Single-Molecule Localization Microscopy of Membrane Proteins using Single-Antibody Labeling

The plasma membrane defines the cell shape and serves as the interface that governs intercellular communication. Membrane proteins constitute a major class of therapeutic targets; therefore, super-resolving the cell membrane through its constitutive proteins holds great promise in advancing cell biology and antibody therapeutics. In this regard, single-molecule localization microscopy (SMLM) enables nanoscale visualization of protein organizations on biological structures. Despite its importance, applying SMLM to plasma membrane proteins poses unique challenges. In this protocol, we present an effective approach using time-lapse single-antibody labeling (SAL) termed membrane SAL (mSAL). We provide detailed step-by-step instructions, including optimization of the antibody concentration, laser power density, duration of non-illumination intervals, image reconstruction, and density-based cluster analysis, to resolve nanoscale membrane protein distribution and membrane morphology. We use the tetraspanin protein CD81 as the model membrane protein to demonstrate the capability of mSAL on both adherent and suspension mammalian cells. In addition to super-resolving the cell membrane and distributions of membrane proteins, our technique enables the investigation of the pharmacodynamics of therapeutic antibodies interacting with their membrane targets in the native membrane environment.