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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<tr><td align="center"><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> About our modeling</font></span></td></tr><tr><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幾丁質酶C的signal peptide (附上氨基酸序列)。這個pre-mature peptide在經過periplasmic space時會被peptidase辨認並且做切割。Peptidase會辨認signal peptide 上Ala-Gln-Ala序列，並且從signal和mature peptide中間的兩個Ala間將之分開。為了使peptidase能夠順利辨認並且切割，我們在AMP的N-terminal多加了一個Ala氨基酸，以確保整個系統能順利運作。
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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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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。
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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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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 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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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 ><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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<tr><td ><span style="font-family:Calibri;text-align:justify;"><font size="5">The first column shows the amino acid sequence we predict.
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Structure state are helix. and third column shows probability of correct prediction.</font></span>
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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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<tr><td align="center"><span style="font-family:Arial Black;"><font size="7"><font-weight: 700;> Conclusion</font></span></td><td></tr><tr><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，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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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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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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Revision as of 02:04, 8 September 2015

About our modeling


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幾丁質酶C的signal peptide (附上氨基酸序列)。這個pre-mature peptide在經過periplasmic space時會被peptidase辨認並且做切割。Peptidase會辨認signal peptide 上Ala-Gln-Ala序列，並且從signal和mature peptide中間的兩個Ala間將之分開。為了使peptidase能夠順利辨認並且切割，我們在AMP的N-terminal多加了一個Ala氨基酸，以確保整個系統能順利運作。 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。

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.

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.

Signiferin
 with Ala attach
N-terminal
Signiferin
 without Ala attach
N-terminal
The first column shows the amino acid sequence 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.



Signiferin以及Epinicidin-1都是由 a helix結構所構成，在我們的模擬分析後，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。

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.

Conclusion


             
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