Difference between revisions of "Part:BBa K4165167"

Revision as of 06:45, 12 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

                  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 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 the dry lab and the wet lab 
                                                  results of His DOC using chemical lysis

@@ Line 4: / Line 4: @@
 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===
@@ Line 15: / Line 12: @@
 <partinfo>BBa_K4165167 SequenceAndFeatures</partinfo>
-===Dry Lab===
+===Modeling===
-<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
+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
-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
+<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>0</td>
+    <td>0.77</td>
+    <td>96</td>
+    <td>0</td>
+    <td>-0.29</td>
+    <td>-0.27</td>
+  </tr>
+</table>
+</body>
+</html>
 <html>
@@ Line 25: / Line 51: @@
-                           Figure 1. The 3D structure of His Docs model visualized by Pymol.
+                              Figure 1. The 3D structure of His Docs model Displayed on Pymol.
 <p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
@@ Line 40: / Line 66: @@
                    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 </p>
@@ Line 47: / Line 71: @@
 <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>
-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
+                   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 sonicator
 <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>
@@ Line 53: / Line 78: @@
 <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 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 the dry lab and the wet lab
+                                                   results of His DOC using chemical lysis