Part:BBa_K4165000
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
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE 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.
| None |