Difference between revisions of "Part:BBa K4165134"
Line 17: Line 17:
 
Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
 
Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
  
−
cbeta_deviations = 0, clashscore = 8.77, molprobity = 3.42, ramachandran_favored = 40, ramachandran_outliers = 40, Qmean_4 = -3.62452, Qmean6 = -2.48071
+
<html>
−
 
+
<style>
 +
table, th, td {
 +
  border:1px solid black; margin-left:auto;margin-right:auto;
 +
}
 +
</style>
 +
<body>
 +
<table style="width:65%">
 +
<table>
 +
  <tr>
 +
    <th>cbeta_deviations</th>
 +
    <th>clashscore</th>
 +
    <th>molprobity</th>
 +
    <th>ramachandran_favored</th>
 +
    <th>ramachandran_outliers</th>
 +
    <th>Qmean_4</th>
 +
    <th>Qmean_6</th>
 +
  </tr>
 +
  <tr>
 +
    <td>0</td>
 +
    <td>8.77</td>
 +
    <td>3.42</td>
 +
    <td>40</td>
 +
    <td>40</td>
 +
    <td>-3.62452</td>
 +
    <td>-2.48071</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
  
−
===Modeling===
+
===Dry Lab===
 +
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 
<html>
 
<html>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2n.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2n.jpg" style="margin-left:200px;" alt="" width="500" /></p>
Line 26: Line 55:
  
  
−
                  Figure 1.: 3D Model of H2N peptide Modelled by AlphaFold2.0 displayed in Pyomol
+
                    Figure 1.: 3D Model of H2N peptide Modelled by AlphaFold2.0 displayed in Pymol.
  
 
===References===
 
===References===

Revision as of 17:53, 11 October 2022


HTRA Binding Peptide 40

part encodes for a synthetic peptide that binds to the PDZ domain of HTRA1 protein

Usage and Biology

A reversed sequence of a high affinity binding peptide is proposed for binding to the PDZ domain of HTRA1.

We were motivated by our chosen Tau binding peptide since it was the inverted sequence of a high affinity peptide that shown better affinity, so we decided to try it with our HTRA1 BP.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Functional Parameters

Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 8.77 3.42 40 40 -3.62452 -2.48071

Dry Lab

Modeling 


                    Figure 1.: 3D Model of H2N peptide Modelled by AlphaFold2.0 displayed in Pymol.

References

Dammers, C., Yolcu, D., Kukuk, L., Willbold, D., Pickhardt, M., Mandelkow, E., ... & Funke, S. A. (2016). Selection and Characterization of Tau Binding ᴅ-Enantiomeric Peptides with Potential for Therapy of Alzheimer Disease. PLoS One, 11(12), e0167432.