ACE: automated CTF estimation

Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function

Transmission electron microscopy, as most imaging devices, introduces optical aberrations that in the case of thin specimens are usually modeled in Fourier space by the so-called contrast transfer function (CTF). Accurate determination of the CTF is crucial for its posterior correction. Furthermore, the CTF estimation must be fast and robust if high-throughput three-dimensional electron microscopy (3DEM) studies are to be carried out. In this paper we present a robust algorithm that fits a theoretical CTF model to the power spectrum density (PSD) measured on a specific micrograph or micrograph area. Our algorithm is capable of estimating the envelope of the CTF which is absolutely needed for the correction of the CTF amplitude changes.

Electron microscopy of integrins

Integrins are a family of heterodimeric, cell-surface receptors that mediate interactions between the cytoskeleton and the extracellular matrix. We have used electron microscopy and single-particle image analysis combined with molecular modeling to investigate the structures of the full-length integrin alpha(IIb)beta(3) and the ectodomain of alpha(V)beta(3) in a complex with fibronectin. The full-length integrin alpha(IIb)beta(3) is purified from human platelets by ion exchange and gel filtration chromatography in buffers containing the detergent octyl-beta-D-glucopyranoside, whereas the recombinant ectodomain of alpha(V)beta(3) is soluble in aqueous buffer. Transmission electron microscopy is performed either in negative stain, where the protein is embedded in a heavy metal such as uranyl acetate, or in the frozen-hydrated state, where the sample is flash-frozen such that the buffer is vitrified and native conditions are preserved. Individual integrin particles are selected from low-dose micrographs, either by manual identification or an automated method using a cross-correlation search of the micrograph against a set of reference images. Due to the small size of integrin heterodimers (approximately 250 kDa) and the low electron dose required to minimize beam damage, the signal-to-noise level of individual particles is quite low, both by negative-stain electron microscopy and electron cryomicroscopy. Consequently, it is necessary to average many particle images with equivalent views. The particle images are subjected to reference-free alignment and classification, in which the particles are aligned to a common view and further grouped by statistical methods into classes with common orientations. Assessment of the structure from a set of two-dimensional averaged projections is often difficult, and a further three-dimensional (3D) reconstruction analysis is performed to classify each particle as belonging to a specific projection from a single 3D model. The 3D reconstruction algorithm is an iterative projection-matching routine in which the classified particles are used to construct a new, 3D map for the next iteration. Docking of known high-resolution structures of individual subdomains within the molecular envelope of the 3D EM map is used to derive a pseudoatomic model of the integrin complex. This approach of 3D EM image analysis and pseudoatomic modeling is a powerful strategy for exploring the structural biology of transmembrane signaling by integrins because it is likely that multiple conformational states will be difficult to crystallize, whereas the different states should be amenable to electron cryomicroscopy.

Bilateral edge filter: photometrically weighted, discontinuity based edge detection

Edge-detection algorithms have the potential to play an increasingly important role both in single particle analysis (for the detection of randomly oriented particles), and in tomography (for the segmentation of 3D volumes). However, the majority of traditional linear filters are significantly affected by noise as well as artefacts, and offer limited selectivity. The Bilateral edge filter presented here is an adaptation of the Bilateral filter [Jiang, W., Baker, M.L., Wu, Q., Bajaj, C., Chiu, W., 2003. Applications of a bilateral denoising filter in biological electron microscopy. J. Struct. Biol. 144, 114-122] designed for enhanced edge detection. It uses photometric weighting to identify significant discontinuities (representing edges), minimizing artefacts and noise. Compared with common edge-detectors (LoG, Marr-Hildreth) the Bilateral edge filter yielded significantly better results. Indeed data was of a similar quality to that of the Canny edge-detector, which is considered as a leading standard in edge detection [Basu, M., 2002. Gaussian-based edge-detection methods-a survey. IEEE Trans. Syst. Man Cybern. C Appl. Rev. 32, 252-260]. Compared to the Canny edge-detector the Bilateral edge-detector has the advantages that it only requires the adjustment of a single parameter, is theoretically faster for reasonably sized images, and can be used in selective contrast enhancement of images. The simplicity and speed of the filter for single particle and tomographic analysis are discussed.

3D electron microscopy of biological nanomachines: principles and applications

Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.

Automated cryoelectron microscopy of "single particles" applied to the 26S proteasome

The 26S proteasome is a large molecular machine with a central role in intracellular protein degradation in eukaryotes. The 2.5 MDa complex, which is built from two copies each of more than 30 different subunits, is labile and prone to dissociation into subcomplexes. Hence it is difficult if not impossible, to obtain structurally homogeneous preparations and, as a consequence, it is very cumbersome to obtain large numbers of images of the holocomplex. In this communication, we describe an automated procedure for the acquisition of large data sets of cryoelectron micrographs. The application of this procedure to the 26S proteasome from Drosophila has allowed us to determine the three-dimensional structure of the complex to a resolution of 2.9 nm and the prospects for further improvements are good.

Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation

Visualization by electron microscopy has provided many insights into the composition, quaternary structure, and mechanism of macromolecular assemblies. By preserving samples in stain or vitreous ice it is possible to image them as discrete particles, and from these images generate three-dimensional structures. This 'single-particle' approach suffers from two major shortcomings; it requires an initial model to reconstitute 2D data into a 3D volume, and it often fails when faced with conformational variability. Random conical tilt (RCT) and orthogonal tilt (OTR) are methods developed to overcome these problems, but the data collection required, particularly for vitreous ice specimens, is difficult and tedious. In this paper, we present an automated approach to RCT/OTR data collection that removes the burden of manual collection and offers higher quality and throughput than is otherwise possible. We show example datasets collected under stain and cryo conditions and provide statistics related to the efficiency and robustness of the process. Furthermore, we describe the new algorithms that make this method possible, which include new calibrations, improved targeting and feature-based tracking.

