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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCRJ 2024; 11:140-151. [PMID: 38358351 PMCID: PMC10916293 DOI: 10.1107/s2052252524001246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D. Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Maya Topf
- Birkbeck, University of London, London, United Kingdom
| | | | | | | | | | | | | | | | - Sai J. Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ryan Pye
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | - Zhe Wang
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | - Martyn D. Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, United Kingdom
| | - Jasmine Y. Young
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation. ARXIV 2024:arXiv:2311.17640v3. [PMID: 38076521 PMCID: PMC10705588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D Adams
- Lawrence Berkeley Laboratory, Berkeley, CA, USA and University of California, Berkeley, CA, USA
| | | | - Catherine L Lawson
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | | | | | | | - Maya Topf
- Birkbeck, University of London, London, UK
| | | | | | | | | | | | | | | | - Sai J Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John D Westbrook
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Martyn D Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, UK
| | - Jasmine Y Young
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
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Turner J, Abbott S, Fonseca N, Pye R, Carrijo L, Duraisamy AK, Salih O, Wang Z, Kleywegt GJ, Morris KL, Patwardhan A, Burley SK, Crichlow G, Feng Z, Flatt JW, Ghosh S, Hudson BP, Lawson CL, Liang Y, Peisach E, Persikova I, Sekharan M, Shao C, Young J, Velankar S, Armstrong D, Bage M, Bueno WM, Evans G, Gaborova R, Ganguly S, Gupta D, Harrus D, Tanweer A, Bansal M, Rangannan V, Kurisu G, Cho H, Ikegawa Y, Kengaku Y, Kim JY, Niwa S, Sato J, Takuwa A, Yu J, Hoch JC, Baskaran K, Xu W, Zhang W, Ma X. EMDB-the Electron Microscopy Data Bank. Nucleic Acids Res 2024; 52:D456-D465. [PMID: 37994703 PMCID: PMC10767987 DOI: 10.1093/nar/gkad1019] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023] Open
Abstract
The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.
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Iudin A, Korir PK, Somasundharam S, Weyand S, Cattavitello C, Fonseca N, Salih O, Kleywegt GJ, Patwardhan A. EMPIAR: the Electron Microscopy Public Image Archive. Nucleic Acids Res 2023; 51:D1503-D1511. [PMID: 36440762 PMCID: PMC9825465 DOI: 10.1093/nar/gkac1062] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 11/29/2022] Open
Abstract
Public archiving in structural biology is well established with the Protein Data Bank (PDB; wwPDB.org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; emdb-empiar.org) for 3D reconstructions from cryo-EM experiments. Even before the recent rapid growth in cryo-EM, there was an expressed community need for a public archive of image data from cryo-EM experiments for validation, software development, testing and training. Concomitantly, the proliferation of 3D imaging techniques for cells, tissues and organisms using volume EM (vEM) and X-ray tomography (XT) led to calls from these communities to publicly archive such data as well. EMPIAR (empiar.org) was developed as a public archive for raw cryo-EM image data and for 3D reconstructions from vEM and XT experiments and now comprises over a thousand entries totalling over 2 petabytes of data. EMPIAR resources include a deposition system, entry pages, facilities to search, visualize and download datasets, and a REST API for programmatic access to entry metadata. The success of EMPIAR also poses significant challenges for the future in dealing with the very fast growth in the volume of data and in enhancing its reusability.
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Affiliation(s)
- Andrii Iudin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Paul K Korir
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Sriram Somasundharam
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Simone Weyand
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Cesare Cattavitello
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Neli Fonseca
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Osman Salih
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
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Loconte V, Chen J, Vanslembrouck B, Ekman AA, McDermott G, Le Gros MA, Larabell CA. Soft X-ray tomograms provide a structural basis for whole-cell modeling. FASEB J 2023; 37:e22681. [PMID: 36519968 PMCID: PMC10107707 DOI: 10.1096/fj.202200253r] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Developing in silico models that accurately reflect a whole, functional cell is an ongoing challenge in biology. Current efforts bring together mathematical models, probabilistic models, visual representations, and data to create a multi-scale description of cellular processes. A realistic whole-cell model requires imaging data since it provides spatial constraints and other critical cellular characteristics that are still impossible to obtain by calculation alone. This review introduces Soft X-ray Tomography (SXT) as a powerful imaging technique to visualize and quantify the mesoscopic (~25 nm spatial scale) organelle landscape in whole cells. SXT generates three-dimensional reconstructions of cellular ultrastructure and provides a measured structural framework for whole-cell modeling. Combining SXT with data from disparate technologies at varying spatial resolutions provides further biochemical details and constraints for modeling cellular mechanisms. We conclude, based on the results discussed here, that SXT provides a foundational dataset for a broad spectrum of whole-cell modeling experiments.
