151
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Sachse C. Single-particle based helical reconstruction—how to make the most of real and Fourier space. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.2.219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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152
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Wagenknecht T, Hsieh C, Marko M. Skeletal muscle triad junction ultrastructure by Focused-Ion-Beam milling of muscle and Cryo-Electron Tomography. Eur J Transl Myol 2015; 25:4823. [PMID: 26052414 PMCID: PMC4748973 DOI: 10.4081/ejtm.2015.4823] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/09/2015] [Accepted: 01/15/2015] [Indexed: 11/23/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) has emerged as perhaps the only practical technique for revealing nanometer-level three-dimensional structural details of subcellular macromolecular complexes in their native context, inside the cell. As currently practiced, the specimen should be 0.1- 0.2 microns in thickness to achieve optimal resolution. Thus, application of cryo-ET to intact frozen (vitreous) tissues, such as skeletal muscle, requires that they be sectioned. Cryo-ultramicrotomy is notoriously difficult and artifact-prone when applied to frozen cells and tissue, but a new technique, focused ion beam milling (cryo-FIB), shows great promise for "thinning" frozen biological specimens. Here we describe our initial results in applying cryo-FIB and cryo-ET to triad junctions of skeletal muscle.
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Affiliation(s)
- Terence Wagenknecht
- New York State Department of Health, Wadsworth Cente, Empire State Plaza, Albany, NY, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Chyongere Hsieh
- New York State Department of Health, Wadsworth Cente, Empire State Plaza, Albany, NY, USA
| | - Michael Marko
- New York State Department of Health, Wadsworth Cente, Empire State Plaza, Albany, NY, USA
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153
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The amphipathic helix of adenovirus capsid protein VI contributes to penton release and postentry sorting. J Virol 2014; 89:2121-35. [PMID: 25473051 DOI: 10.1128/jvi.02257-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Nuclear delivery of the adenoviral genome requires that the capsid cross the limiting membrane of the endocytic compartment and traverse the cytosol to reach the nucleus. This endosomal escape is initiated upon internalization and involves a highly coordinated process of partial disassembly of the entering capsid to release the membrane lytic internal capsid protein VI. Using wild-type and protein VI-mutated human adenovirus serotype 5 (HAdV-C5), we show that capsid stability and membrane rupture are major determinants of entry-related sorting of incoming adenovirus virions. Furthermore, by using electron cryomicroscopy, as well as penton- and protein VI-specific antibodies, we show that the amphipathic helix of protein VI contributes to capsid stability by preventing premature disassembly and deployment of pentons and protein VI. Thus, the helix has a dual function in maintaining the metastable state of the capsid by preventing premature disassembly and mediating efficient membrane lysis to evade lysosomal targeting. Based on these findings and structural data from cryo-electron microscopy, we suggest a refined disassembly mechanism upon entry. IMPORTANCE In this study, we show the intricate connection of adenovirus particle stability and the entry-dependent release of the membrane-lytic capsid protein VI required for endosomal escape. We show that the amphipathic helix of the adenovirus internal protein VI is required to stabilize pentons in the particle while coinciding with penton release upon entry and that release of protein VI mediates membrane lysis, thereby preventing lysosomal sorting. We suggest that this dual functionality of protein VI ensures an optimal disassembly process by balancing the metastable state of the mature adenovirus particle.
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154
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Schur FKM, Hagen WJH, Rumlová M, Ruml T, Müller B, Kräusslich HG, Briggs JAG. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature 2014; 517:505-8. [PMID: 25363765 DOI: 10.1038/nature13838] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 09/03/2014] [Indexed: 12/16/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments.
