Difference between revisions of "Part:BBa K4165012"
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<p style=" font-weight: bold; font-size:14px;"> Docking </p>
 
<p style=" font-weight: bold; font-size:14px;"> Docking </p>
  
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<p style=" font-weight: bold; font-size:14px;"> ΔG = -168.522 </p>
  
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===Functional Parameters===
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<p><img src="https://static.igem.wiki/teams/4165/wiki/seeddocking/tau-seed.png" style="margin-left:200px;" alt="" width="500" /></p>
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<partinfo>BBa_K4165012 parameters</partinfo>
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                          Figure 1. Docked structure of seed peptide against whole tau aggregates
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<p style=" font-weight: bold; font-size:14px;"> ΔG = -4.301 </p>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/seeddocking/phf-seed-cluspro.png" style="margin-left:200px;" alt="" width="500" /></p>
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                          Figure 1. Docked structure of seed peptide against PHF of fibrils
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<p style=" font-weight: bold; font-size:14px;"> ΔG = -2.769 </p>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/seeddocking/phfa-seed-galaxy.png" style="margin-left:200px;" alt="" width="500" /></p>
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                          Figure 1. Docked structure of seed peptide against PHF* of fibrils
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<p style=" font-weight: bold; font-size:14px;"> ΔG = -44.19 </p>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/seeddocking/ab-seed-lightdock.png" style="margin-left:200px;" alt="" width="500" /></p>
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                          Figure 1. Docked structure of seed peptide against amyloid beta
  
 
===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 18:10, 10 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)


Docking

ΔG = -168.522 

                         Figure 1. Docked structure of seed peptide against whole tau aggregates


ΔG = -4.301 

                         Figure 1. Docked structure of seed peptide against PHF of fibrils


ΔG = -2.769 

                         Figure 1. Docked structure of seed peptide against PHF* of fibrils

ΔG = -44.19 

                         Figure 1. Docked structure of seed peptide against amyloid beta

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