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van der Ven AM, Gyamfi H, Suttisansanee U, Ahmad MS, Su Z, Taylor RM, Poole A, Chiorean S, Daub E, Urquhart T, Honek JF. Molecular Engineering of E. coli Bacterioferritin: A Versatile Nanodimensional Protein Cage. Molecules 2023; 28:4663. [PMID: 37375226 DOI: 10.3390/molecules28124663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, intense interest is focused on the discovery and application of new multisubunit cage proteins and spherical virus capsids to the fields of bionanotechnology, drug delivery, and diagnostic imaging as their internal cavities can serve as hosts for fluorophores or bioactive molecular cargo. Bacterioferritin is unusual in the ferritin protein superfamily of iron-storage cage proteins in that it contains twelve heme cofactors and is homomeric. The goal of the present study is to expand the capabilities of ferritins by developing new approaches to molecular cargo encapsulation employing bacterioferritin. Two strategies were explored to control the encapsulation of a diverse range of molecular guests compared to random entrapment, a predominant strategy employed in this area. The first was the inclusion of histidine-tag peptide fusion sequences within the internal cavity of bacterioferritin. This approach allowed for the successful and controlled encapsulation of a fluorescent dye, a protein (fluorescently labeled streptavidin), or a 5 nm gold nanoparticle. The second strategy, termed the heme-dependent cassette strategy, involved the substitution of the native heme with heme analogs attached to (i) fluorescent dyes or (ii) nickel-nitrilotriacetate (NTA) groups (which allowed for controllable encapsulation of a histidine-tagged green fluorescent protein). An in silico docking approach identified several small molecules able to replace the heme and capable of controlling the quaternary structure of the protein. A transglutaminase-based chemoenzymatic approach to surface modification of this cage protein was also accomplished, allowing for future nanoparticle targeting. This research presents novel strategies to control a diverse set of molecular encapsulations and adds a further level of sophistication to internal protein cavity engineering.
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Affiliation(s)
- Anton M van der Ven
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Hawa Gyamfi
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | | | - Muhammad S Ahmad
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Zhengding Su
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Robert M Taylor
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Amanda Poole
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Elisabeth Daub
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Taylor Urquhart
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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Diociaiuti M, Bombelli C, Zanetti-Polzi L, Belfiore M, Fioravanti R, Macchia G, Giordani C. The Interaction between Amyloid Prefibrillar Oligomers of Salmon Calcitonin and a Lipid-Raft Model: Molecular Mechanisms Leading to Membrane Damage, Ca 2+-Influx and Neurotoxicity. Biomolecules 2019; 10:biom10010058. [PMID: 31905804 PMCID: PMC7022306 DOI: 10.3390/biom10010058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/19/2019] [Accepted: 12/27/2019] [Indexed: 12/14/2022] Open
Abstract
To investigate the interaction between amyloid assemblies and “lipid-rafts”, we performed functional and structural experiments on salmon calcitonin (sCT) solutions rich in prefibrillar oligomers, proto- and mature-fibers interacting with liposomes made of monosialoganglioside-GM1 (4%), DPPC (48%) and cholesterol (48%). To focus on the role played by electrostatic forces and considering that sCT is positive and GM1 is negative at physiologic pH, we compared results with those relative to GM1-free liposomes while, to assess membrane fluidity effects, with those relative to cholesterol-free liposomes. We investigated functional effects by evaluating Ca2+-influx in liposomes and viability of HT22-DIFF neurons. Only neurotoxic solutions rich in unstructured prefibrillar oligomers were able to induce Ca2+-influx in the “lipid-rafts” model, suggesting that the two phenomena were correlated. Thus, we investigated protein conformation and membrane modifications occurring during the interaction: circular dichroism showed that “lipid-rafts” fostered the formation of β-structures and energy filtered-transmission electron microscopy that prefibrillar oligomers formed pores, similar to Aβ did. We speculate that electrostatic forces between the positive prefibrillar oligomers and the negative GM1 drive the initial binding while the hydrophobic profile and flexibility of prefibrillar oligomers, together with the membrane fluidity, are responsible for the subsequent pore formation leading to Ca2+-influx and neurotoxicity.
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Affiliation(s)
- Marco Diociaiuti
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, I-00161 Roma, Italy; (M.B.); (R.F.)
