Difference between revisions of "Part:BBa K4165173"
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===Usage and Biology===
 
===Usage and Biology===
  
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The protac in our snitch system is responsible for connecting the target protein (tau) to the tTrim21 which binds to E2 conjugating enzymes and put tau and ubiquitin in proximity to each other resulting in ubiquitination of the tau at lysine residue and after ubiquitination the tau will be degraded by 26S proteasome.
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The protac in our snitch system is responsible for connecting the target protein (tau) to the Trim21 which binds to E2 conjugating enzymes and put tau and ubiquitin in proximity to each other resulting in ubiquitination of the tau at lysine residue and after ubiquitination the tau will be degraded by 26S proteasome.
 
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Revision as of 12:06, 12 October 2022


Biobrick GST - CoH2 - Linker - WWW

This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), GST (BBa_K4165070), CoH2 (BBa_K4165003), GGGGSx3 (BBa_K4165068), WWW (BBa_K4165007), and T7 terminator (BBa_K731721).

Usage and Biology

The protac in our snitch system is responsible for connecting the target protein (tau) to the Trim21 which binds to E2 conjugating enzymes and put tau and ubiquitin in proximity to each other resulting in ubiquitination of the tau at lysine residue and after ubiquitination the tau will be degraded by 26S proteasome.

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
    Illegal SapI.rc site found at 189

Dry Lab

Modeling

From 3 models out of 16 Models modeled in 4 software, 1 Model ranked best according to its Q_Mean values 4 and 6. The best Model has values of :

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
1 3.08 1.35 96.31 0.79 -0.01 -0.29 


                          Figure 1. The 3D structure of the COH-Linker-WWW 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 1. 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 GST COH WWW using sonicator

Figure 2. This graph shows that the mathematical model of the dry lab and the wet lab results of GST COH WWW using sonicator correlate with each other

Comparison between the mathematical model of dry lab and the wet lab results of GST COH WWW using chemical lysis

Figure 3. This Graph shows that the mathematical model of the dry lab and the results of the wet lab of GST COH WWW using chemical lysis don't correlate with each other as there is a great difference between the results