Discovering new proteins through modular assembly, inspired by both nature's evolution and protein engineering, offers exciting possibilities. By leveraging information on subdomain-sized fragments from the database Fuzzle, we seamlessly integrated a flavodoxin-like fragment into a periplasmic binding protein. The resulting chimera exhibits remarkable folding and stable interfaces, showcasing the adaptability of α/β-proteins. Our work pioneers novel avenues in protein engineering and sheds light on the evolutionary origins of periplasmic binding proteins.
Modular assembly is a compelling pathway to create new proteins, a concept supported by protein engineering and millennia of evolution. Natural evolution provided a repository of building blocks, known as domains, which trace back to even shorter segments that underwent numerous ‘copy-paste’ processes culminating in the scaffolds we see today. Utilizing the subdomain-database Fuzzle, we constructed a fold-chimera by integrating a flavodoxin-like fragment into a periplasmic binding protein. This chimera is well-folded and a crystal structure reveals stable interfaces between the fragments. These findings demonstrate the adaptability of α/β-proteins and offer a stepping stone for optimization. By emphasizing the practicality of fragment databases, our work pioneers new pathways in protein engineering. Ultimately, the results substantiate the conjecture that periplasmic binding proteins originated from a flavodoxin-like ancestor.