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

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<tr><td align="center"><h1><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> About our modeling</font></span></h1></td></tr>
 
<tr><td align="center"><h1><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> About our modeling</font></span></h1></td></tr>
 
<tr><td><h1><span style="font-family:Calibri;text-align:left;"><font size="5">
 
<tr><td><h1><span style="font-family:Calibri;text-align:left;"><font size="5">
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In order to have more efficient to get our AMPs, we treated signal peptide upstream of the N-terminal of mature antimicrobial peptides. This signal peptide is comes from chitinase C of S.lividans (MGFRHKAAALAATLALPLAGLVGLASPAQA). When the pre-mature peptides go through the periplasmic space, peptidase will identified the cleavage site Ala-Gln-Ala and cut at the double Ala between the signal and mature peptide. </br></br>
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To increase efficiency in isolating our AMPs, we introduced a signal peptide upstream of the N-terminal of mature antimicrobial peptides. This signal peptide is obtained from chitinase C of S.lividans (MGFRHKAAALAATLALPLAGLVGLASPAQA). When the premature peptides enter the periplasmic space, peptidase will identify the cleavage site Ala-Gln-Ala and cut at the double Ala between the signal and mature peptide. </br></br>
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To make sure the secretion system is work we attach an Ala at the N-terminal of AMPs. We used protein secondary structure prediction software base on the known peptide structure to analysis whether the attached Ala affect the peptide folding process or not.
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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">
 
<table width="95%"  align="center">
 
<tr><td><h1><span style="font-family:Calibri;text-align:justify;"><font size="5"></br>
 
<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 we predict.
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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 second column shows that AMPs corresponding secondary structure state are still a-helix.  
 
The third column shows the probability of correct prediction.
 
The third column shows the probability of correct prediction.
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<table width="95%"  align="center">
 
<table width="95%"  align="center">
 
<tr><td><h1><span style="font-family:Calibri;text-align:justify;"><font size="5"></br>
 
<tr><td><h1><span style="font-family:Calibri;text-align:justify;"><font size="5"></br>
−
The first column shows the amino acid sequence we predict.
+
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 second column shows that AMPs corresponding secondary structure state are still a-helix.  
 
The third column shows the probability of correct prediction.
 
The third column shows the probability of correct prediction.
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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>
 
<tr><td align="center"><h1><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> Conclusion</font></span></h1></td></tr>
 
<tr><td><h1><span style="font-family:Calibri;text-align:justify;"><font size="5"></br>
 
<tr><td><h1><span style="font-family:Calibri;text-align:justify;"><font size="5"></br>
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Through the secondary structure predicted. The result shows whatever Signiferin or Epinecidin-1 the attached of Ala didn’t affect peptide-folding process. They are still a-helix structure.
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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.
 
</br></br>
 
</br></br>
 
</font></span></h1></td></tr>  
 
</font></span></h1></td></tr>  

Revision as of 15:19, 15 September 2015

About our modeling

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

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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