Coding

Part:BBa_K4165007

Designed by: Hossam Hatem   Group: iGEM22_CU_Egypt   (2022-09-29)
Revision as of 15:13, 5 October 2022 by Amr Gouda (Talk | contribs)


WWW (Tau binding peptide)

Synthetic peptide used to bind to the aggregations of misfolded tau protein (BBa_K4165009) and toxic Amyloid beta plaques (BBa_).


Usage and Biology

WWW peptide is designed to inhibit the fibrilization of tau which is one of the main drivers of Alzheimer’s disease and other dementia diseases. PHF* (VQIINK) is the site that derives tau aggregation. WWW can bind to PHF* in a means that can disrupt the interface between each PHF* and consequently reduce the aggregates. Accordingly, this peptide would be suitable to act as the targeting domain in our systems.


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

Modeling

WWW peptide has been designed using AlphaFold2, Apptest, RosettaFold and TRrosetta. the best model obtained from AlphaFold2 with parameters values: cbeta_deviations 0, clashscore 0, molprobity 1.26, ramachandran_favored 100, ramachandran_outliers 0,Qmean4 -2.60904, and Qmean6 -1.56177 


                            Figure 1.: Predicted 3D structure of Synthetic peptide WWW.


Docking

We docked WWW with whole tau, paired helical filaments (PHF) of tau and (PHF*)

ΔG = -173.217 

                      Figure 2.: Docked structure of WWW and whole tau designed by Galaxy docking tool.


ΔG = -8.45 

                      Figure 3.: Docked structure of WWW and PHF* of tau designed by Galaxy docking tool.


ΔG = -8.255 

                      Figure 4.: Docked structure of WWW and PHF of tau designed by Galaxy docking tool.


All of binding energies were calculated using prodigy tool.



References

1. Goedert, M., & Spillantini, M. G. (2017). Propagation of Tau aggregates. Molecular Brain, 10. https://doi.org/10.1186/s13041-017-0298-7

2. Etienne, M. A., Edwin, N. J., Aucoin, J. P., Russo, P. S., McCarley, R. L., & Hammer, R. P. (2007). Beta-amyloid protein aggregation. Methods in molecular biology (Clifton, N.J.), 386, 203–225. https://doi.org/10.1007/1-59745-430-3_7

3. Seidler, P., Boyer, D., Rodriguez, J., Sawaya, M., Cascio, D., Murray, K., Gonen, T., & Eisenberg, D. (2018). Structure-based inhibitors of tau aggregation. Nature chemistry, 10(2), 170. https://doi.org/10.1038/nchem.2889





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