Sequence-developability mapping of affibody and fibronectin paratopes via library-scale variant characterization

Abstract Protein developability is requisite for use in therapeutic, diagnostic, or industrial applications. Many developability assays are low throughput, which limits their utility to the later stages of protein discovery and evolution. Recent approaches enable experimental or computational assess...

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Bibliographic Details
Published in:Protein engineering, design and selection design and selection, 2024-01, Vol.37
Main Authors: Nielsen, Gregory H, Schmitz, Zachary D, Hackel, Benjamin J
Format: Article
Language:English
Subjects:
Fibronectins - chemistry
Fibronectins - genetics
Fibronectins - metabolism
Green Fluorescent Proteins - chemistry
Green Fluorescent Proteins - genetics
Green Fluorescent Proteins - metabolism
Humans
Peptide Library
Protein Binding
Protein Engineering - methods
Protein Stability
Recombinant Fusion Proteins - chemistry
Recombinant Fusion Proteins - genetics
Recombinant Fusion Proteins - metabolism
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Summary:Abstract Protein developability is requisite for use in therapeutic, diagnostic, or industrial applications. Many developability assays are low throughput, which limits their utility to the later stages of protein discovery and evolution. Recent approaches enable experimental or computational assessment of many more variants, yet the breadth of applicability across protein families and developability metrics is uncertain. Here, three library-scale assays—on-yeast protease, split green fluorescent protein (GFP), and non-specific binding—were evaluated for their ability to predict two key developability outcomes (thermal stability and recombinant expression) for the small protein scaffolds affibody and fibronectin. The assays’ predictive capabilities were assessed via both linear correlation and machine learning models trained on the library-scale assay data. The on-yeast protease assay is highly predictive of thermal stability for both scaffolds, and the split-GFP assay is informative of affibody thermal stability and expression. The library-scale data was used to map sequence-developability landscapes for affibody and fibronectin binding paratopes, which guides future design of variants and libraries. Graphical Abstract Graphical Abstract
ISSN:1741-0126
1741-0134
1741-0134
DOI:10.1093/protein/gzae010