Difference between revisions of "Team:TecCEM/Basic Part"

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{{TecCEM}}
 
{{TecCEM}}
 
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    div.parts-div a:vistied {
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<div class="column full_size judges-will-not-evaluate">
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        color: #333333 !important;
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<h3>★  ALERT! </h3>
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        text-decoration: none !important;
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<div id="gif-title" class="text-parts">
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    <img src="https://static.igem.org/mediawiki/2018/4/4e/T--TecCEM--Cells--Interlab.gif" alt="Cell Gif">
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    <h1>Basic Parts</h1>
 
</div>
 
</div>
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<div class="wrapper">
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    <nav class="sidebar-index d-none d-md-block">
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        <div class="sidebar-header">
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            <h3>Parts/ Basic Parts</h3>
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        </div>
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        <a href="#partsSubmenu" data-toggle="collapse" aria-expanded="false" data-offset="100" data-change="sidemenu">
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            <span data-change="el" class="d-inline-block open"></span>
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            Index
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        </a>
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        <ul class="collapse list-unstyled" id="partsSubmenu">
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            <li>
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                <a data-target="#K2719000">BBa_K2719000</a>
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            </li>
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            <li>
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                <a data-target="#K2719001">BBa_K2719001</a>
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            </li>
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            <li>
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                <a data-target="#K2719002">BBa_K2719002</a>
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            </li>
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            <li>
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                <a data-target="#K2719003">BBa_K2719003</a>
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            </li>
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            <li>
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                <a data-target="#K2719004">BBa_K2719004</a>
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            </li>
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            <li>
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                <a data-target="#K2719006">BBa_K2719006</a>
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            </li>
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            <li>
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                <a data-target="#K2719008">BBa_K2719008</a>
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            </li>
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        </ul>
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    </nav>
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    <div class="content parts-div">
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        <div class="container">
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            <div class="row">
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                <div class="col">
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                    <h1>Basic Parts</h1>
  
