Difference between revisions of "Part:BBa K4165008"
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<partinfo>BBa_K4165008 short</partinfo>
 
<partinfo>BBa_K4165008 short</partinfo>
  
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This basic part encodes Human serine protease inhibitor WAP-four disulfide core domain 13 which is able to inhibit HtrA1 (BBa_K4165004).
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This basic part encodes Human serine protease inhibitor WAP-four disulfide core domain 13 which is able to inhibit trypsin-like proteases like serine protease HtrA1 (BBa_K4165004).
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===Usage and Biology===
 
===Usage and Biology===
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This type of family 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].
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This type of family encodes 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.
  
  
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===Dry Lab Characterization===
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
  
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===Functional Parameters===
 
  
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Isoelectric point (PI)
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This inhibitor was modeled using different software (trRosetta - AlphaFold2 - RosettaFold - Modeller) and the top model was acquired from trRosetta ranking 6 out of 6 according to our Quality Assesment code.
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7.763
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Charge at pH 7
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<html>
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2.506
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<p><img src="https://static.igem.wiki/teams/4165/wiki/q8iub5-trrosetta-model3.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
  
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Molecular Weight (Protein)
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                          Figure 1. Predicted 3D structure of WAP inhibitor by trRosetta
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10.386 kDa
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===PDB Structure===
 
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Homology and denovo modelling - (TRrosetta - AlphaFold2 - RosettaFold - Modeller)
 
  
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===Functional Parameters===
  
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Structure assessment results
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Isoelectric point (PI):
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Q_Mean =
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7.763
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Ramachandran Favoured =
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Ramachandran Outliers =
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Clash Score =
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C-beta Deviation =
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Total Score =
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Charge at pH 7:
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2.506
  
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Molecular Weight (Protein):
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10.386 kDa
  
  
 
===References===
 
===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.
 
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.
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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.
 
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.
 
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.
  

Revision as of 17:20, 10 October 2022


WAP-four disulfide core domain 13 serine protease inhibitor.

This basic part encodes Human serine protease inhibitor WAP-four disulfide core domain 13 which is able to inhibit trypsin-like proteases like serine protease HtrA1 (BBa_K4165004).

Usage and Biology

This type of family encodes 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.


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
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 270
    Illegal AgeI site found at 6
  • 1000
    COMPATIBLE WITH RFC[1000]


Dry Lab Characterization

Modeling


This inhibitor was modeled using different software (trRosetta - AlphaFold2 - RosettaFold - Modeller) and the top model was acquired from trRosetta ranking 6 out of 6 according to our Quality Assesment code. 

                          Figure 1. Predicted 3D structure of WAP inhibitor by trRosetta


Functional Parameters

Isoelectric point (PI): 7.763

Charge at pH 7: 2.506

Molecular Weight (Protein): 10.386 kDa


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.