Difference between revisions of "Part:BBa K4165256"

Revision as of 13:13, 13 October 2022

GST-Coh2-G4S-WWW

This composite part encodes for Cohesin 2 module (BBa_K4165003) which is connected to the tau binding peptide WWW (BBa_K4165007) with a flexible linker of GGGGS (BBa_K4165068) repeated 3 times and tagged with a GST tag (BBa_K4165070).

Usage and Biology

The part is considered an integral part of the snitch system in which it 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 proteins which causes Alzheimer's Diseases at lysine residue and after ubiquitination the tau will be degraded by 26S proteasome.

The protac in our snitch system is Sequence and Features

Dry Lab characterization

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 :

                          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 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

In the wet lab we started with cloning in the pJET vector followed by the expression in the pgs21a, then we performed two different kinds of lysis to extract the protein to find which lysis buffer will give better yield, and quantified the protein expression before and after induction using BCA assay, in the end, we tested the GST COH WWW affinity by the pulldown assay against the His Trim21 (L) DOC and against the tau aggregates which showed that WWW could bind to the tau aggregates effectively

Ligation of GST Coh WWW with pJET cloning vector

We used T4 ligase to ligate GST Coh WWW with pJET cloning vector so, we incubated Gst Coh WWW with pJET overnight at 15°C.

           Figure 3. This figure shows the ligation between GST Coh WWW with pJET cloning vector, Our band is expected to be 
             at 4284 (A faint band appears). The ligation reaction didn’t ligate all the inserts so we will find two bands 
             of the vector and the insert at 2974 and 1310 respectively 

Transformation of GST COH WWW in BL-21 using pGS-21a vector

The transformation was done using TSS buffer protocol, after trying three buffers which are Calcium chloride, Magnesium chloride and a combination between Calcium chloride and Magnesium chloride, we optimized our protocol to use the TSS buffer protocol as it showed the best results with a transformation efficiency of GST COH WWW in DH-5 alpha using pJET vector is 142x10⁵ transformants/µg while that of GST COH WWW in BL-21 using pGS-21a vector is 700 transformants/µg , you can find the complete protocol in our wiki page

Transformation of GST COH WWW in DH-5 alpha using pJET vector

                                   Figure 4. Transformed plate of GST COH (L) WWW + pJET

                                    Figure 5. Transformed plate of GST COH (L) WWW + pGS-21a

Miniprep for Gst Coh WWW in pJET cloning vector

Miniprep is a technique used to extract the plasmid containing our protein so, we performed miniprep to extract the pJET cloning vector containing our Gst Coh WWW.

           Figure 6. This figure shows the miniprep of pJET containing the GST Coh WWW, Our mini prep band appears at 
                                                4284 (A faint band appears)

Comparison between chemical lysis and sonication for GST COH WWW

Chemical lysis and sonication were done to check which of them gives better results in the protein extraction, and after comparing the results we optimized our protocol to use chemical lysis for GST COH WWW

                  Figure 7. This graph shows a significant difference between chemical lysis and sonication for GST COH 
                     WWW, after we had the results we optimized our protocol to use chemical lysis for GST COH WWW 

SDS PAGE for induced and non induced samples of GST COH WWW

SDS PAGE depends on the molecular weight of the protein, we performed SDS to make sure that our protein is in the exact size and to show the difference between induced and non induced samples of GST COH WWW.

               Figure 8. This figure shows the comparison between induced and non induced samples of GST COH WWW, where well 
                 no.1 is the induced sample while well no.5 is the non induced sample showing that our protein is induced 
                 effectively owing to our right choice of IPTG, time interval and concentration

BCA assay results of GST COH WWW

BCA assay is a technique that is performed to quantify the proteins, and it depends on the color of the BCA dye which is directly proportional with the quantity of the protein, we performed BCA for GST COH WWW to know its concentration and it is found to be 0.719466667

             Figure 9. This graph illustrates the results of BCA assay for GST COH WWW showing that our protein 
                                       concentration is expected to be 0.719466667 mg/ml

Pull down assay of His Trim21 (L) DocS against GST COH WWW and GST COH TD28Rev

Pull down assay is a technique performed to check the interactions between the proteins and to check if they bind properly, we performed pull down assay to check the binding between GST COH WWW against His Trim21 (L) DOC, and between Tau aggregates and GST COH WWW, where WWW was found to be a proper candidate of Tau (Illustrated in figure 5 and 6)

              Figure 10. This graph shows the comparison of pull down assay between His trim21(L) DOC with GST COH WWW and 
               GST COH TD28Rev, showing that the interaction between His Trim21 (L) DOC and GST COH WWW is better than that 
               of His Trim21 (L) DOC and GST COH TD28Rev as the concentration of the elution of His Trim21 (L) DOC with GST 
               COH WWW is more than that of His Trim21 (L) DOC with GST COH TD28Rev

Pull down assay of Tau aggregates against GST COH WWW and GST COH TD28Rev

              Figure 11. This graph shows the comparison of pull down assay between Tau aggregates with GST COH WWW and GST 
               COH TD28Rev, showing that the interaction between Tau aggregates with GST COH WWW is better than that of Tau 
               aggregates with GST COH TD28Rev as the concentration of elution of Tau aggregates with GST COH WWW is more 
               than that of Tau aggregates with GST COH TD28Rev, illustrating that WWW could be a better candidate for 
               binding to the Tau aggregates