Difference between revisions of "Part:BBa K4165042"
 
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===Usage and Biology===
 
===Usage and Biology===
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Switch 22 plays a role in mediating HTRA1's function. For HTRA1 to become active, a conformational modification in the linker is necessary, which displaces the associated inhibitor from the active site. The conformational rearrangement can be mediated through the affinity clamp for tau and beta-amyloid binding. These clamps are used for stabilizing the inhibitor away from the active site. These two domains (inhibitor and affinity clamp connected with linker1 beside with amyloid beta binding peptide connected to tau binding peptide by linker 2). Additionally, (H1A) binding peptide bound to the PDZ domain and connected to the affinity clamp on the other side with linker3.
+
Switch # is used to mediate the activity of HTRA1. It is composed of 3 parts connected by different linkers; an HtrA1 peptide binding PDZ, a clamp of two targeting peptides for tau or amyloid beta, and a catalytic domain inhibitor. Activating HTRA1 upon clamp binding to the target protein 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 tau or beta-amyloid. This binding will result in a tension that detaches the inhibitor from the active site.
  
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===dry lab===
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The TD28REV and WWW peptides considered as tau binding peptides are proved experimentally to bind with tau inhibit the aggregations of tau aggregations respectively. The H1A peptide was also proven to bind with the PDZ of HtrA1 experimentally. The last part is the inhibitor, which is mainly a serine protease inhibitor, and since our protease is a serine protease, it will act and inhibit the Protein. The whole construction was similarly proved from literature. The process of assembly of the whole switch was done according to both CAPRI and NCBI protocols.
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
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we modeled this switch to see the final structure of the switch, the top model which has score 3 out of 6 from RosettaFold.
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===<span class='h3bb'>Sequence and Features</span>===
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<partinfo>BBa_K4165042 SequenceAndFeatures</partinfo>
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===Dry-Lab Characterization===
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<p style=" font-weight: bold; font-size:14px;">Top model</p>
  
 
<html>
 
<html>
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</html>
 
</html>
  
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                          Figure 1.: The 3D structure of switch22 modeled by RosettaFold.
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                    Figure 1.: The 3D structure of the top model of switch22 modeled by RosettaFold.
 +
 
 +
 
 +
The pipeline for creating this model is discussed in details in the section below.
 +
 
 +
<h1>Switch construction Pipeline</h1>
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 +
 
 +
<html>
 +
<img src="https://static.igem.wiki/teams/4165/wiki/registry/dry-lab-modelling-pipeline.png" style="margin-left:200px;" alt="" width="500" /> <br>
 +
 
 +
 
 +
 
 +
<p style="text-align:center;">Figure 2. A figure which dsecribes our Dry-Lab Modelling Pipeline. By team CU_Egypt 2022.</p>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;"> 1) Modelling </p>
 +
<p> Since our parts do not have experimentally acquired structures, we have to model them. This approach is done using both denovo modelling (ab initio) and template-based modelling. For modelling small peptides of our system  we used AppTest and Alphafold.</p>
 +
<p style=" font-weight: bold; font-size:14px;"> 2) Structure Assessment </p>
 +
<p>In order to assess the quality of our structures we used the Swiss-Model tool which gives an overall on quality of any 3D structure (For more information:
 +
<a href="https://2022.igem.wiki/cu-egypt/ProteinModelling.html">Modeling </a>.</p>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;"> 3) Quality Assessment </p>
 +
<p>Using the code created by us (CU_Egypt 2022), we use the JSON files created from the structure assessment step in Swiss-Model to rank all the models For more information: (Link software page) under the name of Modric.</p>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">4) Filtering</p>
 +
<p>We take the top ranked models from the previous steps.</p>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">5) Docking</p>
 +
<p>The top models of inhibitor and HTRA Binding Peptide are docked with HtrA1 (BBa_K4165004).</p>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">6) Ranking</p>
 +
<p>The docking results are ranked according to their PRODIGY results. For more information: <a href="https://2022.igem.wiki/cu-egypt/Docking.html"> Docking</a>.</p>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">7) Top Models</p>
 +
<p>The results that came out from PRODIGY are ranked and top models are chosen to proceed with to the next step. For more information: (Link Docking page).</p>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">8) Alignment</p>
 +
<p>Docked structures are aligned. This means that the HtrA1- binding peptide complex is aligned with the second complex which is the HtrA1-inhibitor complex to check whether they bonded to the same site or not.</p>
 +
 
 +
<img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/switch31/picture10.png" style="margin-left:300px;" alt="" width="300" /></p>
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 +
 
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<p style="text-align:center;"> Figure 3. Aligned structures of HtrA1 binding peptide 1 docked to HtrA1 and inhibitor docked to HtrA1. </p>
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<p style=" font-weight: bold; font-size:14px;">9) Linker length</p>
 +
<p>The linker lengths are acquired by seeing the distance between the inhibitor and the HtrA1 binding peptide which is between both C terminals, N terminals, C- and N- terminal, and N- and C-terminals the linker length is calculated to be between 14.5 and 20.7 angstrom.</p>
 +
 
