Difference between revisions of "Part:BBa K4165131"
 
(7 intermediate revisions by 4 users not shown)
Line 6: Line 6:
  
 
===Usage and Biology===
 
===Usage and Biology===
−
Synthetic peptide acquired by Phage display, Binds specifically to the water-sites of PDZ domain of HTRA1 Protein with IC50 of 2.0 ± 0.1 and G of 100
+
Synthetic peptide acquired by Phage display, Binds specifically to the water-sites of PDZ domain of HTRA1 Protein with IC50 of 2.0 ± 0.1 and ΔG of 100 kcal/mol.
  
 
<!-- -->
 
<!-- -->
Line 13: Line 13:
  
  
−
===Functional Parameters===
+
===Dry lab characterizations===
 +
===Modeling===
 
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 = 0, molprobity = 2.71, ramachandran_favored = 0, ramachandran_outliers = 0, Qmean_4 = -6.45183, Qmean6 = -5.51397
 
  
−
===Modeling===
+
 
 +
<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>2.71</td>
 +
    <td>0</td>
 +
    <td>0</td>
 +
    <td>-6.45183</td>
 +
    <td>-5.513969</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
 +
 
 +
 
 
<html>
 
<html>
−
<p><img src="" style="margin-left:200px;" alt="" width="500" /></p>
+
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2k.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
  
  
−
                  Figure 1.: 3D Model of H2K peptide Modelled by AlphaFold2.0 displayed in Pyomol
+
                    Figure 1.: 3D Model of H2K peptide Modelled by AlphaFold2.0 displayed in Pymol
  
 
===References===
 
===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.
+
1. 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.
  
 
<partinfo>BBa_K4165131 parameters</partinfo>
 
<partinfo>BBa_K4165131 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 09:17, 13 October 2022


HTRA Binding Peptide 37

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 2.0 ± 0.1 and ΔG of 100 kcal/mol.

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]


Dry lab characterizations

Modeling

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 0 2.71 0 0 -6.45183 -5.513969 



                    Figure 1.: 3D Model of H2K peptide Modelled by AlphaFold2.0 displayed in Pymol

References

1. 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.