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Förster F. Subtomogram analysis: The sum of a tomogram's particles reveals molecular structure in situ. J Struct Biol X 2022; 6:100063. [PMID: 36684812 PMCID: PMC9846452 DOI: 10.1016/j.yjsbx.2022.100063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/25/2023] Open
Abstract
Cryo-electron tomography is uniquely suited to provide insights into the molecular architecture of cells and tissue in the native state. While frozen hydrated specimens tolerate sufficient electron doses to distinguish different types of particles in a tomogram, the accumulating beam damage does not allow resolving their detailed molecular structure individually. Statistical methods for subtomogram averaging and classification that coherently enhance the signal of particles corresponding to copies of the same type of macromolecular allow obtaining much higher resolution insights into macromolecules. Here, I review the developments in subtomogram analysis at Wolfgang Baumeister's laboratory that make the dream of structural biology in the native cell become reality.
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Affiliation(s)
- Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Uni-versiteitsweg 99, 3584 CG Utrecht, the Netherlands
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2
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Investigating the Structure of Neurotoxic Protein Aggregates Inside Cells. Trends Cell Biol 2020; 30:951-966. [PMID: 32981805 DOI: 10.1016/j.tcb.2020.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022]
Abstract
Neurodegenerative diseases affect the lives of millions of people across the world, being particularly prevalent in the aging population. Despite huge research efforts, conclusive insights into the disease mechanisms are still lacking. Therefore, therapeutic strategies are limited to symptomatic treatments. A common histopathological hallmark of many neurodegenerative diseases is the presence of large pathognomonic protein aggregates, but their role in the disease pathology is unclear and subject to controversy. Here, we discuss imaging methods allowing investigation of these structures within their cellular environment: conventional electron microscopy (EM), super-resolution light microscopy (SR-LM), and cryo-electron tomography (cryo-ET). Multidisciplinary approaches are key for understanding neurodegenerative diseases and may contribute to the development of effective treatments. For simplicity, we focus on huntingtin aggregates, characteristic of Huntington's disease.
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3
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Abstract
Dark microglia, a recently described phenotype, are found in high numbers in nonhomeostatic conditions (e.g., Alzheimer's disease pathology, aging, chronic stress). As a specific protein marker has not yet been defined, they cannot be studied using conventional cellular biology techniques. They are recognized by their unique ultrastructural features visible under electron microscopy. This nanoscale resolution imaging technique allows the identification of cells based on their ultrastructure or immunoreactivity to certain proteins. In this protocol, we describe the steps necessary for the preparation of high-quality brain tissues for transmission electron microscopy, the imaging, the identification of dark microglia, and the ultrastructural analysis of various parameters that can be studied in these cells.
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Affiliation(s)
- Marie-Kim St-Pierre
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Maude Bordeleau
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montréal, QC, Canada
| | - Marie-Ève Tremblay
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC, Canada.
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Grandfield K, Palmquist A, Engqvist H. High-resolution three-dimensional probes of biomaterials and their interfaces. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:1337-1351. [PMID: 22349245 DOI: 10.1098/rsta.2011.0253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Interfacial relationships between biomaterials and tissues strongly influence the success of implant materials and their long-term functionality. Owing to the inhomogeneity of biological tissues at an interface, in particular bone tissue, two-dimensional images often lack detail on the interfacial morphological complexity. Furthermore, the increasing use of nanotechnology in the design and production of biomaterials demands characterization techniques on a similar length scale. Electron tomography (ET) can meet these challenges by enabling high-resolution three-dimensional imaging of biomaterial interfaces. In this article, we review the fundamentals of ET and highlight its recent applications in probing the three-dimensional structure of bioceramics and their interfaces, with particular focus on the hydroxyapatite-bone interface, titanium dioxide-bone interface and a mesoporous titania coating for controlled drug release.
