Difference between revisions of "Part:BBa K4165000"

Revision as of 16:12, 10 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 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 = 0, clashscore = 69.77, molprobity = 4.26, ramachandran_favored = 40, ramachandran_outliers = 60, Qmean_4 = -6.45183, Qmean6 = -5.51397)

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

Docking

ΔG= -32.8 kcal/mol

                     Figure 1.: 3D Model of H1A peptide Docked against HTRA1 displayed in Pymol

@@ Line 18: / Line 18: @@
 ===Dry Lab Characterization===
-Got score of 5 out of 6 in our Quality assessment code after modeling by AlphaFold2.0
-cbeta_deviations = 0, clashscore = 69.77, molprobity = 4.26, ramachandran_favored = 40, ramachandran_outliers = 60, Qmean_4 = -6.45183, Qmean6 = -5.51397
 <p style=" font-weight: bold; font-size:14px;"> Modeling </p>
+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 = 0, clashscore = 69.77, molprobity = 4.26, ramachandran_favored = 40, ramachandran_outliers = 60, Qmean_4 = -6.45183, Qmean6 = -5.51397)
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 <p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1b.jpg" style="margin-left:200px;" alt="" width="500" /></p>