Difference between revisions of "Part:BBa K4165210"
 
(2 intermediate revisions by one other user not shown)
Line 4: Line 4:
  
 
Fusion protein consists of Tau binding peptide (WINK) 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 (WINK) for tau targeting and Coh2 protein [BBa_K4165003] that bind to Docs [BBa_K3396000] to form the protac system.
−
 
−
 
  
 
===Usage and Biology===
 
===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.
+
Protac system is known to be a promising one for targeting and signalling 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.
  
  
 
<!-- -->
 
<!-- -->
−
<span class='h3bb'>Sequence and Features</span>
+
===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165210 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165210 SequenceAndFeatures</partinfo>
  
  
 
===3D Modeling and Ranking===
 
===3D Modeling and Ranking===
−
Fused protein consists of WINK tau binding peptide (BBa_K4165146) with linker (GS)2 (BBa_K4165065) to link between the binding peptide and Coh2 (BBa_K4165003). this model was designed by Modeller tool with QA 5 out of 6 according to our parameters in QA code: C-beta deviations , clash score, Molprobity, Ramachandran favored, Ramachandran outliers, Q mean 4, and Q mean 6.
+
Fused protein consists of WINK tau binding peptide (BBa_K4165146) with linker (GS)<sub>2</sub> (BBa_K4165065) to link between the binding peptide and Coh2 (BBa_K4165003). this model was designed by Modeller tool with QA 5 out of 6 according to our parameters in 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 decrease in the overall protein stability as compared to other models. C-beta deviations = 2 , clash score = 39.86 , Molprobity = 2.08 , Ramachandran favored = 98.67 , Ramachandran outliers = 0 , Q mean 4 = 0.1 ,  Q mean 6 = -0.01
+
This protein was excluded due to its decrease in the overall protein stability as compared to other models.
 +
 
 +
<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>2</td>
 +
    <td>39.86</td>
 +
    <td>2.08</td>
 +
    <td>98.67</td>
 +
    <td>0</td>
 +
    <td>0.1</td>
 +
    <td>-0.01</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
 +
 
  
 
<html>
 
<html>
Line 24: Line 54:
 
</html>
 
</html>
  
−
                          Figure 1.: Predicted 3D structure of CoH2-(GS)2-WINK protein.
+
                      Figure 1.: Predicted 3D structure of CoH2-(GS)2-WINK protein Visualized by Pymol.
  
  

Latest revision as of 08:49, 13 October 2022


Coh2 linked with tau binding peptide (WINK) & GSGS linker

Fusion protein consists of Tau binding peptide (WINK) 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 signalling 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

Fused protein consists of WINK tau binding peptide (BBa_K4165146) with linker (GS)2 (BBa_K4165065) to link between the binding peptide and Coh2 (BBa_K4165003). this model was designed by Modeller tool with QA 5 out of 6 according to our parameters in 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 decrease in the overall protein stability as compared to other models.

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
2 39.86 2.08 98.67 0 0.1 -0.01 


                      Figure 1.: Predicted 3D structure of CoH2-(GS)2-WINK protein Visualized by Pymol.