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Adamoski D, Dias MM, Quesñay JEN, Yang Z, Zagoriy I, Steyer AM, Rodrigues CT, da Silva Bastos AC, da Silva BN, Costa RKE, de Abreu FMO, Islam Z, Cassago A, van Heel MG, Consonni SR, Mattei S, Mahamid J, Portugal RV, Ambrosio ALB, Dias SMG. Molecular mechanism of glutaminase activation through filamentation and the role of filaments in mitophagy protection. Nat Struct Mol Biol 2023; 30:1902-1912. [PMID: 37857822 DOI: 10.1038/s41594-023-01118-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/06/2023] [Indexed: 10/21/2023]
Abstract
Glutaminase (GLS), which deaminates glutamine to form glutamate, is a mitochondrial tetrameric protein complex. Although inorganic phosphate (Pi) is known to promote GLS filamentation and activation, the molecular basis of this mechanism is unknown. Here we aimed to determine the molecular mechanism of Pi-induced mouse GLS filamentation and its impact on mitochondrial physiology. Single-particle cryogenic electron microscopy revealed an allosteric mechanism in which Pi binding at the tetramer interface and the activation loop is coupled to direct nucleophile activation at the active site. The active conformation is prone to enzyme filamentation. Notably, human GLS filaments form inside tubulated mitochondria following glutamine withdrawal, as shown by in situ cryo-electron tomography of cells thinned by cryo-focused ion beam milling. Mitochondria with GLS filaments exhibit increased protection from mitophagy. We reveal roles of filamentous GLS in mitochondrial morphology and recycling.
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Affiliation(s)
- Douglas Adamoski
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Marilia Meira Dias
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Jose Edwin Neciosup Quesñay
- Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Brazil
- Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Zhengyi Yang
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna M Steyer
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Camila Tanimoto Rodrigues
- Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Brazil
- Biological Sciences Department, School of Science, Purdue University, Lafayette, IN, USA
| | - Alliny Cristiny da Silva Bastos
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Division of Medical Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bianca Novaes da Silva
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Renna Karoline Eloi Costa
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Zeyaul Islam
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Alexandre Cassago
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Marin Gerard van Heel
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Sílvio Roberto Consonni
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Simone Mattei
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rodrigo Villares Portugal
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | | | - Sandra Martha Gomes Dias
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil.
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2
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Smith PR, Loerch S, Kunder N, Stanowick AD, Lou TF, Campbell ZT. Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance. Nat Commun 2021; 12:6789. [PMID: 34815424 PMCID: PMC8611098 DOI: 10.1038/s41467-021-27160-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/07/2021] [Indexed: 11/09/2022] Open
Abstract
Processing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible for coordinate control of the two processes are unclear. Here, we uncover key roles for eEF2 kinase (eEF2K) in the control of ribosome availability and p-body abundance. eEF2K acts on a sole known substrate, eEF2, to inhibit translation. We find that the eEF2K agonist nelfinavir abolishes p-bodies in sensory neurons and impairs translation. To probe the latter, we used cryo-electron microscopy. Nelfinavir stabilizes vacant 80S ribosomes. They contain SERBP1 in place of mRNA and eEF2 in the acceptor site. Phosphorylated eEF2 associates with inactive ribosomes that resist splitting in vitro. Collectively, the data suggest that eEF2K defines a population of inactive ribosomes resistant to recycling and protected from degradation. Thus, eEF2K activity is central to both p-body abundance and ribosome availability in sensory neurons.
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Affiliation(s)
- Patrick R. Smith
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA
| | - Sarah Loerch
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA ,grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA USA
| | - Nikesh Kunder
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA
| | - Alexander D. Stanowick
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA
| | - Tzu-Fang Lou
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA
| | - Zachary T. Campbell
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA ,grid.267323.10000 0001 2151 7939The Center for Advanced Pain Studies (CAPS), University of Texas at Dallas, Richardson, TX USA
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3
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Spectroscopic Approach to Correction and Visualisation of Bright-Field Light Transmission Microscopy Biological Data. PHOTONICS 2021. [DOI: 10.3390/photonics8080333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The most realistic information about a transparent sample such as a live cell can be obtained using bright-field light microscopy. Under high-intensity pulsing LED illumination, we captured a primary 12-bit-per-channel (bpc) response from an observed sample using a bright-field microscope equipped with a high-resolution (4872 × 3248) image sensor. In order to suppress data distortions originating from the light interactions with elements in the optical path, poor sensor reproduction (geometrical defects of the camera sensor and some peculiarities of sensor sensitivity), we propose a spectroscopic approach for the correction of these uncompressed 12 bpc data by simultaneous calibration of all parts of the experimental arrangement. Moreover, the final intensities of the corrected images are proportional to the photon fluxes detected by a camera sensor. It can be visualized in 8 bpc intensity depth after the Least Information Loss compression.
