Atom Probe Tomography for 3D Structural and Chemical Analysis of Individual Proteins

Abstract

Determination of the 3D structure of proteins and other biomolecules is a major goal in structural biology, to provide insights to their biological function. Such structures are historically unveiled experimentally by X‐ray crystallography or NMR spectroscopy, and in recent years using cryo‐electron microscopy. Here, a method for structural analysis of individual proteins on the sub‐nanometer scale using atom probe tomography is described. This technique offers a combination of high‐resolution analysis of biomolecules in 3D, and the chemical sensitivity of mass spectrometry. As a model protein, the well‐characterized antibody IgG is used. IgG is encapsulated in an amorphous solid silica matrix via a sol–gel process to provide the requisite support for atom probe analysis. The silica synthesis is tuned to resemble physiological conditions. The 3D reconstructions show good agreement with the protein databank IgG crystal structure. This suggests that the silica‐embedding strategy can open the field of atom probe tomography to the analysis of biological molecules. In addition to high‐resolution structural information, the technique may potentially provide chemical information on the atomic scale using isotopic labeling. It is envisaged that this method may constitute a useful complement to existing tools in structural biology, particularly for the examination of proteins with low propensity for crystallization.

A Liquid Metal Encapsulation for Analyzing Porous Nanomaterials by Atom Probe Tomography

“…According to Seol et al (2016), the surface modification from the conductive layer coating improves the overall evaporation sequences. Unlike ceramic coating approaches (Sundell et al, 2019;Webel et al, 2021), a high quality data could be acquired here because a fusible alloy has relatively high thermal (0.19 W/cm °C) and electrical conductivity (0.57 nΩ m) which allows to dissipate the energy and electrons quickly to the base of the specimen (Lipchitz et al, 2015). This can explain the high (3:3) success rate of sample preparation in this investigation, with over 10 million ions collected for each specimen, and without premature or microfractures.…”

Field evaporation and atom probe tomography of pure water tips

“…Instead, they were deposited and measured e.g. in crystalline form 20 , embedded in resin 21 or silica glass 22 or attached by adhesion to the tip surface 23 . Several attempts have been made to investigate the evaporation behavior of ice under high field conditions 24,25 .…”

Three-Dimensional Chemical Mapping of a Single Protein in the Hydrated State with Atom Probe Tomography

“…Alternatively, laser pulsing can also achieve field evaporation by lowering the thermal barrier for field ionization to occur . Application of APT imaging has been extended to dehydrated biological specimens including proteins, mammalian, and bacterial cells. − However, the challenge of applying APT to biological samples in their near-native state still remains. In order to achieve the large electrostatic field suitable for field ionization and evaporation, the APT specimen must be electrically conductive and prepared into a needle shape with an end radius of <75 nm.…”