Protocol for AFM Nanoindentation of Viruses and Protein Cages

Protein-based nanocompartments are ubiquitous in nature. They include both viruses as well as protein cages from non-viral origin. To broaden our knowledge on viruses and non-viral protein nanoshells, a profound insight into their mechanical properties is required. Nanoindentation measurements with an atomic force microscope (AFM) are increasingly being performed to probe such material properties. This single-particle approach allows for determining the shell's spring constant, their Young's modulus, as well as the force and deformation at which failure occurs. The experimental procedures for nanoshell mechanical characterization are described here in detail, focusing on surface preparation, AFM imaging, and nanoindentation and the subsequent data analysis of the force-distance curves. Whereas AFM can be operated in air and in liquid, the described methods are for probing single viruses and nanocages in liquid to enable working in a physiologically relevant environment.