Difference between revisions of "Part:BBa K4165006"
 
(12 intermediate revisions by 5 users not shown)
Line 5: Line 5:
 
A synthetic peptide that is used for targeting misfolded tau protein (BBa_K4165009) as it binds to PHF6 of tau fibrils.
 
A synthetic peptide that is used for targeting misfolded tau protein (BBa_K4165009) as it binds to PHF6 of tau fibrils.
  
−
<partinfo>BBa_K4165006 SequenceAndFeatures</partinfo>
 
  
  
 
===Usage and Biology===
 
===Usage and Biology===
  
−
A short synthetic peptide acquired by mirror image phage display for binding to tau fibrils at its seed sequence ‘VQIVYK’ called the PHF6. The aggregation of microtubule-associated tau protein starts at this seed to form neurofibrillary tangles inside the brain, which are the main cause of Alzheimer’s disease (AD). Accordingly, this peptide would be suitable to act as our targeting domain for the aggregations.
+
This is the reversed sequence of peptide TD28 (BBa_K4165145) which is a short synthetic peptide acquired by mirror image phage display for binding to tau fibrils at its seed sequence ‘VQIVYK’ called the PHF6. The aggregation of microtubule-associated tau protein starts at this seed to form neurofibrillary tangles inside the brain, which are the main cause of Alzheimer’s disease (AD). Accordingly, this peptide would be suitable to act as our targeting domain for the aggregations.
 +
 
 +
 
 +
===Sequence and features===
 +
 
 +
<partinfo>BBa_K4165006 SequenceAndFeatures</partinfo>
  
  
Line 17: Line 21:
 
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
 
<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
  
−
We modeled the peptide with (Alphafold2, Apptest, iTASSER, and trRrosetta) and our top model was obtained from Apptest scoring 6 out of 6 according to our quality assessment code.  
+
We modeled the peptide with (Alphafold2, Apptest, iTASSER, and TRrosetta) and our top model was obtained from Apptest scoring 6 out of 6 according to our quality assessment code.  
  
 
<html>
 
<html>
Line 23: Line 27:
 
</html>
 
</html>
  
−
                                    Figure 1.: Predicted 3D structure of TD28REV peptide.
+
                              Figure 1.: Predicted 3D structure of TD28REV peptide visualized by Pymol.
−
 
+
  
 +
<html>
 
<p style=" font-weight: bold; font-size:14px;"> Docking </p>
 
<p style=" font-weight: bold; font-size:14px;"> Docking </p>
  
−
Docking was performed using three different algorithms (Lightdock, Cluspro, and Galaxy web server) to test the interaction and binding affinity of TD28REV to both tau PHF filament and amyloid beta aggregates, this was followed by ranking of docked models and selection of models with the lowest free energy of binding.
+
Docking was performed using three different algorithms (Lightdock, Cluspro, and Galaxy web server) to test the interaction and binding affinity of TD28REV to both tau PHF filament and amyloid beta aggregates, this was followed by ranking of docked models and selection of models with the lowest free energy of binding, please find the code for docking and ranking at <a href="https://2022.igem.wiki/cu-egypt/ProgrammingClub.html">Programming club page.</a>.</p>
 +
.
  
  
Line 40: Line 45:
 
</html>
 
</html>
  
−
                                  Figure 2.: Visualization of TD28REV docked with Tau PHF.
+
                              Figure 2.: Visualization of TD28REV docked with Tau PHF visualized by Pymol.
  
  
Line 51: Line 56:
 
</html>
 
</html>
  
−
                                  Figure 2.: Visualization of TD28REV docked with Amyloid beta.
+
                              Figure 3.: Visualization of TD28REV docked with Amyloid beta visualized by Pymol.
  
 +
<html>
 +
<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
 +
<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promotor </p>
 +
the mathematical modeling was based on our code for the calculation of transcription and translation you can find it in<a href="https://2022.igem.wiki/cu-egypt/ProgrammingClub.html">Programming club page</a>
 +
besides the estimated results from the wet lab.</p>
 +
 +
<html>
 +
<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/td28rev2.png" style="margin-left:200px;" alt="" width="500" /></p>
 +
</html>
 +
  
 +
                    Figure 4. this figure shows the results from the transcription and translation code showing the
 +
                        mRNA and protein concentrations variation with time compared with the wet lab results.
  
 
===References===
 
===References===

Latest revision as of 01:01, 14 October 2022


TD28rev (Tau binding peptide)

A synthetic peptide that is used for targeting misfolded tau protein (BBa_K4165009) as it binds to PHF6 of tau fibrils.


Usage and Biology

This is the reversed sequence of peptide TD28 (BBa_K4165145) which is a short synthetic peptide acquired by mirror image phage display for binding to tau fibrils at its seed sequence ‘VQIVYK’ called the PHF6. The aggregation of microtubule-associated tau protein starts at this seed to form neurofibrillary tangles inside the brain, which are the main cause of Alzheimer’s disease (AD). Accordingly, this peptide would be suitable to act as our targeting domain for the aggregations.


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

We modeled the peptide with (Alphafold2, Apptest, iTASSER, and TRrosetta) and our top model was obtained from Apptest scoring 6 out of 6 according to our quality assessment code. 

                             Figure 1.: Predicted 3D structure of TD28REV peptide visualized by Pymol.

Docking

Docking was performed using three different algorithms (Lightdock, Cluspro, and Galaxy web server) to test the interaction and binding affinity of TD28REV to both tau PHF filament and amyloid beta aggregates, this was followed by ranking of docked models and selection of models with the lowest free energy of binding, please find the code for docking and ranking at Programming club page..

.

TD28REV vs Tau seed (PHF):

ΔG = -170.825 

                              Figure 2.: Visualization of TD28REV docked with Tau PHF visualized by Pymol.


TD28REV vs Amyloid beta:

ΔG = -40.34 

                             Figure 3.: Visualization of TD28REV docked with Amyloid beta visualized by Pymol.

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 inProgramming club page besides the estimated results from the wet lab.


                   Figure 4. this figure shows the results from the transcription and translation code showing the 
                       mRNA and protein concentrations variation with time compared with the wet lab results.

References

Dammers, C., Yolcu, D., Kukuk, L., Willbold, D., Pickhardt, M., Mandelkow, E., ... & Funke, S. A. (2016). Selection and Characterization of Tau Binding ᴅ-Enantiomeric Peptides with Potential for Therapy of Alzheimer Disease. PLoS One, 11(12), e0167432.