Difference between revisions of "Part:BBa K4165032"
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This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), SPINK8 Inhibitor (BBa_K4165010), GS Linker (BBa_K4165017), seed peptide (BBa_K4165012), GS Linker (BBa_K4165019), seed peptide (BBa_K4165012), GS Linker (BBa_K4165017), H1A (BBa_K4165000) and T7 terminator (BBa_K731721). | This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), SPINK8 Inhibitor (BBa_K4165010), GS Linker (BBa_K4165017), seed peptide (BBa_K4165012), GS Linker (BBa_K4165019), seed peptide (BBa_K4165012), GS Linker (BBa_K4165017), H1A (BBa_K4165000) and T7 terminator (BBa_K731721). | ||
+ | ===Source=== | ||
+ | Synthesised | ||
===Usage and Biology=== | ===Usage and Biology=== | ||
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− | === | + | ===Dry Lab=== |
+ | <p style=" font-weight: bold; font-size:14px;"> Modeling </p> | ||
TRrosetta models this composite part with a score of 6 out of 6 according to our quality assessment code (you can find the python script file on the programming club page with further explanation of how you can optimize it to your needs). | TRrosetta models this composite part with a score of 6 out of 6 according to our quality assessment code (you can find the python script file on the programming club page with further explanation of how you can optimize it to your needs). | ||
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<html> | <html> | ||
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</html> | </html> | ||
− | + | Figure 1. The 3D structure of switch 12 is visualized by Pymol. Red: Tau binding peptides, | |
− | blue: H1A peptide, cyan: inhibitor and green: linkers | + | blue: H1A peptide, cyan: inhibitor, and green: linkers |
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Figure 2. The 3D structure of switch 12 docked to HtrA1 | Figure 2. The 3D structure of switch 12 docked to HtrA1 | ||
+ | |||
+ | <p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p> | ||
+ | <p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promotor </p> | ||
+ | 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. | ||
+ | |||
+ | <html> | ||
+ | <p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/peptide-1o2.png" style="margin-left:200px;" alt="" width="500" /></p> | ||
+ | </html> | ||
+ | |||
+ | |||
+ | Figure 1. 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. | ||
+ | |||
+ | |||
<!-- Uncomment this to enable Functional Parameter display | <!-- Uncomment this to enable Functional Parameter display |
Revision as of 17:40, 10 October 2022
HtrA1 Switch number 12
This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), SPINK8 Inhibitor (BBa_K4165010), GS Linker (BBa_K4165017), seed peptide (BBa_K4165012), GS Linker (BBa_K4165019), seed peptide (BBa_K4165012), GS Linker (BBa_K4165017), H1A (BBa_K4165000) and T7 terminator (BBa_K731721).
Source
Synthesised
Usage and Biology
Switch 12 is used to mediate the activity of HTRA1. 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 affinity clamp for tau and beta-amyloid binding. These clamps are used for stabilizing the inhibitor away from the active site. These two domains (inhibitor and affinity clamp connected with linker1). Additionally, (H1A) binding peptide bound to the PDZ domain and connected to the affinity clamp on the other side with linker3
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
TRrosetta models this composite part with a score of 6 out of 6 according to our quality assessment code (you can find the python script file on the programming club page with further explanation of how you can optimize it to your needs).
Figure 1. The 3D structure of switch 12 is visualized by Pymol. Red: Tau binding peptides, blue: H1A peptide, cyan: inhibitor, and green: linkers
Docking
switch12 vs HtrA1 trimer:
ΔG = -22.315
Figure 2. The 3D structure of switch 12 docked to HtrA1
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 1. 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.