Dieter Typke

Identification of macromolecular complexes in cryoelectron tomograms of phantom cells

Electron tomograms of intact frozen-hydrated cells are essentially three-dimensional images of the entire proteome of the cell, and they depict the whole network of macromolecular interactions. However, this information is not easily accessible because of the poor signal-to-noise ratio of the tomograms and the crowded nature of the cytoplasm. Here, we describe a template matching algorithm that is capable of detecting and identifying macromolecules in tomographic volumes in a fully automated manner. The algorithm is based on nonlinear cross correlation and incorporates elements of multivariate statistical analysis. Phantom cells, i.e., lipid vesicles filled with macromolecules, provide a realistic experimental scenario for an assessment of the fidelity of this approach. At the current resolution of ≈4 nm, macromolecules in the size range of 0.5–1 MDa can be identified with good fidelity.

Electron Tomography of Ice-Embedded Prokaryotic Cells

Whole cells of archaea were embedded in vitreous ice by plunge freezing and investigated by automated energy-filtered electron tomography at 120 kV. The embedded cells were between 300 and 750 nm thick, and their structures were reconstructed to a resolution of 20-40 nm from tilt series comprising 50-140 images. The dose was kept within tolerable limits. A resolution of 20 nm allowed visualization of the individual stalks of the S-layer of Pyrobaculum aerophilum cells, which had undergone partial lysis, in three dimensions. The attainable resolution for low-dose electron tomography under different experimental conditions was theoretically investigated in terms of the specimen thickness. To obtain 2-nm resolution at 120 kV (300 kV), the specimen must not be thicker than 100 nm (150 nm). For a resolution of 10 nm, the maximum thickness is 450 nm (700 nm). An accelerating voltage of 300 kV is advantageous, mainly for specimens thicker than 100 nm. Experimental investigations so far have resulted in a resolution that is worse by a factor of 2-5 as compared to theory.

Towards automatic electron tomography

Electron microscope control, that allows the automatic recording of tilt series for the 3D reconstruction of individual objects, has been realized. The experimental set-up includes a 200 kV TEM equipped with a 1K x 1K CCD camera, both controlled externally by a fast dedicated image-processing computer. For the goniometer control an accurate electronic readout of the tilt angle and a board driving the goniometer motor have been installed. For low-dose imaging, three to five different specimen areas are used: one (or two) for the determination of object displacements during tilting, one (or two) for autofocusing, and another one for recording the tilt series to be used for the 3D reconstruction. Tilt series can be recorded with a rather low total dose, the lower limit being set by the requirement that subsequent projection images have to be aligned by means of cross-correlation functions. The method has been tested with graphitized carbon particles on carbon film and with negatively stained proteasomes from the archaebacterium Thermoplasma acidophilum. Some future developments towards fully automatic electron tomography are discussed.

Towards automatic electron tomography II. Implementation of autofocus and low-dose procedures

Abstract Automatic electron tomography involves the compensation for lateral specimen displacements and, at higher resolution, refocusing. Improved automatic procedures are described and the accuracy and reliability of the basic steps is assessed. It is demonstrated that the cumulative dose in collecting tomographic 3D data sets can be kept small enough for the investigation of ice-embedded specimens.

Crystal structure of coagulogen, the clotting protein from horseshoe crab - a structural homologue of nerve growth factor

The clotting cascade system of the horseshoe crab (Limulus) is involved in both haemostasis and host defence. The cascade results in the conversion of coagulogen, a soluble protein, into an insoluble coagulin gel. The clotting enzyme excises the fragment peptide C from coagulogen, giving rise to aggregation of the monomers. The crystal structure of coagulogen reveals an elongated molecule that embraces the helical peptide C fragment. Cleavage and removal of the peptide C would expose an extended hydrophobic cove, which could interact with the hydrophobic edge of a second molecule, leading to a polymeric fibre. The C‐terminal half of the coagulogen molecule exhibits a striking topological similarity to the neurotrophin nerve growth factor (NGF), providing the first evidence for a neurotrophin fold in invertebrates. Similarities between coagulogen and Spatzle, the Drosophila ligand of the receptor Toll, suggest that the neurotrophin fold might be considered more ancient and widespread than previously realized.

Determination of the inelastic mean free path in ice by examination of tilted vesicles and automated most probable loss imaging

Using electron microscopy, the thickness of ice-embedded vesicles is estimated examining tilted and untilted views and assuming an ellipsoidal shape of the vesicles that appear to be circular in the untilted view. Another thickness measure is obtained from the ratio of the unfiltered and zero-loss-filtered image intensities of the vesicle. From these two measurements, the mean free path A for inelastic scattering of electrons in ice is calculated as 203 +/- 33 nm for 120 kV acceleration voltage. It is found that vesicles in thin ice films (< or = 1.5 lambda) significantly protrude out of the ice film. Due to surface tension the shape becomes an oblate ellipsoid. In holes covered with a thick ice film (> or = 3 lambda) and strong thickness gradients, vesicles are predominantly found in regions where the ice thickness is appropriate for their size. Also, a way of imaging the most probable loss under low-dose conditions involving thickness measurement is proposed. Even at large ice thicknesses zero-loss filtering always gives better image contrast. Most probable loss imaging can only help where there is no intensity in the zero-loss image, at very large thicknesses (lambda > 8).

Structure of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum as studied by electron tomography

Valosine‐containing protein‐like ATPase from Thermoplasma acidophilum is a member of the superfamily of ATPases associated with a diversity of cellular activities and is closely related to CDC48 from yeast and p97 from higher eukaryotes and more distantly to N‐ethylmaleimide‐sensitive fusion protein. We have used electron tomography to obtain low‐resolution (2–2.5 nm) three‐dimensional maps of both the whole 500 kDa complex and the N‐terminally truncated valosine‐containing protein‐like ATPase from T. acidophilum complex lacking the putative substrate binding domain.

Cryoelectron microscopy and cryoelectron tomography of the nuclear pre-mRNA processing machine

Large nuclear ribonucleoprotein particles, which can be viewed as the naturally assembled precursor messenger RNA (pre-mRNA) processing machine, were analyzed in frozen-hydrated preparations by cryoelectron microscopy. A general and reproducible strategy for preparing ice-embedded large nuclear ribonucleoprotein (lnRNP) particles at sufficiently high concentration was developed. Taking advantage of their negatively charged components, the lnRNP particles are adsorbed and thus concentrated on a positively charged lipid monolayer while preserving their native structure. Using this approach we carried out cryoelectron tomography and three-dimensional image reconstruction of individual lnRNP particles. The study revealed a structure similar to that of negatively stained particles studied previously, yet with additional features. The small additional domain visualized in negative stain appeared to be larger in the ice preparations. In addition, using image restoration from focus series of ice-embedded lnRNP particles, new features such as holes within the subunits were visualized in two dimensions, and it was shown that the subunits are interconnected via a fiber, very likely formed by the pre-mRNA. This finding supports the model that each subunit represents a spliceosome that splices out the intron wound around it.

Determination of the wave aberration of electron lenses from superposition diffractograms of images with differently tilted illumination

The wave aberration of an objective lens may be determined from superposition diffractograms of bright-field images with different tilt direction of the primary beam and single-sideband transfer. The theory of superposition diffractograms is sketched and some experimental aspects are discussed.

Survey of large protein complexes in D. vulgaris reveals great structural diversity

An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr ≈ 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate ≈10 times greater than that of previous “proteomic” screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.