Difference between revisions of "Part:BBa K4165032"
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                   Figure 1.  The 3D structure of switch 12 is visualized by Pymol. Red: Tau binding peptides,  
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                   Figure 1.  The 3D structure of switch 12 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
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                                Figure 2. The 3D structure of switch 12 docked to HtrA1
  
  
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                     Figure 1. this figure shows the results from the transcription and translation code showing  
 
                     Figure 1. this figure shows the results from the transcription and translation code showing  
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                  the variation of mRNA and protein concentrations with time compared with the wet lab results.
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                                the variation of mRNA and protein concentrations with time.
  
 
   
 
   

Revision as of 17:07, 11 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).

Usage and Biology

Switch 12 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


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]


Dry Lab

Modeling

The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta with a score of 6 out of 6 according to our quality assessment code. 

                  Figure 1.  The 3D structure of switch 12 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.