Difference between revisions of "Part:BBa K4165085"

(→‎Dry-Lab Characterization)
 
Line 4: Line 4:
  
 
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).
−
 
−
 
−
 
  
 
===Usage and Biology===
 
===Usage and Biology===
Line 25: Line 22:
 
<p style=" font-weight: bold; font-size:14px;"> Quality Assessment </p>
 
<p style=" font-weight: bold; font-size:14px;"> Quality Assessment </p>
  
−
<p> C-beta deviation: 0 </p>
+
<html>
−
<p> Clash score: 50.77 </p>
+
<style>
−
<p> Molprobity: 3.2 </p>
+
table, th, td {
−
<p> Ramachandran favored: 78.95 </p>
+
  border:1px solid black; margin-left:auto;margin-right:auto;
−
<p> Ramachandran outliers: 8.42 </p>
+
}
−
<p> QMean_4: -3.71517 </p>
+
</style>
−
<p> QMean_6: -3.3123 </p>
+
<body>
 +
<table style="width:65%">
 +
<table>
 +
  <tr>
 +
    <th>cbeta_deviations</th>
 +
    <th>clashscore</th>
 +
    <th>molprobity</th>
 +
    <th>ramachandran_favored</th>
 +
    <th>ramachandran_outliers</th>
 +
    <th>Qmean_4</th>
 +
    <th>Qmean_6</th>
 +
  </tr>
 +
  <tr>
 +
    <td>0</td>
 +
    <td>50.77</td>
 +
    <td>3.2</td>
 +
    <td>78.95</td>
 +
    <td>8.42</td>
 +
    <td>-3.71517</td>
 +
    <td>-3.3123</td>
 +
  </tr>
 +
</table>
 +
</body>
 +
</html>
  
  
Line 38: Line 58:
 
</html>
 
</html>
  
−
                  Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 4-AlphaFold).
+
              Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 4-AlphaFold).
  
  

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.