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  1. AU="Scheres, Sjors H W"
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  1. Article ; Online: High-throughput cryo-EM structure determination of amyloids.

    Lövestam, Sofia / Scheres, Sjors H W

    Faraday discussions

    2022  Volume 240, Page(s) 243–260

    Abstract: The formation of amyloid filaments is characteristic of various degenerative diseases. Recent breakthroughs in electron cryo-microscopy (cryo-EM) have led to atomic structure determination of multiple amyloid filaments, both of filaments ... ...

    Abstract The formation of amyloid filaments is characteristic of various degenerative diseases. Recent breakthroughs in electron cryo-microscopy (cryo-EM) have led to atomic structure determination of multiple amyloid filaments, both of filaments assembled
    MeSH term(s) Cryoelectron Microscopy/methods ; Algorithms
    Language English
    Publishing date 2022-11-08
    Publishing country England
    Document type Journal Article
    ISSN 1364-5498
    ISSN (online) 1364-5498
    DOI 10.1039/d2fd00034b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Amyloid structure determination in RELION-3.1.

    Scheres, Sjors H W

    Acta crystallographica. Section D, Structural biology

    2020  Volume 76, Issue Pt 2, Page(s) 94–101

    Abstract: Helical reconstruction in RELION is increasingly being used to determine the atomic structures of amyloid filaments from electron cryo-microscopy (cryo-EM) images. However, because the energy landscape of amyloid refinements is typically fraught with ... ...

    Abstract Helical reconstruction in RELION is increasingly being used to determine the atomic structures of amyloid filaments from electron cryo-microscopy (cryo-EM) images. However, because the energy landscape of amyloid refinements is typically fraught with local optima, amyloid structure determination is often difficult. This paper aims to help RELION users in this process. It discusses aspects of helical reconstruction that are particularly relevant to amyloids, it illustrates the problem of local optima in refinement and how to detect them, and it introduces a new method to calculate 3D initial models from reference-free 2D class averages. By providing starting models that are closer to the global optimum, this method makes amyloid structure determination easier. All methods described are open-source and distributed within RELION-3.1. Their use is illustrated using a publicly available data set on tau filaments from the brain of an individual with Alzheimer's disease.
    MeSH term(s) Algorithms ; Alzheimer Disease ; Amyloid/chemistry ; Amyloid/ultrastructure ; Cryoelectron Microscopy/methods ; Humans ; Imaging, Three-Dimensional/methods ; Software ; tau Proteins/chemistry
    Chemical Substances Amyloid ; tau Proteins
    Language English
    Publishing date 2020-01-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S2059798319016577
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  3. Article ; Online: Molecular pathology of neurodegenerative diseases by cryo-EM of amyloids.

    Scheres, Sjors H W / Ryskeldi-Falcon, Benjamin / Goedert, Michel

    Nature

    2023  Volume 621, Issue 7980, Page(s) 701–710

    Abstract: Abnormal assembly of tau, α-synuclein, TDP-43 and amyloid-β proteins into amyloid filaments defines most human neurodegenerative diseases. Genetics provides a direct link between filament formation and the causes of disease. Developments in cryo-electron ...

    Abstract Abnormal assembly of tau, α-synuclein, TDP-43 and amyloid-β proteins into amyloid filaments defines most human neurodegenerative diseases. Genetics provides a direct link between filament formation and the causes of disease. Developments in cryo-electron microscopy (cryo-EM) have made it possible to determine the atomic structures of amyloids from postmortem human brains. Here we review the structures of brain-derived amyloid filaments that have been determined so far and discuss their impact on research into neurodegeneration. Whereas a given protein can adopt many different filament structures, specific amyloid folds define distinct diseases. Amyloid structures thus provide a description of neuropathology at the atomic level and a basis for studying disease. Future research should focus on model systems that replicate the structures observed in disease to better understand the molecular mechanisms of disease and develop improved diagnostics and therapies.
    MeSH term(s) Humans ; alpha-Synuclein ; Amyloid/chemistry ; Amyloid/classification ; Amyloid/ultrastructure ; Amyloid beta-Peptides ; Cryoelectron Microscopy ; Neurodegenerative Diseases/metabolism ; Neurodegenerative Diseases/pathology ; Pathology, Molecular ; Protein Folding
    Chemical Substances alpha-Synuclein ; Amyloid ; Amyloid beta-Peptides ; MAPT protein, human ; TARDBP protein, human
    Language English
    Publishing date 2023-09-27
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-06437-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 26: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
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    Zs.MO 244: Show issues

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  4. Article ; Online: Automated model building and protein identification in cryo-EM maps.

