Difference between revisions of "Part:BBa K4165107"

Latest revision as of 09:45, 13 October 2022

HTRA Binding Peptide 13

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 –6.9 kcal/mol and IC₅₀ of 40 ± 5.

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	0	1.42	60	20	-3.533754	-1.924678

                 Figure 1.: 3D Model of H1M peptide Modelled by AlphaFold2.0 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.

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K4165107 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===
-Synthetic peptide acquired by Phage display, Binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins with G of –6.9 and IC50 of 40 ± 5
+Synthetic peptide acquired by Phage display, Binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins with ΔG of –6.9 kcal/mol and IC<sub>50</sub> of 40 ± 5.
 <!-- -->
-<span class='h3bb'>Sequence and Features</span>
+===<span class='h3bb'>Sequence and Features</span>===
 <partinfo>BBa_K4165107 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
-cbeta_deviations = 0, clashscore = 0, molprobity = 1.42, ramachandran_favored = 60, ramachandran_outliers = 20, Qmean_4 = -3.533754, Qmean6 = -1.924678
-===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>0</td>
+    <td>1.42</td>
+    <td>60</td>
+    <td>20</td>
+    <td>-3.533754</td>
+    <td>-1.924678</td>
+  </tr>
+</table>
+</body>
+</html>
 <html>
 <p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1m.jpg" style="margin-left:200px;" alt="" width="500" /></p>
@@ Line 23: / Line 54: @@
-                   Figure 1.: 3D Model of H1M peptide Modelled by AlphaFold2.0 displayed in Pyomol
+                   Figure 1.: 3D Model of H1M peptide Modelled by AlphaFold2.0 displayed in Pymol.
+===References===
+.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.
+.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_K4165107 parameters</partinfo>
 <!-- -->