Difference between revisions of "Part:BBa K4165000"

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This peptide was modeled using different software and the top model from Alphafold2 got score 5 out of 6 in our Quality assessment code.
 
This peptide was modeled using different software and the top model from Alphafold2 got score 5 out of 6 in our Quality assessment code.
  
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(cbeta_deviations = 0, clashscore = 69.77, molprobity = 4.26, ramachandran_favored = 40, ramachandran_outliers = 60, Qmean_4 = -6.45183, Qmean6 = -5.51397)
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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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  <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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    <td>0</td>
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    <td>69.77</td>
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    <td>4.26</td>
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    <td>40</td>
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    <td>60</td>
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    <td>-6.45183</td>
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    <td>-5.513969</td>
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                       Figure 2.: 3D Model of H1A peptide Docked against HTRA1 displayed in Pymol  
 
                       Figure 2.: 3D Model of H1A peptide Docked against HTRA1 displayed in Pymol  
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<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
 
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<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promotor </p>
 
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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.
 
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<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/mathematical-modeling/h1a2.png" style="margin-left:200px;" alt="" width="500" /></p>
 
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                  Figure 3. this figure shows the results from the transcription and translation code showing
 
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                  the variation of mRNA and protein concentrations with time compared with the wet lab results.
 
  
 
===References===
 
===References===
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1.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.
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1.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.<br>
 
2.Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu, P., Pan, B., ... & Sidhu, S. S. (2007). Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Science, 16(11), 2454-2471.
 
2.Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu, P., Pan, B., ... & Sidhu, S. S. (2007). Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Science, 16(11), 2454-2471.
  
 
<partinfo>BBa_K4165000 parameters</partinfo>
 
<partinfo>BBa_K4165000 parameters</partinfo>
 
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Latest revision as of 13:57, 13 October 2022


HTRA Binding Peptide 1

Part encodes a synthetic peptide that binds to the PDZ domain of serine protease HTRA1.

Usage and Biology

Synthetic peptide acquired by Phage display, binds specifically to PDZ domain of HTRA1 and HTRA3 Proteins.

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]


Functional Parameters

ΔG of –8.8 Kcal/mol and IC50 of 0.9 ± 0.1

Dry Lab Characterization

Modeling

This peptide was modeled using different software and the top model from Alphafold2 got score 5 out of 6 in our Quality assessment code.


cbeta_deviations clashscore molprobity ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 69.77 4.26 40 60 -6.45183 -5.513969 


                     Figure 1.: 3D Model of H1A peptide Modelled by AlphaFold2.0 displayed in Pymol

Docking

ΔG= -32.8 kcal/mol 

                     Figure 2.: 3D Model of H1A peptide Docked against HTRA1 displayed in Pymol

References

1.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.
2.Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu, P., Pan, B., ... & Sidhu, S. S. (2007). Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Science, 16(11), 2454-2471.