- Correspondence: ; Tel.: +39-06-49902981
| | - Cecilia Bombelli
- CNR-Istituto per i Sistemi Biologici, UOS di Roma, c/o Dipartimento di Chimica, Sapienza Università di Roma, I-00185 Roma, Italy;
| | - Laura Zanetti-Polzi
- Dipartimento di Fisica e Scienze Chimiche, Università dell’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy;
| | - Marcello Belfiore
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, I-00161 Roma, Italy; (M.B.); (R.F.)
| | - Raoul Fioravanti
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, I-00161 Roma, Italy; (M.B.); (R.F.)
- Dipartimento di Chimica, Sapienza Università di Roma, I-00185 Roma, Italy
| | - Gianfranco Macchia
- Centro Grandi Strumentazioni e Core Facilities, Istituto Superiore di Sanità, I-00161 Roma, Italy;
| | - Cristiano Giordani
- Grupo Productos Naturales Marinos, Facultad de Ciencias Farmacéuticas y Alimentarias, Instituto de Física, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia;
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Mansouri K, Edwards RJ. Suspending samples over carbon holey films increases heterogeneity of molecular orientations in negative stain electron microscopy. MethodsX 2019; 6:582-586. [PMID: 30976531 PMCID: PMC6439206 DOI: 10.1016/j.mex.2019.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/27/2019] [Indexed: 11/15/2022] Open
Abstract
Negative stain electron microscopy (NSEM) is a simple and cost effective method to analyze a wide variety of specimens, especially proteins. In traditional NSEM, the protein sample is applied to and supported by a continuous carbon film. Unfortunately, many proteins stick to the carbon film with a limited number of orientations. Because the restricted orientation limits the available views of the molecule, information about the three-dimensional structure of the molecule is likewise limited. The method presented here overcomes this limitation by using a carbon holey film combined with 1-octadecanol as a spreading agent. We demonstrate this method with solubilized envelope (Env) proteins from HIV, which typically show a restricted orientation on continuous carbon film, and show the following: 1-octadecanol added to negative stain aids the formation of a continuous sample-stain layer spanning the holes of a holey carbon film. Samples negatively stained over holes show less restricted orientation, resulting in better single particle reconstructions.
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Flexible Hinges in Bacterial Chemoreceptors. J Bacteriol 2018; 200:JB.00593-17. [PMID: 29229700 DOI: 10.1128/jb.00593-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/30/2017] [Indexed: 12/26/2022] Open
Abstract
Transmembrane bacterial chemoreceptors are extended, rod-shaped homodimers with ligand-binding sites at one end and interaction sites for signaling complex formation and histidine kinase control at the other. There are atomic-resolution structures of chemoreceptor fragments but not of intact, membrane-inserted receptors. Electron tomography of in vivo signaling complex arrays lack distinct densities for chemoreceptor rods away from the well-ordered base plate region, implying structural heterogeneity. We used negative staining, transmission electron microscopy, and image analysis to characterize the molecular shapes of intact homodimers of the Escherichia coli aspartate receptor Tar rendered functional by insertion into nanodisc-provided E. coli lipid bilayers. Single-particle analysis plus tomography of particles in a three-dimensional matrix revealed two bend loci in the chemoreceptor cytoplasmic domain, (i) a short, two-strand gap between the membrane-proximal, four-helix-bundle HAMP (histidine kinases, adenylyl cyclases, methyl-accepting chemoreceptors, and phosphatases) domain and the membrane-distal, four-helix coiled coil and (ii) aligned glycines in the extended, four-helix coiled coil, the position of a bend noted in the previous X-ray structure of a receptor fragment. Our images showed HAMP bends from 0° to ∼13° and glycine bends from 0° to ∼20°, suggesting that the loci are flexible hinges. Variable hinge bending explains indistinct densities for receptor rods outside the base plate region in subvolume averages of chemotaxis arrays. Bending at flexible hinges was not correlated with the chemoreceptor signaling state. However, our analyses showed that chemoreceptor bending avoided what would otherwise be steric clashes between neighboring receptors that would block the formation of core signaling complexes and chemoreceptor arrays.IMPORTANCE This work provides new information about the shape of transmembrane bacterial chemoreceptors, crucial components in the molecular machinery of bacterial chemotaxis. We found that intact, lipid-bilayer-inserted, and thus functional homodimers of the Escherichia coli chemoreceptor Tar exhibited bends at two flexible hinges along their ∼200-Å, rod-like, cytoplasmic domains. One hinge was at the short, two-strand gap between the membrane-proximal, four-helix-bundle HAMP (histidine kinases, adenylyl cyclases, methyl-accepting chemoreceptors, and phosphatases) domain and the membrane-distal, four-helix coiled coil. The other hinge was at aligned glycines in the extended, four-helix coiled coil, where a bend had been identified in the X-ray structure of a chemoreceptor fragment. Our analyses showed that flexible hinge bending avoided structural clashes in chemotaxis core complexes and their arrays.