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Affiliation(s)
- Florian K M Schur
- 1] Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany [2] Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Michaela Rumlová
- 1] Institute of Organic Chemistry and Biochemistry (IOCB), Academy of Sciences of the Czech Republic, v.v.i., IOCB &Gilead Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic [2] Department of Biotechnology, Institute of Chemical Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Barbara Müller
- 1] Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany [2] Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- 1] Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany [2] Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - John A G Briggs
- 1] Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany [2] Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany
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155
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Zeev-Ben-Mordehai T, Vasishtan D, Siebert CA, Whittle C, Grünewald K. Extracellular vesicles: a platform for the structure determination of membrane proteins by Cryo-EM. Structure 2014; 22:1687-92. [PMID: 25438672 PMCID: PMC4229021 DOI: 10.1016/j.str.2014.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/09/2014] [Accepted: 09/12/2014] [Indexed: 01/13/2023]
Abstract
Membrane protein-enriched extracellular vesicles (MPEEVs) provide a platform for studying intact membrane proteins natively anchored with the correct topology in genuine biological membranes. This approach circumvents the need to conduct tedious detergent screens for solubilization, purification, and reconstitution required in classical membrane protein studies. We have applied this method to three integral type I membrane proteins, namely the Caenorhabditis elegans cell-cell fusion proteins AFF-1 and EFF-1 and the glycoprotein B (gB) from Herpes simplex virus type 1 (HSV1). Electron cryotomography followed by subvolume averaging allowed the 3D reconstruction of EFF-1 and HSV1 gB in the membrane as well as an analysis of the spatial distribution and interprotein interactions on the membrane. MPEEVs have many applications beyond structural/functional investigations, such as facilitating the raising of antibodies, for protein-protein interaction assays or for diagnostics use, as biomarkers, and possibly therapeutics. Intact membrane proteins with correct topology in genuine biological membranes Display system circumvents need for detergent solubilization and reconstitution 3D reconstruction of proteins in the membrane by subvolume averaging Mapping spatial distribution and relationships between proteins on the membrane
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Affiliation(s)
- Tzviya Zeev-Ben-Mordehai
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Daven Vasishtan
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - C Alistair Siebert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Cathy Whittle
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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156
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Huiskonen JT, Parsy ML, Li S, Bitto D, Renner M, Bowden TA. Averaging of viral envelope glycoprotein spikes from electron cryotomography reconstructions using Jsubtomo. J Vis Exp 2014:e51714. [PMID: 25350719 PMCID: PMC4353292 DOI: 10.3791/51714] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enveloped viruses utilize membrane glycoproteins on their surface to mediate entry into host cells. Three-dimensional structural analysis of these glycoprotein ‘spikes’ is often technically challenging but important for understanding viral pathogenesis and in drug design. Here, a protocol is presented for viral spike structure determination through computational averaging of electron cryo-tomography data. Electron cryo-tomography is a technique in electron microscopy used to derive three-dimensional tomographic volume reconstructions, or tomograms, of pleomorphic biological specimens such as membrane viruses in a near-native, frozen-hydrated state. These tomograms reveal structures of interest in three dimensions, albeit at low resolution. Computational averaging of sub-volumes, or sub-tomograms, is necessary to obtain higher resolution detail of repeating structural motifs, such as viral glycoprotein spikes. A detailed computational approach for aligning and averaging sub-tomograms using the Jsubtomo software package is outlined. This approach enables visualization of the structure of viral glycoprotein spikes to a resolution in the range of 20-40 Å and study of the study of higher order spike-to-spike interactions on the virion membrane. Typical results are presented for Bunyamwera virus, an enveloped virus from the family Bunyaviridae. This family is a structurally diverse group of pathogens posing a threat to human and animal health.