    Jamali, Kiarash / Käll, Lukas / Zhang, Rui / Brown, Alan / Kimanius, Dari / Scheres, Sjors H W

    Nature

    2024  Volume 628, Issue 8007, Page(s) 450–457

    Abstract: Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics ... ...

    Abstract Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs
    MeSH term(s) Amino Acid Sequence ; Cryoelectron Microscopy/methods ; Cryoelectron Microscopy/standards ; Machine Learning ; Markov Chains ; Models, Molecular ; Neural Networks, Computer ; Protein Conformation ; Proteins/chemistry ; Proteins/ultrastructure ; Computer Graphics
    Chemical Substances Proteins
    Language English
    Publishing date 2024-02-26
    Publishing country England
    Document type Comparative Study ; Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-024-07215-4
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    ab Jg. 2022: Lesesaal (EG)
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  5. Article ; Online: Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir.

    Shi, Yang / Ghetti, Bernardino / Goedert, Michel / Scheres, Sjors H W

    Journal of molecular biology

    2023  Volume 435, Issue 11, Page(s) 168025

    Abstract: Positron emission tomography (PET) imaging allows monitoring the progression of amyloid aggregation in the living brain. [ ...

    Abstract Positron emission tomography (PET) imaging allows monitoring the progression of amyloid aggregation in the living brain. [
    MeSH term(s) Humans ; Alzheimer Disease/metabolism ; Alzheimer Disease/pathology ; Brain/metabolism ; Chronic Traumatic Encephalopathy/metabolism ; Chronic Traumatic Encephalopathy/pathology ; Cryoelectron Microscopy ; Ligands ; Positron-Emission Tomography/methods ; tau Proteins/chemistry ; Tauopathies/metabolism ; Tauopathies/pathology ; Intermediate Filaments/chemistry ; Carbolines/chemistry ; Protein Binding ; Radioactive Tracers
    Chemical Substances 7-(6-fluoropyridin-3-yl)-5H-pyrido(4,3-b)indole (J09QS3Z3WB) ; Ligands ; tau Proteins ; Carbolines ; Radioactive Tracers
    Language English
    Publishing date 2023-06-16
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2023.168025
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 867: Show issues Location:
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  6. Article ; Online: Tau and neurodegeneration.

    Goedert, Michel / Crowther, R Anthony / Scheres, Sjors H W / Spillantini, Maria Grazia

    Cytoskeleton (Hoboken, N.J.)

    2023  Volume 81, Issue 1, Page(s) 95–102

    Abstract: First identified in 1975, tau was implicated in Alzheimer's disease 10 years later. Filamentous tangle inclusions were known to be made of hyperphosphorylated tau by 1991, with similar inclusions gaining recognition for being associated with other ... ...

    Abstract First identified in 1975, tau was implicated in Alzheimer's disease 10 years later. Filamentous tangle inclusions were known to be made of hyperphosphorylated tau by 1991, with similar inclusions gaining recognition for being associated with other neurodegenerative diseases. In 1998, mutations in MAPT, the gene that encodes tau, were identified as the cause of a dominantly inherited form of frontotemporal dementia with abundant filamentous tau inclusions. While this result indicated that assembly of tau into aberrant filaments is sufficient to drive neurodegeneration and dementia, most cases of tauopathy are sporadic. More recent work in experimental systems showed that filamentous assemblies of tau may first form in one brain area, and then spread to others in a prion-like fashion. Beginning in 2017, work on human brains using high-resolution techniques has led to a structure-based classification of tauopathies, which has opened the door to a better understanding of the significance of tau filament formation.
    MeSH term(s) Humans ; tau Proteins/genetics ; Tauopathies/genetics ; Brain/metabolism ; Cytoskeleton/metabolism ; Mutation
    Chemical Substances tau Proteins
    Language English
    Publishing date 2023-12-10
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2534372-5
    ISSN 1949-3592 ; 1949-3584
    ISSN (online) 1949-3592
    ISSN 1949-3584
    DOI 10.1002/cm.21812
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    Zs.A 1840: Show issues Location:
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  7. Article ; Online: Multi-body Refinement of Cryo-EM Images in RELION.

