Difference between revisions of "Part:BBa K4165124"
Omnia Alaa11 (Talk | contribs) |
Omnia Alaa11 (Talk | contribs) |
||
| (4 intermediate revisions by 2 users not shown) | |||
| Line 10: | Line 10: | ||
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. | 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. | ||
<!-- --> | <!-- --> | ||
| − | <span class='h3bb'>Sequence and Features</span> | + | ===<span class='h3bb'>Sequence and Features</span>=== |
<partinfo>BBa_K4165124 SequenceAndFeatures</partinfo> | <partinfo>BBa_K4165124 SequenceAndFeatures</partinfo> | ||
| − | === | + | ===Dry lab characterizations=== |
| + | ===Modeling=== | ||
Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0. | Got score of 4 out of 6 in our Quality assessment code after modeling by AlphaFold2.0. | ||
| + | |||
<html> | <html> | ||
| Line 48: | Line 50: | ||
</html> | </html> | ||
| − | + | ||
| − | + | ||
<html> | <html> | ||
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2d.jpg" style="margin-left:200px;" alt="" width="500" /></p> | <p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h2d.jpg" style="margin-left:200px;" alt="" width="500" /></p> | ||
</html> | </html> | ||
| − | |||
Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pymol. | Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pymol. | ||
===References=== | ===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. | + | 1. 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. |
<!-- --> | <!-- --> | ||
<partinfo>BBa_K4165124 parameters</partinfo> | <partinfo>BBa_K4165124 parameters</partinfo> | ||
<!-- --> | <!-- --> | ||
Latest revision as of 09:12, 13 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 reversed sequence 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
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Dry lab characterizations
Modeling
Got score of 4 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 | 16 | 3.73 | 20 | 60 | -5.832 | -3.92999 |
Figure 1.: 3D Model of H2D peptide Modelled by AlphaFold2.0 displayed in Pymol.
References
1. 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.