Rapid Production and Cryo-EM Structure Determination of GPCR-Nanodisc Complexes via Cell-Free Synthesis

Abstract

G protein-coupled receptors (GPCRs) represent major therapeutic targets, yet cryo-EM structure determination of unliganded or antagonist-bound GPCRs remains severely bottlenecked by small receptor mass, detergent-induced instability, and multi-week cell-based production pipelines. Here, we combine intracellular loop 3 (ICL3) rigid fiducial engineering with a high-throughput, cell-free protein synthesis workflow to rapidly generate cryo-EM-ready GPCR-nanodisc assemblies. Using the eProtein Discovery(TM) digital microfluidics system, we performed automated nanoliter-scale screening of construct fusions and nanodisc lipid compositions, establishing that co-translational insertion into nanodiscs is strictly required for receptor solubilization and affinity purification. Direct scale-up of screening conditions yielded structural-grade protein within four days from gene assembly to grid vitrification. We demonstrate this workflow with a 3.38 Angstrom cryo-EM structure of antagonist-bound human adenosine A2A receptor (A2AR)-beta-lactamase fusion in complex with beta-lactamase inhibitory protein II (BLIP-II). To demonstrate generalizability of protein quality, we extended this detergent-free co-translational pipeline to an expanded panel of 12 wild-type GPCRs spanning Classes A, B, and C, as well as six orphan receptors. All targets were purified with biophysical quality comparable to the A2AR benchmark. By removing the reliance on cellular expression or agonist/G-protein stabilization and compressing construct assembly, nanodisc screening, biophysical quality control, and grid vitrification into a four-day turnaround, this detergent-free cell-free pipeline provides a rapid Design-Build-Test-Learn (DBTL) engine to accelerate structure-based drug discovery for challenging and unliganded GPCR targets.