Abstract

Discriminating native, large protein assemblies from their oligomeric intermediates is inherently challenging as minor differences in size and shape often limit the resolution of routine analytical methods. Here, we present conformation-specific electrophoresis (CSE), a multistack gel strategy enabling quantitative, subunit-resolution separation of native complex oligomers in a simple slab-gel format. CSE employs tailored polyacrylamide stacks imposing iterative focusing and differential sieving, thereby sharpening and sorting analytes based on subtle differences in shape and mass. Using a pore-forming toxin as a model system, CSE fully resolved all structurally unique assembly intermediates, whereas conventional electrophoresis methods typically yielded only one or two overlapping bands. The method provides high resolution, analytical linearity, and sensitivity for quantifying trace oligomers. We further demonstrate its broad applicability for nondestructive gel excision to isolate functional oligomers, confirming the method’s nondenaturing nature and providing material for subsequent advanced analysis, such as single-molecule nanopore techniques. By integrating high analytical performance and compatibility with standard electrophoresis equipment, CSE provides a practical platform for investigating assembly mechanisms and serving as an effective tool for characterizing molecular heterogeneity in macromolecular chemistry, structural biology, and pharmaceutical science.