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

 
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<td align="center"><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> About our modeling</font></span></td><td><span style="font-family:Calibri;text-align:justify;"><font size="5"></br></br>為了能夠使我們更有效地拿到我們的指定抗菌肽，我們在設計序列時在AMPs的N-terminal加上了來自S.lividans的signal peptide。這個signal peptide在經過periplasmic space時會被peptidase辨認並且做切割。Peptidase會辨認signal peptide與相聯蛋白相接處的雙Ala，然後從中間將兩者分開。為了使peptidase能夠順利辨認signal peptide與target AMPs，我們在AMP的N-terminal多加了一個Ala氨基酸，供給辨認的切位點。
 
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我們利用模擬技術，利用原本的已知結構，去推測在我們多加了一個Ala的情況下，是否會影響AMPs的蛋白結構折疊。</br></br>
 
  
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In order to make us more efficient to get our peptide，so when we design our AMPs’s N-terminal.We add the signal peptide from S.lividans.When the signal peptide go through the periplasmic space, peptidase will identified it and cut. Peptidase will  identified signal peptide and connection protein’s double Ala at convergence. Then separate two parts. In order to make peptidase can be more success to  identify signal peptide and target AMPs. We add an Ala attach N-terminal in our AMP.To identify cutting site.</br></br>
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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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We ues protein secondary structure prediction,used known peptide structure.To surmise,if we add more Ala, whether it will affect our AMPs ‘protein structure folding.</br></br>
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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 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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<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:Arial Black;"><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:Arial Black;"><font size="7"><font-weight: 800;> with Ala attach </br>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:Arial Black;"><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:Arial Black;"><font size="7"><font-weight: 800;> without Ala attach </br>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 ><span style="font-family:Calibri;text-align:justify;"><font size="5">The 2nd column result shows most of our AMP corresponding seconadry
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Structure state are helix. and third column shows probability of correct prediction.</font></span>
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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 align="center"><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> Conclusion</font></span></td><td><span style="font-family:Calibri;text-align:justify;"><font size="5"></br></br>Signiferin以及Epinicidin-1都是由 a helix結構所構成，在我們的模擬分析後（寫上用什麼軟體分析），不管是signiferin還是Epinecidin-1在N-terminal多加了一個Ala後並不影響蛋白的摺疊結構。</br></br>
 
  
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Through the protein secondary structure prediction. The result shows both of Signiferin and Epinicidin-1 are a helix structure.
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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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Whatever is signiferin or Epinicidin-1,after we add an ala N-terminal, it won’t affect our AMPs ‘protein structure folding.
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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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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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