 +
 
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">10) Assembly</p>
 +
<p>After settling on the linkers lengths, now we will proceed to the assembly step of the whole system which is done using TRrosetta, AlphaFold, RosettaFold, and Modeller.</p>
 +
 
 +
 
 +
<p>a<img src="https://static.igem.wiki/teams/4165/wiki/ahmed-sameh/tau1.png
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" style="margin-left:50px;" alt="" width="150"/> b<img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/htra1-bp/h1b.jpg" style="margin-left:50px;" alt="" width="150" />c<img src="https://static.igem.wiki/teams/4165/wiki/q8iub5-trrosetta-model3.png" style="margin-left:50px;" alt="" width="150" /></p>
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Figure 4. a) TD28REV_GGSGGGG_WWW clamp b) HTRA Binding Peptide 1 c) WAP-four disulfide core domain 13 serine protease inhibitor.
 +
 
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">11) Structure Assessment</p>
 +
<p>In order to assess the quality of our structures we used the Swiss-Model tool which gives an overall on quality of any 3D structure (For more information: (<a href="https://2022.igem.wiki/cu-egypt/ProteinModelling.html">Modeling </a>).</p>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">12) Quality Assessment </p>
 +
<p>Using the code created by us (CU_Egypt 2022), we use the JSON files created from the structure assessment step in Swiss-Model to rank all the models For more information: (<a href="https://2022.igem.wiki/cu-egypt/software.html">Software </a>) under the name of Modric.</p>
 +
 
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">13) Ranking</p>
 +
<p>Using the code created by us (CU_Egypt 2022), we use the JSON files created from the structure assessment step in Swiss-Model to rank all the models For more information: (Link software page) under the name of Abu Trika.</p>
 +
<p style=" font-weight: bold; font-size:14px;">Table 1. quality assessment parameters of switch 31.</p>
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<table style="width:65%">
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<table>
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  <tr>
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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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  </tr>
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  <tr>
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    <td>0</td>
 +
    <td>184.32</td>
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    <td>3.07</td>
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    <td>94.96</td>
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    <td>0</td>
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    <td>0.425854</td>
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    <td>-0.07431</td>
 +
  </tr>
 +
</table>
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">14) Alignment</p>
 +
<p>The docked structures are then aligned and compared to the basic parts which are docked with protein of interest (HtrA1). The structures with least RMSD are chosen.</p>
 +
 
 +
 
 +
 
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<p style=" font-weight: bold; font-size:14px;">Conclusion</p>
 +
The top model was HtrA1 switch 10 (BBa_K4165030) since it was the best switch fulfilling the criteria of structure assessment, docking, and RMSD.
 +
 
 +
 
 +
 
 +
<p style=" font-weight: bold; font-size:14px;">References</p>
 +
 
 +
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
 +
 
 +
4. 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
 +
 
 +
5. 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.
 +
 
 +
6. Stein, V., & Alexandrov, K. (2014). Protease-based synthetic sensing and signal amplification. Proceedings of the National Academy of Sciences, 111(45), 15934-15939
 +
 
 +
7. Rey, J., Breiden, M., Lux, V., Bluemke, A., Steindel, M., & Ripkens, K. et al. (2022). An allosteric HTRA1-calpain 2 complex with a restricted activation profile. Proceedings Of The National Academy Of Sciences, 119(14). doi: 10.1073/pnas.2113520119<br><br>
 +
 
 +
8. Santos, L. H., Ferreira, R. S., & Caffarena, E. R. (2019). Integrating molecular docking and molecular dynamics simulations. In Docking screens for drug discovery (pp. 13-34). Humana, New York, NY.
 +
 
 +
 
 +
 
  
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<!-- -->
 
−
<span class='h3bb'>Sequence and Features</span>
 
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<partinfo>BBa_K4165042 SequenceAndFeatures</partinfo>
 
  
  

Latest revision as of 03:57, 14 October 2022


HtrA1 Switch 22

This composite part consists of T7 promoter (BBa_K3633015), lac operator (BBa_K4165062), pGS-21a RBS (BBa_K4165016), 6x His-tag (BBa_K4165020), H1A (BBa_K4165000), GGGGSG Linker (BBa_K4165017), TD28REV, (BBa_K4165006), GGSGGGG Linker (BBa_K4165018), WWW (BBa_K4165007), GGGGSG Linker (BBa_K4165017), WAP inhibitor (BBa_K4165008), and T7 terminator (BBa_K731721).

