Week 5 HW: Protein Design Part II

Table of Contents

• Part A: SOD1 Binder Peptide Design
• Part B: BRD4 Drug Discovery Platform Tutorial
• Part C: Final Project: L-Protein Mutants

Part A: SOD1 Binder Peptide Design

• Part 1: Generate Binders with PepMLM

1. UniProt P00441 without the header:

MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

The mutation “A4V” means the alanine at codon 4 (position) is changed to a valine. The M at the beginning is Methionine (coded by the codon AUG) but this is commonly ignored in canonical numbering since it’s the start codon. It’s there to signal the start of protein translation.

The mutated SOD1 sequence:

MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEEHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

Part B: BRD4 Drug Discovery Platform Tutorial

Part C: Final Project: L-Protein Mutants