Team:Gothenburg-Sweden/Results

From 2010.igem.org

(Difference between revisions)
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                                          <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us#intro">Introduction</a>
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                                          <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us#cth">CHALMERS</a></li>
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                                          <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us#svs">Supervisors</a></li>
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                                          <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us#sts">Students</a>
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                              <div class="Title1">FUSS</div>
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                                            <a href="#">What's all about?</a>
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                                            <a href="#">Background</a>
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                                            <a href="#">Protein Fusion</a>
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                                            <a href="#"> Methods</a>
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                                            <a href="#">Preliminary Results</a>
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                      <p>coming soon...</p>
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                                          <p>11</p>
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                                          <div class="newsright"><a href="#">August 11, 2010</a>
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                                          <p> The PCR reaction from yesterday was checked on a gel. α should be ... </p>
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<td><p>Since the structure of the subunits in our protein complex is not  complete and the fluorescent proteins are to be studied along with the complex,  we have modeled the entire complex along with the FPs computationally. There  are two main steps involved in the process of modeling this complex  computationally. First step is to predict the structure of each subunit and  then to dock them to find how they bind to each other.</p>
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    We obtained the entire primary structure (protein sequence) of all three  subunits (snf1, sip2, snf4) and the fluorescent proteins (ECFP and EYFP) from  the Protein Database (PDB). We need to find the structure of the 3 subunits and  also the fusion proteins which are ECFP-snf1, EYFP-snf4 and ECFP-snf4-EYFP. So,  here for the fusion protein sequence we combined the sequence of FPs and the  subunits accordingly.<br>
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    Now we just have the sequence of all 6 proteins including the fusion  proteins and we need to find the structure of each one separately. The most  prominent method used to find the tertiary structure of the proteins from its  sequence is “homology modeling”.  Here  they compare the target sequence to the database and they find the alignment  and predict the structure from that alignment. We used this method and found  the following predictions using soft-wares.</p>
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  <div class="Title3">News</div>
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  <p><strong>Structure Predictions in  2D</strong></p>
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                                    <p>Göteborgs-Posten, a major daily newspaper in Sweden with the second largest national circulation, published an article involving the interview with our team...
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    Alpha                                    Beta                            Gamma<br>
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                                    <br><br> </p>
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  <img width="205" height="189" src="http://2010.igem.org/wiki/images/3/31/Results_clip_image008.jpg" alt="cfp_alpha.jpg"><img width="201" height="188" src="http://2010.igem.org/wiki/images/1/1f/Results_clip_image010.jpg" alt="yfp_gamma.jpg"><img width="205" height="189" src="http://2010.igem.org/wiki/images/7/73/Results_clip_image012.jpg" alt="cfp_gamma_yfp.jpg"> <br>
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<div class="read"><a href="#">read more</a></div>
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      ECFP_Alpha                    EYFP_Gamma                  ECFP_Gamma_EYFP</p>
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  <p align="center"><strong>DOCKING</strong><br>
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    We have got the structures so far and  now we have to find how they can bind to each other. This can be obtained by  means of “Protein Docking”. This method will obtain the surface of the  molecules and try to bind them together by considering various factors like  surface complementarily, electrostatics, bond angles etc. Here, we found the  appropriate docking for two different approaches of tagging the FPs and just  the subunits.</p>
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  <p>First, we docked all three subunits  without the FPs. This is just to study how the subunits bind themselves  normally. This is the predicted structure of the entire complex.</p>
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      Predicted  SNF1 Complex</p>
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  <p>Secondly, we docked the alpha subunit with  ECFP on its N-terminal end, beta subunit and gamma subunit with EYFP on its  N-terminal end. Here, from the picture below you can see that the distance  between the FPs is 51.10Å. This would give some good results for the FRET  analysis.</p>
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  <div id="myfooter">  <p>   <a href="#">Home</a> | <a href="#">CTH</a> | <a href="#">Sponsors</a> | <a href="#">About Us</a> | <a href="#">Contact Us</a></p> <p>Chalmers University of Technology, Gothenburg, SWEDEN</p>
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                          <strong><em>Predicted FPs  orientation with SNF1 complex when they are tagged to alpha (snf1) and gamma (snf4)  subunits to their N-terminal ends</em></strong></p>
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  <p>The third docking is to find the binding of alpha, beta and gamma with FPs on its N- and C- terminal ends. Here, the  distance between the two chromophores is shown as 92.70Å in the figure below.  This is because of the reason that the FPs are oriented exactly in opposite  directions. But in reality it might be closer than predicted which would help  in FRET analysis. </p>
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                          <strong><em>Predicted FPs  orientation in the SNF1 complex when they are tagged to the N- and C- terminal  ends of the gamma (snf4) subunit</em></strong></p>
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<td align="center" class="style1"><a href="http://2010.igem.org/Team:Gothenburg-Sweden">Home</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      <a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us">About us </a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      |      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://www.chalmers.se/en/">Chalmers</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      |      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://2010.igem.org/Team:Gothenburg-Sweden/Sponsors">Sponsors</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;      |      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://2010.igem.org/Team:Gothenburg-Sweden/Contact">Contact Us</a></td>
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