Usage and Biology

Switch # is used to mediate the activity of HTRA1. It is composed of 3 parts connected by different linkers; an HtrA1 peptide binding PDZ, a clamp of two targeting peptides for tau or amyloid beta, and a catalytic domain inhibitor. Activating HTRA1 upon clamp binding to the target protein 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 tau or beta-amyloid. This binding will result in a tension that detaches the inhibitor from the active site.

The TD28REV and WWW peptides considered as tau binding peptides are proved experimentally to bind with tau inhibit the aggregations of tau aggregations respectively. The H1A peptide was also proven to bind with the PDZ of HtrA1 experimentally. The last part is the inhibitor, which is mainly a serine protease inhibitor, and since our protease is a serine protease, it will act and inhibit the Protein. The whole construction was similarly proved from literature. The process of assembly of the whole switch was done according to both CAPRI and NCBI protocols.



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 538
    Illegal AgeI site found at 274
  • 1000
    COMPATIBLE WITH RFC[1000]

Dry-Lab Characterization

Top model

                    Figure 1.: The 3D structure of the top model of switch22 modeled by RosettaFold.


The pipeline for creating this model is discussed in details in the section below.

Switch construction Pipeline



Figure 2. A figure which dsecribes our Dry-Lab Modelling Pipeline. By team CU_Egypt 2022.

1) Modelling

Since our parts do not have experimentally acquired structures, we have to model them. This approach is done using both denovo modelling (ab initio) and template-based modelling. For modelling small peptides of our system we used AppTest and Alphafold.

2) Structure Assessment

In order to assess the quality of our structures we used the Swiss-Model tool which gives an overall on quality of any 3D structure (For more information: Modeling .

3) Quality Assessment

Using the code created by us (CU_Egypt 2022), we use the JSON files created from the structure assessment step in Swiss-Model to rank all the models For more information: (Link software page) under the name of Modric.

4) Filtering

We take the top ranked models from the previous steps.

5) Docking

The top models of inhibitor and HTRA Binding Peptide are docked with HtrA1 (BBa_K4165004).

6) Ranking

The docking results are ranked according to their PRODIGY results. For more information: Docking.

7) Top Models

The results that came out from PRODIGY are ranked and top models are chosen to proceed with to the next step. For more information: (Link Docking page).

8) Alignment

Docked structures are aligned. This means that the HtrA1- binding peptide complex is aligned with the second complex which is the HtrA1-inhibitor complex to check whether they bonded to the same site or not.

Figure 3. Aligned structures of HtrA1 binding peptide 1 docked to HtrA1 and inhibitor docked to HtrA1.

9) Linker length

The linker lengths are acquired by seeing the distance between the inhibitor and the HtrA1 binding peptide which is between both C terminals, N terminals, C- and N- terminal, and N- and C-terminals the linker length is calculated to be between 14.5 and 20.7 angstrom.

10) Assembly

After settling on the linkers lengths, now we will proceed to the assembly step of the whole system which is done using TRrosetta, AlphaFold, RosettaFold, and Modeller.

a bc

Figure 4. a) TD28REV_GGSGGGG_WWW clamp b) HTRA Binding Peptide 1 c) WAP-four disulfide core domain 13 serine protease inhibitor.

11) Structure Assessment

In order to assess the quality of our structures we used the Swiss-Model tool which gives an overall on quality of any 3D structure (For more information: (Modeling ).

12) Quality Assessment

Using the code created by us (CU_Egypt 2022), we use the JSON files created from the structure assessment step in Swiss-Model to rank all the models For more information: (Software ) under the name of Modric.

13) Ranking

Using the code created by us (CU_Egypt 2022), we use the JSON files created from the structure assessment step in Swiss-Model to rank all the models For more information: (Link software page) under the name of Abu Trika.

Table 1. quality assessment parameters of switch 31.

cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 184.32 3.07 94.96 0 0.425854 -0.07431

14) Alignment

The docked structures are then aligned and compared to the basic parts which are docked with protein of interest (HtrA1). The structures with least RMSD are chosen.

Conclusion

The top model was HtrA1 switch 10 (BBa_K4165030) since it was the best switch fulfilling the criteria of structure assessment, docking, and RMSD.

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 4. 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 5. 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. 6. Stein, V., & Alexandrov, K. (2014). Protease-based synthetic sensing and signal amplification. Proceedings of the National Academy of Sciences, 111(45), 15934-15939 7. Rey, J., Breiden, M., Lux, V., Bluemke, A., Steindel, M., & Ripkens, K. et al. (2022). An allosteric HTRA1-calpain 2 complex with a restricted activation profile. Proceedings Of The National Academy Of Sciences, 119(14). doi: 10.1073/pnas.2113520119

8. Santos, L. H., Ferreira, R. S., & Caffarena, E. R. (2019). Integrating molecular docking and molecular dynamics simulations. In Docking screens for drug discovery (pp. 13-34). Humana, New York, NY.