Difference between revisions of "Part:BBa K4165048"
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===Usage and Biology===
 
===Usage and Biology===
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Switch 28 plays a role in mediating HTRA1's function. For HTRA1 to become active, a conformational modification in the linker is necessary, which displaces the associated 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 beside with amyloid beta binding peptide connected to tau binding peptide by linker 2). 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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Switch 28 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===
 
===Dry lab===
 
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
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we modeled this switch to see the final structure of the switch, the top model which has score 4 out of 6 from RosettaFold.
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The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from Rossetafold with a score of 4 out of 6 according to our quality assessment code.
  
  
 
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switch28.png" style="margin-left:200px;" alt="" width="500" /></p>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switch28.png" style="margin-left:220px;" alt="" width="500" /></p>
 
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                            Figure 1. The 3D structure of switch 28 modeled by RosettaFold.  
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                              Figure 1. The 3D structure of switch 28 modeled by RosettaFold.  
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Revision as of 17:53, 11 October 2022


HtrA1 Switch 28

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), GSGSG Linker (BBa_K4165066), TD28REV (BBa_K4165006), GGSGGGGG Linker (BBa_K4165019), WWW (BBa_K4165007), GSGSG Linker (BBa_K4165066), WAP inhibitor (BBa_K4165008), and T7 terminator (BBa_K731721).

Usage and Biology

Switch 28 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
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 532
    Illegal AgeI site found at 268
  • 1000
    COMPATIBLE WITH RFC[1000]

Dry lab

Modeling

The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from Rossetafold with a score of 4 out of 6 according to our quality assessment code. 


                             Figure 1. The 3D structure of switch 28 modeled by RosettaFold.