Coding

Part:BBa_K4165124

Designed by: Esraa Elmligy   Group: iGEM22_CU_Egypt   (2022-09-30)
Revision as of 13:42, 9 October 2022 by Salma Sobhy (Talk | contribs)


HTRA Binding Peptide 30

part encodes for a synthetic peptide that binds to the PDZ domain of HTRA1 protein

Usage and Biology

A reversal of a high affinity binding peptide is proposed for binding to the PDZ domain of HTRA1.

We were motivated by our chosen Tau binding peptide since it was the inverted sequence of a high affinity peptide that shown better affinity, so we decided to try it with our HTRA1 BP. 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

Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0

cbeta_deviations = 0, clashscore = 16, molprobity = 3.73, ramachandran_favored = 20, ramachandran_outliers = 60, Qmean_4 = -5.832, Qmean6 = -3.92999


Modeling


                 Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pyomol

References

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.

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Categories
Parameters
None