Difference between revisions of "Team:Queens Canada/Parts"

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{{Queens_Canada}}
 
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        <nav id="qgemnav">
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        <ul>
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            <li><a href="https://2015.igem.org/Main_Page"><img src="https://static.igem.org/mediawiki/2015/f/fa/Qqq_IGEM_official_logo.png" /></a></li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada/Sponsorship">Sponsorship</a></li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada/Attributions">Attributions</a></li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada/Safety">Safety</a></li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada/Practices">Human Practices</a>
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                <ul>
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                    <li><a href="https://2015.igem.org/Team:Queens_Canada/Practices/Academics">Academics</a></li>
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                    <li><a href="https://2015.igem.org/Team:Queens_Canada/Practices/Outreach">Community Outreach</a></li>
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                    <li><a href="https://2015.igem.org/Team:Queens_Canada/Practices/IP">Intellectual Property</a></li>
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                </ul>
  
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<h2> Part Documentation</h2>
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            </li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada/Notebook">Notebook</a></li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada/Parts">Parts</a></li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada/Description">Project</a>
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                <ul>
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                    <li><a href="https://2015.igem.org/Team:Queens_Canada/Background">Background</a></li>
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                    <li><a href="https://2015.igem.org/Team:Queens_Canada/Modeling">Modeling</a></li>
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                    <li><a href="https://2015.igem.org/Team:Queens_Canada/AFP_Scaffold"> The Ice Queen</a></li>
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                    <li><a href="https://2015.igem.org/Team:Queens_Canada/Circ_AFP"> Icefinity</a></li>
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                </ul>
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            </li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada/Team">Team</a></li>
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            <li><a href="https://2015.igem.org/Team:Queens_Canada">Home</a></li>
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        </ul>
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    </nav>
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    </div>
  
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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        <img src="https://static.igem.org/mediawiki/2015/0/0e/Qqq_QGEM_Banner.png"/>
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    </div>
  
