Difference between revisions of "Part:BBa K4165202"

Revision as of 14:07, 13 October 2022

Trim-(GGGGS)3-Docs

This parts code for the Trim21 E3 ligase with the PRYSPRY domain truncated (BBa_K3396007), fused to type 1 Dockerin module derived from Clostridium thermocellum cellulosome scaffoldin by a Glycine Serine flexible linker repeated three times to maintain part flexibility needed during target ubiquitination.

Usage and Biology

This fusion protein is part of our Trim System (Snitch System), it is a modified version of the NUDT 2020 part (BBa_K3396005). It is supposed to bind to the PROTAC (Coh2-linker-tau_binding_peptide) to assemble a full system that will be able to target Tau protein through the binding peptide and recruit ubiquitin to tag the whole protein to initiate degradation by proteasomes through Trim21.

Trim21 (E3) is an integral part of the protein turnover processes which serves as a quality control step. In order to be degraded by proteasome 26S, the protein must be tagged with a ubiquitin tail. E3 ligase serves the function of transferring the ubiquitin to the protein of interest. So, in order for the process to be directed more specifically at certain proteins, we took advantage of the high affinity between the two modules (DocS and Coh2) which make up the cellulosome, to act as a protein pair that will guide trim to any chosen protein.

This process could be done by anchoring Trim21 to either one of the modules and anchoring its other counterpart with a targeting domain for the protein of interest, more feasible and directed ubiquitination of the target protein has been achieved, which eventually leads to specific degradation.

Sequence and Features

Improvement

There seemed to be some mistakes in the original sequence uploaded by NUDT 2020 (BBa_K3396005), there was an additional stop codon in the middle of the fusion protein and an extra Tyrosine residue in their Glycine-Serine Linker. These misconceptions hinder the usage of this part by any iGEM team, so we ought to provide them with the correct sequence that they could use easily if they want to assemble this part.

           Figure 1.: Alignment of modified Trim-G4S-DocS sequence with the original sequence from of NUDT_2020
(BBa_K3396007) showing the extra amino acid residues (Valine-Leucine-Glutamic acid- Lysine) and the stop codon in the middle.

Modeling

tTrim21-(G₄S)₃-DocS is modeled by AlphaFold2, ITASSER, MODELLER, Robetta and TrRosetta, best model obtained from TrRosetta. We assembled this part with different linker and substituted the DocS with Coh2 (BBa_K4165200), (BBa_K4165201), and (BBa_K4165203). The results of model assessment showed that this part is the best one.

                   Figure 2.: Predicted 3D structure of our fusion protein tTrim21-(G4S)3-DocS.

Table 1: Quality assessment parameters of tTrim21-(G₄S)₃-DocS. model.

The modeling results show that fusing DocS to tTrim21 by (G4S)3 linker improves the quality of the model than DocS basic part (BBa_K3396000).

1.2. Docking

Docking is done to test the interaction of the whole fusion proteins together, and how it can change the binding affinity from the tagged part in our contribution to DocS (BBa_K3396000). The results prove that when DocS is fused to tTrim21, the resulted protein has higher affinity to GST-Coh2-linker-WWW than basic DocS and Coh2.

               Figure 3.: All docked structure of TLD by Galaxy and ClusPro displayed by Pymol.

Table 2: Binding affinity of tTrim21-(G₄S)₃-DocS to protacs with different tau binding peptides models.

1.2. Mathematical modeling

The rate of formation of the complex of Trim21-linker-DocS and GST-Coh2-linker-tau binding peptide is modeled using our Ubiquitin proteasome system simulating mathematical model

               Figure 4.: Graphical representation showing the change in concentration of Trim21-linker-DocS, GST-Coh2- 
                                     linker-tau binding peptides and their complex with time.

               Figure 5.: Graphical representation showing the change in concentration of Tau with time when it is added to 
                                       the Ubiquitin proteasome system for degradation.

the high decline in the tau concentration at the beginning of simulation is due to its binding with the complex formed above, then the rate of decrease slow down as all complex binds to tau, the slow decrease is dependent on the degradation of tau mainly.