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Affiliation(s)
- Valentina Loconte
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Jian‐Hua Chen
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Bieke Vanslembrouck
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Axel A. Ekman
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Gerry McDermott
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Mark A. Le Gros
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Carolyn A. Larabell
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
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Schmidt M. Biological function investigated by time-resolved structure determination. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:010901. [PMID: 36846099 PMCID: PMC9946696 DOI: 10.1063/4.0000177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life. This is illustrated by examples where chemical and physical stimuli spawn biological responses on various length and time-scales, from fractions of Ångströms to micro-meters and from femtoseconds to hours.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, USA
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7
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van Belkum A, Almeida C, Bardiaux B, Barrass SV, Butcher SJ, Çaykara T, Chowdhury S, Datar R, Eastwood I, Goldman A, Goyal M, Happonen L, Izadi-Pruneyre N, Jacobsen T, Johnson PH, Kempf VAJ, Kiessling A, Bueno JL, Malik A, Malmström J, Meuskens I, Milner PA, Nilges M, Pamme N, Peyman SA, Rodrigues LR, Rodriguez-Mateos P, Sande MG, Silva CJ, Stasiak AC, Stehle T, Thibau A, Vaca DJ, Linke D. Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens. Diagnostics (Basel) 2021; 11:diagnostics11071259. [PMID: 34359341 PMCID: PMC8305138 DOI: 10.3390/diagnostics11071259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022] Open
Abstract
Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen–surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin–ligand interaction, supported by present high-throughput “omics” technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.
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Affiliation(s)
- Alex van Belkum
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
- Correspondence: (A.v.B.); (D.L.)
| | | | - Benjamin Bardiaux
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Sarah V. Barrass
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Sarah J. Butcher
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Tuğçe Çaykara
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Sounak Chowdhury
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Rucha Datar
- BioMérieux, Microbiology R&D, 38390 La Balme Les Grottes, France;
| | | | - Adrian Goldman
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Manisha Goyal
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Theis Jacobsen
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Pirjo H. Johnson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Volkhard A. J. Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Andreas Kiessling
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Juan Leva Bueno
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Anchal Malik
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Ina Meuskens
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
| | - Paul A. Milner
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Michael Nilges
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Nicole Pamme
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Sally A. Peyman
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Ligia R. Rodrigues
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Pablo Rodriguez-Mateos
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Maria G. Sande
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Carla Joana Silva
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Aleksandra Cecylia Stasiak
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Arno Thibau
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Diana J. Vaca
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
- Correspondence: (A.v.B.); (D.L.)
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Kepsutlu B, Wycisk V, Achazi K, Kapishnikov S, Pérez-Berná AJ, Guttmann P, Cossmer A, Pereiro E, Ewers H, Ballauff M, Schneider G, McNally JG. Cells Undergo Major Changes in the Quantity of Cytoplasmic Organelles after Uptake of Gold Nanoparticles with Biologically Relevant Surface Coatings. ACS NANO 2020; 14:2248-2264. [PMID: 31951375 DOI: 10.1021/acsnano.9b09264] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Here, we use cryo soft X-ray tomography (cryo-SXT), which delivers 3D ultrastructural volumes of intact cells without chemical fixation or staining, to gain insight about nanoparticle uptake for nanomedicine. We initially used dendritic polyglycerol sulfate (dPGS) with potential diagnostic and therapeutic applications in inflammation. Although dPGS-coated gold nanoparticle (dPGS-AuNP) uptake followed a conventional endocytic/degradative pathway in human lung epithelial cell lines (A549), with cryo-SXT, we detected ∼5% of dPGS-AuNPs in the cytoplasm, a level undetectable by confocal light microscopy. We also observed ∼5% of dPGS-AuNPs in a rarely identified subcellular site, namely, lipid droplets, which are important for cellular energy metabolism. Finally, we also found substantial changes in the quantity of cytoplasmic organelles upon dPGS-AuNP uptake over the 1-6 h incubation period; the number of small vesicles and mitochondria significantly increased, and the number of multivesicular bodies and the number and volume of lipid droplets significantly decreased. Although nearly all organelle numbers at 6 h were still significantly different from controls, most appeared to be returning to normal levels. To test for generality, we also examined cells after uptake of gold nanoparticles coated with a different agent, polyethylenimine (PEI), used for nucleic acid delivery. PEI nanoparticles did not enter lipid droplets, but they induced similar, albeit less pronounced, changes in the quantity of cytoplasmic organelles. We confirmed these changes in organelle quantities for both nanoparticle coatings by confocal fluorescence microscopy. We suggest this cytoplasmic remodeling could reflect a more common cellular response to coated gold nanoparticle uptake.
