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 de novo 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 de novo structures demonstrate good in silico 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.