Difference between revisions of "Part:BBa K4165077"
 
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This basic part encodes Human serine protease inhibitor WAP-four disulfide core domain 10A which is able to inhibit HtrA1 (BBa_K4165004).
 
This basic part encodes Human serine protease inhibitor WAP-four disulfide core domain 10A which is able to inhibit HtrA1 (BBa_K4165004).
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===Usage and Biology===
 
===Usage and Biology===
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===<span class='h3bb'>Sequence and Features</span>===
 
===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165077 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165077 SequenceAndFeatures</partinfo>
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−
 
  
 
===Functional Parameters===
 
===Functional Parameters===
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Isoelectric point (PI)
 
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8.121
 
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Charge at pH 7
 
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4.499
 
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Molecular Weight (Protein)
 
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8.943
 
  
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Homology and denovo modelling - AlphaFold2
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<html>
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PDB structure
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<style>
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https://drive.google.com/drive/folders/1Xzf25fsOO8fyS0w3xAookPZnMpGQ6vrQ
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table, th, td {
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Structure assessment results
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  border:1px solid black; margin-left:auto;margin-right:auto;
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Molprobity = 1.62
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}
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Q_Mean = 0.6 土 0.1
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</style>
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Ramachandran Favoured = 89.61%
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<body>
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Ramachandran Outliers = 0
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<table style="width:65%">
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Clash Score = 0
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<table>
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C-beta Deviation = 0
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  <tr>
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Total Score =
+
    <th>Isoelectric point (PI)</th>
 +
    <th>Charge at pH 7</th>
 +
    <th>Molecular Weight (Protein)</th>
 +
  </tr>
 +
  <tr>
 +
    <td>8.121</td>
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    <td>4.499</td>
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    <td>8.943</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
  
 +
===Dry Lab Characterization===
 +
This inhibitor was modeled by several software and the top model was acquired by Alphafold2
 +
Structure assessment results: <br>
  
 
<html>
 
<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/q9h1f0-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
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<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>Q_Mean</th>
 +
    <th>Total Score</th>
 +
  </tr>
 +
  <tr>
 +
    <td>0</td>
 +
    <td>0</td>
 +
    <td>1.62</td>
 +
    <td>89.61%</td>
 +
    <td>0</td>
 +
    <td>0.6 土 0.1</td>
 +
    <td>5</td>
 +
  </tr>
 +
</table>
 +
</body>
 
</html>
 
</html>
  
−
                  Figure 1.: A graphical illustration showing the structure of the inhibitor (AlphaFold).
 
  
 +
<html>
 +
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/q9h1f0-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
 +
</html>
 +
 +
                    Figure 1.: A graphical illustration showing the structure of the inhibitor (AlphaFold).
  
  

Latest revision as of 12:47, 13 October 2022


WAP-four disulphide core domain 10A serine protease inhibitor.

This basic part encodes Human serine protease inhibitor WAP-four disulfide core domain 10A which is able to inhibit HtrA1 (BBa_K4165004).

Usage and Biology

This gene encodes for a type of inhibitor that contains a motif which consists of 8 cysteine residues capable of forming four disulfide bonds at the core of the protease, thus inhibiting its action. This type of inhibitor is very effective and has high affinity for trypsin-like proteases (serine proteases), and in our case it would act as an inhibitor for the trypsin-like catalytic domain of serine protease HtrA1[1]-[3].

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 49
    Illegal PstI site found at 198
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 49
    Illegal PstI site found at 198
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 49
    Illegal PstI site found at 198
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 49
    Illegal PstI site found at 198
  • 1000
    COMPATIBLE WITH RFC[1000]

Functional Parameters

Isoelectric point (PI) Charge at pH 7 Molecular Weight (Protein)
8.121 4.499 8.943

Dry Lab Characterization

This inhibitor was modeled by several software and the top model was acquired by Alphafold2 Structure assessment results:

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Q_Mean Total Score
0 0 1.62 89.61% 0 0.6 土 0.1 5 


                    Figure 1.: A graphical illustration showing the structure of the inhibitor (AlphaFold).


References

1. Clauss, A., Lilja, H., & Lundwall, Å. (2005). The evolution of a genetic locus encoding small serine proteinase inhibitors. Biochemical and biophysical research communications, 333(2), 383-389. 2. Eigenbrot, C., Ultsch, M., Lipari, M. T., Moran, P., Lin, S. J., Ganesan, R., ... & Kirchhofer, D. (2012). Structural and functional analysis of HtrA1 and its subdomains. Structure, 20(6), 1040-1050. 3. Grau, S., Baldi, A., Bussani, R., Tian, X., Stefanescu, R., Przybylski, M., ... & Ehrmann, M. (2005). Implications of the serine protease HtrA1 in amyloid precursor protein processing. Proceedings of the National Academy of Sciences, 102(17), 6021-6026.