Difference between revisions of "Part:BBa K4165124"
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===Functional Parameters===
 
===Functional Parameters===
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Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
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Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0.
  
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cbeta_deviations = 0, clashscore = 16, molprobity = 3.73, ramachandran_favored = 20, ramachandran_outliers = 60, Qmean_4 = -5.832, Qmean6 = -3.92999
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table, th, td {
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}
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<table style="width:65%">
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<table>
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  <tr>
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    <th>cbeta_deviations</th>
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    <th>clashscore</th>
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    <th>molprobity</th>
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    <th>ramachandran_favored</th>
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    <th>ramachandran_outliers</th>
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    <th>Qmean_4</th>
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    <th>Qmean_6</th>
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  </tr>
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  <tr>
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    <td>0</td>
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    <td>16</td>
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    <td>3.73</td>
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    <td>20</td>
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    <td>60</td>
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    <td>-5.832</td>
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    <td>-3.92999</td>
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  </tr>
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</table>
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</body>
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</html>
  
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===Dry Lab===
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===Modeling===
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 
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<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>
 
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</html>
  
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                  Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pyomol
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                    Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pymol.
  
 
===References===
 
===References===

Revision as of 17:40, 11 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]


Functional Parameters

Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0.

tml> <style> table, th, td { 

 border:1px solid black; margin-left:auto;margin-right:auto;

} </style> <body>

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 16 3.73 20 60 -5.832 -3.92999

</body> </html>

Dry Lab

Modeling 


                    Figure 1.: 3D Model of H2D 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.