Difference between revisions of "Part:BBa K4165030"

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===Usage and Biology===
 
===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.
 
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.
 
 
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<span class='h3bb'><p style=" font-weight: bold; font-size:17px;"> Sequence and Features</p></span>
 
<partinfo>BBa_K4165030 SequenceAndFeatures</partinfo>
 
 
  
 
===Dry Lab===
 
===Dry Lab===
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                              Figure 1. The 3D structure of switch 10 modeled by TRrosetta. Red: Tau binding peptides,  
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                        Figure 1. The 3D structure of switch 10 protein 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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<p style=" font-weight: bold; font-size:14px;"> Docking </p>
 
<p style=" font-weight: bold; font-size:14px;"> Docking </p>
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</html>
  
                              Figure 2. The 3D structure of switch 10 docked to HtrA1
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                          Figure 2. The 3D structure of switch 10 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;"> Mathematical modeling </p>
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               Figure 3. this figure shows the results from the transcription and translation code showing the  
 
               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.
 
                       variation of mRNA and protein concentrations with time compared with the wet lab results.
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 +
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 +
<span class='h3bb'><p style=" font-weight: bold; font-size:17px;"> Sequence and Features</p></span>
 +
<partinfo>BBa_K4165030 SequenceAndFeatures</partinfo>
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 +
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Revision as of 14:16, 10 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), 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).

Source

Synthesized

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 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 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]