Difference between revisions of "Part:BBa K4165046"
 
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===Usage and Biology===
 
===Usage and Biology===
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Switch 26 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 26 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 seed peptide is considered as an amyloid binding peptide and is proved experimentally to inhibit the aggregations of amyloid beta through cell viability assays with a survival rate values nearly 100%. The H1A peptide was validated to bind with the PDZ of HtrA1 experimentally. The last part, which is the inhibitor, which is mainly a serine protease inhibitor, and since our protease is a serine protease, so 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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===Dry lab===
 
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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  out of 6 from        .
 
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<p><img src="" style="margin-left:200px;" alt="" width="500" /></p>
 
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</html>
 
  
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                                      Figure 1. The 3D structure of switch 26 modeled by
 
  
 
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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165046 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165046 SequenceAndFeatures</partinfo>
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===Dry-lab Characterization===
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<p style=" font-weight: bold; font-size:14px;">Top model</p>
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switch26.png" style="margin-left:220px;" alt="" width="500" /></p>
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</html>
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                                Figure 1. The 3D structure of switch 26 modeled by TRrosetta
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The pipeline for creating this model is discussed in details in the section below
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<h1>Switch construction Pipeline</h1>
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<html>
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<img src="https://static.igem.wiki/teams/4165/wiki/registry/dry-lab-modelling-pipeline.png" style="margin-left:200px;" alt="" width="500" /> <br>
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 +
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<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>
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<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:
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<a href="https://2022.igem.wiki/cu-egypt/ProteinModelling.html">Modeling </a>.</p>
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<p style=" font-weight: bold; font-size:14px;"> 3) Quality Assessment </p>
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<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>
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<p>We take the top ranked models from the previous steps.</p>
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<p style=" font-weight: bold; font-size:14px;">5) Docking</p>
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<p>The top models of inhibitor and HTRA Binding Peptide are docked with HtrA1 (BBa_K4165004).</p>
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<p style=" font-weight: bold; font-size:14px;">6) Ranking</p>
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<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>
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<p style=" font-weight: bold; font-size:14px;">7) Top Models</p>
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<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>
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<p style=" font-weight: bold; font-size:14px;">8) Alignment</p>
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<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 binded to the same site or not.</p>
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<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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<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>
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<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 13 and 25 angstrom.</p>
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<p style=" font-weight: bold; font-size:14px;">10) Assembly</p>
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<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>
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<p>a<img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/switch31/ninhiibitor31-clamp.png" 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) Seed_GGSGGGGG_seed clamp b) HTRA Binding Peptide 1 c) WAP-four disulfide core domain 13 serine protease inhibitor.
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<p style=" font-weight: bold; font-size:14px;">11) Structure Assessment</p>
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<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>
 +
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<p style=" font-weight: bold; font-size:14px;">12) Quality Assessment </p>
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<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>
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 +
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<p style=" font-weight: bold; font-size:14px;">13) Ranking</p>
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<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>
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The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta with a score of 5 out of 6 according to our quality assessment code.
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<html>
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<style>
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table, th, td {
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  border:1px solid black; margin-left:auto;margin-right:auto;
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}
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</style>
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<body>
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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>1</td>
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    <td>2.15</td>
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    <td>1.46</td>
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    <td>92.42</td>
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    <td>1.52</td>
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    <td>-2.28826</td>
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    <td>-2.8186</td>
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  </tr>
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</table>
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</body>
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</html>
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<p style=" font-weight: bold; font-size:14px;">14) Alignment</p>
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<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>
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The top model was HtrA1 switch 10 (BBa_K4165030) since it was the best switch fulfilling the criteria of structure assessment, docking, and RMSD.
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<p style=" font-weight: bold; font-size:14px;">References</p>
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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.
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 +
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
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 +
4. 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>
 +
 +
5. 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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Latest revision as of 03:59, 14 October 2022


HtrA1 Switch 26

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), GGGGSGG Linker (BBa_K4165064), Seed peptide (BBa_K4165012), GGSGGGGG Linker (BBa_K4165019), Seed peptide (BBa_K4165012), GGGGSGG Linker (BBa_K4165064), WAP inhibitor (BBa_K4165008), and T7 terminator (BBa_K731721).

Usage and Biology

Switch 26 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 seed peptide is considered as an amyloid binding peptide and is proved experimentally to inhibit the aggregations of amyloid beta through cell viability assays with a survival rate values nearly 100%. The H1A peptide was validated to bind with the PDZ of HtrA1 experimentally. The last part, which is the inhibitor, which is mainly a serine protease inhibitor, and since our protease is a serine protease, so 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 379
    Illegal AgeI site found at 115
  • 1000
    COMPATIBLE WITH RFC[1000]

Dry-lab Characterization

Top model

                               Figure 1. The 3D structure of switch 26 modeled by TRrosetta


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 binded 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 13 and 25 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) Seed_GGSGGGGG_seed 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.

The switch was modeled by (Alphafold - Rosettafold - tRrosetta) and the top model was obtained from tRrosseta with a score of 5 out of 6 according to our quality assessment code.
cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
1 2.15 1.46 92.42 1.52 -2.28826 -2.8186

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. 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

4. 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

5. 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.