Membrane Proteins at Scale: Automated Copolymer Nanodisc Purification for Structure and Function

Membrane proteins (MPs) remain among the most important yet least accessible classes of drug targets. Traditional detergent solubilization strips away native lipids, destabilizing proteins and limiting subsequent work. Amphiphilic copolymers offer a powerful alternative, directly extracting MPs in their native lipid environment. However, because each target protein responds differently to individual copolymers, solubilization outcomes have remained unpredictable, turning every new project into a slow, empirical search. Here, we introduce an automated, plate-based copolymer screening platform that accelerates this process from days to hours, using only milliliter-scale volumes. The system integrates lyophilized copolymer libraries with magnetic-bead affinity purification, enabling parallel testing of dozens of copolymers against multiple MPs in a single run. Applied to 14 diverse, full-length wildtype human MPs, including GPCRs, solute carriers, ion channels, and claudins, we find that next-generation copolymers (AASTY, CyclAPol (UltrasoluteTM Amphipol), and Cubipol) systematically outperform classical copolymers. As a detailed case study, we focus on the full-length human P2X4 receptor, a purinergic channel implicated in neuropathic pain and inflammation. Using our automated workflow, P2X4 could be extracted in multiple copolymers with high purity and stability, retaining its native state. NanoDSF confirmed that the native lipid belt conferred significant thermostabilization without engineered mutations. The channel also retains ligand binding, with consistent affinities measured across different methods. Finally, cryo-EM analysis of P2X4 in Cubipol nanodiscs yielded reconstructions at up to 2.9 [A] resolution, capturing both apo and ligand-bound states. Together, these results highlight how automation and modern copolymer chemistry converge to transform membrane protein biochemistry. With throughput scalable to thousands of targets annually, this approach lays the foundation for systematic, genome-wide exploration of the membrane proteome.