Difference between revisions of "Part:BBa K4165130"

(→‎Modeling)
Line 15: Line 15:
 
Got score of 5 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
 
Got score of 5 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
  
−
cbeta_deviations = 0, clashscore = 0, molprobity = 1.37, ramachandran_favored = 66.67, ramachandran_outliers = 0, Qmean_4 = 2.023586, Qmean6 = 1.78381
+
<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>0</td>
 +
    <td>1.37</td>
 +
    <td>66.67</td>
 +
    <td>0</td>
 +
    <td>2.023486</td>
 +
    <td>1.78381</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/h2j.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2j.jpg" style="margin-left:200px;" alt="" width="500" /></p>
Line 23: Line 53:
  
  
−
                  Figure 1.: 3D Model of H2J peptide Modelled by AlphaFold2.0 displayed in Pyomol
+
                    Figure 1.: 3D Model of H2J peptide Modelled by AlphaFold2.0 displayed in Pymol.
  
 
===References===
 
===References===

Revision as of 16:51, 11 October 2022


HTRA Binding Peptide 36

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

Usage and Biology

Synthetic peptide acquired by Phage display, Binds specifically to the water-sites of PDZ domain of HTRA1 Protein with IC50 of 2.8 ± 0.7 and G of 140

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 5 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 0 1.37 66.67 0 2.023486 1.78381

Dry Lab

Modeling 


                    Figure 1.: 3D Model of H2J peptide Modelled by AlphaFold2.0 displayed in Pymol.

References

Beuming, T., Farid, R., & Sherman, W. (2009). High‐energy water sites determine peptide binding affinity and specificity of PDZ domains. Protein Science, 18(8), 1609-1619.