Difference between revisions of "Part:BBa K4165000"
Line 51: Line 51:
 
                   Figure 3. this figure shows the results from the transcription and translation code showing  
 
                   Figure 3. this figure shows the results from the transcription and translation code showing  
 
                   the variation of mRNA and protein concentrations with time compared with the wet lab results.
 
                   the variation of mRNA and protein concentrations with time compared with the wet lab results.
 +
 +
===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.
  
 
<partinfo>BBa_K4165000 parameters</partinfo>
 
<partinfo>BBa_K4165000 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Revision as of 21:47, 11 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 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 = 0, clashscore = 69.77, molprobity = 4.26, ramachandran_favored = 40, ramachandran_outliers = 60, Qmean_4 = -6.45183, Qmean6 = -5.51397) 

                     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

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 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 compared with the wet lab results.

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.