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Franken LE, Boekema EJ, Stuart MCA. Transmission Electron Microscopy as a Tool for the Characterization of Soft Materials: Application and Interpretation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1600476. [PMID: 28546914 PMCID: PMC5441488 DOI: 10.1002/advs.201600476] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/02/2016] [Indexed: 05/22/2023]
Abstract
Transmission electron microscopy (TEM) provides direct structural information on nano-structured materials and is popular as a characterization tool in soft matter and supramolecular chemistry. However, technical aspects of sample preparation are overlooked and erroneous image interpretations are regularly encountered in the literature. There are three most commonly used TEM methods as we derived from literature: drying, staining and cryo-TEM, which are explained here with respect to their application, limitations and interpretation. Since soft matter chemistry relies on a lot of indirect evidence, the role of TEM for the correct evaluation of the nature of an assembly is very large. Mistakes in application and interpretation can therefore have enormous impact on the quality of present and future studies. We provide helpful background information of these three techniques, the information that can and cannot be derived from them and provide assistance in selecting the right technique for soft matter imaging. This essay warns against the use of drying and explains why. In general cryo-TEM is by far the best suited method and many mistakes and over-interpretations can be avoided by the use of this technique.
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Affiliation(s)
- Linda E. Franken
- Electron Microscopy GroupGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Egbert J. Boekema
- Electron Microscopy GroupGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Marc C. A. Stuart
- Electron Microscopy GroupGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
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Renz P, Kokkinopoulou M, Landfester K, Lieberwirth I. Imaging of Polymeric Nanoparticles: Hard Challenge for Soft Objects. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201600246] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Patricia Renz
- Max-Planck Institute for Polymer Research; Ackermannweg 10 5130 Mainz Germany
| | - Maria Kokkinopoulou
- Max-Planck Institute for Polymer Research; Ackermannweg 10 5130 Mainz Germany
| | | | - Ingo Lieberwirth
- Max-Planck Institute for Polymer Research; Ackermannweg 10 5130 Mainz Germany
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7
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Transmission electron microscopy in molecular structural biology: A historical survey. Arch Biochem Biophys 2015; 581:3-18. [DOI: 10.1016/j.abb.2014.11.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/14/2014] [Accepted: 11/21/2014] [Indexed: 01/21/2023]
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Kokkinopoulou M, Güler MA, Lieb B, Barbeck M, Ghanaati S, Markl J. 3D-ultrastructure, functions and stress responses of gastropod (Biomphalaria glabrata) rhogocytes. PLoS One 2014; 9:e101078. [PMID: 24971744 PMCID: PMC4074132 DOI: 10.1371/journal.pone.0101078] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/03/2014] [Indexed: 11/18/2022] Open
Abstract
Rhogocytes are pore cells scattered among the connective tissue of different body parts of gastropods and other molluscs, with great variation in their number, shape and size. They are enveloped by a lamina of extracellular matrix. Their most characteristic feature is the "slit apparatus", local invaginations of the plasma membrane bridged by cytoplasmic bars, forming slits of ca. 20 nm width. A slit diaphragm creates a molecular sieve with permeation holes of 20×20 nm. In blue-blooded gastropods, rhogocytes synthesize and secrete the respiratory protein hemocyanin, and it has been proposed-though not proven-that in the rare red-blooded snail species they might synthesize and secrete the hemoglobin. However, the cellular secretion pathway for respiratory proteins, and the functional role(s) of the enigmatic rhogocyte slit apparatus are still unclear. Additional functions for rhogocytes have been proposed, notably a role in protein uptake and degradation, and in heavy metal detoxification. Here we provide new structural and functional information on the rhogocytes of the red-blooded freshwater snail Biomphalaria glabrata. By in situ hybridization of mantle tissues, we prove that rhogocytes indeed synthesize hemoglobin. By electron tomography, the first three dimensional (3D) reconstructions of the slit apparatus are provided, showing detail of highly dense material in the cytoplasmic bars close to the slits. By immunogold labelling, we collected evidence that a major component of this material is actin. By genome databank mining, the complete sequence of a B. glabrata nephrin was obtained, and localized to the rhogocytes by immunofluorescence microscopy. The presence of both proteins fit the ultrastructure-based hypothesis that rhogocytes are related to mammalian podocytes and insect nephrocytes. Reactions of the rhogocytes to deprivation of food and cadmium toxification are also documented, and a possible secretion pathway of newly synthesized respiratory proteins through the slit apparatus is discussed.
