Difference between revisions of "Part:BBa K4165167"
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                   the variation of mRNA and protein concentrations with time compared with the wet lab results.
 
                   the variation of mRNA and protein concentrations with time compared with the wet lab results.
 
   
 
   
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===WetLab Results===
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<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 </p>
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<html>
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<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>
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</html>
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Figure 3. This graph shows the correlation between the mathematical model of dry lab and the wet lab results of the His DOC using sonicator
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<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 chemical lysis </p>
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<html>
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<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>
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</html>
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Figure 4. This graph shows the correlation between the mathematical model of dry lab and the wet lab results of His DOC using chemical lysis
  
  

Revision as of 17:15, 11 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).

Source

Synthesized

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

Dry Lab

Modeling

Model “peptide (His_DocS) modeled by TRrosetta model1” Ranked Third model from our 4 ones with score 5 out of 6 and values of C Beta deviasion = 0 , clash score = 0 , molprobitey = 0.77 , Ramachandran favored = 96 , Ramachandran outlier = 0 , Q Mean_4 = -0.29 , Q Mean_6 = -0.27 



                          Figure 1. The 3D structure of His Docs model visualized by 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

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

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

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