Cryogenic light microscopy of vitrified samples with Angstrom precision

Abstract

High-resolution studies in structural biology are commonly based on diffraction methods and on electron microscopy. However, these approaches are limited by the difficulty in crystallization of biomolecules or by a low contrast that makes high-resolution measurements very challenging in crowded samples such as a cell membrane. The exquisite labeling specificity of fluorescence microscopy gets around these issues. Indeed, several recent reports have reached resolutions down to the [A]ngstrom level in super-resolution microscopy, but to date, these works used fixed samples. To establish light microscopy as a workhorse in structural biology, two main requirements must be fulfilled: near-native sample preservation and near-atomic optical resolution. Here, we demonstrate a technique that satisfies these key criteria with particular promise for conformational studies on membrane proteins and their complexes. To prepare cell membranes in their near-native state, we adapt established protocols from cryogenic electron microscopy (Cryo-EM) for shock-freezing and transfer of samples. We developed a high-vacuum cryogenic shuttle system that allows us to transfer vitrified samples in and out of a liquid-helium cryostat that houses a super-resolution fluorescence microscope. Sample temperatures below 10 K help dissipate the heat from laser illumination, thus maintaining intact vitreous ice. We utilize the photoblinking of organic dye molecules attached to well-defined positions of a protein to localize one label fluorophore at a time. We present various characterization studies of the vitreous ice, photoblinking behavior, and the effects of the laser intensity. Moreover, we benchmark our method by demonstrating [A]ngstrom precision in resolving the full assembled configuration of the heptameric membrane protein alpha-hemolysin (HL) in a synthetic lipid membrane as a model system. Additionally, we report on the techniques capability to resolve membrane proteins in their native cellular membrane environment. Our method, which we term single-particle cryogenic light microscopy (spCryo-LM), enables structural studies of membrane protein tertiary and quaternary conformations without the need for chemical fixation or protein isolation. The approach can also integrate other super-resolution or spectroscopic techniques with particular promise in correlative microscopy with images from Cryo-EM and related techniques.