Difference between revisions of "Part:BBa K4165072"
(→Mathematical Modeling) |
(→Mathematical Modeling) |
||
| Line 56: | Line 56: | ||
===Mathematical Modeling=== | ===Mathematical Modeling=== | ||
<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promoter </p> | <p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promoter </p> | ||
| − | + | The mathematical modeling was based on our code for the calculation of transcription and translation according to thermodynamic laws and ODE (You can find it on our wiki) and compared the results with the wet lab. | |
<html> | <html> | ||
| Line 63: | Line 63: | ||
| − | + | ||
| − | + | Figure 2. This figure shows the results from the transcription and translation code showing | |
| − | Figure 2. | + | |
the variation of mRNA and protein concentrations with time compared with the wet lab results (1mM IPTG concentration) | the variation of mRNA and protein concentrations with time compared with the wet lab results (1mM IPTG concentration) | ||
Latest revision as of 11:12, 12 October 2022
T7 promoter-GST-DocS-T7 terminator
This composite part is composed of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), RBS 4 (BBa_K4165264), GST-tag (BBa_K4165070), DocS (BBa_K3396000), 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]
- 12COMPATIBLE WITH RFC[12]
- 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_DocS) modeled by Rosettafold full_model_407305_3” Ranked the fourth model from our 4 ones with a score 4 out of 6 and values of:
| cbeta_deviations | clashscore | molprobity | ramachandran_favored | ramachandran_outliers | Qmean_4 | Qmean_6 |
|---|---|---|---|---|---|---|
| 0 | 182.78 | 2.72 | 98.25 | 0.7 | 0.75 | 1.02 |
Figure 1. The 3D structure of the GST-DOCs model Displayed on Pymol.
Mathematical Modeling
Transcription rate and translation rate under T7 promoter
The mathematical modeling was based on our code for the calculation of transcription and translation according to thermodynamic laws and ODE (You can find it on our wiki) and compared the results with 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 (1mM IPTG concentration)
Figure 3. 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 (2mM IPTG concentration)