Week 5 HW: Protein Design Part ii

Part 1: Generate Binders with PepMLM

Human SOD1 sequence (without A4V):

>sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2

MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

A4V represents a point mutation within the 4th codon of the human SOD1 gene. This results in the substitution of the conventional alanine for a valine amino acid.

Mutant SOD1 sequence (with A4V):

MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

Four experimental peptides were then generated using the PepMLM tool:

Evaluate Binders with AlphaFold3

Entry	Binder	Pseudo Perplexity	ipTM	Description	Image
🎮	FLYRWLPSRRGG	—	0.31
0	HRYYPVAVRLKE	11.513239315710866	0.26
1	HRYPVVAVAWKE	14.299230176233568	0.26
2	KRYPPVAARWKE	20.264871722997526	0.34
3	WLYPVAAARHKE	20.749563629245603	0.35

Part 3: Evaluate Properties of Generated Peptides in the PeptiVerse