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Affiliation(s)
| | | | - Bernhard Lieb
- Institute of Zoology, Johannes Gutenberg University, Mainz, Germany
| | - Mike Barbeck
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Shahram Ghanaati
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jürgen Markl
- Institute of Zoology, Johannes Gutenberg University, Mainz, Germany
- * E-mail:
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Harris JR, De Carlo S. Negative staining and cryo-negative staining: applications in biology and medicine. Methods Mol Biol 2014; 1117:215-258. [PMID: 24357366 DOI: 10.1007/978-1-62703-776-1_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Negative staining is widely applicable to isolated viruses, protein molecules, macromolecular assemblies and fibrils, subcellular membrane fractions, liposomes and artificial membranes, synthetic DNA arrays, and also to polymer solutions and a variety of nanotechnology samples. Techniques are provided for the preparation of the necessary support films (continuous carbon and holey/perforated carbon). The range of suitable negative stains is presented, with some emphasis on the benefit of using ammonium molybdate and of negative stain-trehalose combinations. Protocols are provided for the single droplet negative staining technique (on continuous and holey carbon support films), the floating and carbon sandwich techniques in addition to the negative staining-carbon film (NS-CF) technique for randomly dispersed fragile molecules, 2D crystallization of proteins and for cleavage of cells and organelles. Immuno-negative staining and negative staining of affinity labeled complexes (e.g., biotin-streptavidin) are presented in some detail. The formation of immune complexes in solution for droplet negative staining is given, as is the use of carbon-plastic support films as an adsorption surface on which to perform immunolabeling or affinity experiments, prior to negative staining. Dynamic biological systems can be investigated by negative staining, where the time period is in excess of a few minutes, but there are possibilities to greatly reduce the time by rapid stabilization of molecular systems with uranyl acetate or tannic acid. The more recently developed cryo-negative staining procedures are also included: first, the high concentration ammonium molybdate procedure on holey carbon films and second, the carbon sandwich procedure using uranyl formate. Several electron micrographs showing examples of applications of negative staining techniques are included and the chapter is thoroughly referenced.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, Mainz, Germany
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Orlova EV, Saibil HR. Structural analysis of macromolecular assemblies by electron microscopy. Chem Rev 2011; 111:7710-48. [PMID: 21919528 PMCID: PMC3239172 DOI: 10.1021/cr100353t] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Indexed: 12/11/2022]
Affiliation(s)
- E. V. Orlova
- Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - H. R. Saibil
- Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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Harris JR, Soliakov A, Lewis RJ, Depoix F, Watkinson A, Lakey JH. Alhydrogel® adjuvant, ultrasonic dispersion and protein binding: a TEM and analytical study. Micron 2011; 43:192-200. [PMID: 21831642 DOI: 10.1016/j.micron.2011.07.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 07/10/2011] [Accepted: 07/11/2011] [Indexed: 01/25/2023]
Abstract
Aluminium-based vaccine adjuvants have been in use since the 1920s. Aluminium hydroxide (alum) that is the chemical basis of Alhydrogel, a widely used adjuvant, is a colloid that binds proteins to the particular surface for efficient presentation to the immune system during the vaccination process. Using conventional TEM and cryo-TEM we have shown that Alhydrogel can be finely dispersed by ultrasonication of the aqueous suspension. Clusters of ultrasonicated aluminium hydroxide micro-fibre crystals have been produced (∼ 10-100 nm), that are significantly smaller than those present the untreated Alhydrogel (∼ 2-12 μm). However, even prolonged ultrasonication did not produce a homogenous suspension of single aluminium hydroxide micro-fibres. The TEM images of unstained and negatively stained air-dried Alhydrogel are very similar to those obtained by cryo-electron microscopy. Visualization of protein on the surface of the finely dispersed Alhydrogel by TEM is facilitated by prior ultrasonication. Several examples are given, including some of medical relevance, using proteins of widely ranging molecular mass and oligomerization state. Even with the smaller mass proteins, their presence on the Alhydrogel surface can be readily defined by TEM. It has been found that low quantities of protein tend to cross-link and aggregate the small Alhydogel clusters, in a more pronounced manner than high protein concentrations. This indicates that complete saturation of the available Alhydrogel surface with protein may be achieved, with minimal cross-linkage, and future exploitation of this treatment of Alhydrogel is likely to be of immediate value for more efficient vaccine production.
