Difference between revisions of "Part:BBa K4165113"
 
(5 intermediate revisions by 3 users not shown)
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 IC50 of 7.7 ± 0.6
+
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_K4165113 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165113 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 = 179.69, molprobity = 3.76, ramachandran_favored = 33.33, ramachandran_outliers = 66.67, Qmean_4 = -1.899134, Qmean6 = -0.607119
+
 
 +
<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>179.69</td>
 +
    <td>3.76</td>
 +
    <td>33.33</td>
 +
    <td>66.67</td>
 +
    <td>-1.89913</td>
 +
    <td>-0.60712</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
 +
 
  
  
−
===Modeling===
 
 
<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/h1s.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
  
  
−
                   Figure 1.: 3D Model of H1S peptide Modelled by AlphaFold2.0 displayed in Pyomol
+
                   Figure 1.: 3D Model of H1S 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.
+
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_K4165113 parameters</partinfo>
 
<partinfo>BBa_K4165113 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 09:07, 13 October 2022


HTRA Binding Peptide 19

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
0 179.69 3.76 33.33 66.67 -1.89913 -0.60712 



                 Figure 1.: 3D Model of H1S 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.