Week 5 HW:Protein-design-part-ii
Part 1: Generate binders with PepMLM
Step 1 — Get the mutant SOD1 sequence
Original SOD1 sequence from Uniprot
sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
A4V mutant SOD1 sequence
MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Step 2 — Run PepMLM
Used google colab notebook for the step.
https://colab.research.google.com/drive/1j4HO5MPdIlCLZFvqYnjy_Ug--8oxTB9Z#scrollTo=VtfbXYndhyle
| # | Binder | Pseudo Perplexity |
|---|---|---|
| 1 | WLSYPVVLEWGE | 16.4334209 |
| 2 | WHYYVVAVRWKE | 31.112519 |
| 3 | WHSYAAAAALWE | 12.9540785 |
| 4 | WLYYAVGLAWKX | 14.2779037 |
| 5 | FLYRWLPSRRGG | XXXX |
(lower perplexity = the model is more confident the peptide is a good binder)
Part 2: AlphaFold3 structure prediction
For each result, I looked at the below: The ipTM score (higher is better, closer to 1.0 means confident binding prediction)
| Binder | Pseudo Perplexity | ipTM score |
|---|---|---|
| WLSYPVVLEWGE | 16.4334209 | 0.21 |
| WHYYVVAVRWKE | 31.112519 | 0.35 |
| WHSYAAAAALWE | 12.9540785 | 0.27 |
| WLYYAVGLAWKX | 14.2779037 | Could not be generated because it had a letter X |
| FLYRWLPSRRGG | XXXX | 0.3 |
The ipTM score (interface predicted TM-score) measures how confidently AlphaFold3 predicts the two chains interact. It ranges from 0 to 1. Below 0.4 = poor 0.4–0.6 = moderate Above 0.6 = good
Where the peptide appears to dock (look at the 3D viewer — is it near position 4 at the N-terminus? At the dimer interface? Surface-exposed?)
I have a question on the fact that my second binder has a high Pseudo Perplexity value of 31 therefore the assumption is that the binding confidence level is very low. However through alphafold it has the best ipTM score suggesting that it had the best confident binding prediction
Part 3: PeptiVerse therapeutic properties
| Binder | Solubility | Hemolysis | Binding Affinity | Length | Molecular Weight | Net Charge (pH 7) | Isoelectric Point | Hydrophobicity (GRAVY) |
|---|---|---|---|---|---|---|---|---|
| WLSYPVVLEWGE | Soluble - 1.00 | Non-hemolytic 0.112 | Weak binding - 5.952 | 12 | 1477.7 | -2.23 | 4.24 | 0.26 |
| WHYYVVAVRWKE | Soluble - 1.00 | Non-hemolytic 0.069 | Weak binding - 6.345 | 12 | 1635.9 | 0.85 | 8.5 | -0.42 |
| WHSYAAAAALWE | Soluble - 1.00 | Non-hemolytic 0.035 | Weak binding - 5.863 | 12 | 1375.5 | -1.15 | 5.47 | 0.18 |
| WLYYAVGLAWKX | Soluble - 1.00 | Non-hemolytic 0.115 | Medium binding - 7.101 | 12 | 1351.8 | 0.76 | 8.5 | 0.56 |
the best one balances strong binding + not hemolytic + good solubility.