Symposium on Subtomogram Averaging in Electron Tomography

Dr. Thomas Hrabe
Cryo-electron tomography (CET) is a three-dimensional imaging technique for structural studies of protein complexes. In-depth analysis of these macromolecules depicted in tomograms requires localization of putative particles (subtomograms), averaging of subtomograms to enhance their signal and classification to capture the structural variations among them. Here, we introduce the open-source platform PyTom that unifies these standard processing steps in an open-source python toolbox.
Cryo-electron tomography towards rational drug design
Dr. Massimiliano Maletta
During the last 50 years, novel drug therapeutics have been, for the most part discovered, serendipitously in laboratory research. Advancements in structural techniques has allowed for high-resolution structural characterization of druggable targets making it possible to design new drugs using a rational approach. The high-resolution information of drug-targets makes it possible to predict further favorable interactions and based on these predictions, a new compound with the desired features is designed. Unfortunately this rational approach has lead to the discovery of very few drugs. Despite the incredible amount of effort that has been dedicated to rational drug design, the recent statistics show that the two main reasons for drug candidate failure are inefficiency (66%) and toxicity (21%). Either the drug is not interacting as we expect with the target or it has unexpected cross-reactivity with other molecules. Drug inefficiency and toxicity is mainly due to our lack in understanding of what is exactly going on in the cell at macromolecular level when exposed to these compounds. Our approach is to use the technique cryo-electron tomography of vitreous section (CETOVIS) as a novel method to visualize the effects of drugs on macromolecular complexes within the cell. Because the resolution of cryo-ET is reaching 2 nm, we anticipate this approach can be used to observe structural changes that occur within the cell when exposed to various drug compounds in order to test for the potential efficiency and toxicity of these compounds.
Fast alignment of 3D volumes using generalized convolution theorem: theory and app.
Yuxiang Chen
In cryo-electron tomography (CET) alignment and averaging of subtomograms, each depicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. We propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics.
Modelling of image formation in cryo-electron microscopy
Dr. Miloš Vulović
We present a platform for simulation of cryo-electron microscopy (cryo-EM) images based on physical principles. The model takes into account the parameters of the specimen, contrast transfer function (CTF), and detector response. Such a model is essential for optimizing the acquisition strategy, assisting the regularization in the 3D reconstruction, improving image interpretation, and achieving a resolution beyond the limits imposed by the oscillatory CTF. The full model was validated against experimental images. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.
CTF correction of large data sets
Dr. Raimond Ravelli
The oscillating contrast transfer function (CTF) should be accounted for if one wants to interpret cryo-electron microscopy (cryo-EM) images at frequencies beyond the first zero of the CTF. Estimates provided by the data acquisition software are inaccurate and occasionally even erroneous. Ideally, the data itself can be used to determine the defocus and astigmatism parameters for each particular area of an image. The signal-to-noise ratio of individual cryo-EM images is, however, too low. We present how this problem is overcome in single particle cryo-EM and discuss its relevance for cryo-electron tomography.