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

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 2.: 3D Model of H1A peptide Docked against HTRA1 displayed in Pymol 

Mathematical modeling

Transcription rate and translation rate under T7 promotor

the mathematical modeling was based on our code for the calculation of transcription and translation (you can find it in the code section) beside with the estimated results from the wet lab.

                 Figure 3. this figure shows the results from the transcription and translation code showing 
                 the variation of mRNA and protein concentrations with time compared with the wet lab results.