Difference between revisions of "Part:BBa K4165202"
Line 56: Line 56:
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/data-analysis/sonication-or-chemical/sonication-or-chemical/trim-doc.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/data-analysis/sonication-or-chemical/sonication-or-chemical/trim-doc.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
−
Figure 4. 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
+
                                    Figure 4. 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
 +
 
 +
 
  
 
===References===
 
===References===

Revision as of 19:50, 11 October 2022


Trim-(GGGGS)3-Docs

This parts code for the trim21 E3 ligase having his PRYSPRY domain truncated (BBa_K3396007), fused to type 1 Dockerin module derived from Clostridium thermocellum cellulosome scaffoldin using Glycine serine flexible linker repeated three times to maintain part flexibility needed during target ubiquitination.

Usage and Biology

this part is the main part in our Snitch system, it is supposed to bind to the protac (Coh2-linker-tau_binding_peptide) which in turn will bind to tau protein. The hypothesis is when the binding occurs between the three parts, tTrim21 will recruit E2 conjugating enzyme that carries ubiquitin and move the ubiquitin from the E2 to tau. After ubiquitination, tau protein is supposed to be degraded by 26S proteasome.

source

Synthetic Fusion protein

Sequence and Features

sequence was optimized for E.coli expression


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 535

Dry Lab

Modeling

tTrim21-(G4S)3-DocS is modeled by AlphaFold2, ITASSER, MODELLER, Robetta and TrRosetta, best model obtained from TrRosetta. 


                            Figure 1.: Predicted 3D structure of our fusion protein tTrim21-(G4S)3-DocS.


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



WetLab Results

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

                                   Figure 2. Transformed plate of His Trim21 (L) Doc + pGS-21a

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

                                   Figure 3. Transformed plate of His Trim21 (L) Doc + pJET

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

                                   Figure 4. 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


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.