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Affiliation(s)
- Kathryn Grandfield
- Applied Materials Science, Department of Engineering Sciences, The Ångström Laboratory, Uppsala University, 75121 Uppsala, Sweden.
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6
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Nawa Y, Inami W, Chiba A, Ono A, Miyakawa A, Kawata Y, Lin S, Terakawa S. Dynamic and high-resolution live cell imaging by direct electron beam excitation. OPTICS EXPRESS 2012; 20:5629-35. [PMID: 22418370 DOI: 10.1364/oe.20.005629] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We propose a direct electron-beam excitation assisted optical microscope with a resolution of a few tens of nanometers and it can be applied for observation of dynamic movements of nanoparticles in liquid. The technique is also useful for live cell imaging under physiological conditions as well as observation of colloidal solution, microcrystal growth in solutions, etc. In the microscope, fluorescent materials are directly excited with a focused electron beam. The direct excitation with an electron beam yields high spatial resolution since the electron beam can be focused to a few tens of nanometers in the specimens. In order to demonstrate the potential of our proposed microscope, we observed the movements of fluorescent nanoparticles, which can be used for labelling specimens, in a water-based solution. We also demonstrated an observation result of living CHO cells.
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Affiliation(s)
- Yasunori Nawa
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, 4328561, Japan
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7
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Imaging Specific Protein Labels on Eukaryotic Cells in Liquid with Scanning Transmission Electron Microscopy. ACTA ACUST UNITED AC 2011. [DOI: 10.1017/s1551929511000903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Understanding the structure and dynamics of the protein complexes that underlie cellular function is a central scientific challenge. Biochemical techniques used to identify such complexes would be enhanced by the imaging of specific molecular positions in the context of intact cells, with protein-scale resolution (on the order of a few nanometers). Currently, though, nanometer resolution can only be achieved at the cost of less-direct imaging of the unperturbed cell. Cellular ultrastructure is traditionally studied by transmission electron microscopy (TEM), which yields nanometer resolution on embedded and stained sections, or cryo sections. These cellular samples are neither intact nor in their native liquid state. Light microscopy is used to image protein distributions in fluorescently labeled cells in liquid to investigate cellular function, but even recent improvements in resolution by nanoscopy techniques are still insufficient to resolve the individual constituents of protein complexes. Thus, development of techniques capable of high-resolution imaging in native cellular states would contribute significantly to our understanding of cellular function at the molecular level. The development of liquid compartments that include electron-transparent silicon nitride membrane windows has led to the introduction of a novel concept to achieve nanometer resolution on tagged proteins in cells.
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8
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Three-dimensional reconstruction of nucleolar components by electron microscope tomography. Methods Mol Biol 2010; 463:137-58. [PMID: 18951166 DOI: 10.1007/978-1-59745-406-3_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The nucleus is a complex volume constituted of numerous subcompartments in which specific functions take place due to a specific spatial organization of their molecular components. To understand how these molecules are spatially organized within these machineries, it is necessary to investigate their three-dimensional organization at high resolution. To reach this goal, electron tomography appears to be a method of choice; it can generate tomograms with a resolution of a few nanometers by using multiple projections of a tilted section several hundred to several thousand nanometers in thickness imaged by transmission electron microscopy (TEM).Specific identification of molecules of interest contained within such thick sections requires their specific immunocytochemical labelling using electron-dense markers. We recently demonstrated that electron tomography of proteins immunostained with nanogold particles before embedding, and subsequently amplified with silver, was very fruitful due to the inherently high spatial resolution of the medium-voltage scanning and transmission electron microscope (STEM). Here we describe this approach, which is very efficient for tracing the 3D organization of proteins within complex machineries by using antibodies raised against one of the proteins, or against GFP to analyse GFP-tagged proteins.
