Difference between revisions of "Part:BBa K4165038"

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The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta with a score of 4 out of 6 according to our quality assessment code.
 
The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta with a score of 4 out of 6 according to our quality assessment code.
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    <th>cbeta_deviations</th>
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    <th>clashscore</th>
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    <th>molprobity</th>
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    <th>ramachandran_favored</th>
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    <th>ramachandran_outliers</th>
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    <th>Qmean_4</th>
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    <th>Qmean_6</th>
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    <td>0</td>
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    <td>1.61</td>
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    <td>0.91</td>
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    <td>98.46</td>
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    <td>1.585746</td>
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    <td>0.26107</td>
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                 Figure 3. this figure shows the results from the transcription and translation code showing the  
 
                 Figure 3. this figure shows the results from the transcription and translation code showing the  
 
                                   variation of mRNA and protein concentrations with time.
 
                                   variation of mRNA and protein concentrations with time.
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===Refernces===
 
===Refernces===

Revision as of 14:03, 13 October 2022


HtrA1 Switch number 18

This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), WAP inhibitor (BBa_K4165008), GSGSGS linker (BBa_J18921), seed peptide (BBa_K4165012), GGSGGGGG linker (BBa_K4165019), seed peptide (BBa_K4165012), GSGSGS linker (BBa_J18921), H1A (BBa_K4165000) and T7 terminator (BBa_K731721).

Usage and Biology

Switch 18 is used to mediate the activity of HTRA1 (BBa_K4165004). It is composed of 3 parts connected by different linkers; an HtrA1 PDZ domain binding peptide (BBa_K4165000), a clamp of two targeting peptides for amyloid beta 42 which is neurotoxic fragment when accumulated in the extracellular matrix of the neurons, and a catalytic domain inhibitor (WAP inhibitor). this part is constructed to make our protease HtrA1 switched off as long as the target of the clamp does not exist. The method of inhibition depends on the binding of the inhibitor to the catalytic domain and PDZ peptide (BBa_K4165000) to PDZ. Activating HTRA1 requires a conformational change in the linker, eliminating the attached inhibitor from the active site. The conformational rearrangement can be mediated through the binding of affinity clamp to beta-amyloid. This binding will result in a tension that detaches the inhibitor from the active site.

This part or its concept can be used by next iGEM teams to use in constructing target specific switchable protease system specially with HtrA1 protease.

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
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 379
    Illegal AgeI site found at 115
  • 1000
    COMPATIBLE WITH RFC[1000]

Dry Lab

Modeling

The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta with a score of 4 out of 6 according to our quality assessment code.

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 1.61 0.91 98.46 0 1.585746 0.26107 

                  Figure 1. The 3D structure of switch 18 modeled by TRrosetta. Red: Tau binding peptides, 
                                  blue: H1A peptide, cyan: inhibitor, and green: linkers


Docking

switch 18 vs HtrA1:

The binding affinity of switch 18 to HtrA1 is calculated as ΔG = -19.516 kcal/mol. 

                      Figure 2. The 3D structure of switch 18 docked to HtrA1 Visualized by Pymol.


Mathematical modeling

Transcription rate and translation rate under T7 promoter

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 3. this figure shows the results from the transcription and translation code showing the 
                                  variation of mRNA and protein concentrations with time.

Refernces

1. Lu, J., Cao, Q., Wang, C., Zheng, J., Luo, F., Xie, J., ... & Li, D. (2019). Structure-based peptide inhibitor design of amyloid-β aggregation. Frontiers in molecular neuroscience, 12, 54.

2. Romero-Molina, S., Ruiz-Blanco, Y. B., Mieres-Perez, J., Harms, M., Münch, J., Ehrmann, M., & Sanchez-Garcia, E. (2022). PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity. Journal of Proteome Research.

3. Stein, V., & Alexandrov, K. (2014). Protease-based synthetic sensing and signal amplification. Proceedings of the National Academy of Sciences, 111(45), 15934-15939