Difference between revisions of "Part:BBa K4165138"
 
(3 intermediate revisions by 2 users not shown)
Line 8: Line 8:
 
A reversed sequence of a high affinity binding peptide is proposed for binding to the PDZ domain of HTRA1.
 
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.
+
We were motivated by our chosen Tau binding peptide since it was the inverted sequence of a high affinity peptide that showed better affinity, so we decided to try it with our HTRA1 BP.
  
 
<!-- -->
 
<!-- -->
Line 14: Line 14:
 
<partinfo>BBa_K4165138 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165138 SequenceAndFeatures</partinfo>
  
−
===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 = 8.2, molprobity = 3.7, ramachandran_favored = 0, ramachandran_outliers = 80, Qmean_4 = -5.42217, Qmean6 = -4.10711
+
 
 +
<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>8.2</td>
 +
    <td>3.7</td>
 +
    <td>0</td>
 +
    <td>80</td>
 +
    <td>-5.42217</td>
 +
    <td>-4.10711</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
 +
 
  
  
−
===Modeling===
 
 
<html>
 
<html>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2r.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2r.jpg" style="margin-left:200px;" alt="" width="500" /></p>
Line 26: Line 57:
  
  
−
                  Figure 1.: 3D Model of H2R peptide Modelled by AlphaFold2.0 displayed in Pyomol
+
                    Figure 1.: 3D Model of H2R peptide Modelled by AlphaFold2.0 displayed in Pymol.
  
 
===References===
 
===References===

Latest revision as of 09:08, 13 October 2022


HTRA Binding Peptide 44

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 showed 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]

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 8.2 3.7 0 80 -5.42217 -4.10711 



                   Figure 1.: 3D Model of H2R 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.