Difference between revisions of "Part:BBa K4165219"
 
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Fusion protein consists of Tau binding peptide (TD28rev) for tau targeting and Coh2 protein [BBa_K4165003] that bind to Docs [BBa_K3396000] to form the protac system.
 
Fusion protein consists of Tau binding peptide (TD28rev) for tau targeting and Coh2 protein [BBa_K4165003] that bind to Docs [BBa_K3396000] to form the protac system.
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===Usage and Biology===
 
===Usage and Biology===
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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165219 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165219 SequenceAndFeatures</partinfo>
  
  
 
===3D Modeling and Ranking===
 
===3D Modeling and Ranking===
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This fused protein was modeled using Modeller software and after running our quality assessment code it got a score of 5 out of 6 according to the parameters of the QA code: C-beta deviations, clash score, Molprobity, Ramachandran favored, Ramachandran outliers, Q mean 4, and Q mean 6. This protein was excluded due to its low QA score as compared to other models. C-beta deviations = 1 , clash score = 37.89, Molprobity = 2.2 , Ramachandran favored = 98.16 , Ramachandran outliers = 0 , Q mean 4 = -0.84 , Q mean 6 = -1.25.
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This fused protein was modeled using Modeller software and after running our quality assessment code it got a score of 5 out of 6 according to the parameters of the QA code: C-beta deviations, clash score, Molprobity, Ramachandran favored, Ramachandran outliers, Q mean 4, and Q mean 6. This protein was excluded due to its low QA score as compared to other models.
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<html>
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<style>
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table, th, td {
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  border:1px solid black; margin-left:auto;margin-right:auto;
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}
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</style>
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<body>
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<table style="width:65%">
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<table>
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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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  </tr>
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  <tr>
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    <td>1</td>
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    <td>37.89</td>
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    <td>2.2</td>
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    <td>98.16</td>
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    <td>0</td>
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    <td>-0.84</td>
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    <td>-1.25</td>
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  </tr>
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</table>
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</body>
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</html>
  
  
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</html>
 
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                                    Figure 1.: Predicted 3D Structure of COH2_G4S_TD28rev
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                                Figure 1.: Predicted 3D Structure of COH2_G4S_TD28rev Visualized by Pymol.
  
  

Latest revision as of 08:28, 13 October 2022


Coh2 linked with tau binding peptide (TD28rev) & G4S linker

Fusion protein consists of Tau binding peptide (TD28rev) for tau targeting and Coh2 protein [BBa_K4165003] that bind to Docs [BBa_K3396000] to form the protac system.

Usage and Biology

Protac system is known to be a promising one for targeting and signaling many diseases and biological application so according to our project aim, we introduced this fusion protein with different linker length and tau binding peptide to be a target for degradation of Tau aggregation in our updated protac version system "Snitch system". Furthermore, that can be validated by wet-lab results by in vitro or in vivo testing.


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
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


3D Modeling and Ranking

This fused protein was modeled using Modeller software and after running our quality assessment code it got a score of 5 out of 6 according to the parameters of the QA code: C-beta deviations, clash score, Molprobity, Ramachandran favored, Ramachandran outliers, Q mean 4, and Q mean 6. This protein was excluded due to its low QA score as compared to other models.


cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
1 37.89 2.2 98.16 0 -0.84 -1.25 


                               Figure 1.: Predicted 3D Structure of COH2_G4S_TD28rev Visualized by Pymol.