Difference between revisions of "Part:BBa K4165000"
 
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<partinfo>BBa_K4165000 short</partinfo>
 
<partinfo>BBa_K4165000 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 a synthetic peptide that binds to the PDZ domain of serine protease HTRA1.
  
 
===Usage and Biology===
 
===Usage and Biology===
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Synthetic peptide acquired by Phage display, Binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins with G of –8.8 and IC50 of 0.9 ± 0.1
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Synthetic peptide acquired by Phage display, binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins.  
  
 
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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165000 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165000 SequenceAndFeatures</partinfo>
 +
  
 
===Functional Parameters===
 
===Functional Parameters===
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Got score of 5 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
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ΔG of –8.8 Kcal/mol and IC50 of 0.9 ± 0.1
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cbeta_deviations = 0, clashscore = 69.77, molprobity = 4.26, ramachandran_favored = 40, ramachandran_outliers = 60, Qmean_4 = -6.45183, Qmean6 = -5.51397
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 +
===Dry Lab Characterization===
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 +
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
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This peptide was modeled using different software and the top model from Alphafold2 got score 5 out of 6 in our Quality assessment code.
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 +
 
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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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</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>69.77</td>
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    <td>4.26</td>
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    <td>40</td>
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    <td>60</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===
 
 
<html>
 
<html>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1b.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1b.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
  
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                  Figure 1.: 3D Model of H1A peptide Modelled by AlphaFold2.0 displayed in Pyomol
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                      Figure 1.: 3D Model of H1A peptide Modelled by AlphaFold2.0 displayed in Pymol
  
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===Docking===
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<p style=" font-weight: bold; font-size:14px;"> Docking </p>
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G= 1.266
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ΔG= -32.8 kcal/mol
  
 
<html>
 
<html>
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</html>
 
</html>
  
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                  Figure 1.: 3D Model of H1A peptide Docked against HTRA1 displayed in Pyomol
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                      Figure 2.: 3D Model of H1A peptide Docked against HTRA1 displayed in Pymol
 +
 
 +
===References===
 +
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.<br>
 +
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.
 +
 
 
<partinfo>BBa_K4165000 parameters</partinfo>
 
<partinfo>BBa_K4165000 parameters</partinfo>
 
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Latest revision as of 13:57, 13 October 2022


HTRA Binding Peptide 1

Part encodes a synthetic peptide that binds to the PDZ domain of serine protease HTRA1.

Usage and Biology

Synthetic peptide acquired by Phage display, binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins.

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

ΔG of –8.8 Kcal/mol and IC50 of 0.9 ± 0.1

Dry Lab Characterization

Modeling

This peptide was modeled using different software and the top model from Alphafold2 got score 5 out of 6 in our Quality assessment code.


cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 69.77 4.26 40 60 -6.45183 -5.513969 


                     Figure 1.: 3D Model of H1A peptide Modelled by AlphaFold2.0 displayed in Pymol

Docking

ΔG= -32.8 kcal/mol 

                     Figure 2.: 3D Model of H1A peptide Docked against HTRA1 displayed in Pymol

References

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.