Difference between revisions of "Part:BBa K4165109"
 
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<partinfo>BBa_K4165109 short</partinfo>
 
<partinfo>BBa_K4165109 short</partinfo>
  
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part encodes for a synthetic peptide that binds to the PDZ domain of HTRA1 protein
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Part encodes for a synthetic peptide that binds to the PDZ domain of HTRA1 protein
  
 
===Usage and Biology===
 
===Usage and Biology===
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decameric peptide, Binds specifically to PDZ domain of HTRA1 Protein with G of 10.3 ± 0.2 kcal/mol.
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Decameric peptide, Binds specifically to PDZ domain of HTRA1 Protein with ΔG of 10.3 ± 0.2 kcal/mol.
  
 
<!-- -->
 
<!-- -->
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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165109 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165109 SequenceAndFeatures</partinfo>
  
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===Functional Parameters===
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===Dry Lab Characterization===
 +
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 
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
  
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cbeta_deviations = 0, clashscore = 17.86, molprobity = 4, ramachandran_favored = 62.5, ramachandran_outliers = 12.5, Qmean_4 = -6.45183, Qmean6 = -5.513969
 
  
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−
===Modeling===
 
 
<html>
 
<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1o.jpg" style="margin-left:200px;" alt="" width="500" /></p>
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<style>
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table, th, td {
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  border:1px solid black; margin-left:auto;margin-right:auto;
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}
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</style>
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<body>
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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>17.86</td>
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    <td>4</td>
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    <td>62.5</td>
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    <td>12.5</td>
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    <td>-6.45183</td>
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    <td>-5.513969</td>
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  </tr>
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</table>
 +
</body>
 
</html>
 
</html>
  
  
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                  Figure 1.: 3D Model of H1O peptide Modelled by AlphaFold2.0 displayed in Pyomol
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1o.jpg" style="margin-left:250px;" alt="" width="500" /></p>
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</html>
  
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===Docking===
 
  
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                        Figure 1.: 3D Model of H1O peptide Modelled by AlphaFold2.0 displayed in Pymol.
  
 
===References===
 
===References===

Latest revision as of 09:39, 13 October 2022


HTRA Binding Peptide 15

Part encodes for a synthetic peptide that binds to the PDZ domain of HTRA1 protein

Usage and Biology

Decameric peptide, Binds specifically to PDZ domain of HTRA1 Protein with ΔG of 10.3 ± 0.2 kcal/mol.

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 Characterization

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 17.86 4 62.5 12.5 -6.45183 -5.513969 



                       Figure 1.: 3D Model of H1O peptide Modelled by AlphaFold2.0 displayed in Pymol.

References

Rey, J., Breiden, M., Lux, V., Bluemke, A., Steindel, M., Ripkens, K., ... & Ehrmann, M. (2022). An allosteric HTRA1-calpain 2 complex with restricted activation profile. Proceedings of the National Academy of Sciences, 119(14), e2113520119.