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TitleADAPT-M: A workflow for rapid, quantitative measurements of enriched protein libraries.
Journal, issue, pagesbioRxiv, Year 2025
Publish dateOct 22, 2025
AuthorsCarla P Perez / Nicole V DelRosso / Cameron L Noland / Udit Parekh / Christian A Choe / Raphael R Eguchi / Qi Wen / Polly M Fordyce / Po-Ssu Huang /
PubMed AbstractProtein-protein interactions underpin most cellular interactions, and engineered binders present powerful tools for probing biology and developing novel therapeutics. One bottleneck in binder ...Protein-protein interactions underpin most cellular interactions, and engineered binders present powerful tools for probing biology and developing novel therapeutics. One bottleneck in binder generation is the scalable, quantitative characterization of these interactions. We present ADAPT-M (ffinity etermination by daptation of roein binders for icrofluidics), a streamlined workflow that connects yeast surface display (YSD) with affinity and kinetic measurements using the high-throughput STAMMPPING microfluidic platform. ADAPT-M quantifies s and dissociation kinetic parameters for hundreds of enriched protein variants in under one week without requiring hands-on protein purification. We applied ADAPT-M to a computationally designed library targeting the SARS-CoV-2 Omicron BA.1 receptor binding domain, successfully recovering and measuring s for most highly enriched YSD variants. Measurements correlate strongly with biolayer interferometry and yeast titration assays. ADAPT-M further enabled selection of lead candidates for structural and mutational analysis, which revealed designed paratopes were preserved despite binding to off-target epitopes. By bridging YSD screening and validation, ADAPT-M accelerates protein binder discovery and supports data-driven protein engineering.
External linksbioRxiv / PubMed:41279512 / PubMed Central
MethodsEM (single particle)
Resolution3.16 Å
Structure data

72524

9y5y

EMDB-72524, PDB-9y5y:
Structure of the Omicron Spike RBD bound by the monobody s19382 (local refinement from dimerized Spike protein ECDs)
Method: EM (single particle) / Resolution: 3.16 Å

Source
  • severe acute respiratory syndrome coronavirus 2
  • synthetic construct (others)
KeywordsANTIVIRAL PROTEIN/VIRAL PROTEIN / Inhibitor / Complex / Viral Spike Protein / Monobody / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-VIRAL PROTEIN complex

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