Difference between revisions of "Part:BBa K4165098"

Revision as of 20:29, 11 October 2022

HTRA Binding Peptide 4

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 –8.1 kJ.mol^-1 and IC₅₀ of 2.8 ± 0.3

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	30,53	3.76	60	40	-6.45183	-5.435502

                     Figure 1.: 3D Model of H1D 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_K4165098 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===
@@ Line 14: / Line 14: @@
-===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.
@@ Line 49: / Line 52: @@
-===Modeling===
 <html>
 <p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1d.jpg" style="margin-left:200px;" alt="" width="500" /></p>
@@ Line 55: / Line 57: @@
-                       Figure 1.: 3D Model of H1D peptide Modelled by AlphaFold2.0 displayed in Pyomol.
+                       Figure 1.: 3D Model of H1D peptide Modelled by AlphaFold2.0 displayed in Pymol.
 ===References===