A Next-Generation qPlus-Sensor-Based AFM Setup: Resolving Archaeal S-Layer Protein Structures in Air and Liquid

Surface-layer (S-layer) proteins form the outermost envelopeinmany bacteria and most archaea and arrange in two-dimensional quasicrystallinestructures via self-assembly. We investigated S-layer proteins extractedfrom the archaeon Pyrobaculum aerophilium with aqPlus sensor-based atomic force microscope (AFM) in both liquid andambient conditions and compared it to transmission electron microscopy(TEM) images under vacuum conditions. For AFM scanning, a next-generationliquid cell and a new protocol for creating long and sharp sapphiretips was introduced. Initial AFM images showed only layers of residualdetergent molecules (sodium dodecyl sulfate, SDS), which are usedto isolate the S-layer proteins from the cells. SDS was not visiblein the TEM images, requiring more thorough sample preparation forAFM measurements. These improvements allowed us to resolve the crystallikestructure of the S-layer samples with frequency-modulation AFM inboth air and liquid.