Difference between revisions of "Part:BBa K4165102"
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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
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===Usage and Biology===
 
===Usage and Biology===
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Got least score of 1 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
 
Got least score of 1 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
  
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cbeta_deviations = 0, clashscore = 0, molprobity = 1.42, ramachandran_favored = 60, ramachandran_outliers = 40, Qmean_4 = -6.45183, Qmean6 = -5.513969
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<html>
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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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<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>0</td>
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    <td>1.42</td>
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    <td>60</td>
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    <td>40</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>
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</body>
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</html>
  
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===Modeling===
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===Dry Lab===
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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/h1h.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1h.jpg" style="margin-left:200px;" alt="" width="500" /></p>
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                  Figure 1.: 3D Model of H1H peptide Modelled by AlphaFold2.0 displayed in Pyomol  
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                    Figure 1.: 3D Model of H1H peptide Modelled by AlphaFold2.0 displayed in Pyomol.
  
 
===Reference===
 
===Reference===

Revision as of 14:31, 11 October 2022


HTRA Binding Peptide 8

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 PDZ domain of HTRA1 and HTRA3 Proteins with ΔG of –7.3 kJ.mol-1 and IC50 of 7.7 ± 0.6

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 least score of 1 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 0 1.42 60 40 -6.45183 -5.513969

Dry Lab

Modeling 


                   Figure 1.: 3D Model of H1H peptide Modelled by AlphaFold2.0 displayed in Pyomol.

Reference

1.Romero-Molina, S., Ruiz-Blanco, Y. B., Mieres-Perez, J., Harms, M., Münch, J., Ehrmann, M., & Sanchez-Garcia, E. (2022). PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity. Journal of Proteome Research.

2.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.