Difference between revisions of "Team:TCU Taiwan/Modeling/Protein structure"

 
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<h2 align="center";><span style="font-family:AR BONNIE,Comic Sans MS;"><font size="10"><font-weight: 1000;> </br>Secondary Structure Prediction
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</h2>
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<tr><td align="justify" ><h1><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> About our modeling</font></span></h1></td></tr>
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<tr><td><h1><span style="font-family:Calibri;text-align:left;"><font size="5">
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To increase efficiency in isolating our AMPs, we introduced a signal peptide upstream of the N-terminal of our AMPs. This signal peptide is obtained from chitinase C of S.lividans (MGFRHKAAALAATLALPLAGLVGLASPAQA). When the fusion peptides enter the periplasmic space, peptidase will identify the cleavage site Ala-Gln-Ala and cut at the double Ala between the signal and AMPs. </br></br>
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To ensure and verify this process, we have attached an Ala at the N-terminal of AMPs. When applying a protein secondary structure prediction software base on the known peptide structure, we can analyze whether the attached Ala may have an effect on the peptide folding process.
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<table width="95%"  align="center">
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<tr><td align="left"><h1><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> Signiferin peptide structure analysis</font></span></h1></td></tr>
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    <td width="90%" align="center"><img src="https://static.igem.org/mediawiki/2015/e/ee/2015tcutaiwanModelingwithoutA1.jpg" align=center width="80%"  title="Result 1"></td>
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<td align="center"><span style="font-family:AR BONNIE,Comic Sans MS;"><font size="7"><font-weight: 700;> About our modeling</br></br></br></br></br></br></br></font></span></td>
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  </tr>
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    <td width="45%" align="center"><img src="https://static.igem.org/mediawiki/2015/f/f8/2015tcutaiwanModelingwithA1.jpg" align=center width="80%"  title="Result 1"></td>
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<table width="95%"  align="center">
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<tr><td><h1><span style="font-family:Calibri;text-align:justify;"><font size="5"></br>
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The first column shows the amino acid sequence that we predict.
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The second column shows that AMPs corresponding secondary structure state are still a-helix.
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The third column shows the probability of correct prediction.
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    <td width="45%" align="center"><span style="font-family:AR BONNIE,Comic Sans MS;"><font size="7"><font-weight: 800;> Signiferin</br></font></span><img src="https://static.igem.org/mediawiki/2015/1/17/2015tcutaiwanmodelingsigaddA.JPG" align=center width="72%"  title="with amino acid A"></td>
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<tr><td align="left"><h1><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> Epinicedin-1 pepetide structure analysis</font></span></h1></td></tr>
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    <td width="45%" align="center"><span style="font-family:AR BONNIE,Comic Sans MS;"><font size="7"><font-weight: 800;> with Ala attach N-terminal</br></font></span><img src="https://static.igem.org/mediawiki/2015/2/2a/2015tcutaiwanmodelingdataSigaddA.JPG" align=center width="72%"  title="Result 1"></td>
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  <td width="45%" align="center"><img src="https://static.igem.org/mediawiki/2015/8/82/2015tcutaiwanModelingepi-1withoutA1.jpg" align=center width="80%"  title="Result 4"></td>
 
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<td width="45%" align="center"><span style="font-family:AR BONNIE,Comic Sans MS;"><font size="7"><font-weight: 800;> Signiferin</br></font></span><img src="https://static.igem.org/mediawiki/2015/6/67/2015tcutaiwanmodelingsigwithoutA.JPG" align=center width="72%"  title="without amino acid A"></td>
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<td width="90%" align="center"><img src="https://static.igem.org/mediawiki/2015/1/10/2015tcutaiwanigemModelingepi-1withA1.jpg" align=center width="80%"  title="Result 3"></td>
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     <td width="45%"  align="center"><span style="font-family:AR BONNIE,Comic Sans MS;"><font size="7"><font-weight: 800;> without Ala attach N-terminal</br><img src="https://static.igem.org/mediawiki/2015/1/12/2015tcutaiwanmodelingdataSigwithoutA.JPG" align=center width="72%"  title="Result 2"></font></span></td>
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<tr><td><h1><span style="font-family:Calibri;text-align:justify;"><font size="5"></br>
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    <td align="center"><span style="font-family:AR BONNIE,Comic Sans MS;"><font size="7"><font-weight: 800;> Summary</br></br></br></br></br></br></br></font></span></td>
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The first column shows the amino acid sequence that we predict.
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  </tr>  
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The second column shows that AMPs corresponding secondary structure state are still a-helix.
 +
The third column shows the probability of correct prediction.
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</br></br>
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</font></span></h1></td></tr>
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<table width="95%"  align="center">
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<tr><td align="center"><h1><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> Conclusion</font></span></h1></td></tr>
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<tr><td><h1><span style="font-family:Calibri;text-align:justify;"><font size="5"></br>
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Through the analysis of the peptide secondary structure and confirmation of the -helix structure, the results show whether Ala is attached to Signiferin or Epinecidin-1, the peptide did not affect the peptide folding process. process.
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</br></br>
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</font></span></h1></td></tr>  
 
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Latest revision as of 16:38, 18 September 2015

About our modeling

To increase efficiency in isolating our AMPs, we introduced a signal peptide upstream of the N-terminal of our AMPs. This signal peptide is obtained from chitinase C of S.lividans (MGFRHKAAALAATLALPLAGLVGLASPAQA). When the fusion peptides enter the periplasmic space, peptidase will identify the cleavage site Ala-Gln-Ala and cut at the double Ala between the signal and AMPs.

To ensure and verify this process, we have attached an Ala at the N-terminal of AMPs. When applying a protein secondary structure prediction software base on the known peptide structure, we can analyze whether the attached Ala may have an effect on the peptide folding process.

Signiferin peptide structure analysis


The first column shows the amino acid sequence that we predict. The second column shows that AMPs corresponding secondary structure state are still a-helix. The third column shows the probability of correct prediction.

Epinicedin-1 pepetide structure analysis


The first column shows the amino acid sequence that we predict. The second column shows that AMPs corresponding secondary structure state are still a-helix. The third column shows the probability of correct prediction.

Conclusion


Through the analysis of the peptide secondary structure and confirmation of the -helix structure, the results show whether Ala is attached to Signiferin or Epinecidin-1, the peptide did not affect the peptide folding process. process.



             
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