Difference between revisions of "Part:BBa K4165047"
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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 tRrosseta with a score of 4 out of 6 according to our quality assessment code.
 
The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta with a score of 4 out of 6 according to our quality assessment code.
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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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    <td>0</td>
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    <td>4.89</td>
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    <td>1.65</td>
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    <td>94.07</td>
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    <td>0.74</td>
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    <td>-0.032774</td>
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    <td>-1.3494</td>
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Revision as of 14:24, 13 October 2022


HtrA1 Switch 27

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), GSGS Linker (BBa_K4165065), TD28REV (BBa_K4165006), GGSGGGGG Linker (BBa_K4165019), WWW (BBa_K4165007), GSGS Linker (BBa_K4165065), WAP inhibitor (BBa_K4165008), and T7 terminator (BBa_K731721).

Usage and Biology

Switch 27 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 526
    Illegal AgeI site found at 262
  • 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 4 out of 6 according to our quality assessment code.

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 4.89 1.65 94.07 0.74 -0.032774 -1.3494 

                               Figure 1. The 3D structure of switch 27 modeled by TRrosetta.