Difference between revisions of "Part:BBa K4165217"
 
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<partinfo>BBa_K4165217 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165217 SequenceAndFeatures</partinfo>
  
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===3D Modeling and Ranking===
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===Dry lab===
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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, Qmean4, and Qmean6. This protein was excluded due to its low QA score as compared to other models. C-beta deviations = 0, clash score = 39.57, Molprobity = 2.23, Ramachandran favored = 98.14, Ramachandran outliers = 0, Qmean4 = -0.51, Qmean6 = -0.98
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<p style=" font-weight: bold; font-size:14px;"> 1.1. 3D Modeling and Ranking </p>
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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, Qmean4, and Qmean6. This protein was excluded due to its low QA score as compared to other models.
  
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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>39.57</td>
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    <td>2.23</td>
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    <td>98.14</td>
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    <td>0</td>
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    <td>-0.51</td>
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    <td>-0.98</td>
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                          Figure 1.: Predicted 3D structure of CoH_(G4S)<sub>3</sub>_WWW Protein
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                  Figure 1.: Predicted 3D structure of CoH_(G4S) <sub>3</sub>_WWW Protein Visualized by Pymol.
  
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<p style=" font-weight: bold; font-size:14px;"> 1.2. Docking </p>
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Coh2-(G4S)3-WWW (CLW) is docked to trim-(G4S)3-DocS (TLD) on LightDock standalone vesrion and ClusPro2.0 web server, the binding affinity were calculated using prodigy to be -14.13 and -15.23 kcal/mol respectively. 
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                            Figure 2.: CoH_(G4S)<sub>3</sub>_WWW docked to trim21-(G4S)-DocS on LightDock.
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                              Figure 3.: CoH_(G4S)<sub>3</sub>_WWW docked to trim21-(G4S)-DocS on CusPro.
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the results of the binding affinity indicate that CLW can bind to TLD with high affinity, the next step is investigating the affinity of WWW in the whole docked structure to its targets (PHF, PHF* and tau aggregates). the docking is done on Galaxy and ClusPro.
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/tldgcw-phf-cluspro.png" style="margin-left:200px;" alt="" width="500" /></p>
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                            Figure 4.: Whole system docked with PHF seed of tau on ClusPro2.0, ΔG = -8.06 kcal/mol.
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/tldgcw-phfa-galaxy.png" style="margin-left:200px;" alt="" width="500" /></p>
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                            Figure 5.: Whole system docked with PHFa seed of tau on Galaxy, ΔG = -7.29 kcal/mol.
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                          Figure 6.: Whole system docked with tau aggregates on ClusPro, ΔG = -12.27 kcal/mol.
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in the 3 figures above GST is colored in grey, Coh2 is colored in orange, trim21 is colored in green, DocS is colored in light blue, WWW is colored in red, and ligands are colored in cyan.
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Latest revision as of 08:35, 13 October 2022


Coh2 linked with tau binding peptide (WWW) & (G4S)3

Fusion protein consists of Tau binding peptide (WWW) 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]

Dry lab

1.1. 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, Qmean4, and Qmean6. 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
0 39.57 2.23 98.14 0 -0.51 -0.98 

                  Figure 1.: Predicted 3D structure of CoH_(G4S) 3_WWW Protein Visualized by Pymol.

1.2. Docking

Coh2-(G4S)3-WWW (CLW) is docked to trim-(G4S)3-DocS (TLD) on LightDock standalone vesrion and ClusPro2.0 web server, the binding affinity were calculated using prodigy to be -14.13 and -15.23 kcal/mol respectively. 

                           Figure 2.: CoH_(G4S)3_WWW docked to trim21-(G4S)-DocS on LightDock. 


                             Figure 3.: CoH_(G4S)3_WWW docked to trim21-(G4S)-DocS on CusPro.

the results of the binding affinity indicate that CLW can bind to TLD with high affinity, the next step is investigating the affinity of WWW in the whole docked structure to its targets (PHF, PHF* and tau aggregates). the docking is done on Galaxy and ClusPro. 

                            Figure 4.: Whole system docked with PHF seed of tau on ClusPro2.0, ΔG = -8.06 kcal/mol. 


                           Figure 5.: Whole system docked with PHFa seed of tau on Galaxy, ΔG = -7.29 kcal/mol. 


                         Figure 6.: Whole system docked with tau aggregates on ClusPro, ΔG = -12.27 kcal/mol.

in the 3 figures above GST is colored in grey, Coh2 is colored in orange, trim21 is colored in green, DocS is colored in light blue, WWW is colored in red, and ligands are colored in cyan.