Difference between revisions of "Part:BBa K4165124"

 
 
(9 intermediate revisions by 3 users not shown)
Line 5: Line 5:
 
part encodes for a synthetic peptide that binds to the PDZ domain of HTRA1 protein
 
part encodes for a synthetic peptide that binds to the PDZ domain of HTRA1 protein
  
−
<!-- Add more about the biology of this part here
 
 
===Usage and Biology===
 
===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.   
 
<!-- -->
 
<!-- -->
−
<span class='h3bb'>Sequence and Features</span>
+
===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165124 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165124 SequenceAndFeatures</partinfo>
  
  
−
<!-- Uncomment this to enable Functional Parameter display
+
===Dry lab characterizations===
−
===Functional Parameters===
+
===Modeling===
 +
Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0.
 +
 
 +
 
 +
<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>
 +
 
 +
 
 +
<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>
 +
</html>
 +
 
 +
                    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.
 +
<!-- -->
 +
 
 
<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.