Cryo-EM – Bartesaghi Lab

- Accurate Detection of Proteins in Cryo-Electron Tomograms from Sparse Labels
- Cryo-EM, Methods
- Accurate Detection of Proteins in Cryo-Electron Tomograms from Sparse Labels Cryo-electron tomography (CET) combined with sub-volume averaging (SVA), is currently the only imaging technique capable of de-termining the structure of proteins imaged inside cells at molecular reso-lution. To obtain high-resolution reconstructions, sub-volumes containing randomly distributed copies of the protein of interest need be identified, extracted and subjected to SVA,…
- High-resolution structure determination using high-throughput electron cryo-tomography
- Cryo-EM, Methods
- High-resolution structure determination using high-throughput electron cryo-tomography The low throughput characteristic of tomographic data acquisition combined with the complex data-analysis pipeline that is required to obtain high-resolution maps, has limited the applicability of this technique to favorable samples or to resolutions that are too low to provide useful mechanistic information. Recently, beam image-shift electron cryo-tomography (BISECT), a strategy to…
- Data-driven determination of number of discrete conformations in single-particle cryo-EM
- Cryo-EM, Methods
- Data-driven determination of number of discrete conformations in single-particle cryo-EM Single-particle cryo-EM can be used to image heterogeneous samples containing multiple molecular species, different oligomeric states or distinct conformations. This, however, requires expert-user knowledge and trial-and-error experimentation to determine the correct number of conformations present in a mixture. Here, we propose an approach to address the problem of automatically…
- Automated systematic evaluation of cryo-EM specimens with SmartScope
- Cryo-EM, Machine learning and artificial intelligence, Methods
- Automated systematic evaluation of cryo-EM specimens with SmartScope We present SmartScope, the first framework to streamline, standardize, and automate specimen evaluation in cryo-electron microscopy. SmartScope employs deep-learning-based object detection to identify and classify features suitable for imaging, allowing it to perform thorough specimen screening in a fully automated manner. A web interface provides remote control over the automated operation…
- Cryo-ZSSR: multiple-image super-resolution based on deep internal learning
- Cryo-EM, Machine learning and artificial intelligence, Methods
- Cryo-ZSSR: multiple-image super-resolution based on deep internal learning We present a multiple-image super-resolution (SR) algorithm based on deep internal learning designed specifically to work under low-SNR conditions typical of cryo-EM data. Our approach leverages the internal image statistics of cryo-EM movies and does not require training on ground-truth data. When applied to a single-particle dataset of apoferritin, we show…
- Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography
- Cryo-EM, Methods
- Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography To overcome the inherent low-throughput characteristic of CET data collection, improve the resolution of SVA and extend its application to a wider set of samples including low molecular weight targets, here, we: (1) use beam-image shift navigation to multiply the number of regions of interest imaged at each…
- Single-Particle Cryo-Electron Microscopy
- Cryo-EM, Methods
- Mathematical Theory, Computational Challenges, and Opportunities Structural biology studies the structure and dynamics of macromolecules to broaden our knowledge about the mechanisms of life and impact the drug-discovery process. Owing to recent groundbreaking developments, chiefly in hardware technologies and data processing techniques, many new molecular structures have been elucidated to near-atomic resolutions using cryo-EM. The main goal of this article…
- Unsupervised particle sorting for high-resolution single-particle cryo-EM
- Cryo-EM, Machine learning and artificial intelligence, Methods
- Unsupervised particle sorting for high-resolution single-particle cryo-EM Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both in data collection and data processing, have significantly lowered the barrier for non-expert users to successfully execute the structure determination workflow. Many critical data processing…
- Atomic Resolution Cryo-EM Structure of B-galactosidase
- Cryo-EM, Methods
- Atomic Resolution Cryo-EM Structure of B-galactosidase We report methods to account for radiation damage and local changes in defocus and image drift, enabling visualization of atomic resolution features in a cryo-EM density map of inhibitor-bound b-galactosidase, and measuring of local flexibility of the bound inhibitor using constrained molecular dynamics simulations. Structure, 26(6), 2018.
- Fundamental Limits in Multi-Image Alignment
- Cryo-EM, Methods
- Fundamental Limits in Multi-Image Alignment IEEE Trans on Signal Process, 64(21):5707-5722, 2016.
- Constrained Single-Particle Cryo-Electron Tomography
- Cryo-EM, Methods
- Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography We propose a hybrid strategy, constrained single-particle tomography (CSPT), that combines the advantages of cryo-electron tomography and subvolume averaging with those of traditional single-particle reconstruction and projection matching refinement. Its key components are the effective manipulation of images from tomographic tilt series to successfully extract high-resolution information and correct for…
- Collaborative Framework for Alignment and Classification of Sub-Tomograms
- Cryo-EM, Methods
- A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography Journal of Structural Biology 181(2):116-27, 2013.
- Sub-Tomogram Alignment Using Spherical Harmonics
- Cryo-EM, Methods
- Classification and 3D Averaging with Missing Wedge Correction in Biological Electron Tomography Journal of Structural Biology 162(3):436-50, 2008.
- Energy-Based Segmentation of Cryo-EM Tomograms
- Cryo-EM, Methods
- An Energy-based Three-dimensional Segmentation Approach for the Quantitative Interpretation of Electron Tomograms IEEE Trans Image Process,14(9):1314-23, 2005.