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Affiliation(s)
- Juha T Huiskonen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford;
| | - Marie-Laure Parsy
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Sai Li
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| | - David Bitto
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Max Renner
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Thomas A Bowden
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford
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157
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Chen Y, Pfeffer S, Fernández J, Sorzano C, Förster F. Autofocused 3D Classification of Cryoelectron Subtomograms. Structure 2014; 22:1528-37. [DOI: 10.1016/j.str.2014.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/03/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
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158
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Structural differences observed in arboviruses of the alphavirus and flavivirus genera. Adv Virol 2014; 2014:259382. [PMID: 25309597 PMCID: PMC4182009 DOI: 10.1155/2014/259382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/28/2014] [Accepted: 08/18/2014] [Indexed: 12/22/2022] Open
Abstract
Arthropod borne viruses have developed a complex life cycle adapted to alternate between insect and vertebrate hosts. These arthropod-borne viruses belong mainly to the families Togaviridae, Flaviviridae, and Bunyaviridae. This group of viruses contains many pathogens that cause febrile, hemorrhagic, and encephalitic disease or arthritic symptoms which can be persistent. It has been appreciated for many years that these viruses were evolutionarily adapted to function in the highly divergent cellular environments of both insect and mammalian phyla. These viruses are hybrid in nature, containing viral-encoded RNA and proteins which are glycosylated by the host and encapsulate viral nucleocapsids in the context of a host-derived membrane. From a structural perspective, these virus particles are macromolecular machines adapted in design to assemble into a packaging and delivery system for the virus genome and, only when associated with the conditions appropriate for a productive infection, to disassemble and deliver the RNA cargo. It was initially assumed that the structures of the virus from both hosts were equivalent. New evidence that alphaviruses and flaviviruses can exist in more than one conformation postenvelopment will be discussed in this review. The data are limited but should refocus the field of structural biology on the metastable nature of these viruses.
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159
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Davies KM, Daum B, Gold VAM, Mühleip AW, Brandt T, Blum TB, Mills DJ, Kühlbrandt W. Visualization of ATP synthase dimers in mitochondria by electron cryo-tomography. J Vis Exp 2014:51228. [PMID: 25285856 PMCID: PMC4828066 DOI: 10.3791/51228] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Electron cryo-tomography is a powerful tool in structural biology, capable of visualizing the three-dimensional structure of biological samples, such as cells, organelles, membrane vesicles, or viruses at molecular detail. To achieve this, the aqueous sample is rapidly vitrified in liquid ethane, which preserves it in a close-to-native, frozen-hydrated state. In the electron microscope, tilt series are recorded at liquid nitrogen temperature, from which 3D tomograms are reconstructed. The signal-to-noise ratio of the tomographic volume is inherently low. Recognizable, recurring features are enhanced by subtomogram averaging, by which individual subvolumes are cut out, aligned and averaged to reduce noise. In this way, 3D maps with a resolution of 2 nm or better can be obtained. A fit of available high-resolution structures to the 3D volume then produces atomic models of protein complexes in their native environment. Here we show how we use electron cryo-tomography to study the in situ organization of large membrane protein complexes in mitochondria. We find that ATP synthases are organized in rows of dimers along highly curved apices of the inner membrane cristae, whereas complex I is randomly distributed in the membrane regions on either side of the rows. By subtomogram averaging we obtained a structure of the mitochondrial ATP synthase dimer within the cristae membrane.
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Affiliation(s)
- Karen M Davies
- Department of Structural Biology, Max Planck Institute of Biophysics
| | - Bertram Daum
- Department of Structural Biology, Max Planck Institute of Biophysics
| | - Vicki A M Gold
- Department of Structural Biology, Max Planck Institute of Biophysics
| | | | - Tobias Brandt
- Department of Structural Biology, Max Planck Institute of Biophysics
| | - Thorsten B Blum
- Department of Structural Biology, Max Planck Institute of Biophysics
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics;
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160
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Durrant JD, Amaro RE. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput Biol 2014; 10:e1003720. [PMID: 25032790 PMCID: PMC4102414 DOI: 10.1371/journal.pcbi.1003720] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/21/2014] [Indexed: 11/19/2022] Open
Abstract
As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. In order to build accurate large-scale models of subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature will be essential. In the current work, we present a multi-scale utility called LipidWrapper capable of creating curved membrane models with geometries derived from various sources, both experimental and theoretical. To demonstrate its utility, we use LipidWrapper to examine an important mechanism of influenza virulence. A copy of the program can be downloaded free of charge under the terms of the open-source FreeBSD License from http://nbcr.ucsd.edu/lipidwrapper. LipidWrapper has been tested on all major computer operating systems.
