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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===<span class='h3bb'>Sequence and Features</span>===
 
===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165008 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165008 SequenceAndFeatures</partinfo>
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===Functional Parameters===
 
===Functional Parameters===
  
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Isoelectric point (PI)
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<html>
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7.763
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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>Isoelectric point (PI)</th>
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    <th>Charge at pH 7</th>
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    <th>Molecular Weight (Protein)</th>
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  </tr>
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  <tr>
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    <td>7.763</td>
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    <td>2.506</td>
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    <td>10.386 kDa</td>
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  </tr>
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</table>
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</body>
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</html>
  
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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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===Dry Lab Characterization===
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10.386 kDa
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
  
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===PDB Structure===
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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 Assessment code.
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Homology and denovo modelling - (TRrosetta - AlphaFold2 - RosettaFold - Modeller)
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Structure assessment results
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<html>
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Q_Mean =  
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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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Ramachandran Favoured =  
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</html>
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Ramachandran Outliers =  
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Clash Score =  
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                          Figure 1. Predicted 3D structure of WAP inhibitor by trRosetta displayed on Pymol.
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C-beta Deviation =  
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Total Score =  
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<p style=" font-weight: bold; font-size:14px;"> Docking </p>
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ΔG = -38.13
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/q8iub5-htra1.jpeg" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
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                            Figure 2. Docked structure of HtrA1 with WAP inhibitor displayed on Pymol.
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<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
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<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promotor </p>
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the mathematical modeling was based on our code for the calculation of transcription and translation (you can find it in the code section) beside with the estimated results from the wet lab.
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/q8iub52.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
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                  Figure 3. this figure shows the results from the transcription and translation code showing the
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                      variation of mRNA and protein concentrations with time compared with the wet lab results.
  
  
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===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.
 +
 
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.
  

Latest revision as of 13:56, 13 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]


Functional Parameters

Isoelectric point (PI) Charge at pH 7 Molecular Weight (Protein)
7.763 2.506 10.386 kDa


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 Assessment code. 


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


Docking

ΔG = -38.13 

                           Figure 2. Docked structure of HtrA1 with WAP inhibitor displayed on Pymol.

Mathematical modeling

Transcription rate and translation rate under T7 promotor

the mathematical modeling was based on our code for the calculation of transcription and translation (you can find it in the code section) beside with the estimated results from the wet lab. 


                  Figure 3. this figure shows the results from the transcription and translation code showing the 
                      variation of mRNA and protein concentrations with time compared with the wet lab results.



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.