Highly Diverse Protein Library Based on the Ubiquitous (β/α)8 Enzyme Fold Yields Well-Structured Proteins through in Vitro Folding Selection

Misha V. Golynskiy, John C. Haugner, Burckhard Seelig

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Proper protein folding is a prerequisite for protein stability and enzymatic activity. Although directed evolution can be a powerful tool to investigate enzymatic function and to isolate novel activities, well-designed libraries of folded proteins are essential. In vitro selection methods are particularly capable of searching for enzymatic activities in libraries of trillions of protein variants, yet high-quality libraries of well-folded enzymes with such high diversity are lacking. We describe the construction and detailed characterization of a folding-enriched protein library based on the ubiquitous (β/α)8 barrel fold, which is found in five of the six enzyme classes. We introduced seven randomized loops on the catalytic face of the monomeric, thermostable (β/α)8 barrel of glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima. We employed in vitro folding selection based on protease digestion to enrich intermediate libraries containing three to four randomized loops for folded variants, and then combined them to assemble the final library (1014 DNA sequences). The resulting library was analyzed by using the in vitro protease assay and an in vivo GFP-folding assay; it contains ∼1012 soluble monomeric protein variants. We isolated six library members and demonstrated that these proteins are soluble, monomeric and show (β/α)8-barrel fold-like secondary and tertiary structure. The quality of the folding-enriched library improved up to 50-fold compared to a control library that was assembled without the folding selection. To the best of our knowledge, this work is the first example of combining the ultra-high throughput mRNA display method with selection for folding. The resulting (β/α)8 barrel libraries provide a valuable starting point to study the unique catalytic capabilities of the (β/α)8 fold, and to isolate novel enzymes.

Original languageEnglish (US)
Pages (from-to)1553-1563
Number of pages11
Issue number13
StatePublished - Sep 2013


  • (beta/alpha) barrel
  • GFP-folding reporter
  • MRNA display
  • Protein engineering
  • Protein folding


Dive into the research topics of 'Highly Diverse Protein Library Based on the Ubiquitous (β/α)8 Enzyme Fold Yields Well-Structured Proteins through in Vitro Folding Selection'. Together they form a unique fingerprint.

Cite this