Difference between revisions of "Part:BBa K4165124"
 
(6 intermediate revisions by 2 users not shown)
Line 10: Line 10:
 
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 shown better affinity, so we decided to try it with our HTRA1 BP.     
 
<!-- -->
 
<!-- -->
−
<span class='h3bb'>Sequence and Features</span>
+
===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165124 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165124 SequenceAndFeatures</partinfo>
  
  
−
===Functional Parameters===
+
===Dry lab characterizations===
−
Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
+
===Modeling===
 +
Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0.
  
−
cbeta_deviations = 0, clashscore = 16, molprobity = 3.73, ramachandran_favored = 20, ramachandran_outliers = 60, Qmean_4 = -5.832, Qmean6 = -3.92999
+
 
 +
<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>16</td>
 +
    <td>3.73</td>
 +
    <td>20</td>
 +
    <td>60</td>
 +
    <td>-5.832</td>
 +
    <td>-3.92999</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
  
  
−
===Modeling===
 
 
<html>
 
<html>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2d.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2d.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
  
−
 
+
                    Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pymol.
−
                  Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pyomol
+
  
 
===References===
 
===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.
+
1. 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.
 
<!-- -->
 
<!-- -->
  
 
<partinfo>BBa_K4165124 parameters</partinfo>
 
<partinfo>BBa_K4165124 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 09:12, 13 October 2022


HTRA Binding Peptide 30

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]


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 16 3.73 20 60 -5.832 -3.92999 


                    Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pymol.

References

1. 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.