Difference between revisions of "Part:BBa K4165081"
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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 is able to inhibit serine proteases and it is predicted to be located extracellularly. The inhibitor binds to trypsin proteases and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a tyrpsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 [1] - [4].
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This type of family encodes for a type of inhibitor that is able to inhibit serine proteases and it is predicted to be located extracellularly. The inhibitor binds to trypsin proteases and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a tyrpsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 <sup>[1-4]</sup>.
  
  
 
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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165081 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165081 SequenceAndFeatures</partinfo>
  
  
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===Functional Parameters===
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===Dry-Lab Charachtarization===
  
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GC% Content
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<p style=" font-weight: bold; font-size:14px;"> Modelling </p>
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58.9%
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Isoelectric point (PI)
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<html>
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7.362
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-inhibitors/rosettafold-model-11.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
  
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Charge at pH 7
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                  Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 2-RosettaFold).
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0.609
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Molecular Weight (Protein)
 
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9.454 kDa
 
  
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Only a predicted model (AlphaFold).
 
  
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<p style=" font-weight: bold; font-size:14px;"> Docking </p>
  
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AlphaFold:
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ΔG = -25.635
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https://alphafold.ebi.ac.uk/entry/O60575
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Molprobity:
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Clash Score:
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Ramachandran Favoured:
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<html>
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Ramachandran Outliers:
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-inhibitors/5.png" style="margin-left:200px;" alt="" width="500" /></p>
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Rotamers Outliers:
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</html>
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C-beta Deviations:
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Q-Mean:  
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                  Figure 2.: A graphical illustration showing the binding of the inhibitor with HtrA1 protein (ClusPro).
  
 
===References===
 
===References===
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1 - Frochaux, V., Hildebrand, D., Talke, A., Linscheid, M. W., & Schlüter, H. (2014). Alpha-1-antitrypsin: a novel human high temperature requirement protease A1 (HTRA1) substrate in human placental tissue. PloS one, 9(10), e109483.
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1 - Frochaux, V., Hildebrand, D., Talke, A., Linscheid, M. W., & Schlüter, H. (2014). Alpha-1-antitrypsin: a novel human high temperature requirement protease A1 (HTRA1) substrate in human placental tissue. PloS one, 9(10), e109483.<br>
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2 - 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.
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2 - 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.<br>
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3 - 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.
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3 - 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.<br>
 
4 - Chen, T. J., Tian, Y. F., Chou, C. L., Chan, T. C., He, H. L., Li, W. S., ... & Lai, H. Y. (2021). High spink4 expression predicts poor outcomes among rectal cancer patients receiving CCRT. Current Oncology, 28(4), 2373-2384.
 
4 - Chen, T. J., Tian, Y. F., Chou, C. L., Chan, T. C., He, H. L., Li, W. S., ... & Lai, H. Y. (2021). High spink4 expression predicts poor outcomes among rectal cancer patients receiving CCRT. Current Oncology, 28(4), 2373-2384.
  

Latest revision as of 05:24, 12 October 2022


SPINK4 (Serine Peptidase Inhibitor Kazal type 4).

This basic part encodes Human serine protease inhibitor known as SPINK4 which is able to inhibit trypsin-like proteases, like HtrA1 (BBa_K4165004).

Usage and Biology

This type of family encodes for a type of inhibitor that is able to inhibit serine proteases and it is predicted to be located extracellularly. The inhibitor binds to trypsin proteases and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a tyrpsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 [1-4].


Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 135
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 135
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 135
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 135
  • 1000
    COMPATIBLE WITH RFC[1000]


Dry-Lab Charachtarization

Modelling 

                 Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 2-RosettaFold).


Docking

ΔG = -25.635 


                 Figure 2.: A graphical illustration showing the binding of the inhibitor with HtrA1 protein (ClusPro).

References

1 - Frochaux, V., Hildebrand, D., Talke, A., Linscheid, M. W., & Schlüter, H. (2014). Alpha-1-antitrypsin: a novel human high temperature requirement protease A1 (HTRA1) substrate in human placental tissue. PloS one, 9(10), e109483.
2 - 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 - 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.
4 - Chen, T. J., Tian, Y. F., Chou, C. L., Chan, T. C., He, H. L., Li, W. S., ... & Lai, H. Y. (2021). High spink4 expression predicts poor outcomes among rectal cancer patients receiving CCRT. Current Oncology, 28(4), 2373-2384.