Determination of astigmatism in TEM images

We have developed a new two-step algorithm to determine the astigmatism of images from transmission electron microscopes (TEMs). Instead of computing the radial average of the power spectrum, we divide the power spectrum of a TEM image 1 to m (typically 32) sectors. We use a technique based on perturbation analysis of the contrast transfer function (CTF) to assimilate sector averages of the power spectrum of an image, which are incoherent in the presence of astigmatism, to a coherent radial average corresponding to a nominal defocus value. This is based on the fact that small defocus change from a nominal value can be considered to be equivalent to a perturbation on the spatial frequency spectra. Thus, instead of measuring the angular defocus variations, we optimise the frequency change required to obtain a coherent radial average. Numerically, this is achieved by minimizing sigma(2)/sigma(1) of a matrix formed from the sector averages, where sigma(i) denotes the ith singular value of the matrix. After the minimisation procedure, the second singular value should be very small compared with the first singular value, indicating that the matrix is nearly rank unity. In the second step, the nominal defocus can be obtained from the coherent radial average using any good defocus estimation program, which assumes zero astigmatism. The defocus value at a sector can be obtained from this nominal defocus value and one of the parameters from the unconstrained optima. Our algorithm is tested on astigmatic images of carbon film, 2D crystals of bacteriorhodopsin and cryo-images of HIV cores.

Electron energy filtering significantly improves amplitude contrast of frozen-hydrated protein at 300kV

The amplitude contrast of frozen-hydrated biological samples was measured using the bacterial flagellar filament embedded in vitreous ice at an accelerating voltage of 300kV. From the mean radial amplitude spectra of overfocused images, amplitude contrast was estimated to be 6.9+/-1.9% and 2.7+/-1.0% of the whole contrast at the low spatial frequency range with and without energy filtering, respectively, and that of the carbon film to be 9.5+/-2.0% and 5.8+/-1.8%. Energy filtering effectively doubled the signal-to-noise ratio in the images of frozen-hydrated filaments, and substantially improved intensity data statistics of layer lines up to at least approximately 25A resolution in their Fourier transforms. It also markedly improved inter-particle fitting phase residuals of averaged data at resolutions up to approximately 15A. Using the energy filtered data recorded on a new high-performance, lens-coupled CCD camera the three-dimensional map of the flagellar filament was calculated at 8A by applying the amplitude contrast of 6.9%. The map and its mean radial density distribution validated the obtained value of the amplitude contrast.

A novel method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas

In a context of automation of cryo-electron microscopy, we developed a novel method for improving visibility of diffraction rings in the power spectra of cryo-electron micrographs of vitreous ice (without carbon film or high concentration of diffracting material). We used these enhanced spectra to semi-automatically detect and remove micrographs and/or local areas introducing errors in the global 3D map (drifted and charged areas) or those unable to increase global signal-to-noise ratio (non-diffracting areas). Our strategy also allows a detection of micrographs/areas with a strong astigmatism. These images should be removed when using algorithms that do not correct astigmatism. Our sorting method is simple and fast since it uses the normalized cross-correlation between enhanced spectra and their copies rotated by 90 degrees. It owes its success mainly to the novel pre-processing of power spectra. The improved visibility also allows an easier visual check of accuracy of sorting. We show that our algorithm can even improve the visibility of diffraction rings of cryo-electron micrographs of pure water. Moreover, we show that this visibility depends strongly on ice thickness. This algorithm is implemented in the Xmipp (open-source image processing package) and is freely available for implementation in any other software package.

CTF determination and correction in electron cryotomography

Electron cryotomography (cryoET) has the potential to elucidate the structure of complex biological specimens at molecular resolution but technical and computational improvements are still needed. This work addresses the determination and correction of the contrast transfer function (CTF) of the electron microscope in cryoET. Our approach to CTF detection and defocus determination depends on strip-based periodogram averaging, extended throughout the tilt series to overcome the low contrast conditions found in cryoET. A method for CTF correction that deals with the defocus gradient in images of tilted specimens is also proposed. These approaches to CTF determination and correction have been applied here to several examples of cryoET of pleomorphic specimens and of single particles. CTF correction is essential for improving the resolution, particularly in those studies that combine cryoET with single particle averaging techniques.

Structure of the Sec13/31 COPII coat cage

Endomembranes of eukaryotic cells are dynamic structures that are in continuous communication through the activity of specialized cellular machineries, such as the coat protein complex II (COPII), which mediates cargo export from the endoplasmic reticulum (ER). COPII consists of the Sar1 GTPase, Sec23 and Sec24 (Sec23/24), where Sec23 is a Sar1-specific GTPase-activating protein and Sec24 functions in cargo selection, and Sec13 and Sec31 (Sec13/31), which has a structural role. Whereas recent results have shown that Sec23/24 and Sec13/31 can self-assemble to form COPII cage-like particles, we now show that Sec13/31 can self-assemble to form minimal cages in the absence of Sec23/24. We present a three-dimensional reconstruction of these Sec13/31 cages at 30 A resolution using cryo-electron microscopy and single particle analysis. These results reveal a novel cuboctahedron geometry with the potential to form a flexible lattice and to generate a diverse range of containers. Our data are consistent with a model for COPII coat complex assembly in which Sec23/24 has a non-structural role as a multivalent ligand localizing the self-assembly of Sec13/31 to form a cage lattice driving ER cargo export.