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            <h1 style="padding: 60px 0px 20px 0px;">OUR PARTS</h1>
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        <table border="2px">
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            <tr>
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                <th>Part Name</th>
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                <th>Type</th>
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                <th>Description</th>
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                <th>Length (bp)</th>
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            </tr>
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            <tr>
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                <td><a href="http://parts.igem.org/Part:BBa_K1831000">BBa_K1831000</a></td>
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                <td>Composite</td>
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                <td>NpuDnaE intein RFC[105] circularization construct using Type III AFP and a computer-optimized linker</td>
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                <td>804</td>
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            </tr>
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            <tr>
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                <td><a href="http://parts.igem.org/Part:BBa_K1831001">BBa_K1831001</a></td>
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                <td>Composite</td>
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                <td>Type III AFP with E-coil + His tag</td>
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                <td>421</td>
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            </tr>
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            <tr>
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                <td><a href="http://parts.igem.org/Part:BBa_K1831002">BBa_K1831002</a></td>
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                <td>Composite</td>
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                <td>T3-10 Scaffold with K-coiled-coil + His tag</td>
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                <td>816</td>
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            </tr>
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            <tr>
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                <td><a href="http://parts.igem.org/Part:BBa_K1831003">BBa_K1831003</a></td>
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                <td>Composite</td>
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                <td>Type III AFP with E-coil</td>
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                <td>407</td>
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            </tr>
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        </table>
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    <div id="Parts" style="padding: 20px 200px 20px 200px;">
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        <h2>BBa_K1831000</h2>
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            <p align="center"><em>NpuDnaE intein circularization construct using Type III AFP and a computer-optimized linker</em></p>
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            <img src="https://static.igem.org/mediawiki/2015/d/dc/Qqq_QGEM_BBa_K1831000.png" style="display: block; margin-left: auto; margin-right: auto;"/>
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            <p><strong>What:</strong> Starting from the NpuDnaE intein RFC [105] circularization construct BioBrick from Team Heidelberg 2014 (<a href="http://parts.igem.org/Part:BBa_K1362000">BBa_K1362000</a>) we developed a computationally-optimized linker sequence to circularize a Type III antifreeze protein. Our linker consists of the tripeptide GAA, which in addition to the extein scar CWE/RGK, links the N and C termini of a the Type III AFP (PDB file: 1AME) without straining the core protein structure or distorting the residues critical for ice-binding. Our BioBrick also added a constitutive T7 promoter (Part BBa_I14018) allowing expression of your circular protein without any additional sub-cloning steps.</p>
 +
            <p><strong>Why:</strong> Type III AFPs have a variety of potential applications in the oil and gas, food, and health industries, however these industries often use processes involving extreme temperatures, pH levels, and salt concentrations. Type III AFP is a particularly fragile protein as it denatures at 37<sup>o</sup>C. Circularizing the protein using our BioBrick affords greater stability at a wider variety of experimental conditions</p>
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<br>
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        <h2>BBa_K1831001</h2>
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            <p align="center"><em>Type III AFP with E-coil + His tag</em></p>
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            <img src="https://static.igem.org/mediawiki/2015/3/31/Qqq_QGEM_BBa_K1831001.png" style="display: block; margin-left: auto; margin-right: auto;"/>
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            <p><strong>What:</strong> This BioBrick is a fusion protein consisting of the E-coil domain of our coiled-coil system fused in-frame to the C-terminus of a Type III AFP. Type III AFP (PDB fIle: 1AME) is a moderately active antifreeze protein from the ocean pout, with a small (7Kb), globular structure. The E-coil refers to the coiled-coil with glutamic acid residues in the 'e' and 'g' positions of the helical wheel first used by Team Calgary 2013 ( <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189011">BBa_K1189011</a>). There is a His-tag at the C-terminus of the E-coil which provides an alternative purification method to ice-affinity.</p>
 +
            <p><strong>Why:</strong> The fusion of the E-coil to the Type III AFP will enable non-covalent, yet high affinity, specific attachment of AFPs to our protein scaffold and K-coil BioBrick (BBa_K1831002, see below). The interaction between the E- and K-coils involved oppositely charged residues, promoting the heterodimeric interaction of the coils that links AFPs to our scaffold. The addition of a His-tag to the C-terminus of the coil will allow for simple purification of the protein even for teams without access to an ice-affinity purification apparatus.</p>
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        <br>
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        <h2>BBa_K1831002</h2>
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            <p align="center"><em>T3-10 Scaffold with K-coiled-coil + His tag</em></p>
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            <img src="https://static.igem.org/mediawiki/2015/a/a3/Qqq_QGEM_BBa_K1831002.jpg" style="display: block; margin-left: auto; margin-right: auto;" />
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            <p><strong>What:</strong> A single subunit of the T3-10 self-assembling protein scaffold (Baker 2008) is fused in-frame to the K-coil from Team Calgary 2013’s parallel coiled-coil proteins (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189010">BBa_K1189010</a>). The 'K' denotes the charged lysine residues in the ‘e’ and ‘g’ positions of the helical wheel representation of the coils. A His-tag fused to the C-terminus of the coils allows quick purification. A flexible linker Gly-Ser between the K-coil and the His-tag prevents potential electrostatic interference between the two domains.</p>
 +
            <p><strong>Why:</strong> This fusion of the K-coil to each individual subunit means that once assembled into a multimer, multiple proteins with a complimentary E-coil domain (such as our Type III AFPs: BBa_K1831001, BBa_K1831003) can be non-covalently attached to the scaffold. By adding a flexible linker of Gly-Ser we incorporated a unique BamHI restriction site. This acts as a diagnostic marker for simplified cloning of our BioBrick into the expression vector of your choosing.</p>
 +
        <br>
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        <h2>BBa_K1831003</h2>
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            <p align="center"><em>Type III AFP with E-coil</em></p>
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            <img src="https://static.igem.org/mediawiki/2015/6/62/Qqq_QGEM_BBa_K1831003.png" style="display: block; margin-left: auto; margin-right: auto;"/>
 +
        <p><strong>What:</strong> This BioBrick is a fusion protein consisting of the E-coil domain of our coiled-coil system fused in-frame to the C-terminus of a Type III AFP. Type III AFP (PDB fIle: 1AME) is a moderately active antifreeze protein from the ocean pout, with a small (7Kb), globular structure. The E-coil refers to the coiled-coil with glutamic acid residues in the ‘e’ and ‘g’ positions of the helical wheel first used by Team Calgary 2013 (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1189011">BBa_K1189011</a>). This protein has been shown to be purified effectively by ice-affinity. If a His-tag is required for your purposes, see BBa_K1831001.</p>
 +
       
 +
        <p><strong>Why:</strong> The fusion of the E-coil to the Type III AFP will enable non-covalent, yet high affinity, specific attachment of AFPs to our protein scaffold and K-coil BioBrick (BBa_K1831002). The interaction between the E- and K-coils involved oppositely charged residues, promoting the heterodimeric interaction of the coils that links AFPs to our scaffold. There is no His-tag, but ice-affinity purification can be used. By including a His-tag on our K-coil fusion protein (our scaffold: BBa_K1831002), and not the AFP with E-coil, we have enabled simple separation of any non-interacting coiled-coil domains.</p>
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    </div>
  
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<h4>Note</h4>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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</div>
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    <div class="footer">
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        <a href="https://www.facebook.com/iGEMQueens?fref=ts"><img src="https://static.igem.org/mediawiki/2015/2/29/Qqq_QGEM_FB_FindUsOnFacebook.png" /> </a>
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        <a href="https://twitter.com/igemqueens"><img id="twitter" src="https://static.igem.org/mediawiki/2015/3/34/Qqq_QGEM_twitterlogo.png" /></a>
  