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                    <h2 id="K2719000"><a href="http://parts.igem.org/Part:BBa_K2719000">BBa_K2719000</a>: GST Coding
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<div class="clear"></div>
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                        site</h2>
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                    <p>Glutathione S-transferase (GST) is a peptide derived from Schistosoma japonicum, in which a
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                        target
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                        protein may be fused on the N-terminal. This fusion allows the purification of the target
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<div class="column full_size">
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                        protein using
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<h1>Basic Parts</h1>
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                        glutathione affinity and maximize the presence of the protein in soluble state, rather than on
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<p>
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                        inclusion bodies. This tag may be later removed by adding a protease recognition site between
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A <b>basic part</b> is a functional unit of DNA that cannot be subdivided into smaller component parts. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_R0051">BBa_R0051</a> is an example of a basic part, a promoter regulated by lambda cl.
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                        GST and
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</p>
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                        the target protein (Harper & Speicher, 2013).</p>
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                    <div class="text-center">
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<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are <b>many</b> opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. </p>
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                        <figure class="figure text-left">
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                            <img src="https://static.igem.org/mediawiki/2018/4/4f/T--TecCEM--GST3DStructure.png" class="figure-img img-fluid rounded"
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                                alt="GST Coding Site">
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                            <figcaption class="figure-caption">Figure 1. GST 3D structure, modelled with Swiss-Model</figcaption>
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                        </figure>
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                    </div>
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                    <h2 id="K2719001"><a href="http://parts.igem.org/Part:BBa_K2719001">BBa_K2719001</a>: Tenascin
 +
                        Domain V</h2>
 +
                    <p>Tenascin is a human protein that is involved in tissue regeneration processes. The domain V
 +
                        contains
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                        heparin binding sites that are fundamental for our scaffold.
 +
                        Also contains multiple growth factor binding sites and, even when we are only working with
 +
                        leptin is
 +
                        important because it would help in the improvement of tissue regeneration. In addition, it has
 +
                        been
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                        reported that it participated stem cells signalling.</p>
 +
                    <div class="text-center">
 +
                        <figure class="figure text-left">
 +
                            <img src="https://static.igem.org/mediawiki/2018/3/30/T--TecCEM--TCD5DomainV3DStructure.png"
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                                class="figure-img img-fluid rounded" alt="Tenascin
 +
                                Domain V">
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                            <figcaption class="figure-caption">Figure 2. Tenascin 5 domain V 3D structure, modelled
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                                with Swiss-Model</figcaption>
 +
                        </figure>
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                    </div>
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                    <h2 id="K2719002"><a href="http://parts.igem.org/Part:BBa_K2719002">BBa_K2719002</a>: GST-Tenascin
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                        Domain V Fusion Protein</h2>
 +
                    <p>This part is the fusion between both proteins and that helps us to simplify tenascin
 +
                        purification. GST
 +
                        has tenascin fused on the N-terminal. For more information see BBa_K2719001 and BBa_K2719003.</p>
 +
                    <div class="text-center">
 +
                        <figure class="figure text-left">
 +
                            <img src="https://static.igem.org/mediawiki/2018/1/10/T--TecCEM--TCD5%2BGST3DStructure.png" class="figure-img img-fluid rounded"
 +
                                alt="GST-Tenascin Domain V Fusion Protein">
 +
                            <figcaption class="figure-caption">Figure 3. Tenascin V- GST fusion protein 3D structure,
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                                modeled with Swiss-Model</figcaption>
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                        </figure>
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                    </div>
 +
                    <h2 id="K2719003"><a href="http://parts.igem.org/Part:BBa_K2719003">BBa_K2719003</a>: Optimized GST
 +
                        Coding
 +
                        site</h2>
 +
                    <p>GST coding sequence (see part BBa_K2719000) with codon optimization for <i>E.coli</i> BL21 (DE3) to
 +
                        avoid
 +
                        complications in the production of this recombinant protein.</p>
 +
                    <div class="text-center">
 +
                        <figure class="figure text-left">
 +
                            <img src="https://static.igem.org/mediawiki/2018/4/4f/T--TecCEM--GST3DStructure.png" class="figure-img img-fluid rounded"
 +
                                alt="GST 3D structure, modelled with Swiss-Model">
 +
                            <figcaption class="figure-caption">Figure 4. GST 3D structure, modelled with Swiss-Model</figcaption>
 +
                        </figure>
 +
                    </div>
 +
                    <h2 id="K2719004"><a href="http://parts.igem.org/Part:BBa_K2719004">BBa_K2719004</a>: Tenascin
 +
                        Fibronectin
 +
                        Domains</h2>
 +
                    <p>Coding sequence from tenascin fibronectin domains I-V have the property of interacting with the
 +
                        proliferation of fibroblast, but the domain with the main characteristic previously mentioned
 +
                        is domain
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                        V (see part BBa_K2719001).</p>
 +
                    <div class="text-center">
 +
                        <figure class="figure text-left">
 +
                            <img src="https://static.igem.org/mediawiki/2018/e/e9/T--TecCEM--TCD53DStructure.png" class="figure-img img-fluid rounded"
 +
                                alt="Tenascin Fibronectin Domains">
 +
                            <figcaption class="figure-caption">Figura 5. Tenascin V Fibronectin Domains 3D Structure.
 +
                                Modelled with Swiss-Model</figcaption>
 +
                        </figure>
 +
                    </div>
 +
                    <h2 id="K2719006"><a href="http://parts.igem.org/Part:BBa_K2719006">BBa_K2719006</a>: Collagen V-
 +
                        like
 +
                        protein coding
 +
                        site</h2>
 +
                    <p>Collagen V is one of the main proteins involved in the extracellular matrix, thus it would be
 +
                        important
 +
                        in the structure of our scaffold. The main challenge for producing recombinant collagen V is
 +
                        that for
 +
                        its correct structure it requires post-traductional modifications, specially the hydroxylation
 +
                        of
 +
                        proline. To overcome this challenge, we designed this part to incorporate hydroxyproline, a
 +
                        non-canonical amino acid. For its proper incorporation, this part is optimized for its use on
 +
                        <i>E.coli</i>
 +
                        Rosetta (DE3).</p>
 +
                    <div class="text-center">
 +
                        <figure class="figure text-left">
 +
                            <img src="https://static.igem.org/mediawiki/2018/0/0e/T--TecCEM--ColV2DStructure.png" class="figure-img img-fluid rounded"
 +
                                alt="Collagen V-
 +
                                like
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                                protein coding
 +
                                site">
 +
                            <figcaption class="figure-caption">Figure 6. 2D structure of Collagen V-like</figcaption>
 +
                        </figure>
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                    </div>
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                    <h2 id="K2719008"><a href="http://parts.igem.org/Part:BBa_K2719008">BBa_K2719008</a>: Leptin coding
 +
                        site.</h2>
 +
                    <p>This is one of the most important parts because is the growth factor that we are using for
 +
                        accelerating
 +
                        the process of skin regeneration. Is a protein that is found in adipocytes cells on many living
 +
                        beings
 +
                        and it has been discovered that it has a regenerating property, because it has been found in
 +
                        many wound
 +
                        repair processes. It has been shown that it increases glucose intake speeding up metabolism,
 +
                        thus,
 +
                        accelerating cell proliferation.</p>
 +
                    <div class="text-center">
 +
                        <figure class="figure text-left">
 +
                            <img src="https://static.igem.org/mediawiki/2018/d/d3/T--TecCEM--Lep3DStructure.png" class="figure-img img-fluid rounded"
 +
                                alt="Leptin coding site">
 +
                            <figcaption class="figure-caption">Figure 7. Leptin 3D prediction modelled with Swiss Model</figcaption>
 +
                        </figure>
 +
                    </div>
 +
                </div>
 +
            </div>
 +
        </div>
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    </div>
 