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Gangodkar S, Jain P, Dixit N, Ghosh K, Basu A. Dengue virus-induced autophagosomes and changes in endomembrane ultrastructure imaged by electron tomography and whole-mount grid-cell culture techniques. JOURNAL OF ELECTRON MICROSCOPY 2010; 59:503-11. [PMID: 20705752 PMCID: PMC7793021 DOI: 10.1093/jmicro/dfq063] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 07/06/2010] [Accepted: 07/14/2010] [Indexed: 05/29/2023]
Abstract
The biogenesis events and formation of dengue virus (DENV) in the infected host cells remain incompletely understood. In the present study, we examined the ultrastructural changes associated with DENV-2 replication in three susceptible host cells, C6/36, Vero and SK Hep1, a cell line of human endothelial origin, using transmission electron microscopy, whole-mount grid-cell culture techniques and electron tomography (ET). The prominent feature in C6/36 cells was the formation of large perinuclear vacuoles with mature DENV particles, and on-grid whole-mount examination of the infected Vero cells showed different forms of DENV core structures associated with cellular membranes within 48 h after infection. Distinct multivesicular structures and prominent autophagic vesicles were seen in the infected SK Hep1 cells when compared with the other two cell lines. ET showed the three-dimensional organization of these vesicles as a continuous system. This is the first report of ET-based analysis of DENV-2 replication in a human endothelial cell line. These results further emphasizes the strong role played by intracellular host membranes-virus interactions in the biogenesis of DENV and strongly argues for the possibility of targeting compounds to block such structure formation as key anti-dengue agents.
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Affiliation(s)
- Shobha Gangodkar
- Electron Microscopy Group, National Institute of Virology (ICMR), 20A Dr Ambedkar Road, Pune 411001,India
| | - Preksha Jain
- Electron Microscopy Group, National Institute of Virology (ICMR), 20A Dr Ambedkar Road, Pune 411001,India
| | - Nishikant Dixit
- Electron Microscopy Group, National Institute of Virology (ICMR), 20A Dr Ambedkar Road, Pune 411001,India
| | - Kanjaksha Ghosh
- National Institute of Immunohematology (ICMR), 13th Floor KEM Hospital, Parel, Mumbai, India
| | - Atanu Basu
- Electron Microscopy Group, National Institute of Virology (ICMR), 20A Dr Ambedkar Road, Pune 411001,India
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de Jonge N, Poirier-Demers N, Demers H, Peckys DB, Drouin D. Nanometer-resolution electron microscopy through micrometers-thick water layers. Ultramicroscopy 2010; 110:1114-9. [PMID: 20542380 DOI: 10.1016/j.ultramic.2010.04.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Revised: 03/17/2010] [Accepted: 04/05/2010] [Indexed: 11/29/2022]
Abstract
Scanning transmission electron microscopy (STEM) was used to image gold nanoparticles on top of and below saline water layers of several micrometers thickness. The smallest gold nanoparticles studied had diameters of 1.4 nm and were visible for a liquid thickness of up to 3.3 microm. The imaging of gold nanoparticles below several micrometers of liquid was limited by broadening of the electron probe caused by scattering of the electron beam in the liquid. The experimental data corresponded to analytical models of the resolution and of the electron probe broadening as function of the liquid thickness. The results were also compared with Monte Carlo simulations of the STEM imaging on modeled specimens of similar geometry and composition as used for the experiments. Applications of STEM imaging in liquid can be found in cell biology, e.g., to study tagged proteins in whole eukaryotic cells in liquid and in materials science to study the interaction of solid:liquid interfaces at the nanoscale.
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Affiliation(s)
- Niels de Jonge
- Vanderbilt University Medical Center, Department of Molecular Physiology and Biophysics, Nashville, TN 37232-0615, USA.
