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.
  
  
 
===Usage and Biology===
 
===Usage and Biology===
  
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TLKIVW is a hexapeptide designed using Rosetta software to bind to VQIVYK steric zipper motif of tau fibers, which is from primarily reasons for the Alzheimer’s disease and other dementia related diseases, also it can prevent further accumulation of tau fibrils.
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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'> <p style=" font-weight: bold; font-size:17px;"> Sequence and Features</p> </span>
 
<span class='h3bb'> <p style=" font-weight: bold; font-size:17px;"> Sequence and Features</p> </span>
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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. The best model obtained from 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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table, th, td {
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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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    <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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Revision as of 11:35, 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.


Table 1: Quality assessment parameters of TLKIVW model.


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.