Difference between revisions of "Part:BBa K4165124"

Revision as of 13:57, 9 October 2022

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

Dammers, C., Yolcu, D., Kukuk, L., Willbold, D., Pickhardt, M., Mandelkow, E., ... & Funke, S. A. (2016). Selection and Characterization of Tau Binding ᴅ-Enantiomeric Peptides with Potential for Therapy of Alzheimer Disease. PLoS One, 11(12), e0167432.

@@ Line 29: / Line 29: @@
 ===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.
+Dammers, C., Yolcu, D., Kukuk, L., Willbold, D., Pickhardt, M., Mandelkow, E., ... & Funke, S. A. (2016). Selection and Characterization of Tau Binding ᴅ-Enantiomeric Peptides with Potential for Therapy of Alzheimer Disease. PLoS One, 11(12), e0167432.
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 <partinfo>BBa_K4165124 parameters</partinfo>
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