    Nakane, Takanori / Scheres, Sjors H W

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2215, Page(s) 145–160

    Abstract: Single-particle analysis of electron cryo-microscopy (cryo-EM) images allows structure determination of macromolecular complexes. But when these molecules adopt many different conformations, traditional image processing approaches often lead to blurred ... ...

    Abstract Single-particle analysis of electron cryo-microscopy (cryo-EM) images allows structure determination of macromolecular complexes. But when these molecules adopt many different conformations, traditional image processing approaches often lead to blurred reconstructions. By considering complexes to be comprised of multiple, independently moving rigid bodies, multi-body refinement in RELION enables structure determination of highly flexible complexes, while at the same time providing a characterization of the motions in the complex. Here, we describe how to perform multi-body refinement in RELION using a publicly available example. We outline how to prepare the necessary files, how to run the actual multi-body calculation, and how to interpret its output. This method can be applied to any cryo-EM data set of flexible complexes that can be divided into two or more bodies, each with a minimum molecular weight of 100-150 kDa.
    MeSH term(s) Cryoelectron Microscopy ; Image Processing, Computer-Assisted/methods ; Macromolecular Substances/chemistry ; Models, Molecular ; Molecular Conformation ; Single Molecule Imaging/methods ; Software
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2020-12-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0966-8_7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir

    Shi, Yang / Ghetti, Bernardino / Goedert, Michel / Scheres, Sjors H.W.

    Journal of Molecular Biology. 2023 June, v. 435, no. 11 p.168025-

    2023  

    Abstract: Positron emission tomography (PET) imaging allows monitoring the progression of amyloid aggregation in the living brain. [¹⁸F]-Flortaucipir is the only approved PET tracer compound for the visualisation of tau aggregation. Here, we describe cryo-EM ... ...

    Abstract Positron emission tomography (PET) imaging allows monitoring the progression of amyloid aggregation in the living brain. [¹⁸F]-Flortaucipir is the only approved PET tracer compound for the visualisation of tau aggregation. Here, we describe cryo-EM experiments on tau filaments in the presence and absence of flortaucipir. We used tau filaments isolated from the brain of an individual with Alzheimer’s disease (AD), and from the brain of an individual with primary age-related tauopathy (PART) with a co-pathology of chronic traumatic encephalopathy (CTE). Unexpectedly, we were unable to visualise additional cryo-EM density for flortaucipir for AD paired helical or straight filaments (PHFs or SFs), but we did observe density for flortaucipir binding to CTE Type I filaments from the case with PART. In the latter, flortaucipir binds in a 1:1 molecular stoichiometry with tau, adjacent to lysine 353 and aspartate 358. By adopting a tilted geometry with respect to the helical axis, the 4.7 Å distance between neighbouring tau monomers is reconciled with the 3.5 Å distance consistent with π-π-stacking between neighbouring molecules of flortaucipir.
    Keywords amyloid ; aspartic acid ; brain ; encephalopathy ; geometry ; ligands ; lysine ; molecular biology ; positron-emission tomography ; stoichiometry ; cryo-EM ; Tau ; Flortaucipir ; PET compounds
    Language English
    Dates of publication 2023-06
    Publishing place Elsevier Ltd
    Document type Article ; Online
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2023.168025
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  9. Article: Automated model building and protein identification in cryo-EM maps.

    Jamali, Kiarash / Käll, Lukas / Zhang, Rui / Brown, Alan / Kimanius, Dari / Scheres, Sjors H W

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. ... ...

    Abstract Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality as those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy as humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will thus remove bottlenecks and increase objectivity in cryo-EM structure determination.
    Language English
    Publishing date 2023-10-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.16.541002
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  10. Article ; Online: Structures, Distributions, and Conformations of SARS-CoV-2 Spike Proteins on Intact Virions by Cryo-EM and Cryo-ET.

    Ke, Zunlong / Oton, Joaquin / Qu, Kun / Scheres, Sjors H W / Briggs, John A G

    Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

    2023  Volume 29, Issue 29 Suppl 1, Page(s) 902–903

    Language English
    Publishing date 2023-08-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 1385710-1
    ISSN 1435-8115 ; 1431-9276
    ISSN (online) 1435-8115
    ISSN 1431-9276
    DOI 10.1093/micmic/ozad067.448
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