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Affiliation(s)
- Burcu Kepsutlu
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Virginia Wycisk
- Organische Chemie, Institut für Chemie und Biochemie , Freie Universität Berlin , Takustrasse 3 , D-14195 Berlin , Germany
| | - Katharina Achazi
- Organische Chemie, Institut für Chemie und Biochemie , Freie Universität Berlin , Takustrasse 3 , D-14195 Berlin , Germany
| | - Sergey Kapishnikov
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Ana Joaquina Pérez-Berná
- ALBA Synchrotron Light Source , MISTRAL Beamline Experiments Division , Cerdanyola del Vallès , 08290 Barcelona , Spain
| | - Peter Guttmann
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Antje Cossmer
- Division 1.1 - Inorganic Trace Analysis , Federal Institute for Materials Research and Testing (BAM) , Richard-Willstätter-Str. 11 , 12489 Berlin , Germany
| | - Eva Pereiro
- ALBA Synchrotron Light Source , MISTRAL Beamline Experiments Division , Cerdanyola del Vallès , 08290 Barcelona , Spain
| | - Helge Ewers
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Chemistry and Biochemisty, Department of Biology, Chemistry and Pharmacy , Freie Universität Berlin , Thielallee 63 , 14195 Berlin , Germany
| | - Matthias Ballauff
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Physics , Humboldt Universität zu Berlin , Newtonstraße 15 , 12489 Berlin , Germany
| | - Gerd Schneider
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Physics , Humboldt Universität zu Berlin , Newtonstraße 15 , 12489 Berlin , Germany
| | - James G McNally
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
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9
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Lawson CL, Berman HM, Chiu W. Evolving data standards for cryo-EM structures. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014701. [PMID: 32002441 PMCID: PMC6980868 DOI: 10.1063/1.5138589] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/07/2020] [Indexed: 05/04/2023]
Abstract
Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration have been twofold: to develop the necessary infrastructure for archiving cryo-EM-derived density maps and models, and to promote development of cryo-EM structure validation standards. We describe how cryo-EM data archiving and validation have been developed and jointly coordinated for the Electron Microscopy Data Bank and Protein Data Bank archives over the past two decades, as well as the impact of evolving technology on data standards. Just as for X-ray crystallography and nuclear magnetic resonance, engaging the scientific community via workshops and challenging activities has played a central role in developing recommendations and requirements for the cryo-EM structure data archives.
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Affiliation(s)
- Catherine L. Lawson
- Institute for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 2019; 27:1745-1759. [PMID: 31780431 DOI: 10.1016/j.str.2019.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/31/2019] [Accepted: 11/06/2019] [Indexed: 12/23/2022]
Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.
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Affiliation(s)
- Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA.