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Affiliation(s)
- Jacob D. Durrant
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Rommie E. Amaro
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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161
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Risco C, de Castro IF, Sanz-Sánchez L, Narayan K, Grandinetti G, Subramaniam S. Three-Dimensional Imaging of Viral Infections. Annu Rev Virol 2014; 1:453-73. [PMID: 26958730 DOI: 10.1146/annurev-virology-031413-085351] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Three-dimensional (3D) imaging technologies are beginning to have significant impact in the field of virology, as they are helping us understand how viruses take control of cells. In this article we review several methodologies for 3D imaging of cells and show how these technologies are contributing to the study of viral infections and the characterization of specialized structures formed in virus-infected cells. We include 3D reconstruction by transmission electron microscopy (TEM) using serial sections, electron tomography, and focused ion beam scanning electron microscopy (FIB-SEM). We summarize from these methods selected contributions to our understanding of viral entry, replication, morphogenesis, egress and propagation, and changes in the spatial architecture of virus-infected cells. In combination with live-cell imaging, correlative microscopy, and new techniques for molecular mapping in situ, the availability of these methods for 3D imaging is expected to provide deeper insights into understanding the structural and dynamic aspects of viral infection.
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Affiliation(s)
- Cristina Risco
- Cell Structure Laboratory, National Center for Biotechnology (CNB-CSIC), Madrid 28049, Spain;
| | | | - Laura Sanz-Sánchez
- Cell Structure Laboratory, National Center for Biotechnology (CNB-CSIC), Madrid 28049, Spain;
| | - Kedar Narayan
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892;
| | - Giovanna Grandinetti
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892;
| | - Sriram Subramaniam
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892;
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162
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Abstract
![]()
The flagellum is one of the most
sophisticated self-assembling
molecular machines in bacteria. Powered by the proton-motive force,
the flagellum rapidly rotates in either a clockwise or counterclockwise
direction, which ultimately controls bacterial motility and behavior. Escherichia coli and Salmonella enterica have served as important model systems for extensive genetic, biochemical,
and structural analysis of the flagellum, providing unparalleled insights
into its structure, function, and gene regulation. Despite these advances,
our understanding of flagellar assembly and rotational mechanisms
remains incomplete, in part because of the limited structural information
available regarding the intact rotor–stator complex and secretion
apparatus. Cryo-electron tomography (cryo-ET) has become a valuable
imaging technique capable of visualizing the intact flagellar motor
in cells at molecular resolution. Because the resolution that can
be achieved by cryo-ET with large bacteria (such as E. coli and S. enterica) is limited, analysis of small-diameter
bacteria (including Borrelia burgdorferi and Campylobacter jejuni) can provide additional insights into
the in situ structure of the flagellar motor and
other cellular components. This review is focused on the application
of cryo-ET, in combination with genetic and biophysical approaches,
to the study of flagellar structures and its potential for improving
the understanding of rotor–stator interactions, the rotational
switching mechanism, and the secretion and assembly of flagellar components.
