Difference between revisions of "Part:BBa K4165105"
 
(6 intermediate revisions by 4 users not shown)
Line 3: Line 3:
 
<partinfo>BBa_K4165105 short</partinfo>
 
<partinfo>BBa_K4165105 short</partinfo>
  
−
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
  
 
===Usage and Biology===
 
===Usage and Biology===
−
Synthetic peptide acquired by Phage display, Binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins with  ΔG of –7.1 kJ.mol<sup>-1</sup> and IC<sub>50<sub> of 23 ± 3
+
Synthetic peptide acquired by Phage display, Binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins with  ΔG of –7.1 kcal/mol and IC<sub>50</sub> of 23 ± 3.
  
 
<!-- -->
 
<!-- -->
Line 12: Line 12:
 
<partinfo>BBa_K4165105 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165105 SequenceAndFeatures</partinfo>
  
−
===Functional Parameters===
+
===Dry Lab Characterization===
 +
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 +
 
 
Got score of 5 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
 
Got score of 5 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
  
−
cbeta_deviations = 0, clashscore = 25, molprobity = 3.86, ramachandran_favored = 66.67, ramachandran_outliers = 16.67, Qmean_4 = -6.45183, Qmean6 = -5.513969
 
  
−
===Modeling===
+
<html>
 +
<style>
 +
table, th, td {
 +
  border:1px solid black; margin-left:auto;margin-right:auto;
 +
}
 +
</style>
 +
<body>
 +
<table style="width:65%">
 +
<table>
 +
  <tr>
 +
    <th>cbeta_deviations</th>
 +
    <th>clashscore</th>
 +
    <th>molprobity</th>
 +
    <th>ramachandran_favored</th>
 +
    <th>ramachandran_outliers</th>
 +
    <th>Qmean_4</th>
 +
    <th>Qmean_6</th>
 +
  </tr>
 +
  <tr>
 +
    <td>0</td>
 +
    <td>25</td>
 +
    <td>3.86</td>
 +
    <td>66.67</td>
 +
    <td>16.67</td>
 +
    <td>-6.45183</td>
 +
    <td>-5.513969</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
 +
 
 +
 
 
<html>
 
<html>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1k.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1k.jpg" style="margin-left:200px;" alt="" width="500" /></p>
Line 23: Line 55:
  
  
−
                  Figure 1.: 3D Model of H1K peptide Modelled by AlphaFold2.0 displayed in Pyomol  
+
                      Figure 1.: 3D Model of H1K peptide Modelled by AlphaFold2.0 displayed in Pyomol.
 +
 
 +
===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.
  
 
<partinfo>BBa_K4165105 parameters</partinfo>
 
<partinfo>BBa_K4165105 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 10:46, 13 October 2022


HTRA Binding Peptide 11

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 –7.1 kcal/mol and IC50 of 23 ± 3.

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 5 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 25 3.86 66.67 16.67 -6.45183 -5.513969 



                      Figure 1.: 3D Model of H1K peptide Modelled by AlphaFold2.0 displayed in Pyomol.

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.