Difference between revisions of "Part:BBa K4165085"
 
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This basic part encodes Human serine protease inhibitor known as SPINK14 which is able to inhibit trypsin-like proteases, like HtrA1 (BBa_K4165004).
 
This basic part encodes Human serine protease inhibitor known as SPINK14 which is able to inhibit trypsin-like proteases, like 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 is predicted to be able to inhibit serine peptidases. The inhibitor is present extracellularly. The inhibitor binds to trypsin-like proteases (serine proteases) and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a trypsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 [1] - [3].
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This type of family encodes for a type of inhibitor that is predicted to be able to inhibit serine peptidases. The inhibitor is present extracellularly. The inhibitor binds to trypsin-like proteases (serine proteases) and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a trypsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 <sup>[1-3]</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_K4165085 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165085 SequenceAndFeatures</partinfo>
  
  
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===Functional Parameters===
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===Dry-Lab Characterization===
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GC% Content
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62.2%
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Isoelectric point (PI)
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<p style=" font-weight: bold; font-size:14px;"> Modelling </p>
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8.767
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Charge at pH 7
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This inhibitor was modeled by several software and the top model was acquired by Alphafold
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5.898
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Molecular Weight (Protein)
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<p style=" font-weight: bold; font-size:14px;"> Quality Assessment </p>
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11.057 kDa
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===PDB Structure===
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<html>
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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>cbeta_deviations</th>
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    <th>clashscore</th>
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    <th>molprobity</th>
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    <th>ramachandran_favored</th>
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    <th>ramachandran_outliers</th>
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    <th>Qmean_4</th>
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    <th>Qmean_6</th>
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  </tr>
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  <tr>
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    <td>0</td>
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    <td>50.77</td>
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    <td>3.2</td>
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    <td>78.95</td>
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    <td>8.42</td>
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    <td>-3.71517</td>
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    <td>-3.3123</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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It has a predicted sturcture (AlphaFold2)
 
  
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-inhibitors/model4-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
  
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AlphaFold:
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              Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 4-AlphaFold).
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https://alphafold.ebi.ac.uk/entry/Q6IE38
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Molprobity:  
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Clash Score:
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Ramachandran Favoured:
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Ramachandran Outliers:
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Rotamers Outliers:
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C-beta Deviations:
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Q-Mean:
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<p style=" font-weight: bold; font-size:14px;"> Docking </p>
  
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<html>
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<p> ΔG = -37.794 </p>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/5-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
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                  Figure 1.: A graphical illustration showing the structure of the inhibitor (AlphaFold).
 
  
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<html>
 +
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-inhibitors/dry-lab/dock-q6ie38.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
  
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                  Figure 2.: A graphical illustration showing the binding of the inhibitor with HtrA1 (Galaxy).
  
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===Reference===:
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===Reference:===
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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>
  
  
 
<partinfo>BBa_K4165085 parameters</partinfo>
 
<partinfo>BBa_K4165085 parameters</partinfo>
 
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Latest revision as of 12:36, 13 October 2022


SPINK14 (Serine Peptidase Inhibitor Kazal type 14).

This basic part encodes Human serine protease inhibitor known as SPINK14 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 predicted to be able to inhibit serine peptidases. The inhibitor is present extracellularly. The inhibitor binds to trypsin-like proteases (serine proteases) and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a trypsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 [1-3].

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
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Dry-Lab Characterization

Modelling

This inhibitor was modeled by several software and the top model was acquired by Alphafold

Quality Assessment

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 50.77 3.2 78.95 8.42 -3.71517 -3.3123 


              Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 4-AlphaFold).


Docking

ΔG = -37.794 


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

Reference:

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.