Difference between revisions of "Part:BBa K4165001:Design"
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===Dry Lab Characterization=== | ===Dry Lab Characterization=== | ||
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Firstly, we removed the last nucleotide in the original sequence from NUDT team 2020 to avoid the frame-shifting and preparing to codon 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. | ||
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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. | 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. | 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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===Source=== | ===Source=== | ||
Revision as of 18:14, 4 October 2022
Truncated tripartite motif-containing 21 (TRIM21)
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE 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.
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