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Nel AE, Mädler L, Velegol D, Xia T, Hoek EMV, Somasundaran P, Klaessig F, Castranova V, Thompson M. Understanding biophysicochemical interactions at the nano-bio interface. NATURE MATERIALS 2009; 8:543-57. [PMID: 19525947 DOI: 10.1038/nmat2442] [Citation(s) in RCA: 4548] [Impact Index Per Article: 303.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Rapid growth in nanotechnology is increasing the likelihood of engineered nanomaterials coming into contact with humans and the environment. Nanoparticles interacting with proteins, membranes, cells, DNA and organelles establish a series of nanoparticle/biological interfaces that depend on colloidal forces as well as dynamic biophysicochemical interactions. These interactions lead to the formation of protein coronas, particle wrapping, intracellular uptake and biocatalytic processes that could have biocompatible or bioadverse outcomes. For their part, the biomolecules may induce phase transformations, free energy releases, restructuring and dissolution at the nanomaterial surface. Probing these various interfaces allows the development of predictive relationships between structure and activity that are determined by nanomaterial properties such as size, shape, surface chemistry, roughness and surface coatings. This knowledge is important from the perspective of safe use of nanomaterials.
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Affiliation(s)
- Andre E Nel
- Division of NanoMedicine, David Geffen School of Medicine and California NanoSystems Institute at UCLA, Los Angeles, California 90095, USA.
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Composition and three-dimensional architecture of the dengue virus replication and assembly sites. Cell Host Microbe 2009; 5:365-75. [PMID: 19380115 PMCID: PMC7103389 DOI: 10.1016/j.chom.2009.03.007] [Citation(s) in RCA: 801] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 02/02/2009] [Accepted: 03/13/2009] [Indexed: 01/31/2023]
Abstract
Positive-strand RNA viruses are known to rearrange cellular membranes to facilitate viral genome replication. The biogenesis and three-dimensional organization of these membranes and the link between replication and virus assembly sites is not fully clear. Using electron microscopy, we find Dengue virus (DENV)-induced vesicles, convoluted membranes, and virus particles to be endoplasmic reticulum (ER)-derived, and we detect double-stranded RNA, a presumed marker of RNA replication, inside virus-induced vesicles. Electron tomography (ET) shows DENV-induced membrane structures to be part of one ER-derived network. Furthermore, ET reveals vesicle pores that could enable release of newly synthesized viral RNA and reveals budding of DENV particles on ER membranes directly apposed to vesicle pores. Thus, DENV modifies ER membrane structure to promote replication and efficient encapsidation of the genome into progeny virus. This architecture of DENV replication and assembly sites could explain the coordination of distinct steps of the flavivirus replication cycle.
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14
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Tchélidzé P, Chatron-Colliet A, Thiry M, Lalun N, Bobichon H, Ploton D. Tomography of the cell nucleus using confocal microscopy and medium voltage electron microscopy. Crit Rev Oncol Hematol 2009; 69:127-43. [DOI: 10.1016/j.critrevonc.2008.07.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 07/18/2008] [Indexed: 12/18/2022] Open
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15
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Engel A. Chapter 9 Scanning Transmission Electron Microscopy. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1076-5670(09)59009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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16
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Müller SA, Aebi U, Engel A. What transmission electron microscopes can visualize now and in the future. J Struct Biol 2008; 163:235-45. [PMID: 18614377 DOI: 10.1016/j.jsb.2008.05.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 05/21/2008] [Indexed: 11/18/2022]
Abstract
Our review concentrates on the progress made in high-resolution transmission electron microscopy (TEM) in the past decade. This includes significant improvements in sample preparation by quick-freezing aimed at preserving the specimen in a close-to-native state in the high vacuum of the microscope. Following advances in cold stage and TEM vacuum technology systems, the observation of native, frozen hydrated specimens has become a widely used approach. It fostered the development of computer guided, fully automated low-dose data acquisition systems allowing matched pairs of images and diffraction patterns to be recorded for electron crystallography, and the collection of entire tilt-series for electron tomography. To achieve optimal information transfer to atomic resolution, field emission electron guns combined with acceleration voltages of 200-300 kV are now routinely used. The outcome of these advances is illustrated by the atomic structure of mammalian aquaporin-O and by the pore-forming bacterial cytotoxin ClyA resolved to 12 A. Further, the Yersinia injectisome needle, a bacterial pseudopilus and the binding of phalloidin to muscle actin filaments were chosen to document the advantage of the high contrast offered by dedicated scanning transmission electron microscopy (STEM) and/or the STEM's ability to measure the mass of protein complexes and directly link this to their shape. Continued progress emerging from leading research laboratories and microscope manufacturers will eventually enable us to determine the proteome of a single cell by electron tomography, and to more routinely solve the atomic structure of membrane proteins by electron crystallography.