| | - Paul D Adams
- Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Alexandre A Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Wah Chiu
- Department of Bioengineering, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5447, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Margaret J Gabanyi
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Thomas D Goddard
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | | | - Juergen Haas
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Christian A Hanke
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Catherine L Lawson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - John L Markley
- BioMagResBank (BMRB), Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytech Institute, Troy, NY 12180, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3JR, Scotland
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Torsten Schwede
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | | | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Brinda Vallat
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK
| | - Geerten W Vuister
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Benjamin Webb
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kate L White
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrej Sali
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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Kingsley LJ, Brunet V, Lelais G, McCloskey S, Milliken K, Leija E, Fuhs SR, Wang K, Zhou E, Spraggon G. Development of a virtual reality platform for effective communication of structural data in drug discovery. J Mol Graph Model 2019; 89:234-241. [DOI: 10.1016/j.jmgm.2019.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 10/27/2022]
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Gan L, Ng CT, Chen C, Cai S. A collection of yeast cellular electron cryotomography data. Gigascience 2019; 8:giz077. [PMID: 31247098 PMCID: PMC6596884 DOI: 10.1093/gigascience/giz077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/09/2019] [Accepted: 06/10/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cells are powered by a large set of macromolecular complexes, which work together in a crowded environment. The in situ mechanisms of these complexes are unclear because their 3D distribution, organization, and interactions are largely unknown. Electron cryotomography (cryo-ET) can address these knowledge gaps because it produces cryotomograms-3D images that reveal biological structure at ∼4-nm resolution. Cryo-ET uses no fixation, dehydration, staining, or plastic embedment, so cellular features are visualized in a life-like, frozen-hydrated state. To study chromatin and mitotic machinery in situ, we subjected yeast cells to genetic and chemical perturbations, cryosectioned them, and then imaged the cells by cryo-ET. FINDINGS Here we share >1,000 cryo-ET raw datasets of cryosectioned budding yeast Saccharomyces cerevisiaecollected as part of previously published studies. These data will be valuable to cell biologists who are interested in the nanoscale organization of yeasts and of eukaryotic cells in general. All the unpublished tilt series and a subset of corresponding cryotomograms have been deposited in the EMPIAR resource for the community to use freely. To improve tilt series discoverability, we have uploaded metadata and preliminary notes to publicly accessible Google Sheets, EMPIAR, and GigaDB. CONCLUSIONS Cellular cryo-ET data can be mined to obtain new cell-biological, structural, and 3D statistical insights in situ. These data contain structures not visible in traditional electron-microscopy data. Template matching and subtomogram averaging of known macromolecular complexes can reveal their 3D distributions and low-resolution structures. Furthermore, these data can serve as testbeds for high-throughput image-analysis pipelines, as training sets for feature-recognition software, for feasibility analysis when planning new structural-cell-biology projects, and as practice data for students.
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Affiliation(s)
- Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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Leng J, Shoura M, McLeish TCB, Real AN, Hardey M, McCafferty J, Ranson NA, Harris SA. Securing the future of research computing in the biosciences. PLoS Comput Biol 2019; 15:e1006958. [PMID: 31095554 PMCID: PMC6521984 DOI: 10.1371/journal.pcbi.1006958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Improvements in technology often drive scientific discovery. Therefore, research requires sustained investment in the latest equipment and training for the researchers who are going to use it. Prioritising and administering infrastructure investment is challenging because future needs are difficult to predict. In the past, highly computationally demanding research was associated primarily with particle physics and astronomy experiments. However, as biology becomes more quantitative and bioscientists generate more and more data, their computational requirements may ultimately exceed those of physical scientists. Computation has always been central to bioinformatics, but now imaging experiments have rapidly growing data processing and storage requirements. There is also an urgent need for new modelling and simulation tools to provide insight and understanding of these biophysical experiments. Bioscience communities must work together to provide the software and skills training needed in their areas. Research-active institutions need to recognise that computation is now vital in many more areas of discovery and create an environment where it can be embraced. The public must also become aware of both the power and limitations of computing, particularly with respect to their health and personal data.
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Affiliation(s)
- Joanna Leng
- School of Computing, University of Leeds, Leeds, United Kingdom
| | - Massa Shoura
- School of Pathology, Stanford University, Palo Alto, California, United States of America
| | | | - Alan N. Real
- Advanced Research Computing, University of Durham, Durham, United Kingdom
| | - Mariann Hardey
- Advanced Research Computing, University of Durham, Durham, United Kingdom
- School of Business, University of Durham, Durham, United Kingdom
| | | | - Neil A. Ranson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sarah A. Harris
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
- * E-mail:
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Ortega DR, Oikonomou CM, Ding HJ, Rees-Lee P, Jensen GJ. ETDB-Caltech: A blockchain-based distributed public database for electron tomography. PLoS One 2019; 14:e0215531. [PMID: 30986271 PMCID: PMC6464211 DOI: 10.1371/journal.pone.0215531] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/03/2019] [Indexed: 01/12/2023] Open
Abstract
Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets.
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Affiliation(s)
- Davi R. Ortega
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Catherine M. Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - H. Jane Ding
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Prudence Rees-Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | | | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, Pasadena, California, United States of America
- * E-mail:
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15
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Smith D, Starborg T. Serial block face scanning electron microscopy in cell biology: Applications and technology. Tissue Cell 2019; 57:111-122. [DOI: 10.1016/j.tice.2018.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/22/2018] [Accepted: 08/26/2018] [Indexed: 10/28/2022]
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16
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Ekman A, Weinhardt V, Chen JH, McDermott G, Le Gros MA, Larabell C. PSF correction in soft X-ray tomography. J Struct Biol 2018; 204:9-18. [PMID: 29908247 DOI: 10.1016/j.jsb.2018.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 11/29/2022]
Abstract
In this article, we introduce a linear approximation of the forward model of soft X-ray tomography, such that the reconstruction is solvable by standard iterative schemes. This linear model takes into account the three-dimensional point spread function (PSF) of the optical system, which consequently enhances the reconstruction of data. The feasibility of the model is demonstrated on both simulated and experimental data, based on theoretically estimated and experimentally measured PSFs.
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Affiliation(s)
- Axel Ekman
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Venera Weinhardt
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Gerry McDermott
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Mark A Le Gros
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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17
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Kleywegt GJ, Velankar S, Patwardhan A. Structural biology data archiving - where we are and what lies ahead. FEBS Lett 2018; 592:2153-2167. [PMID: 29749603 PMCID: PMC6019198 DOI: 10.1002/1873-3468.13086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 12/31/2022]
Abstract
For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank, Electron Microscopy Data Bank and Biological Magnetic Resonance Data Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilized to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists.
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Affiliation(s)
- Gerard J. Kleywegt
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Sameer Velankar
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
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19
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Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. Building bridges between cellular and molecular structural biology. eLife 2017; 6:e25835. [PMID: 28682240 PMCID: PMC5524535 DOI: 10.7554/elife.25835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/30/2017] [Indexed: 11/13/2022] Open
Abstract
The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.
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Affiliation(s)
- Ardan Patwardhan
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Sarah J Butcher
- Institute of Biotechnology and the Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, United Kingdom
| | - David Gault
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Corey Hecksel
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrii Iudin
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Martin L Jones
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, United Kingdom
| | - Paul K Korir
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Abraham J Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingvar Lagerstedt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Catherine L Lawson
- Center for Integrative Proteomics Research and the Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Piscataway, United States
| | - David Mastronarde
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, United States
| | | | - Helen Parkinson
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses, Francis Crick Institute, London, United Kingdom
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Helen R Saibil
- Institute of Structural and Molecular Biology, Department of Crystallography, Birkbeck College, London, United Kingdom
| | - Sirarat Sarntivijai
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Irene Solanes Valero
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Sriram Subramaniam
- Laboratory for Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression and the Division of Computational Biology, University of Dundee, Dundee, United Kingdom
| | - Ilinca Tudose
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Martyn Winn
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
| | - Gerard J Kleywegt
- Molecular and Cellular Structure Cluster, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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Patwardhan A. Trends in the Electron Microscopy Data Bank (EMDB). ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:503-508. [PMID: 28580912 PMCID: PMC5458492 DOI: 10.1107/s2059798317004181] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/14/2017] [Indexed: 12/11/2022]
Abstract
The Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions, is an invaluable resource for obtaining a birds-eye view of trends affecting the field of cryo-EM. EMDB is growing rapidly, with almost a quarter of the entries having been released over the past year. Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%. The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from FEI have an overwhelming lead in terms of usage, and the use of the RELION software package continues to grow rapidly after having attained a leading position in the field. China is rapidly emerging as a major player in the field, supplementing the US, Germany and the UK as the big four. Similarly, Tsinghua University ranks only second to the MRC Laboratory for Molecular Biology in terms of involvement in publications associated with cryo-EM structures at better than 4 Å resolution. Overall, the numbers point to a rapid democratization of the field, with more countries and institutes becoming involved.
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Affiliation(s)
- Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, England
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21
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Multi-color electron microscopy by element-guided identification of cells, organelles and molecules. Sci Rep 2017; 7:45970. [PMID: 28387351 PMCID: PMC5384080 DOI: 10.1038/srep45970] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/07/2017] [Indexed: 12/31/2022] Open
Abstract
Cellular complexity is unraveled at nanometer resolution using electron microscopy (EM), but interpretation of macromolecular functionality is hampered by the difficulty in interpreting grey-scale images and the unidentified molecular content. We perform large-scale EM on mammalian tissue complemented with energy-dispersive X-ray analysis (EDX) to allow EM-data analysis based on elemental composition. Endogenous elements, labels (gold and cadmium-based nanoparticles) as well as stains are analyzed at ultrastructural resolution. This provides a wide palette of colors to paint the traditional grey-scale EM images for composition-based interpretation. Our proof-of-principle application of EM-EDX reveals that endocrine and exocrine vesicles exist in single cells in Islets of Langerhans. This highlights how elemental mapping reveals unbiased biomedical relevant information. Broad application of EM-EDX will further allow experimental analysis on large-scale tissue using endogenous elements, multiple stains, and multiple markers and thus brings nanometer-scale 'color-EM' as a promising tool to unravel molecular (de)regulation in biomedicine.
