Difference between revisions of "Part:BBa K4165171"
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This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), GST tag (BBa_K4165070), CoH2 (BBa_K4165003), and T7 terminator (BBa_K731721). | This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), GST tag (BBa_K4165070), CoH2 (BBa_K4165003), and T7 terminator (BBa_K731721). | ||
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===Usage and Biology=== | ===Usage and Biology=== | ||
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<partinfo>BBa_K4165171 SequenceAndFeatures</partinfo> | <partinfo>BBa_K4165171 SequenceAndFeatures</partinfo> | ||
− | === | + | ===Modeling=== |
− | + | Model “peptide (GST_Coh2) modeled by Alphafold GST_Coh2_f66fb_unrelaxed_rank_3_model_2” Ranked first model from our 4 ones with score 5 out of 6 and values of | |
− | Model “peptide (GST_Coh2) modeled by Alphafold GST_Coh2_f66fb_unrelaxed_rank_3_model_2” Ranked first model from our 4 ones with score 5 out of 6 and values of | + | |
+ | <html> | ||
+ | <style> | ||
+ | table, th, td { | ||
+ | border:1px solid black; margin-left:auto;margin-right:auto; | ||
+ | } | ||
+ | </style> | ||
+ | <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>13.59</td> | ||
+ | <td>1.64</td> | ||
+ | <td>98.31</td> | ||
+ | <td>0.56</td> | ||
+ | <td>0.643</td> | ||
+ | <td>0.914</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </body> | ||
+ | </html> | ||
+ | |||
<html> | <html> | ||
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− | Figure 1. The 3D structure of COH model | + | Figure 1. The 3D structure of GST-COH model Displayed on Pymol. |
<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p> | <p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p> | ||
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− | Figure | + | 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. | variation of mRNA and protein concentrations with time compared with the wet lab results. | ||
===WetLab Results=== | ===WetLab Results=== | ||
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<p><img src="https://static.igem.wiki/teams/4165/wiki/data-analysis/tir-wet-expression/gst-coh-chem.jpg" style="margin-left:200px;" alt="" width="500" /></p> | <p><img src="https://static.igem.wiki/teams/4165/wiki/data-analysis/tir-wet-expression/gst-coh-chem.jpg" style="margin-left:200px;" alt="" width="500" /></p> | ||
</html> | </html> | ||
− | Figure | + | Figure 3. This graph shows the correlation between the mathematical model of the dry lab and the wet lab |
+ | results of GST COH using chemical lysis | ||
<p style=" font-weight: bold; font-size:14px;">Comparison between the mathematical model of dry lab and the wet lab results of GST COH using sonicator </p> | <p style=" font-weight: bold; font-size:14px;">Comparison between the mathematical model of dry lab and the wet lab results of GST COH using sonicator </p> | ||
<html> | <html> | ||
<p><img src="https://static.igem.wiki/teams/4165/wiki/data-analysis/tir-wet-expression/gst-coh2-son.jpg" style="margin-left:200px;" alt="" width="500" /></p> | <p><img src="https://static.igem.wiki/teams/4165/wiki/data-analysis/tir-wet-expression/gst-coh2-son.jpg" style="margin-left:200px;" alt="" width="500" /></p> | ||
</html> | </html> | ||
− | Figure | + | Figure 5. This graph shows that the mathematical model of the dry lab and the wet lab results of GST COH using |
+ | sonicator don't correlate with each as there is a difference between the results | ||
Revision as of 10:43, 12 October 2022
Biobrick GST - CoH2
This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), GST tag (BBa_K4165070), CoH2 (BBa_K4165003), and T7 terminator (BBa_K731721).
Usage and Biology
COH protein is a part of the Snitch system, which binds to the GST tag for the purification of the COH.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 1172
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI.rc site found at 45
Illegal SapI.rc site found at 189
Modeling
Model “peptide (GST_Coh2) modeled by Alphafold GST_Coh2_f66fb_unrelaxed_rank_3_model_2” Ranked first model from our 4 ones with score 5 out of 6 and values of
cbeta_deviations | clashscore | molprobity | ramachandran_favored | ramachandran_outliers | Qmean_4 | Qmean_6 |
---|---|---|---|---|---|---|
0 | 13.59 | 1.64 | 98.31 | 0.56 | 0.643 | 0.914 |
Figure 1. The 3D structure of GST-COH 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 GST COH using chemical lysis
Figure 3. This graph shows the correlation between the mathematical model of the dry lab and the wet lab results of GST COH using chemical lysis
Comparison between the mathematical model of dry lab and the wet lab results of GST COH using sonicator
Figure 5. This graph shows that the mathematical model of the dry lab and the wet lab results of GST COH using sonicator don't correlate with each as there is a difference between the results