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Affiliation(s)
- Shirley A Müller
- Maurice E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstr. 70, CH-4056 Basel, Switzerland.
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17
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Imaging of intracellular spherical lamellar structures and tissue gross morphology by a focused ion beam/scanning electron microscope (FIB/SEM). Ultramicroscopy 2008; 108:663-70. [DOI: 10.1016/j.ultramic.2007.10.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 10/12/2007] [Accepted: 10/26/2007] [Indexed: 11/19/2022]
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Sun J, Weinstein H. Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects. J Chem Phys 2007; 127:155105. [PMID: 17949221 DOI: 10.1063/1.2789434] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
One of the major factors distinguishing molecular processes in vivo from biochemical experiments in vitro is the effect of the environment produced by macromolecular crowding in the cell. To achieve a realistic modeling of processes in the living cell based on biochemical data, it becomes necessary, therefore, to consider such effects. We describe a protocol based on Brownian dynamics simulation to characterize and quantify the effect of various forms of crowding on diffusion and bimolecular association in a simple model of interacting hard spheres. We show that by combining the elastic collision method for hard spheres and the mean field approach for hydrodynamic interaction (HI), our simulations capture the correct dynamics of a monodisperse system. The contributions from excluded volume effect and HI to the crowding effect are thus quantified. The dependence of the results on size distribution of each component in the system is illustrated, and the approach is applied as well to the crowding effect on electrostatic-driven association in both neutral and charged environments; values for effective diffusion constants and association rates are obtained for the specific conditions. The results from our simulation approach can be used to improve the modeling of cell signaling processes without additional computational burdens.
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Affiliation(s)
- Jian Sun
- Department of Physiology and Biophysics, Weill Medical College, Cornell University, 1300 York Avenue, New York, New York 10021, USA
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20
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Şener MK, Olsen JD, Hunter CN, Schulten K. Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle. Proc Natl Acad Sci U S A 2007; 104:15723-8. [PMID: 17895378 PMCID: PMC2000399 DOI: 10.1073/pnas.0706861104] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.
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Affiliation(s)
- Melih K. Şener
- *Beckman Institute and
- Department of Physiology and Biophysics, Weill Medical College, Cornell University, New York, NY 10021; and
- To whom correspondence may be addressed. E-mail: or
| | - John D. Olsen
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Klaus Schulten
- *Beckman Institute and
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- To whom correspondence may be addressed. E-mail: or
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Cyrklaff M, Linaroudis A, Boicu M, Chlanda P, Baumeister W, Griffiths G, Krijnse-Locker J. Whole cell cryo-electron tomography reveals distinct disassembly intermediates of vaccinia virus. PLoS One 2007; 2:e420. [PMID: 17487274 PMCID: PMC1855435 DOI: 10.1371/journal.pone.0000420] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 04/03/2007] [Indexed: 11/18/2022] Open
Abstract
At each round of infection, viruses fall apart to release their genome for replication, and then reassemble into stable particles within the same host cell. For most viruses, the structural details that underlie these disassembly and assembly reactions are poorly understood. Cryo-electron tomography (cryo-ET), a unique method to investigate large and asymmetric structures at the near molecular resolution, was previously used to study the complex structure of vaccinia virus (VV). Here we study the disassembly of VV by cryo-ET on intact, rapidly frozen, mammalian cells, infected for up to 60 minutes. Binding to the cell surface induced distinct structural rearrangements of the core, such as a shape change, the rearrangement of its surface spikes and de-condensation of the viral DNA. We propose that the cell surface induced changes, in particular the decondensation of the viral genome, are a prerequisite for the subsequent release of the vaccinia DNA into the cytoplasm, which is followed by its cytoplasmic replication. Generally, this is the first study that employs whole cell cryo-ET to address structural details of pathogen-host cell interaction.