WetLab Results

Trim21 is an E3 ligase that can add ubiquitin molecules to the target protein. We fused this part to the dockerin protein to form the Snitch first composite that can bind to their binding partner Cohesine protein fused to Tau binding peptide, these two partners can trigger the Tau ubiquitination upon the interaction between TBP and tau. We started with making suspension of this part and ligate it with pJET using T4 ligase, then we transform it into DH5 alpha to amplify it. Then we extract the plasmid using manual miniprep protocol and restrict it using XbaI and XhoI to ligate it with pGS-21a, and transformation into BL-21 to induce protein expression using IPTG. We extracted the protein using a chemical lysis buffer and purify the protein using Ni-NTA affinity chromatography. We tested the activity and specificity of this part by using a pull-down assay that detects the protein-protein interaction between Docs linked to Trim21 and Coh2 which is linked to TBP, then we use BCA assay to characterize the interaction.

Transformation of His Trim21 (L) Doc in DH-5 alpha using pJET cloning vector

                              Figure 7. Transformed plate of His Trim21 (L) Doc + pJET 

Transformation of His Trim21 (L) Doc in BL-21 using pGS-21a expression vector

We transformed His Trim21 (L) Doc in BL-21 using the pGS-21a vector, and we used the TSS buffer protocol as it shows the best results compared to Calcium Chloride buffer and the combination between Calcium Chloride and Magnesium Chloride buffer.

                             Figure 6. Transformed plate of His Trim21 (L) Doc + pGS-21a 

Comparison between chemical lysis and sonication for His Trim21 (L) DOC

We extract the protein Trim21 (L) Doc using two methods, the chemical method which is based on the use of lysozyme to lysis the bacterial cell membrane, in the other side the physical method, which used sonication to degrade the bacterial cell membrane. We compared the lysis methods using the BCA assay. The results of the BCA assay show that the extraction using the physical method is more efficient.

                      Figure 8. This graph shows a significant difference between chemical lysis and sonication
                            for His Trim21 (L) DOC, after we had the results, we optimized our protocol to
                                         use sonication for His Trim21 (L) DOC

SDS PAGE of induced and non-induced samples of His Trim 21 (L) DOC

SDS PAGE depends on molecular weight so, we performed SDS PAGE to check our protein size and to compare between induced and non induced samples.

             Figure 9. This figure shows the comparison between the induced and non-induced samples of His Trim21 
              (L) DOC, where well no.1 is the non-induced sample while well no.3 is the induced sample showing that 
              our protein is induced effectively owing to our right choice of IPTG, time interval and concentration

Pull-down assay of His Trim21 (L) DOC against GST COH WWW and GST COH TD28 Rev

Pull-down assay is a one-step assay that is used to detect protein-protein interaction. We incubate Trim (L) Doc with GST Coh WWW and GST Coh TD28rev to see the best interaction, we used the BCA assay to characterize the interaction.

             Figure 10. This graph shows the comparison of pull-down assay between His Trim (L) DOC against GST COH WWW and 
              GST COH TD28 Rev, showing that the interaction between His Trim21 (L) DOC and GST COH WWW is better than that 
              of His Trim (L) DOC and GST COH TD28 Rev as the concentration of the elution coming from the pull-down assay 
              of His Trim21 (L) DOC and GST COH WWW is more than that of His Trim21 (L) DOC and GST COH TD28rev

Gel of Pull down assay of His Trim 21 (L) DOC with GST-Coh2-L-WWW results

We performed SDS PAGE after performing pull-down assay to check the binding between the proteins

     Figure 11. Shows the gel the interaction is done between the Trim21 (L) Doc and GST Coh WWW as there are two bands 
                                                      that appear in the gel  

References

1- Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH. Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain. J Mol Biol. 2001 Mar 30;307(3):745-53. doi: 10.1006/jmbi.2001.4522. PMID: 11273698.

2- Ronchi, V. P., & Haas, A. L. (2012). Measuring rates of ubiquitin chain formation as a functional readout of ligase activity. In Ubiquitin Family Modifiers and the Proteasome (pp. 197-218). Humana Press.

3- Collins, G. A., & Goldberg, A. L. (2017). The logic of the 26S proteasome. Cell, 169(5), 792-806.