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Wang S, Li L, Tao R, Gao Y. Ion channelopathies associated genetic variants as the culprit for sudden unexplained death. Forensic Sci Int 2017; 275:128-137. [PMID: 28363160 DOI: 10.1016/j.forsciint.2017.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/23/2017] [Accepted: 03/13/2017] [Indexed: 11/29/2022]
Abstract
Forensic identification of sudden unexplained death (SUD) has always been a ticklish issue because it used to be defined as sudden death without a conclusive diagnosis after autopsy. However, benefiting from the developments in genome research, a growing body of evidence points to the importance of ion channelopathies associated genetic variants in the pathogenesis of SUD. Genetic diagnosis of the deceased is also a new trend in epidemiological studies, for it enables the undertaking for preventive approach in individuals with high risks. In this review, we briefly discuss the molecular structure of ion channels and the role of genetic variants in regulating their functions as well as the diverse mechanisms underlying the ion channelopathies at gene level.
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Affiliation(s)
- Shouyu Wang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou 215123, Jiangsu, China
| | - Lijuan Li
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou 215123, Jiangsu, China
| | - Ruiyang Tao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou 215123, Jiangsu, China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou 215123, Jiangsu, China.
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Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION. Nat Protoc 2016; 11:2054-65. [PMID: 27685097 DOI: 10.1038/nprot.2016.124] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Electron cryo-tomography (cryo-ET) is a technique that is used to produce 3D pictures (tomograms) of complex objects such as asymmetric viruses, cellular organelles or whole cells from a series of tilted electron cryo-microscopy (cryo-EM) images. Averaging of macromolecular complexes found within tomograms is known as subtomogram averaging, and this technique allows structure determination of macromolecular complexes in situ. Subtomogram averaging is also gaining in popularity for the calculation of initial models for single-particle analysis. We describe herein a protocol for subtomogram averaging from cryo-ET data using the RELION software (http://www2.mrc-lmb.cam.ac.uk/relion). RELION was originally developed for cryo-EM single-particle analysis, and the subtomogram averaging approach presented in this protocol has been implemented in the existing workflow for single-particle analysis so that users may conveniently tap into existing capabilities of the RELION software. We describe how to calculate 3D models for the contrast transfer function (CTF) that describe the transfer of information in the imaging process, and we illustrate the results of classification and subtomogram averaging refinement for cryo-ET data of purified hepatitis B capsid particles and Saccharomyces cerevisiae 80S ribosomes. Using the steps described in this protocol, along with the troubleshooting and optimization guidelines, high-resolution maps can be obtained in which secondary structure elements are resolved subtomogram.
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Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope. Sci Rep 2016; 6:33354. [PMID: 27646194 PMCID: PMC5028842 DOI: 10.1038/srep33354] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 08/22/2016] [Indexed: 01/06/2023] Open
Abstract
The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections.
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Darrow MC, Zhang Y, Cinquin BP, Smith EA, Boudreau R, Rochat RH, Schmid MF, Xia Y, Larabell CA, Chiu W. Visualizing red blood cell sickling and the effects of inhibition of sphingosine kinase 1 using soft X-ray tomography. J Cell Sci 2016; 129:3511-7. [PMID: 27505892 DOI: 10.1242/jcs.189225] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/01/2016] [Indexed: 01/17/2023] Open
Abstract
Sickle cell disease is a destructive genetic disorder characterized by the formation of fibrils of deoxygenated hemoglobin, leading to the red blood cell (RBC) morphology changes that underlie the clinical manifestations of this disease. Using cryogenic soft X-ray tomography (SXT), we characterized the morphology of sickled RBCs in terms of volume and the number of protrusions per cell. We were able to identify statistically a relationship between the number of protrusions and the volume of the cell, which is known to correlate to the severity of sickling. This structural polymorphism allows for the classification of the stages of the sickling process. Recent studies have shown that elevated sphingosine kinase 1 (Sphk1)-mediated sphingosine 1-phosphate production contributes to sickling. Here, we further demonstrate that compound 5C, an inhibitor of Sphk1, has anti-sickling properties. Additionally, the variation in cellular morphology upon treatment suggests that this drug acts to delay the sickling process. SXT is an effective tool that can be used to identify the morphology of the sickling process and assess the effectiveness of potential therapeutics.