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Affiliation(s)
- Xiaowei Zhao
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston , Houston, Texas 77030, United States
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163
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Zeev-Ben-Mordehai T, Vasishtan D, Siebert CA, Grünewald K. The full-length cell-cell fusogen EFF-1 is monomeric and upright on the membrane. Nat Commun 2014; 5:3912. [PMID: 24867324 PMCID: PMC4050280 DOI: 10.1038/ncomms4912] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/17/2014] [Indexed: 01/04/2023] Open
Abstract
Fusogens are membrane proteins that remodel lipid bilayers to facilitate membrane merging. Although several fusogen ectodomain structures have been solved, structural information on full-length, natively membrane-anchored fusogens is scarce. Here we present the electron cryo microscopy three-dimensional reconstruction of the Caenorhabditis elegans epithelial fusion failure 1 (EFF-1) protein natively anchored in cell-derived membrane vesicles. This reveals a membrane protruding, asymmetric, elongated monomer. Flexible fitting of a protomer of the EFF-1 crystal structure, which is homologous to viral class-II fusion proteins, shows that EFF-1 has a hairpin monomeric conformation before fusion. These structural insights, when combined with our observations of membrane-merging intermediates between vesicles, enable us to propose a model for EFF-1 mediated fusion. This process, involving identical proteins on both membranes to be fused, follows a mechanism that shares features of SNARE-mediated fusion while using the structural building blocks of the unilaterally acting class-II viral fusion proteins. Cell–cell fusion in Caenorhabditis elegans is mediated by EFF-1 and AFF-1 proteins. Here, the authors present an electron cryomicroscopy 3D reconstruction of EFF-1 in the membrane, and combine snapshots of membrane fusion in vitro with a recently reported crystal structure to propose a mechanism for the fusion process.
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Affiliation(s)
- Tzviya Zeev-Ben-Mordehai
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Daven Vasishtan
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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164
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Yu Z, Frangakis AS. M-free: scoring the reference bias in sub-tomogram averaging and template matching. J Struct Biol 2014; 187:10-19. [PMID: 24859794 DOI: 10.1016/j.jsb.2014.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/23/2014] [Accepted: 05/15/2014] [Indexed: 11/27/2022]
Abstract
Cryo-electron tomography provides a snapshot of the cellular proteome. With template matching, the spatial positions of various macromolecular complexes within their native cellular context can be detected. However, the growing awareness of the reference bias introduced by the cross-correlation based approaches, and more importantly the lack of a reliable confidence measurement in the selection of these macromolecular complexes, has restricted the use of these applications. Here we propose a heuristic, in which the reference bias is measured in real space in an analogous way to the R-free value in X-ray crystallography. We measure the reference bias within the mask used to outline the area of the template, and do not modify the template itself. The heuristic works by splitting the mask into a working and a testing area in a volume ratio of 9:1. While the working area is used during the calculation of the cross-correlation function, the information from both areas is explored to calculate the M-free score. We show using artificial data, that the M-free score gives a reliable measure for the reference bias. The heuristic can be applied in template matching and in sub-tomogram averaging. We further test the applicability of the heuristic in tomograms of purified macromolecules, and tomograms of whole Mycoplasma cells.
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Affiliation(s)
- Zhou Yu
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str.15, 60438 Frankfurt am Main, Germany
| | - Achilleas S Frangakis
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str.15, 60438 Frankfurt am Main, Germany.
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165
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Schwede T. Protein modeling: what happened to the "protein structure gap"? Structure 2014; 21:1531-40. [PMID: 24010712 DOI: 10.1016/j.str.2013.08.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 11/27/2022]
Abstract
Computational modeling of three-dimensional macromolecular structures and complexes from their sequence has been a long-standing vision in structural biology. Over the last 2 decades, a paradigm shift has occurred: starting from a large "structure knowledge gap" between the huge number of protein sequences and small number of known structures, today, some form of structural information, either experimental or template-based models, is available for the majority of amino acids encoded by common model organism genomes. With the scientific focus of interest moving toward larger macromolecular complexes and dynamic networks of interactions, the integration of computational modeling methods with low-resolution experimental techniques allows the study of large and complex molecular machines. One of the open challenges for computational modeling and prediction techniques is to convey the underlying assumptions, as well as the expected accuracy and structural variability of a specific model, which is crucial to understanding its limitations.
