Browsing by Subject "Cryoelectron microscopy"

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    Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms
    (Nature Research, 2021-10-21) Moebel, Emmanuel; Martínez Sánchez, Antonio; Lamm, Lorenz; Righetto, Ricardo; Wietrzynski, Wojciech; Albert, Sahradha; Lariviere, Damien; Fourmentin, Eric; Pfeffer, Stefan; Ortiz, Julio; Baumeister, Wolfgang; Peng, Tingying; Engel, Benjamin; Kervrann, Charles; Ingeniería de la Información y las Comunicaciones
    Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes. Here, we present DeepFinder, a computational procedure that uses artificial neural networks to simultaneously localize multiple classes of macromolecules. Once trained, the inference stage of DeepFinder is faster than template matching and performs better than other competitive deep learning methods at identifying macromolecules of various sizes in both synthetic and experimental datasets. On cellular cryo-ET data, DeepFinder localized membrane-bound and cytosolic ribosomes (roughly 3.2 MDa), ribulose 1,5-bisphosphate carboxylase–oxygenase (roughly 560 kDa soluble complex) and photosystem II (roughly 550 kDa membrane complex) with an accuracy comparable to expert-supervised ground truth annotations. DeepFinder is therefore a promising algorithm for the semiautomated analysis of a wide range of molecular targets in cellular tomograms.
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    In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment
    (Elsevier, 2018-02-08) Guo, Qiang; Lehmer, Carina; Martinez-Sanchez, Antonio; Rudack, Till; Beck, Florian; Hartmann, Hannelore; Pérez-Berlanga, Manuela; Frédéric, Frottin; Hipp, Mark; Hartl, Ulrich; Edbauer, Dieter; Baumeister, Wolfgang; Fernández-Busnadiego, Rubén; Ingeniería de la Información y las Comunicaciones
    Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. We find that poly-GA aggregates consist of densely packed twisted ribbons that recruit numerous 26S proteasome complexes, while other macromolecules are largely excluded. Proximity to poly-GA ribbons stabilizes a transient substrate-processing conformation of the 26S proteasome, suggesting stalled degradation. Thus, poly-GA aggregates may compromise neuronal proteostasis by driving the accumulation and functional impairment of a large fraction of cellular proteasomes.