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Affiliation(s)
- Michele C Darrow
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yujin Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Bertrand P Cinquin
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elizabeth A Smith
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rosanne Boudreau
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryan H Rochat
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Xia
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA University of Texas at Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA Department of Nephrology, The First Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Carolyn A Larabell
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Abstract
CryoEM in structural biology is currently served by three public archives-EMDB for 3DEM reconstructions, PDB for models built from 3DEM reconstructions, and EMPIAR for the raw 2D image data used to obtain the 3DEM reconstructions. These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed, and integrated with other structural and bioinformatics resources. The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication. The field is currently undergoing transformative changes where on the one hand high-resolution structures are becoming a routine occurrence while on the other hand electron tomography is enabling the study of macromolecules in the cellular context. Concomitantly the archives are evolving to best serve their stakeholder communities. In this chapter, we describe the current state of the archives, resources available for depositing, accessing, searching, visualizing and validating data, on-going community-wide initiatives and opportunities, and challenges for the future.
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Affiliation(s)
- A Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.
| | - C L Lawson
- Research Collaboratory for Structural Bioinformatics, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, United States.
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Application of advanced X-ray methods in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3671-3685. [PMID: 27156488 DOI: 10.1016/j.bbagen.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules. SCOPE OF REVIEW Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples. MAJOR CONCLUSIONS SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures. GENERAL SIGNIFICANCE X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A. Web-based volume slicer for 3D electron-microscopy data from EMDB. J Struct Biol 2016; 194:164-70. [PMID: 26876163 PMCID: PMC4819904 DOI: 10.1016/j.jsb.2016.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 12/05/2022]
Abstract
We describe the functionality and design of the Volume slicer – a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale.
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Affiliation(s)
- José Salavert-Torres
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom; Present address: Universitat Politècnica de València, DISCA, Edificio 1G - Lab 3S-15, Camino de Vera S/N, 46022 València, Spain.
| | - Andrii Iudin
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
| | - Eduardo Sanz-García
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
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30
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Carroni M, Saibil HR. Cryo electron microscopy to determine the structure of macromolecular complexes. Methods 2015; 95:78-85. [PMID: 26638773 PMCID: PMC5405050 DOI: 10.1016/j.ymeth.2015.11.023] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/14/2015] [Accepted: 11/26/2015] [Indexed: 01/28/2023] Open
Abstract
Structural biology. Cryo electron microscopy. Macromolecular complexes. Single particle analysis.
Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field.
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Affiliation(s)
- Marta Carroni
- ISMB, Birkbeck College, Malet St, London WC1E 7HX, UK
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31
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Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W. EMDataBank unified data resource for 3DEM. Nucleic Acids Res 2015; 44:D396-403. [PMID: 26578576 PMCID: PMC4702818 DOI: 10.1093/nar/gkv1126] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/10/2023] Open
Abstract
Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata (emdatabank.org). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.
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Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Corey Hryc
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Eduardo Sanz Garcia
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian P Hudson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Grigore Pintilie
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Raul Sala
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - John D Westbrook
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
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Do M, Isaacson SA, McDermott G, Le Gros MA, Larabell CA. Imaging and characterizing cells using tomography. Arch Biochem Biophys 2015; 581:111-21. [PMID: 25602704 PMCID: PMC4506273 DOI: 10.1016/j.abb.2015.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/29/2014] [Accepted: 01/11/2015] [Indexed: 12/11/2022]
Abstract
We can learn much about cell function by imaging and quantifying sub-cellular structures, especially if this is done non-destructively without altering said structures. Soft X-ray tomography (SXT) is a high-resolution imaging technique for visualizing cells and their interior structure in 3D. A tomogram of the cell, reconstructed from a series of 2D projection images, can be easily segmented and analyzed. SXT has a very high specimen throughput compared to other high-resolution structure imaging modalities; for example, tomographic data for reconstructing an entire eukaryotic cell is acquired in a matter of minutes. SXT visualizes cells without the need for chemical fixation, dehydration, or staining of the specimen. As a result, the SXT reconstructions are close representations of cells in their native state. SXT is applicable to most cell types. The deep penetration of soft X-rays allows cells, even mammalian cells, to be imaged without being sectioned. Image contrast in SXT is generated by the differential attenuation soft X-ray illumination as it passes through the specimen. Accordingly, each voxel in the tomographic reconstruction has a measured linear absorption coefficient (LAC) value. LAC values are quantitative and give rise to each sub-cellular component having a characteristic LAC profile, allowing organelles to be identified and segmented from the milieu of other cell contents. In this chapter, we describe the fundamentals of SXT imaging and how this technique can answer real world questions in the study of the nucleus. We also describe the development of correlative methods for the localization of specific molecules in a SXT reconstruction. The combination of fluorescence and SXT data acquired from the same specimen produces composite 3D images, rich with detailed information on the inner workings of cells.