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4
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Mendonça DC, Guimarães SL, Pereira HD, Pinto AA, de Farias MA, de Godoy AS, Araujo APU, van Heel M, Portugal RV, Garratt RC. An atomic model for the human septin hexamer by cryo-EM. J Mol Biol 2021; 433:167096. [PMID: 34116125 DOI: 10.1016/j.jmb.2021.167096] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 01/22/2023]
Abstract
In order to form functional filaments, human septins must assemble into hetero-oligomeric rod-like particles which polymerize end-to-end. The rules governing the assembly of these particles and the subsequent filaments are incompletely understood. Although crystallographic approaches have been successful in studying the separate components of the system, there has been difficulty in obtaining high resolution structures of the full particle. Here we report a first cryo-EM structure for a hexameric rod composed of human septins 2, 6 and 7 with a global resolution of ~3.6 Å and a local resolution of between ~3.0 Å and ~5.0 Å. By fitting the previously determined high-resolution crystal structures of the component subunits into the cryo-EM map, we are able to provide an essentially complete model for the particle. This exposes SEPT2 NC-interfaces at the termini of the hexamer and leaves internal cavities between the SEPT6-SEPT7 pairs. The floor of the cavity is formed by the two α0 helices including their polybasic regions. These are locked into place between the two subunits by interactions made with the α5 and α6 helices of the neighbouring monomer together with its polyacidic region. The cavity may serve to provide space allowing the subunits to move with respect to one another. The elongated particle shows a tendency to bend at its centre where two copies of SEPT7 form a homodimeric G-interface. Such bending is almost certainly related to the ability of septin filaments to recognize and even induce membrane curvature.
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Affiliation(s)
| | | | | | | | | | | | - Ana P U Araujo
- São Carlos Institute of Physics, USP, São Carlos, SP, Brazil
| | - Marin van Heel
- Brazilian Nanotechnology National Laboratory, CNPEM, Campinas, SP, Brazil
| | - Rodrigo V Portugal
- Brazilian Nanotechnology National Laboratory, CNPEM, Campinas, SP, Brazil.
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5
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Cryo-EM structure of the mature and infective Mayaro virus at 4.4 Å resolution reveals features of arthritogenic alphaviruses. Nat Commun 2021; 12:3038. [PMID: 34031424 PMCID: PMC8144435 DOI: 10.1038/s41467-021-23400-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/27/2021] [Indexed: 12/19/2022] Open
Abstract
Mayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related arthritogenic alphaviruses. Here, we present the structure of MAYV at 4.4 Å resolution, obtained from a preparation of mature, infective virions. MAYV presents typical alphavirus features and organization. Interactions between viral proteins that lead to particle formation are described together with a hydrophobic pocket formed between E1 and E2 spike proteins and conformational epitopes specific of MAYV. We also describe MAYV glycosylation residues in E1 and E2 that may affect MXRA8 host receptor binding, and a molecular “handshake” between MAYV spikes formed by N262 glycosylation in adjacent E2 proteins. The structure of MAYV is suggestive of structural and functional complexity among alphaviruses, which may be targeted for specificity or antiviral activity. Mayaro virus (MAYV) is an emerging arbovirus in Central and South America that is transmitted by mosquitoes and causes arthritogenic disease. Here, the authors present the 4.4 Å resolution cryo-EM structure of MAYV and describe specific features of the virus, which could be exploited for the design of MAYV-specific diagnostics and therapeutics.
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6
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Bao C, Loerch S, Ling C, Korostelev AA, Grigorieff N, Ermolenko DN. mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding. eLife 2020; 9:e55799. [PMID: 32427100 PMCID: PMC7282821 DOI: 10.7554/elife.55799] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022] Open
Abstract
Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Förster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.
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Affiliation(s)
- Chen Bao
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
| | - Sarah Loerch
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Clarence Ling
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
| | - Andrei A Korostelev
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of RochesterRochesterUnited States
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7
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Pertusa JF, Morante-Redolat JM. Main Steps in Image Processing and Quantification: The Analysis Workflow. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 2040:3-21. [PMID: 31432472 DOI: 10.1007/978-1-4939-9686-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In the last decades, the variety of programs, algorithms, and strategies that researchers have at their disposal to process and analyze image files has grown extensively. However, these are only pointless tools if not applied with the careful planning required to achieve a succesful image analysis. In order to do so, the analyst must establish a meaningful and effective sequence of orderly operations that is able to (1) overcome all the problems derived from the image manipulation and (2) successfully resolve the question that was originally posed. In this chapter, the authors suggest a set of strategies and present a reflection on the main milestones that compose the image processing workflow, to help guide the way to obtaining unbiased quantitative data.
