Difference between revisions of "Part:BBa K4165139"
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<partinfo>BBa_K4165139 short</partinfo>
 
<partinfo>BBa_K4165139 short</partinfo>
  
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Tau binding peptide targeting the PHF seed of Tau
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A synthetic peptide that is used for targeting misfolded tau protein (BBa_K4165009) as it binds to PHF6 of tau fibrils.
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===Usage and Biology===
 
===Usage and Biology===
  
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TLKIVW is a hexapeptide designed using Rosetta software and obtained by phage display to bind to VQIVYK (BBa_K4165204) steric zipper motif of tau fibers, which is from the main reasons of the Alzheimer’s disease and other dementia related diseases, this peptide can also prevent further accumulation of tau fibrils.
 
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<span class='h3bb'>Sequence and Features</span>
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<span class='h3bb'> <p style=" font-weight: bold; font-size:17px;"> Sequence and Features</p> </span>
 
<partinfo>BBa_K4165139 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165139 SequenceAndFeatures</partinfo>
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===Dry Lab===
 
===Dry Lab===
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
  
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TLKIVW were modeled by alphafold2 and apptest.
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TLKIVW was modeled by AlphaFold2 and Apptest and the best model was obtained from Apptest ranking 5 out of 6 according to our quality assessment code.
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best model obtained from apptest
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/tlkivw.png" style="margin-left:200px;" alt="" width="500" /></p>
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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>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>0</td>
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    <td>2.11</td>
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    <td>100</td>
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    <td>0</td>
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    <td>-1.97474</td>
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    <td>-0.69185</td>
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  </tr>
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</table>
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</body>
 
</html>
 
</html>
  
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                            Figure 1.: Predicted 3D structure of Synthetic peptide TLKIVW.
 
  
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modeled by alphafold2 and apptest.
 
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best model obtained from apptest
 
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Table 1.: Quality assessment parameters of TLKIVW model.
 
  
 
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/tlkivw-pars.png" style="margin-left:200px;" alt="" width="500" /></p>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/tlkivw.png" style="margin-left:220px;" alt="" width="500" /></p>
 
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</html>
  
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HAmZA
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                                Figure 1: Predicted 3D structure of Synthetic peptide TLKIVW.
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===References===
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1. Sievers, S. A., Karanicolas, J., Chang, H. W., Zhao, A., Jiang, L., Zirafi, O., ... & Eisenberg, D. (2011). Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature, 475(7354), 96-100.
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<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K4165139 parameters</partinfo>
 
<partinfo>BBa_K4165139 parameters</partinfo>
 
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Latest revision as of 11:36, 11 October 2022


TLKIVW Peptide

A synthetic peptide that is used for targeting misfolded tau protein (BBa_K4165009) as it binds to PHF6 of tau fibrils.


Usage and Biology

TLKIVW is a hexapeptide designed using Rosetta software and obtained by phage display to bind to VQIVYK (BBa_K4165204) steric zipper motif of tau fibers, which is from the main reasons of the Alzheimer’s disease and other dementia related diseases, this peptide can also prevent further accumulation of tau fibrils.

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

Modeling

TLKIVW was modeled by AlphaFold2 and Apptest and the best model was obtained from Apptest ranking 5 out of 6 according to our quality assessment code.


cbeta_deviations molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 2.11 100 0 -1.97474 -0.69185 


                                Figure 1: Predicted 3D structure of Synthetic peptide TLKIVW.

References

1. Sievers, S. A., Karanicolas, J., Chang, H. W., Zhao, A., Jiang, L., Zirafi, O., ... & Eisenberg, D. (2011). Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature, 475(7354), 96-100.