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Affiliation(s)
- J Robin Harris
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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Chiu PL, Kelly DF, Walz T. The use of trehalose in the preparation of specimens for molecular electron microscopy. Micron 2011; 42:762-72. [PMID: 21752659 DOI: 10.1016/j.micron.2011.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/09/2011] [Accepted: 06/10/2011] [Indexed: 11/29/2022]
Abstract
Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose.
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Affiliation(s)
- Po-Lin Chiu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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New and unconventional approaches for advancing resolution in biological transmission electron microscopy by improving macromolecular specimen preparation and preservation. Micron 2011; 42:141-51. [DOI: 10.1016/j.micron.2010.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Revised: 05/16/2010] [Accepted: 05/17/2010] [Indexed: 11/21/2022]
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Green DJ, Wang JC, Xiao F, Cai Y, Balhorn R, Guo P, Cheng RH. Self-assembly of heptameric nanoparticles derived from tag-functionalized phi29 connectors. ACS NANO 2010; 4:7651-7659. [PMID: 21080706 DOI: 10.1021/nn1024829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The structure of an induced macromolecular assembly was characterized and found to consist of an ordered heptameric arrangement of recombinant phi29 gp10 connector molecules. Insertion of an N-terminal Strep-II/His(6) tag to the connectors led to the spontaneous formation of large nanoparticles that were distinct from free, wild-type phi29 connectors in both size and symmetry elements. The determination of single-molecule tomograms and image-averaged reconstructions allowed for the stoichiometric and topological characterization of the ordered assemblage, revealing that the nanoparticle is composed of five equatorial connectors arranged with pseudo-5-fold rotational symmetry, capped on its ends by two polar connectors. Additionally, all seven connectors are oriented with their narrower N-terminal necks into the nanoparticle core and wider C-terminal ends out toward the nanoparticle surface, a geometric arrangement accommodated by the shape complementarity of the conical connector profiles. A significant amount of conformational heterogeneity was detected, ranging from changes in overall nanoparticle diameter, to tilting of individual connectors, to variations in connector stoichiometry. Nevertheless, a stable, heptameric nanoparticle was resolved, revealing the significant potential of guided, peptide-mediated supramolecular self-assembly. With this construct, we anticipate the further design of variable N-terminal tags to allow for the generation of nanoparticles with tailored connector stoichiometry and topological arrangements. By modifying the surface-exposed C-terminal ends with application-appropriate moieties, the consistent structure and compact nature of these nanoparticles may prove beneficial in nanotechnological and nanomedical approaches.
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Affiliation(s)
- Dominik J Green
- Department of Molecular & Cellular Biology, University of California, Davis, California 95616, USA
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15
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Sander B, Golas MM. Visualization of bionanostructures using transmission electron microscopical techniques. Microsc Res Tech 2010; 74:642-63. [DOI: 10.1002/jemt.20963] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 10/01/2010] [Indexed: 11/10/2022]
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De Carlo S, Harris JR. Negative staining and cryo-negative staining of macromolecules and viruses for TEM. Micron 2010; 42:117-31. [PMID: 20634082 DOI: 10.1016/j.micron.2010.06.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 06/14/2010] [Accepted: 06/15/2010] [Indexed: 10/19/2022]
Abstract
In this review we cover the technical background to negative staining of biomolecules and viruses, and then expand upon the different possibilities and limitations. Topics range from conventional air-dry negative staining of samples adsorbed to carbon support films, the variant termed the "negative staining-carbon film" technique and negative staining of samples spread across the holes of holey-carbon support films, to a consideration of dynamic/time-dependent negative staining. For each of these approaches examples of attainable data are given. The cryo-negative staining technique for the specimen preparation of frozen-hydrated/vitrified samples is also presented. A detailed protocol to successfully achieve cryo-negative staining with ammonium molybdate is given, as well as examples of data, which support the claim that cryo-negative staining provides a useful approach for the high-resolution study of macromolecular and viral structure.
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Affiliation(s)
- