Interval-zone free-flow electrophoresis as a charge-specific dimension for native isolation of thylakoid membrane protein complexes

Native polyacrylamide gel electrophoresis is the standard first analytical step after detergent solubilization of thylakoid membranes. It separates photosystem supercomplexes by size and shape, but it forces a polydisperse mixture of protein-detergent particles through a gel of limited pore diameter. Interval-zone free-flow electrophoresis (iZE-FFE) performs that first electrophoretic step in free solution, without ampholytes or immobilines, and returns the complexes as a liquid fraction series ordered by net charge. We describe the operational cycle of iZE, show that bromophenol blue reports the charge density of {beta}-dodecylmaltoside micelles, and apply iZE to Arabidopsis thaliana thylakoid extracts from two sequential solubilization campaigns. After a two-step digitonin then digitonin/{beta}-dodecylmaltoside extraction (experiment 6874), SDS-PAGE of the iZE fractions is crowded: high-molecular mass protein-lipid assemblies of photosystem I and photosystem II release the same subunits into many wells. Native-PAGE of the same fractions resolves ATP-synthase from PSI, a free LHCII pool, anodic PSII, and cathodic PSI, including PSI with and without LHCII. A three-step extraction with a single pH working window (experiment 7154) confirms this charge order. Lowering residual detergent in consecutive extracts still produces partly solubilized high-mass assemblies, whereas a final {beta}-dodecylmaltoside step releases the C2S2M2/C2S2M/C2S2 PSII series and a single PSI band. iZE is therefore a charge-first, orthogonal dimension for native thylakoid biochemistry. Native-PAGE, not SDS-PAGE, is the proper second dimension while solubilization remains incomplete.