Part:BBa_K4165030
HtrA1 switch 10
This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), H1A peptide (BBa_K4165000), GGGGSG (BBa_K4165017), TD28rev (BBa_K4165006), GGSGGGG (BBa_K4165018), WWW (BBa_K4165007), SPINK8 inhibitor (BBa_K4165010) and T7 terminator (BBa_K731721).
Usage and Biology
Switch 10 is used to mediate the activity of HTRA1. It is composed of 3 parts connected by different linkers; an HtrA1 PDZ peptide, a clamp of two targeting peptides for tau or amyloid beta, and a catalytic domain inhibitor. Activating HTRA1 requires a conformational change in the linker, eliminating the attached inhibitor from the active site. The conformational rearrangement can be mediated through the binding of affinity clamp to tau or beta-amyloid. This binding will result in a tension that detaches the inhibitor from the active site.
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
Modeling
The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta with a score of 5 out of 6 according to our quality assessment code.
Figure 1. The 3D structure of switch 10 protein Visualized by Pymol. Red: Tau binding peptides,
blue: H1A peptide, cyan: inhibitor, and green: linkers
Docking
switch 10 vs HtrA1 trimer:
ΔG = -20.041
Figure 2. The 3D structure of switch 10 docked to HtrA1 Visualized by Pymol
Mathematical modeling
Transcription rate and translation rate
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.
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