Difference between revisions of "Part:BBa K4165055"
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===Usage and Biology===
 
===Usage and Biology===
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This part performs a multifunction role in our system, the Plug-Sink system. The H1A (BBa_K4165000) peptide directs the whole peptide to bind to the PDZ HtrA1 protein (BBa_K4165004). The second part is the binding peptide which directs the whole peptide-HtrA1 complex to the tau (BBa_K4165009) and amyloid (BBa_K4165005) aggregates. The last part makes the whole system switch on or off based on the presence of the target protein, thus part is the WAP inhibitor (BBa_K4165008).
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Switch 35 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.
  
 
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===Dry-Lab characterization===
 
===Dry-Lab characterization===
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
  
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The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta.
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===Modelling===
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PDB Structure:
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                    Figure 1. The 3D structure of switch 35 modelled by TRrosetta.
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                            Figure 1. The 3D structure of switch 35 modelled by tRrosseta.

Revision as of 18:09, 11 October 2022


HtrA1 Switch 35

This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), H1A (BBa_K4165000), GS Linker (BBa_K4165068), TD28rev peptide (BBa_K4165006), GS Linker (BBa_K4165018), WWW peptide (BBa_K4165007), GS Linker (BBa_K4165068), WAP inhibitor (BBa_K4165008), and T7 terminator (BBa_K731721)


Usage and Biology

Switch 35 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
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 589
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 572
    Illegal AgeI site found at 308
  • 1000
    COMPATIBLE WITH RFC[1000]


Dry-Lab characterization

Modeling

The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta. 

                           Figure 1. The 3D structure of switch 35 modelled by tRrosseta.