Difference between revisions of "Part:BBa K4165042"
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 
The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from Rosettafold with a score of 3 out of 6 according to our quality assessment code.
 
The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from Rosettafold with a score of 3 out of 6 according to our quality assessment code.
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  <tr>
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    <th>cbeta_deviations</th>
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    <th>clashscore</th>
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    <th>molprobity</th>
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    <th>ramachandran_favored</th>
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    <th>ramachandran_outliers</th>
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    <th>Qmean_4</th>
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    <th>Qmean_6</th>
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    <td>0</td>
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    <td>184.32</td>
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    <td>3.07</td>
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    <td>94.96</td>
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    <td>0</td>
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    <td>0.425854</td>
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    <td>-0.07431</td>
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Revision as of 14:18, 13 October 2022


HtrA1 Switch 22

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), GGGGSG Linker (BBa_K4165017), TD28REV, (BBa_K4165006), GGSGGGG Linker (BBa_K4165018), WWW (BBa_K4165007), GGGGSG Linker (BBa_K4165017), WAP inhibitor (BBa_K4165008), and T7 terminator (BBa_K731721).

Usage and Biology

Switch 22 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 538
    Illegal AgeI site found at 274
  • 1000
    COMPATIBLE WITH RFC[1000]

dry lab

Modeling

The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from Rosettafold with a score of 3 out of 6 according to our quality assessment code.

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 184.32 3.07 94.96 0 0.425854 -0.07431 


                             Figure 1.: The 3D structure of switch22 modeled by RosettaFold.