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Affiliation(s)
- Marek Cyrklaff
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
- * To whom correspondence should be addressed. E-mail: (MC); (JK-L)
| | - Alexandros Linaroudis
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Marius Boicu
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Petr Chlanda
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
| | | | - Jacomine Krijnse-Locker
- European Molecular Biology Laboratory, Heidelberg, Germany
- * To whom correspondence should be addressed. E-mail: (MC); (JK-L)
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Cheutin T, Sauvage C, Tchélidzé P, O'Donohue MF, Kaplan H, Beorchia A, Ploton D. Visualizing Macromolecules with Fluoronanogold: From Photon Microscopy to Electron Tomography. Methods Cell Biol 2007; 79:559-74. [PMID: 17327174 DOI: 10.1016/s0091-679x(06)79022-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- T Cheutin
- Institut de Génétique Humaine, CNRS UPR 1142, 34396 Montpellier Cédex 5, France
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Tchelidze P, Sauvage C, Bonnet N, Kilian L, Beorchia A, O'Donohue MF, Ploton D, Kaplan H. Electron tomography of amplified nanogold immunolabelling: Improvement of quality based on alignment of projections with sinograms and use of post-reconstruction deconvolution. J Struct Biol 2006; 156:421-31. [PMID: 16919476 DOI: 10.1016/j.jsb.2006.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 07/06/2006] [Accepted: 07/10/2006] [Indexed: 11/19/2022]
Abstract
Electron tomography of immunolabelled proteins identified with amplified nanogold particles imaged by Scanning and Transmission Electron Microscopy within thick sections is a powerful method to investigate the three-dimensional organization of complex cellular machineries. In order to increase the overall quality of the reconstructed cube, we have developed two methods that improve the tomographic reconstruction process. We first performed a very precise alignment of the projections before reconstruction with a technique using sinograms. After reconstruction, we propose to compute image restoration by calculating the Point Spread Function of the projection/back-projection system and to use it to deblur the reconstructed cubes. Improvement in the quality of the reconstructed cubes is demonstrated on images of nucleolar proteins tagged with EGFP and immunolabelled with nanogold particles.
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Affiliation(s)
- P Tchelidze
- Unité MéDIAN, CNRS UMR 6142, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
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24
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Krijnse Locker J. How viruses use cells. Curr Opin Microbiol 2006. [PMCID: PMC7108241 DOI: 10.1016/j.mib.2006.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Grünewald K, Cyrklaff M. Structure of complex viruses and virus-infected cells by electron cryo tomography. Curr Opin Microbiol 2006; 9:437-42. [PMID: 16829161 DOI: 10.1016/j.mib.2006.06.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 06/26/2006] [Indexed: 11/22/2022]
Abstract
In microbiology, and in particular in virus research, electron microscopy (EM) is an important tool, offering a broad approach for investigating viral structure throughout their intracellular and extracellular life cycles. Currently, molecular tools and rapid developments in advanced light microscopy dominate the field and supply an enormous amount of information concerning virus biology. In recent years, numerous fascinating high-resolution EM structures obtained by single-particle electron cryo microscopy (cryo-EM) were revealed for viral particles that possess icosahedral symmetry. However, no comprehensive three-dimensional analysis of complex viruses or viruses within cells has yet been achieved using EM. Recent developments in electron cryo-tomography render this a proficient tool for the analysis of complex viruses and viruses within cells in greater detail.
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Affiliation(s)
- Kay Grünewald
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
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