PART A (From Pranam)
Find the amino acid sequence for SOD1 in UniProt (ID: P00441), a protein when mutated, can cause Amyotrophic lateral sclerosis (ALS). In fact, the A4V (when you change position 4 from Alanine to Valine) causes the most aggressive form of ALS, so make that change in the sequence
Original sequence
>sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2
MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS
AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV
HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Mutated sequence
>sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2
MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS
AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV
HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Enter your mutated SOD1 sequence into the PepMLM inference API and generate 4 peptides of length 12 amino acids (Step 5 takes a while so you can also just pick 1 or 2 peptides)
| index | Binder | Pseudo Perplexity |
|---|---|---|
| 0 | WHYPAVAVELKE | 14.210624530465688 |
| 1 | WRYYAVAAAWKX | 9.043190779760293 |
| 2 | KRYGAAAVEWGE | 12.789374583596874 |
| 3 | WHSYATGLALKX | 9.729424435586754 |
After running AlphaFold-Multimer with your 5 peptides alongside your mutated SOD1 sequence, plot the ipTM scores, which measures the relative confidence of the binding region.
Provide a 1 paragraph write-up of your results
The AlphaFold Multimer analysis of the interaction between the peptides and the target protein showed pLDDT values above 70, indicating high confidence in the local structure of the subunits. However, the predicted TM-score (pTM) was approximately 0.5, and the interface predicted TM-score (ipTM) was very low, suggesting low confidence in the global organization of the complex and the interaction between subunits. Despite the structural stability of the individual subunits, the low ipTM and pTM values indicate that the predicted interaction is unreliable. This suggests that the peptides may have weak affinity for the protein or that the model configuration does not accurately reflect the real interaction. Further analysis using complementary approaches, such as molecular dynamics simulations or experimental data, is recommended to assess the stability and plausibility of the complex.
PART B: Final Project: L-Protein Mutants
To generate a mutation in the L-Protein of the MS2 bacteriophage to ensure proper structural stability