Difference between revisions of "Part:BBa K4165001:Design"

Revision as of 18:34, 4 October 2022

Truncated tripartite motif-containing 21 (TRIM21)

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 514

Dry Lab Characterization

Optimization

Firstly, we removed the last nucleotide in the original sequence from NUDT team 2020 to avoid the frame-shifting and preparing to codon optimization.

Also, we optimized the sequence to be expressed in E-coli BL21.

Modeling

Through our work, we modeled Trim-21 with Dockerine and cohesin to know which one of them is more stable when it binds to Trim 21, we designed them by 5 tools (Robetta-Itasser-Alphafold-Modeller-TR Rosetta) to reach the best model. The results and literature showed that Trim21 binds to DocS is preferable to Coh2. Our top 2 models ranked 5 out of 6 according to our QA code.

                            Figure 2.: Predicted 3D structure of truncated Trim21 model1.

                            Figure 3.: Predicted 3D structure of truncated Trim21 model2.

Source

original trim is expressed in human and we acquired the sequence from NUDT iGEM team 2020 BBa_K3396007

References

1. Clift, D., McEwan, W. A., Labzin, L. I., Konieczny, V., Mogessie, B., James, L. C., & Schuh, M. (2017). A Method for the Acute and Rapid Degradation of Endogenous Proteins. Cell, 171(7), 1692-1706.e18. https://doi.org/10.1016/j.cell.2017.10.033

2. D.L. Mallery, W.A. McEwan, S.R. Bidgood, G.J. Towers, C.M. Johnson, L.C. James Antibodies mediate intracellular immunity through tripartite motif-containing 21 (TRIM21) Proc. Natl. Acad. Sci. USA, 107 (2010), pp. 19985-19990

3. Kleiger, G., & Mayor, T. (2014). Perilous journey: a tour of the ubiquitin-proteasome system. Trends in cell biology, 24(6), 352. https://doi.org/10.1016/j.tcb.2013.12.003

4. L.C. James, A.H. Keeble, Z. Khan, D.A. Rhodes, J. Trowsdale Structural basis for PRYSPRY-mediated tripartite motif (TRIM) protein function Proc. Natl. Acad. Sci. USA, 104 (2007), pp. 6200-

5. Zhang, Y., Li, L., Munir, M., & Qiu, H. (2018). RING-Domain E3 Ligase-Mediated Host–Virus Interactions: Orchestrating Immune Responses by the Host and Antagonizing Immune Defense by Viruses. Frontiers in Immunology. https://doi.org/10.3389/fimmu.2018.01083

@@ Line 16: / Line 16: @@
 Through our work, we modeled Trim-21 with Dockerine and cohesin to know which one of them is more stable when it binds to Trim 21, we designed them by 5 tools (Robetta-Itasser-Alphafold-Modeller-TR Rosetta)  to reach the best model.
 The results and literature showed that Trim21 binds to DocS is preferable to Coh2. Our top 2 models ranked 5 out of 6 according to our QA code.
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