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Affiliation(s)
- José F Pertusa
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universitat de València, Burjassot, Spain.
| | - Jose M Morante-Redolat
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universitat de València, Burjassot, Spain.,Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Burjassot, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
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8
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Advances in image processing for single-particle analysis by electron cryomicroscopy and challenges ahead. Curr Opin Struct Biol 2018; 52:127-145. [PMID: 30509756 DOI: 10.1016/j.sbi.2018.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/26/2018] [Accepted: 11/17/2018] [Indexed: 12/20/2022]
Abstract
Electron cryomicroscopy (cryoEM) is essential for the study and functional understanding of non-crystalline macromolecules such as proteins. These molecules cannot be imaged using X-ray crystallography or other popular methods. CryoEM has been successfully used to visualize macromolecular complexes such as ribosomes, viruses, and ion channels. Determination of structural models of these at various conformational states leads to insight on how these molecules function. Recent advances in imaging technology have given cryoEM a scientific rebirth. As a result of these technological advances image processing and analysis have yielded molecular structures at atomic resolution. Nevertheless there continue to be challenges in image processing, and in this article we will touch on the most essential in order to derive an accurate three-dimensional model from noisy projection images. Traditional approaches, such as k-means clustering for class averaging, will be provided as background. We will then highlight new approaches for each image processing subproblem, including a 3D reconstruction method for asymmetric molecules using just two projection images and deep learning algorithms for automated particle picking.
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9
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Abstract
Structural studies of biocomplexes using single-particle cryo-electron microscopy (cryo-EM) is now a well-established technique in structural biology and has become competitive with X-ray crystallography. The latest advances in EM enable us to determine structures of protein complexes at 3-5 Å resolution for an extremely broad range of sizes from ~200 kDa up to hundreds of megadaltons (Bartesaghi et al., Science 348(6239):1147-1151, 2051; Bai et al., Nature 525(7568):212-217, 2015; Vinothkumar et al., Nature 515(7525):80-84, 2014; Grigorieff and Harrison, Curr Opin Struct Biol 21(2):265-273, 2011). The majority of biocomplexes comprise a number of different components and are not amenable to crystallisation. Secretion systems are typical examples of such multi-protein complexes, and structural studies of them are extremely challenging. The only feasible approach to revealing their spatial organisation and functional modification is cryo-EM. The development of systems for digital registration of images and algorithms for the fast and efficient processing of recorded images and subsequent analysis facilitated the determination of structures at near-atomic resolution. In this review we will describe sample preparation for cryo-EM, how data are collected by new detectors, and the logistics of image analysis through the basic steps required for reconstructions of both small and large biological complexes and their refinement to nearly atomic resolution. The processing workflow is illustrated using examples of EM analysis of a Type IV Secretion System.
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10
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Sorzano COS, Fernández-Giménez E, Peredo-Robinson V, Vargas J, Majtner T, Caffarena G, Otón J, Vilas JL, de la Rosa-Trevín JM, Melero R, Gómez-Blanco J, Cuenca J, Del Cano L, Conesa P, Marabini R, Carazo JM. Blind estimation of DED camera gain in Electron Microscopy. J Struct Biol 2018; 203:90-93. [PMID: 29551714 DOI: 10.1016/j.jsb.2018.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 12/17/2022]
Abstract
The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras. We propose the algorithm to be used either to validate the experimentally acquired gain image (for instance, to follow its possible change over time) or to verify that there is no residual gain image after experimentally correcting for the camera gain. We show results for a number of DED camera models currently in use (DE, Falcon II, Falcon 3, and K2).
