Difference between revisions of "Part:BBa K4165030"

Revision as of 15:58, 9 October 2022

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), SPINK8 Inhibitor (BBa_K4165010), TD28rev (BBa_K4165006), WWW (BBa_K4165007), H1A peptide (BBa_K4165000) and T7 terminator (BBa_K731721).

Usage and Biology

Switch 10 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.

Dry Lab

Modeling

TRrosetta models this composite part with a score of 5 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 10 modeled by TRrosetta

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 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.

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]

@@ Line 8: / Line 8: @@
 Switch 10 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.
-===Modeling===
+===Dry Lab===
+<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 TRrosetta models this composite part with a score of 5 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).
@@ Line 16: / Line 17: @@
                                 Figure 1. The 3D structure of switch 10 modeled by TRrosetta
+<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
+<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate </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/parts-registry/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.
 <!-- -->
 <span class='h3bb'>Sequence and Features</span>