proteins on each surface. The distances between the potential binding sites can be obtained from the structure in protein data bank (1K4R). DLVO theory can be described as Equation 1.</p>
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                 <p>To assess this potential problem, we used DLVO theory to calculate the repulsion between gold nanoparticles to estimate the number of gold nanoparticles that would bind to a virus particle. The structure of dengue virus is icosahedral, and there are three E proteins on each surface. The distances between the potential binding sites can be obtained from the structure in protein data bank (1K4R). DLVO theory can be described as Equation 1.</p>
 
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                 <br>
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                 <h4>Equation 1. W<sub>total</sub>(D) = W<sub>a</sub>(D) + W<sub>r</sub>(D) = -AR/12D + 2πεε<sub>0</sub>R&Psi;<sub>&delta;</sub><sup>2</sup>exp(-κD)</h4>
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                 <h4>W<sub>total</sub>(D) = W<sub>a</sub>(D) + W<sub>r</sub>(D) = -AR/12D + 2πεε<sub>0</sub>R&Psi;<sub>&delta;</sub><sup>2</sup>exp(-κD) &emsp;&emsp; Equation 1. </h4>
 
                 <br>
 
                 <br>
 
                 <p>W<sub>total</sub>(D): total energy<br>
 
                 <p>W<sub>total</sub>(D): total energy<br>
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                 </p>
 
                 </p>
 
                 <br>
 
                 <br>
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                 <p>We took several representative positions on adjoining faces of the icosahedron to calculate the interactions between the gold nanoparticles based on DLVO theory. We found the total energies are all positive (Table 1), and these total energies are also larger than the typical biological interactions (~0.5 kcal/mol or 3.49 x10<sup>21</sup> J). The results suggest that there will always be free faces on the virus particles to interact with the peptides conjugated on the test line.</p>
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                 <p>We took several representative positions on adjoining faces of the icosahedron to calculate the interactions between the gold nanoparticles based on DLVO theory. We found the total energies are all positive (Table 1), and these total energies are also larger than the typical biological interactions (~0.5 kcal/mol or 3.49 x10<sup>21</sup> J). The results suggest that there will always be free faces on the virus particles to interact with the PTRS-2 conjugated on the test line.</p>
 
                 <br>
 
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Latest revision as of 16:23, 12 December 2020

Model

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