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Affiliation(s)
- Torsten Schwede
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
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166
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Thalassinos K, Pandurangan AP, Xu M, Alber F, Topf M. Conformational States of macromolecular assemblies explored by integrative structure calculation. Structure 2014; 21:1500-8. [PMID: 24010709 PMCID: PMC3988990 DOI: 10.1016/j.str.2013.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 08/10/2013] [Accepted: 08/12/2013] [Indexed: 12/22/2022]
Abstract
A detailed description of macromolecular assemblies in multiple conformational states can be very valuable for understanding cellular processes. At present, structural determination of most assemblies in different biologically relevant conformations cannot be achieved by a single technique and thus requires an integrative approach that combines information from multiple sources. Different techniques require different computational methods to allow efficient and accurate data processing and analysis. Here, we summarize the latest advances and future challenges in computational methods that help the interpretation of data from two techniques—mass spectrometry and three-dimensional cryo-electron microscopy (with focus on alignment and classification of heterogeneous subtomograms from cryo-electron tomography). We evaluate how new developments in these two broad fields will lead to further integration with atomic structures to broaden our picture of the dynamic behavior of assemblies in their native environment.
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Affiliation(s)
- Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
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167
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Harapin J, Eibauer M, Medalia O. Structural analysis of supramolecular assemblies by cryo-electron tomography. Structure 2014; 21:1522-30. [PMID: 24010711 DOI: 10.1016/j.str.2013.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/29/2022]
Abstract
Structural analysis of macromolecular assemblies in their physiological environment is a challenging task that is instrumental in answering fundamental questions in cellular and molecular structural biology. The continuous development of computational and analytical tools for cryo-electron tomography (cryo-ET) enables the study of these assemblies at a resolution of a few nanometers. Through the implementation of thinning procedures, cryo-ET can now be applied to the reconstruction of macromolecular structures located inside thick regions of vitrified cells and tissues, thus becoming a central tool for structural determinations in various biological disciplines. Here, we focus on the successful in situ applications of cryo-ET to reveal structures of macromolecular complexes within eukaryotic cells.
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Affiliation(s)
- Jan Harapin
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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168
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Hoenger A. High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles. PROTOPLASMA 2014; 251:417-427. [PMID: 24390311 PMCID: PMC3927062 DOI: 10.1007/s00709-013-0600-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
Cryo-electron microscopy techniques and computational 3-D reconstruction of macromolecular assemblies are tightly linked tools in modern structural biology. This symbiosis has produced vast amounts of detailed information on the structure and function of biological macromolecules. Typically, one of two fundamentally different strategies is used depending on the specimens and their environment. A: 3-D reconstruction based on repetitive and structurally identical unit cells that allow for averaging, and B: tomographic 3-D reconstructions where tilt-series between approximately ± 60 and ± 70° at small angular increments are collected from highly complex and flexible structures that are beyond averaging procedures, at least during the first round of 3-D reconstruction. Strategies of group A are averaging-based procedures and collect large number of 2-D projections at different angles that are computationally aligned, averaged together, and back-projected in 3-D space to reach a most complete 3-D dataset with high resolution, today often down to atomic detail. Evidently, success relies on structurally repetitive particles and an aligning procedure that unambiguously determines the angular relationship of all 2-D projections with respect to each other. The alignment procedure of small particles may rely on their packing into a regular array such as a 2-D crystal, an icosahedral (viral) particle, or a helical assembly. Critically important for cryo-methods, each particle will only be exposed once to the electron beam, making these procedures optimal for highest-resolution studies where beam-induced damage is a significant concern. In contrast, tomographic 3-D reconstruction procedures (group B) do not rely on averaging, but collect an entire dataset from the very same structure of interest. Data acquisition requires collecting a large series of tilted projections at angular increments of 1-2° or less and a tilt range of ± 60° or more. Accordingly, tomographic data collection exposes its specimens to a large electron dose, which is particularly problematic for frozen-hydrated samples. Currently, cryo-electron tomography is a rapidly emerging technology, on one end driven by the newest developments of hardware such as super-stabile microscopy stages as well as the latest generation of direct electron detectors and cameras. On the other end, success also strongly depends on new software developments on all kinds of fronts such as tilt-series alignment and back-projection procedures that are all adapted to the very low-dose and therefore very noisy primary data. Here, we will review the status quo of cryo-electron microscopy and discuss the future of cellular cryo-electron tomography from data collection to data analysis, CTF-correction of tilt-series, post-tomographic sub-volume averaging, and 3-D particle classification. We will also discuss the pros and cons of plunge freezing of cellular specimens to vitrified sectioning procedures and their suitability for post-tomographic volume averaging despite multiple artifacts that may distort specimens to some degree.
