Difference between revisions of "Part:BBa K4165167"

 
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<partinfo>BBa_K4165167 short</partinfo>
 
<partinfo>BBa_K4165167 short</partinfo>
  
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This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), DocS (BBa_K3396000) and T7 terminator (BBa_K731721).
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This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), 6x His-tag (BBa_K4165020), DocS (BBa_K3396000) and T7 terminator (BBa_K731721).
  
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<!-- Add more about the biology of this part here
 
 
===Usage and Biology===
 
===Usage and Biology===
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DOCs protein is a part of the Snitch system, which binds to the His tag for the purification of the Docs.
  
 
<!-- -->
 
<!-- -->
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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165167 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165167 SequenceAndFeatures</partinfo>
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 +
===Modeling===
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Model “peptide (His_DocS) modeled by TRrosetta model1” Ranked the Third model from our 4 ones with a score 5 out of 6 and values of
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 +
<html>
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<style>
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table, th, td {
 +
  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>0</td>
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    <td>0.77</td>
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    <td>96</td>
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    <td>0</td>
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    <td>-0.29</td>
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    <td>-0.27</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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 +
 +
 +
<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/his-docs.jpg" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
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 +
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                              Figure 1. The 3D structure of His Docs model Displayed on Pymol.
 +
 +
<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.
 +
 +
 +
<html>
 +
<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/his-doc2.png"style="margin-left:200px;" alt="" width="500" /></p>
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</html>
 +
 +
 +
              Figure 2. 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.
 +
 +
===WetLab Results===
 +
<p style=" font-weight: bold; font-size:14px;"> Comparison between the mathematical model of dry lab and the wet lab results of His DOC using sonicator and chemical lysis </p>
 +
We have made a statistical analysis (t-test) to investigate the mathematical model's effectiveness in predicting the amount of the produced protein due to IPTG induction, whereas the test compares the mathematical model expected results to the replicates made in the induction experiment, given that all the condition of the experiment has been input to the model generating the predicted results.
 +
<html>
 +
<p><img src="https://static.igem.wiki/teams/4165/wiki/data-analysis/tir-wet-expression/his-doc-son.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 +
</html>
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              Figure 3. This graph shows the correlation between the mathematical model of the dry lab and the wet lab
 +
                                              results of the His DOC using a sonicator
 +
 +
<html>
 +
<p><img src="https://static.igem.wiki/teams/4165/wiki/data-analysis/tir-wet-expression/his-docs-chem.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 +
</html>
 +
              Figure 4. This graph shows the correlation between the mathematical model of the dry lab and the wet lab
 +
                                                results of His DOC using chemical lysis
 +
  
  

Latest revision as of 23:50, 13 October 2022


His - DocS

This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), 6x His-tag (BBa_K4165020), DocS (BBa_K3396000) and T7 terminator (BBa_K731721).

Usage and Biology

DOCs protein is a part of the Snitch system, which binds to the His tag for the purification of the Docs.

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
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 45

Modeling

Model “peptide (His_DocS) modeled by TRrosetta model1” Ranked the Third model from our 4 ones with a score 5 out of 6 and values of

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 0 0.77 96 0 -0.29 -0.27 



                             Figure 1. The 3D structure of His Docs model 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 2. 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.

WetLab Results

Comparison between the mathematical model of dry lab and the wet lab results of His DOC using sonicator and chemical lysis

We have made a statistical analysis (t-test) to investigate the mathematical model's effectiveness in predicting the amount of the produced protein due to IPTG induction, whereas the test compares the mathematical model expected results to the replicates made in the induction experiment, given that all the condition of the experiment has been input to the model generating the predicted results. 

              Figure 3. This graph shows the correlation between the mathematical model of the dry lab and the wet lab 
                                              results of the His DOC using a sonicator


              Figure 4. This graph shows the correlation between the mathematical model of the dry lab and the wet lab 
                                               results of His DOC using chemical lysis