Difference between revisions of "Part:BBa K4165008"

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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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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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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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                                Figure 1. Predicted 3D structure of WAP inhibitor by trRosetta
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                          Figure 1. Predicted 3D structure of WAP inhibitor by trRosetta displayed on Pymol.
  
  
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                                Figure 2. Docked structure of HtrA1 with WAP inhibitor
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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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<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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                  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.
  
 
===Functional Parameters===
 
===Functional Parameters===

Revision as of 05:20, 11 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 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.

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.