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<h3>Note</h3>
 
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<p>This page should list all the basic parts your team has made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page. Remember judges will only look at the first part in the list for the Best Basic Part award, so put your best part first!</p>
 
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<h3>Best Basic Part Special Prize</h3>
 
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<p> To be eligible for this award, this part must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts. If you have a part you wish to nominate your team for this <a href="https://2018.igem.org/Judging/Awards">special prize</a>, make sure you add your part number to your <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.
 
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<br><br>
 
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<b>Please note:</b> Judges will only look at the first part number you list, so please only enter ONE (1) part number in the judging form for this prize. </p>
 
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{{TecCEM/Footer}}

Latest revision as of 00:44, 18 October 2018

Cell Gif

Basic Parts

Basic Parts

BBa_K2719000: GST Coding site

Glutathione S-transferase (GST) is a peptide derived from Schistosoma japonicum, in which a target protein may be fused on the N-terminal. This fusion allows the purification of the target protein using glutathione affinity and maximize the presence of the protein in soluble state, rather than on inclusion bodies. This tag may be later removed by adding a protease recognition site between GST and the target protein (Harper & Speicher, 2013).

GST Coding Site
Figure 1. GST 3D structure, modelled with Swiss-Model

BBa_K2719001: Tenascin Domain V

Tenascin is a human protein that is involved in tissue regeneration processes. The domain V contains heparin binding sites that are fundamental for our scaffold. Also contains multiple growth factor binding sites and, even when we are only working with leptin is important because it would help in the improvement of tissue regeneration. In addition, it has been reported that it participated stem cells signalling.

Tenascin Domain V
Figure 2. Tenascin 5 domain V 3D structure, modelled with Swiss-Model

BBa_K2719002: GST-Tenascin Domain V Fusion Protein

This part is the fusion between both proteins and that helps us to simplify tenascin purification. GST has tenascin fused on the N-terminal. For more information see BBa_K2719001 and BBa_K2719003.

GST-Tenascin Domain V Fusion Protein
Figure 3. Tenascin V- GST fusion protein 3D structure, modeled with Swiss-Model

BBa_K2719003: Optimized GST Coding site

GST coding sequence (see part BBa_K2719000) with codon optimization for E.coli BL21 (DE3) to avoid complications in the production of this recombinant protein.

GST 3D structure, modelled with Swiss-Model
Figure 4. GST 3D structure, modelled with Swiss-Model

BBa_K2719004: Tenascin Fibronectin Domains

Coding sequence from tenascin fibronectin domains I-V have the property of interacting with the proliferation of fibroblast, but the domain with the main characteristic previously mentioned is domain V (see part BBa_K2719001).

Tenascin Fibronectin Domains
Figura 5. Tenascin V Fibronectin Domains 3D Structure. Modelled with Swiss-Model

BBa_K2719006: Collagen V- like protein coding site

Collagen V is one of the main proteins involved in the extracellular matrix, thus it would be important in the structure of our scaffold. The main challenge for producing recombinant collagen V is that for its correct structure it requires post-traductional modifications, specially the hydroxylation of proline. To overcome this challenge, we designed this part to incorporate hydroxyproline, a non-canonical amino acid. For its proper incorporation, this part is optimized for its use on E.coli Rosetta (DE3).

Collagen V- like protein coding site
Figure 6. 2D structure of Collagen V-like

BBa_K2719008: Leptin coding site.

This is one of the most important parts because is the growth factor that we are using for accelerating the process of skin regeneration. Is a protein that is found in adipocytes cells on many living beings and it has been discovered that it has a regenerating property, because it has been found in many wound repair processes. It has been shown that it increases glucose intake speeding up metabolism, thus, accelerating cell proliferation.

Leptin coding site
Figure 7. Leptin 3D prediction modelled with Swiss Model