Difference between revisions of "Part:BBa K4165120"

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===Usage and Biology===
 
===Usage and Biology===
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Synthetic peptide acquired by Phage display, Binds specifically to the water-sites of PDZ domain of HTRA1 Protein with IC50 of 0.26 ± 0.01 and ΔG of 13 kJ mol-1.
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Synthetic peptide acquired by Phage display, Binds specifically to the water-sites of PDZ domain of HTRA1 Protein with IC<sub>50</sub> of 0.26 ± 0.01 and ΔG of 13 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_K4165120 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165120 SequenceAndFeatures</partinfo>
  
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===Functional Parameters===
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===Dry lab characterizations===
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===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
  
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cbeta_deviations = 0, clashscore = 20.83, molprobity = 3.85, ramachandran_favored = 33.33, ramachandran_outliers = 33.33, Qmean_4 = -6.45183, Qmean6 = -5.51397
 
  
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===Modeling===
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table, th, td {
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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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    <td>0</td>
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    <td>20.83</td>
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    <td>3.85</td>
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    <td>33.33</td>
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    <td>33.33</td>
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    <td>-6.45183</td>
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    <td>-5.513969</td>
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</html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1z.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1z.jpg" style="margin-left:200px;" alt="" width="500" /></p>
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                  Figure 1.: 3D Model of H1Z peptide Modelled by AlphaFold2.0 displayed in Pyomol
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                    Figure 1.: 3D Model of H1Z peptide Modelled by AlphaFold2.0 displayed in Pymol.
  
 
===References===
 
===References===

Latest revision as of 09:21, 13 October 2022


HTRA Binding Peptide 26

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

Usage and Biology

Synthetic peptide acquired by Phage display, Binds specifically to the water-sites of PDZ domain of HTRA1 Protein with IC50 of 0.26 ± 0.01 and ΔG of 13 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 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 20.83 3.85 33.33 33.33 -6.45183 -5.513969 



                   Figure 1.: 3D Model of H1Z peptide Modelled by AlphaFold2.0 displayed in Pymol.

References

Beuming, T., Farid, R., & Sherman, W. (2009). High‐energy water sites determine peptide binding affinity and specificity of PDZ domains. Protein Science, 18(8), 1609-1619.