Part:BBa_K4165008
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
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 270
Illegal AgeI site found at 6 - 1000COMPATIBLE 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.
| None |