Week 5 HW: Protein Design Part 2

Part A : SOD1 Binder Peptide Design

Part 1: Generate Binders with PepMLM

Part 2: Evaluate Binders with AlphaFold3

Part 3: Evaluate Properties of Generated Peptides in the PeptiVerse

Part 4: Generate Optimized Peptides with moPPIt

Part C: Final Project: L-Protein Mutants

L-Protein and DnaJ Sequence Lysis Protein Sequence (UniProtKB ID: https://www.uniprot.org/uniprotkb/P03609/entry)

METRFPQQSQQTPASTNRRRPFKHEDYPCRRQQRSSTLYVLIFLAIFLSKFTNQLLLSLLEAVIRTVTTLQQLLT

Note: Lysis protein contains a soluble N-terminal domain followed by a transmembrane protein (blue/last 35 residues). Transmembrane protein affects the lysis activity. The soluble domain (green) is the domain responsible for interaction with DnaJ.

DnaJ sequence (UniProtKB ID: https://www.uniprot.org/uniprotkb/P03609/entry)

MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYNMELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPAGVDTGDRIRLAGEGEAGEHGAPAGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEIEVPTLDGRVKLKVPGETQTGKLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGGPTGEHNSPRSKSFFDGVKKFFDDLTR