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Affiliation(s)
- Andreas Hoenger
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO, 80309, USA,
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169
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Abstract
Electron cryo tomography (cryoET) is an ideal technique to study virus-host interactions at molecular resolution. Imaging of biological specimens in a frozen-hydrated state assures a close to native environment. Various virus-host cell interactions have been analysed in this way, with the herpesvirus 'life' cycle being the most comprehensively studied. The data obtained were further integrated with fluorescence and soft X-ray cryo microscopy data applied on experimental systems covering a wide range of biological complexity. This hybrid approach combines dynamic with static imaging and spans a resolution range from micrometres to angstroms. Along selected aspects of the herpesvirus replication cycle, we describe dedicated combinations of approaches and how subsequent data integration enables insights towards a functional understanding of the underlying processes.
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170
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Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. J Struct Biol 2013; 184:394-400. [DOI: 10.1016/j.jsb.2013.10.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 11/19/2022]
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171
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Lučič V, Rigort A, Baumeister W. Cryo-electron tomography: the challenge of doing structural biology in situ. ACTA ACUST UNITED AC 2013; 202:407-19. [PMID: 23918936 PMCID: PMC3734081 DOI: 10.1083/jcb.201304193] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Electron microscopy played a key role in establishing cell biology as a discipline, by producing fundamental insights into cellular organization and ultrastructure. Many seminal discoveries were made possible by the development of new sample preparation methods and imaging modalities. Recent technical advances include sample vitrification that faithfully preserves molecular structures, three-dimensional imaging by electron tomography, and improved image-processing methods. These new techniques have enabled the extraction of high fidelity structural information and are beginning to reveal the macromolecular organization of unperturbed cellular environments.
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Affiliation(s)
- Vladan Lučič
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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172
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Han HM, Bouchet-Marquis C, Huebinger J, Grabenbauer M. Golgi apparatus analyzed by cryo-electron microscopy. Histochem Cell Biol 2013; 140:369-81. [PMID: 23954988 PMCID: PMC3787787 DOI: 10.1007/s00418-013-1136-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2013] [Indexed: 11/28/2022]
Abstract
In 1898, the Golgi apparatus was discovered by light microscopy, and since the 1950s, the ultrastructure composition is known by electron microscopic investigation. The complex three-dimensional morphology fascinated researchers and was sometimes even the driving force to develop novel visualization techniques. However, the highly dynamic membrane systems of Golgi apparatus are delicate and prone to fixation artifacts. Therefore, the understanding of Golgi morphology and its function has been improved significantly with the development of better preparation methods. Nowadays, cryo-fixation is the method of choice to arrest instantly all dynamic and physiological processes inside cells, tissues, and small organisms. Embedded in amorphous ice, such samples can be further processed by freeze substitution or directly analyzed in their fully hydrated state by cryo-electron microscopy and tomography. Even though the overall morphology of vitrified Golgi stacks is comparable to well-prepared and resin-embedded samples, previously unknown structural details can be observed solely based on their native density. At this point, any further improvement of sample preparation would gain novel insights, perhaps not in terms of general morphology, but on fine structural details of this dynamic organelle.
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Affiliation(s)
- Hong-Mei Han
- Department of Systemic Cell Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Cedric Bouchet-Marquis
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO USA
- FEI Company, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124 USA
| | - Jan Huebinger
- Department of Systemic Cell Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Markus Grabenbauer
- Institute of Anatomy and Cell Biology, Heidelberg University, INF 307, 69120 Heidelberg, Germany
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173
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Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography. Curr Opin Struct Biol 2013; 23:771-7. [DOI: 10.1016/j.sbi.2013.08.006] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/29/2013] [Indexed: 11/16/2022]
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