Engineered peptide barcodes for in-depth analyses of binding protein libraries

• Published in: Nature methods Vol. 16; no. 5; pp. 421 - 428
• Main Authors: Egloff, Pascal, Zimmermann, Iwan, Arnold, Fabian M., Hutter, Cedric A. J., Morger, Damien, Opitz, Lennart, Poveda, Lucy, Keserue, Hans-Anton, Panse, Christian, Roschitzki, Bernd, Seeger, Markus A.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.05.2019; Nature Publishing Group
• Subjects: 631/1647/2163; 631/45/475; 631/45/612; 631/61/338; Aquaporins; Bacterial Outer Membrane Proteins - genetics; Bar codes; Binders; Binding proteins; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Carrier Proteins - genetics; Cascades; Chromatography, Liquid; DNA Barcoding, Taxonomic - methods; DNA sequencing; Gene expression; Genetic code; High-Throughput Nucleotide Sequencing - methods; Immobilization; Legionella pneumophila - genetics; Life Sciences; Mass spectrometry; Mass spectroscopy; Membrane proteins; Membrane Proteins - genetics; Mining industry; Nanobodies; Peptide Library; Peptides; Protein binding; Proteins; Proteomics; Spectroscopy; Tandem Mass Spectrometry; Target recognition; Technology
• ISSN: 1548-7091; 1548-7105
• DOI: 10.1038/s41592-019-0389-8

Binding protein generation typically relies on laborious screening cascades that process candidate molecules individually. We have developed NestLink, a binder selection and identification technology able to biophysically characterize thousands of library members at once without the need to handle individual clones at any stage of the process. NestLink uses genetically encoded barcoding peptides termed flycodes, which were designed for maximal detectability by mass spectrometry and support accurate deep sequencing. We demonstrate NestLink’s capacity to overcome the current limitations of binder-generation methods in three applications. First, we show that hundreds of binder candidates can be simultaneously ranked according to kinetic parameters. Next, we demonstrate deep mining of a nanobody immune repertoire for membrane protein binders, carried out entirely in solution without target immobilization. Finally, we identify rare binders against an integral membrane protein directly in the cellular environment of a human pathogen. NestLink opens avenues for the selection of tailored binder characteristics directly in tissues or in living organisms. A method for protein binder selection and identification, NestLink, uses barcoding peptides detectable by mass spectrometry to select and biophysically characterize thousands of binders without requiring the handling of individual clones.