Difference between revisions of "Part:BBa K4165043"
(→‎Dry lab)
Line 17: Line 17:
 
<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 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 tRrosseta with a score of 3 out of 6 according to our quality assessment code.
 +
<html>
 +
<style>
 +
table, th, td {
 +
  border:1px solid black; margin-left:auto;margin-right:auto;
 +
}
 +
</style>
 +
<body>
 +
<table style="width:65%">
 +
<table>
 +
  <tr>
 +
    <th>cbeta_deviations</th>
 +
    <th>clashscore</th>
 +
    <th>molprobity</th>
 +
    <th>ramachandran_favored</th>
 +
    <th>ramachandran_outliers</th>
 +
    <th>Qmean_4</th>
 +
    <th>Qmean_6</th>
 +
  </tr>
 +
  <tr>
 +
    <td>0</td>
 +
    <td>5.53</td>
 +
    <td>1.84</td>
 +
    <td>90.48</td>
 +
    <td>0.79</td>
 +
    <td>-2.96616</td>
 +
    <td>-3.24813</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
  
 
<html>
 
<html>

Revision as of 14:20, 13 October 2022


HtrA1 Switch 23

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), GGGG Linker (BBa_K4165067), Seed peptide (BBa_K4165012), GGSGGGG Linker (BBa_K4165018), Seed peptide (BBa_K4165012), GGGG Linker (BBa_K4165067), WAP inhibitor (BBa_K4165008), and T7 terminator (BBa_K731721).

Usage and Biology

Switch 23 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 379
    Illegal AgeI site found at 115
  • 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 3 out of 6 according to our quality assessment code.

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 5.53 1.84 90.48 0.79 -2.96616 -3.24813 

                              Figure 1. The 3D structure of switch 23 modeled by TRrosetta.