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Affiliation(s)
- C O S Sorzano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain.
| | - E Fernández-Giménez
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - V Peredo-Robinson
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - J Vargas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - T Majtner
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - G Caffarena
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - J Otón
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | | | - R Melero
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Gómez-Blanco
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Cuenca
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - L Del Cano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Univ. Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
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11
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McLeod RA, Diogo Righetto R, Stewart A, Stahlberg H. MRCZ - A file format for cryo-TEM data with fast compression. J Struct Biol 2017; 201:252-257. [PMID: 29175288 DOI: 10.1016/j.jsb.2017.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 11/17/2022]
Abstract
The introduction of fast CMOS detectors is moving the field of transmission electron microscopy into the computer science field of big data. Automated data pipelines control the instrument and initial processing steps which imposes more onerous data transfer and archiving requirements. Here we conduct a technical demonstration whereby storage and read/write times are improved 10× at a dose rate of 1 e-/pix/frame for data from a Gatan K2 direct-detection device by combination of integer decimation and lossless compression. The example project is hosted at github.com/em-MRCZ and released under the BSD license.
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Affiliation(s)
- Robert A McLeod
- Center for Cellular Imaging and NanoAnalytics (C-CINA), University of Basel, Basel, Switzerland.
| | - Ricardo Diogo Righetto
- Center for Cellular Imaging and NanoAnalytics (C-CINA), University of Basel, Basel, Switzerland
| | - Andy Stewart
- Department of Physics, University of Limerick, Limerick, Ireland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), University of Basel, Basel, Switzerland
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12
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Afanasyev P, Seer-Linnemayr C, Ravelli RBG, Matadeen R, De Carlo S, Alewijnse B, Portugal RV, Pannu NS, Schatz M, van Heel M. Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin. IUCRJ 2017; 4:678-694. [PMID: 28989723 PMCID: PMC5619859 DOI: 10.1107/s2052252517010922] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/24/2017] [Indexed: 05/12/2023]
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.
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Affiliation(s)
- Pavel Afanasyev
- Institute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands
- Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | | | | | - Rishi Matadeen
- Netherlands Centre for Electron Nanoscopy (NeCEN), Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sacha De Carlo
- Netherlands Centre for Electron Nanoscopy (NeCEN), Einsteinweg 55, 2333 CC Leiden, The Netherlands
- FEI Company/Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Bart Alewijnse
- Institute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands
- FEI Company/Thermo Fisher Scientific, Eindhoven, The Netherlands
| | | | - Navraj S. Pannu
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | | | - Marin van Heel
- Institute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands
- Brazilian Nanotechnology National Laboratory (LNNANO), Campinas, SP, Brazil
- Department of Life Sciences, Imperial College London, England
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13
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The Structural Architecture of an Infectious Mammalian Prion Using Electron Cryomicroscopy. PLoS Pathog 2016; 12:e1005835. [PMID: 27606840 PMCID: PMC5015997 DOI: 10.1371/journal.ppat.1005835] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/01/2016] [Indexed: 12/31/2022] Open
Abstract
The structure of the infectious prion protein (PrPSc), which is responsible for Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy, has escaped all attempts at elucidation due to its insolubility and propensity to aggregate. PrPSc replicates by converting the non-infectious, cellular prion protein (PrPC) into the misfolded, infectious conformer through an unknown mechanism. PrPSc and its N-terminally truncated variant, PrP 27–30, aggregate into amorphous aggregates, 2D crystals, and amyloid fibrils. The structure of these infectious conformers is essential to understanding prion replication and the development of structure-based therapeutic interventions. Here we used the repetitive organization inherent to GPI-anchorless PrP 27–30 amyloid fibrils to analyze their structure via electron cryomicroscopy. Fourier-transform analyses of averaged fibril segments indicate a repeating unit of 19.1 Å. 3D reconstructions of these fibrils revealed two distinct protofilaments, and, together with a molecular volume of 18,990 Å3, predicted the height of each PrP 27–30 molecule as ~17.7 Å. Together, the data indicate a four-rung β-solenoid structure as a key feature for the architecture of infectious mammalian prions. Furthermore, they allow to formulate a molecular mechanism for the replication of prions. Knowledge of the prion structure will provide important insights into the self-propagation mechanisms of protein misfolding. The structure of the infectious prion (PrPSc), which is responsible for Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy, has escaped all attempts at elucidation due to its propensity to aggregate. Here, we use the repetitive organization inherent in amyloid fibrils to analyze the structure of GPI-anchorless PrP 27–30 via electron cryomicroscopy. Fourier-transform analysis of averaged fibril segments indicates a repeating unit of 19.1 Å. In agreement with this observation, 3D reconstructions reveal that each fibril contains two distinct protofilaments and that the height of each PrP 27–30 molecule in these fibrils is ~17.7 Å. Together the data indicate a four-rung β-solenoid structure as a key feature for the architecture of infectious mammalian prions. The data conflict with all previous models for the structure of PrPSc and allow the formulation of a molecular mechanism for the replication of prions.
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