Difference between revisions of "Part:BBa K4165038"

Revision as of 05:14, 11 October 2022

HtrA1 Switch number 18

This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), WAP inhibitor (BBa_K4165008), GSGSGS linker (BBa_J18921), seed peptide (BBa_K4165012), GGSGGGGG linker (BBa_K4165019), seed peptide (BBa_K4165012), GSGSGS linker (BBa_J18921), H1A (BBa_K4165000) and T7 terminator (BBa_K731721).

Source

Synthesized

Usage and Biology

Switch 18 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

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 379
Illegal AgeI site found at 115
1000
COMPATIBLE WITH RFC[1000]

Dry Lab

Modeling

TRrosetta models this composite part with a score of 4 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 18 modeled by TRrosetta. Red: Tau binding peptides, 
                                         blue: H1A peptide, cyan: inhibitor, and green: linkers

Docking

switch 18 vs HtrA1:

ΔG = -19.516

                         Figure 2. The 3D structure of switch 18 docked to HtrA1 Visualized by Pymol.

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 3. 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.

@@ Line 4: / Line 4: @@
 This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), WAP inhibitor (BBa_K4165008), GSGSGS linker (BBa_J18921), seed peptide (BBa_K4165012), GGSGGGGG linker (BBa_K4165019), seed peptide (BBa_K4165012), GSGSGS linker (BBa_J18921), H1A (BBa_K4165000) and T7 terminator (BBa_K731721).
+===Source===
+Synthesized
 ===Usage and Biology===
-Switch 18 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
+Switch 18 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.
 <h2>Sequence and Features</h2>
 <partinfo>BBa_K4165038 SequenceAndFeatures</partinfo>
-===Modeling===
+===Dry Lab===
+<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 TRrosetta models this composite part with a score of 4 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).
 <html>
@@ Line 19: / Line 22: @@
 </html>
-                                    Figure 1. The 3D structure of switch 18 modeled by TRrosetta. Red: Tau binding peptides,
+                           Figure 1. The 3D structure of switch 18 modeled by TRrosetta. Red: Tau binding peptides,
-                                               blue: H1A peptide, cyan: inhibitor and green: linkers
+                                          blue: H1A peptide, cyan: inhibitor, and green: linkers
@@ Line 33: / Line 36: @@
 </html>
-                               Figure 2. The 3D structure of switch 18 docked to HtrA1
+                          Figure 2. The 3D structure of switch 18 docked to HtrA1 Visualized by Pymol.
+<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-182.png" style="margin-left:200px;" alt="" width="500" /></p>
+</html>
+                 Figure 3. 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.