Difference between revisions of "Part:BBa K4165012"

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                                      Figure 1. RCSB model of seed peptide (37-42)  
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                                  Figure 1. RCSB model of seed peptide (37-42) visualized by Pymol.
  
  
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                          Figure 1. Docked structure of seed peptide against whole tau aggregates
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                      Figure 2. Docked structure of seed peptide against whole tau aggregates visualized by Pymol.
  
  
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                          Figure 1. Docked structure of seed peptide against PHF of fibrils
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                      Figure 3. Docked structure of seed peptide against PHF of fibrils visualized by Pymol.
  
  
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                          Figure 1. Docked structure of seed peptide against PHF* of fibrils
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                      Figure 4. Docked structure of seed peptide against PHF* of fibrils visualized by Pymol.
  
  
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                          Figure 1. Docked structure of seed peptide against amyloid beta
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                            Figure 5. Docked structure of seed peptide against amyloid beta.
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<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
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<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promotor </p>
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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.
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<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/seed2.png" style="margin-left:200px;" alt="" width="500" /></p>
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                Figure 6. this figure shows the results from the transcription and translation code showing the
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                    variation of mRNA and protein concentrations with time compared with the wet lab results.
  
 
===References===
 
===References===
 
1. Fradinger, E. A., Monien, B. H., Urbanc, B., Lomakin, A., Tan, M., Li, H., Spring, S. M., Condron, M. M., Cruz, L., Xie, W., Benedek, G. B., & Bitan, G. (2008). C-terminal peptides coassemble into Aβ42 oligomers and protect neurons against Aβ42-induced neurotoxicity. Proceedings of the National Academy of Sciences of the United States of America, 105(37), 14175-14180. https://doi.org/10.1073/pnas.0807163105
 
1. Fradinger, E. A., Monien, B. H., Urbanc, B., Lomakin, A., Tan, M., Li, H., Spring, S. M., Condron, M. M., Cruz, L., Xie, W., Benedek, G. B., & Bitan, G. (2008). C-terminal peptides coassemble into Aβ42 oligomers and protect neurons against Aβ42-induced neurotoxicity. Proceedings of the National Academy of Sciences of the United States of America, 105(37), 14175-14180. https://doi.org/10.1073/pnas.0807163105

Revision as of 05:26, 11 October 2022


Seed peptide (GGVVIA)

This part encodes Amyloid 𝛽 seed (37-42) which has the ability to bind to A𝛽 plaques inside the brain.

Usage and Biology

A short peptide derived from amyloid beta oligomers (A𝛽 37-42), which is proven to bind amyloid beta plaques inside the brain and stop plaque formation. This peptide showed no cytotoxicity when tested inside hippocampal cell lines, so it will be suitable to use as the targeting domain for A𝛽 plaques inside our system.

Sequence and Features


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
    COMPATIBLE WITH RFC[1000]


Dry Lab Characterization

Modeling 


                                 Figure 1. RCSB model of seed peptide (37-42) visualized by Pymol.


Docking

ΔG = -168.522 

                      Figure 2. Docked structure of seed peptide against whole tau aggregates visualized by Pymol.


ΔG = -4.301 

                      Figure 3. Docked structure of seed peptide against PHF of fibrils visualized by Pymol.


ΔG = -2.769 

                     Figure 4. Docked structure of seed peptide against PHF* of fibrils visualized by Pymol.


ΔG = -44.19 

                            Figure 5. Docked structure of seed peptide against amyloid beta.

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 6. 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.

References

1. Fradinger, E. A., Monien, B. H., Urbanc, B., Lomakin, A., Tan, M., Li, H., Spring, S. M., Condron, M. M., Cruz, L., Xie, W., Benedek, G. B., & Bitan, G. (2008). C-terminal peptides coassemble into Aβ42 oligomers and protect neurons against Aβ42-induced neurotoxicity. Proceedings of the National Academy of Sciences of the United States of America, 105(37), 14175-14180. https://doi.org/10.1073/pnas.0807163105