Molecular mass determination by STEM and EFTEM: a critical comparison

Intrinsic linear heterogeneity of amyloid β protein fibrils revealed by higher resolution mass-per-length determinations

Amyloid β proteins spontaneously form fibrils in vitro that vary in their thermodynamic stability and in morphological characteristics such as length, width, shape, longitudinal twist, and the number of component filaments. It is vitally important to determine which variant best represents the type of fibril that accumulates in Alzheimer disease. In the present study, the nature of morphological variation was examined by dark-field and transmission electron microscopy in a preparation of seeded amyloid β protein fibrils that formed at relatively low protein concentrations and exhibited remarkably high thermodynamic stability. The number of filaments comprising these fibrils changed frequently from two to six along their length, and these changes only became apparent when mass-per-length (MPL) determinations are made with sufficient resolution. The MPL results could be reproduced by a simple stochastic model with a single adjustable parameter. The presence of more than two primary filaments could not be discerned by transmission electron microscopy, and they had no apparent relationship to the longitudinal twist of the fibrils. However, the pitch of the twist was strongly affected by the pH of the negative stain. We conclude that highly stable amyloid fibrils may form in which a surprising amount of intrinsic linear heterogeneity may be obscured by MPL measurements of insufficient resolution, and by the negative stains used for imaging fibrils by electron microscopy.

Measurement of amyloid fibril mass-per-length by tilted-beam transmission electron microscopy

We demonstrate that accurate values of mass-per-length (MPL), which serve as strong constraints on molecular structure, can be determined for amyloid fibrils by quantification of intensities in dark-field electron microscope images obtained in the tilted-beam mode of a transmission electron microscope. MPL values for fibrils formed by residues 218-289 of the HET-s fungal prion protein, for 2-fold- and 3-fold-symmetric fibrils formed by the 40-residue beta-amyloid peptide, and for fibrils formed by the yeast prion protein Sup35NM are in good agreement with previous results from scanning transmission electron microscopy. Results for fibrils formed by the yeast prion protein Rnq1, for which the MPL value has not been previously reported, support an in-register parallel beta-sheet structure, with one Rnq1 molecule per 0.47-nm beta-sheet repeat spacing. Since tilted-beam dark-field images can be obtained on many transmission electron microscopes, this work should facilitate MPL determination by a large number of research groups engaged in studies of amyloid fibrils and similar supramolecular assemblies.

Weighing supported nanoparticles: size-selected clusters as mass standards in nanometrology

We present a new approach to quantify the mass and 3D shape of nanoparticles on supports, using size-selected nanoclusters as mass standards in scanning transmission electron microscope. Through quantitative image intensity analysis, we show that the integrated high angle annular dark field intensities of size-selected gold clusters soft-landed on graphite display a monotonic dependence on the cluster size as far as approximately 6500 atoms. We applied this mass standard to study gold nanoparticles prepared by thermal vapor deposition and by colloidal wet chemistry, and from which we deduced the shapes of these two types of nanoparticles as expected.

Quantitative STEM mass measurement of biological macromolecules in a 300 kV TEM

For almost four decades, the scanning transmission electron microscope (STEM) has made significant contributions to structural biology by providing accurate determinations of the molecular masses of large protein assemblies that have arbitrary shapes and sizes. Nevertheless, STEM mass mapping has been implemented in very few laboratories, most of which have employed cold field-emission gun (FEG) electron sources operating at acceleration voltages of 100 kV and lower. Here we show that a 300 kV commercial transmission electron microscope (TEM) equipped with a thermally assisted Shottky FEG can also provide accurate STEM mass measurements. Using the recently published database of elastic-scattering cross sections from the National Institute of Standards and Technology, we show that the measured absolute mass values for tobacco mosaic virus and limpet hemocyanin didecamers agree with the known values to within better than 10%. Applying the established approach, whereby tobacco mosaic virus is added to a specimen as a calibration standard, we find that the measured molecular weight of the hemocyanin assemblies agrees with the known value to within 3%. This accuracy is achievable although only a very small fraction ( approximately 0.002) of the incident probe current of 300 kV electrons is scattered onto the annular dark-field STEM detector. FEG TEMs operating at intermediate voltages (200-400 kV) are becoming common tools for determining the structure of frozen hydrated protein assemblies. The ability to perform mass determination with the same instrument can provide important complementary information about the numbers of subunits comprising the protein assemblies whose structure is being studied.

Structure and mass analysis by scanning transmission electron microscopy

In the scanning transmission electron microscope (STEM) an electron beam of a few angstroms diameter is raster scanned over a thin sample and the scattered electrons are sequentially measured for each sample element irradiated. The mass, the elemental composition and the structure of a protein can be simultaneously assessed if all detector systems of the STEM are used. Aspects affecting the accuracy of the mass measurement technique and the demands placed on the instrument's dark-field detector system are outlined. In addition, the influences of some sample preparation techniques are noted and the mass-loss induced at ambient temperatures by the incidence of 80kV electrons on various biological samples is reported. Finally, the importance of the STEM for the structural analysis of proteins is documented by examples.

The intermediate filament protein consensus motif of helix 2B: its atomic structure and contribution to assembly

Nearly all intermediate filament proteins exhibit a highly conserved amino acid motif (YRKLLEGEE) at the C-terminal end of their central alpha-helical rod domain. We have analyzed its contribution to the various stages of assembly by using truncated forms of Xenopus vimentin and mouse desmin, VimIAT and DesIAT, which terminate exactly before this motif, by comparing them with the wild-type and tailless proteins. It is surprising that in buffers of low ionic strength and high pH where the full-length proteins form tetramers, both VimIAT and DesIAT associated into various high molecular weight complexes. After initiation of assembly, both VimIAT and DesIAT aggregated into unit-length-type filaments, which rapidly longitudinally annealed to yield filaments of around 20 nm in diameter. Mass measurements by scanning transmission electron microscopy revealed that both VimIAT and DesIAT filaments contained considerably more subunits per cross-section than standard intermediate filaments. This indicated that the YRKLLEGEE-motif is crucial for the formation of authentic tetrameric complexes and also for the control of filament width, rather than elongation, during assembly. To determine the structure of the YRKLLEGEE domain, we grew crystals of peptides containing the last 28 amino acid residues of coil 2B, chimerically fused at its amino-terminal end to the 31 amino acid-long leucine zipper domain of the yeast transcription factor GCN4 to facilitate appropriate coiled-coil formation. The atomic structure shows that starting from Tyr400 the two helices gradually separate and that the coiled coil terminates with residue Glu405 while the downstream residues fold away from the coiled-coil axis.