Part:BBa_K4165105

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.