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<h4>Adding parts to the registry</h4>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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<h4>What information do I need to start putting my parts on the Registry?</h4>
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<p>The information needed to initially create a part on the Registry is:</p>
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<ul>
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<li>Part Name</li>
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<li>Part type</li>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<li>Design considerations</li>
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</ul>
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<p>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
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<h4>Inspiration</h4>
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
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<ul>
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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<h4>Part Table </h4>
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<groupparts>iGEM015 Example</groupparts>
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Latest revision as of 02:46, 17 September 2015

OUR PARTS

Part Name Type Description Length (bp)
BBa_K1831000 Composite NpuDnaE intein RFC[105] circularization construct using Type III AFP and a computer-optimized linker 804
BBa_K1831001 Composite Type III AFP with E-coil + His tag 421
BBa_K1831002 Composite T3-10 Scaffold with K-coiled-coil + His tag 816
BBa_K1831003 Composite Type III AFP with E-coil 407

BBa_K1831000

NpuDnaE intein circularization construct using Type III AFP and a computer-optimized linker

What: Starting from the NpuDnaE intein RFC [105] circularization construct BioBrick from Team Heidelberg 2014 (BBa_K1362000) we developed a computationally-optimized linker sequence to circularize a Type III antifreeze protein. Our linker consists of the tripeptide GAA, which in addition to the extein scar CWE/RGK, links the N and C termini of a the Type III AFP (PDB file: 1AME) without straining the core protein structure or distorting the residues critical for ice-binding. Our BioBrick also added a constitutive T7 promoter (Part BBa_I14018) allowing expression of your circular protein without any additional sub-cloning steps.

Why: Type III AFPs have a variety of potential applications in the oil and gas, food, and health industries, however these industries often use processes involving extreme temperatures, pH levels, and salt concentrations. Type III AFP is a particularly fragile protein as it denatures at 37oC. Circularizing the protein using our BioBrick affords greater stability at a wider variety of experimental conditions


BBa_K1831001

Type III AFP with E-coil + His tag

What: This BioBrick is a fusion protein consisting of the E-coil domain of our coiled-coil system fused in-frame to the C-terminus of a Type III AFP. Type III AFP (PDB fIle: 1AME) is a moderately active antifreeze protein from the ocean pout, with a small (7Kb), globular structure. The E-coil refers to the coiled-coil with glutamic acid residues in the 'e' and 'g' positions of the helical wheel first used by Team Calgary 2013 ( BBa_K1189011). There is a His-tag at the C-terminus of the E-coil which provides an alternative purification method to ice-affinity.

Why: The fusion of the E-coil to the Type III AFP will enable non-covalent, yet high affinity, specific attachment of AFPs to our protein scaffold and K-coil BioBrick (BBa_K1831002, see below). The interaction between the E- and K-coils involved oppositely charged residues, promoting the heterodimeric interaction of the coils that links AFPs to our scaffold. The addition of a His-tag to the C-terminus of the coil will allow for simple purification of the protein even for teams without access to an ice-affinity purification apparatus.


BBa_K1831002

T3-10 Scaffold with K-coiled-coil + His tag

What: A single subunit of the T3-10 self-assembling protein scaffold (Baker 2008) is fused in-frame to the K-coil from Team Calgary 2013’s parallel coiled-coil proteins (BBa_K1189010). The 'K' denotes the charged lysine residues in the ‘e’ and ‘g’ positions of the helical wheel representation of the coils. A His-tag fused to the C-terminus of the coils allows quick purification. A flexible linker Gly-Ser between the K-coil and the His-tag prevents potential electrostatic interference between the two domains.

Why: This fusion of the K-coil to each individual subunit means that once assembled into a multimer, multiple proteins with a complimentary E-coil domain (such as our Type III AFPs: BBa_K1831001, BBa_K1831003) can be non-covalently attached to the scaffold. By adding a flexible linker of Gly-Ser we incorporated a unique BamHI restriction site. This acts as a diagnostic marker for simplified cloning of our BioBrick into the expression vector of your choosing.


BBa_K1831003

Type III AFP with E-coil

What: This BioBrick is a fusion protein consisting of the E-coil domain of our coiled-coil system fused in-frame to the C-terminus of a Type III AFP. Type III AFP (PDB fIle: 1AME) is a moderately active antifreeze protein from the ocean pout, with a small (7Kb), globular structure. The E-coil refers to the coiled-coil with glutamic acid residues in the ‘e’ and ‘g’ positions of the helical wheel first used by Team Calgary 2013 (BBa_K1189011). This protein has been shown to be purified effectively by ice-affinity. If a His-tag is required for your purposes, see BBa_K1831001.

Why: The fusion of the E-coil to the Type III AFP will enable non-covalent, yet high affinity, specific attachment of AFPs to our protein scaffold and K-coil BioBrick (BBa_K1831002). The interaction between the E- and K-coils involved oppositely charged residues, promoting the heterodimeric interaction of the coils that links AFPs to our scaffold. There is no His-tag, but ice-affinity purification can be used. By including a His-tag on our K-coil fusion protein (our scaffold: BBa_K1831002), and not the AFP with E-coil, we have enabled simple separation of any non-interacting coiled-coil domains.