Polymerized Short Sequences as a Template for Protein Folding and Evolution.

Abstract

Repeat proteins, known for their functional versatility and modularity, are focal points of <i>de novo</i> protein design. This study explores and discovers proteins with repeated sequences using evolutionary approaches. Leveraging AlphaFold 2, our initial sequence design integrates amyloid β42 with a random hexapeptide linker through polymerization, achieving high foldability in more than 12% of cases. We further evolve these structures into a mosaic of folds using segmental mutations and genetic algorithms. The majority of these <i>de novo</i> structures demonstrate good <i>in silico</i> stability through molecular dynamics simulation. Additionally, we investigate the compatibility of medial strands to assess potential variations in structural integrity upon mutation, revealing a trade-off among foldability, structural variation, and sequence similarity. This evolutionary approach not only underscores the evolvability and versatility of repeat proteins but also highlights the potential for developing peptide-based pharmaceuticals and functional materials.