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Affiliation(s)
- Myan Do
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Samuel A Isaacson
- Department of Mathematics and Statistics, Boston University, Boston, MA 02215, United States
| | - Gerry McDermott
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Mark A Le Gros
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Carolyn A Larabell
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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Abriel H, Rougier JS, Jalife J. Ion channel macromolecular complexes in cardiomyocytes: roles in sudden cardiac death. Circ Res 2015; 116:1971-88. [PMID: 26044251 DOI: 10.1161/circresaha.116.305017] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The movement of ions across specific channels embedded on the membrane of individual cardiomyocytes is crucial for the generation and propagation of the cardiac electric impulse. Emerging evidence over the past 20 years strongly suggests that the normal electric function of the heart is the result of dynamic interactions of membrane ion channels working in an orchestrated fashion as part of complex molecular networks. Such networks work together with exquisite temporal precision to generate each action potential and contraction. Macromolecular complexes play crucial roles in transcription, translation, oligomerization, trafficking, membrane retention, glycosylation, post-translational modification, turnover, function, and degradation of all cardiac ion channels known to date. In addition, the accurate timing of each cardiac beat and contraction demands, a comparable precision on the assembly and organizations of sodium, calcium, and potassium channel complexes within specific subcellular microdomains, where physical proximity allows for prompt and efficient interaction. This review article, part of the Compendium on Sudden Cardiac Death, discusses the major issues related to the role of ion channel macromolecular assemblies in normal cardiac electric function and the mechanisms of arrhythmias leading to sudden cardiac death. It provides an idea of how these issues are being addressed in the laboratory and in the clinic, which important questions remain unanswered, and what future research will be needed to improve knowledge and advance therapy.
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Affiliation(s)
- Hugues Abriel
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (H.A., J.-S.R.); Center for Arrhythmia Research, Department of Internal Medicine, University of Michigan, Ann Arbor (J.J.); and Area of Myocardial Pathophysiology, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.J.)
| | - Jean-Sébastien Rougier
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (H.A., J.-S.R.); Center for Arrhythmia Research, Department of Internal Medicine, University of Michigan, Ann Arbor (J.J.); and Area of Myocardial Pathophysiology, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.J.)
| | - José Jalife
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (H.A., J.-S.R.); Center for Arrhythmia Research, Department of Internal Medicine, University of Michigan, Ann Arbor (J.J.); and Area of Myocardial Pathophysiology, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain (J.J.).
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34
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de Boer P, Hoogenboom JP, Giepmans BNG. Correlated light and electron microscopy: ultrastructure lights up! Nat Methods 2015; 12:503-13. [PMID: 26020503 DOI: 10.1038/nmeth.3400] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/15/2015] [Indexed: 12/15/2022]
Abstract
Microscopy has gone hand in hand with the study of living systems since van Leeuwenhoek observed living microorganisms and cells in 1674 using his light microscope. A spectrum of dyes and probes now enable the localization of molecules of interest within living cells by fluorescence microscopy. With electron microscopy (EM), cellular ultrastructure has been revealed. Bridging these two modalities, correlated light microscopy and EM (CLEM) opens new avenues. Studies of protein dynamics with fluorescent proteins (FPs), which leave the investigator 'in the dark' concerning cellular context, can be followed by EM examination. Rare events can be preselected at the light microscopy level before EM analysis. Ongoing development-including of dedicated probes, integrated microscopes, large-scale and three-dimensional EM and super-resolution fluorescence microscopy-now paves the way for broad CLEM implementation in biology.
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Affiliation(s)
- Pascal de Boer
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jacob P Hoogenboom
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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35
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Hanein D. Further closing the resolution gap: integrating cryo-soft x-ray and light microscopies. Biophys J 2014; 107:2745-2746. [PMID: 25517139 DOI: 10.1016/j.bpj.2014.10.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 10/28/2014] [Indexed: 10/24/2022] Open
Affiliation(s)
- Dorit Hanein
- Bioinformatics and Structural Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, California.
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