Difference between revisions of "Part:BBa K4165111"
Line 6: Line 6:
  
 
===Usage and Biology===
 
===Usage and Biology===
−
Synthetic peptide acquired by Phage display, Binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins with IC<sub>50</sub> of 0.9 ± 0.1
+
Synthetic peptide acquired by Phage display, Binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins with IC<sub>50</sub> of 0.9 ± 0.1.
  
  
Line 16: Line 16:
 
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 = 30.53, molprobity = 3.76, ramachandran_favored = 60, ramachandran_outliers = 40, Qmean_4 = -6.45183, Qmean6 = -5.435502
+
<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>30.53</td>
 +
    <td>3.76</td>
 +
    <td>60</td>
 +
    <td>40</td>
 +
    <td>-6.45183</td>
 +
    <td>-5.513969</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/h1q.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1q.jpg" style="margin-left:200px;" alt="" width="500" /></p>
Line 25: Line 54:
  
  
−
                  Figure 1.: 3D Model of H1Q peptide Modelled by AlphaFold2.0 displayed in Pyomol
+
                    Figure 1.: 3D Model of H1Q peptide Modelled by AlphaFold2.0 displayed in Pymol.
  
 
===References===
 
===References===
 
Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu, P., Pan, B., ... & Sidhu, S. S. (2007). Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Science, 16(11), 2454-2471.
 
Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu, P., Pan, B., ... & Sidhu, S. S. (2007). Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Science, 16(11), 2454-2471.
 
<!-- -->
 
<!-- -->

Revision as of 15:32, 11 October 2022


HTRA Binding Peptide 17

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 PDZ domain of HTRA1 and HTRA3 Proteins with IC50 of 0.9 ± 0.1.


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 30.53 3.76 60 40 -6.45183 -5.513969

Dry Lab

Modeling 


                   Figure 1.: 3D Model of H1Q peptide Modelled by AlphaFold2.0 displayed in Pymol.

References

Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu, P., Pan, B., ... & Sidhu, S. S. (2007). Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Science, 16(11), 2454-2471.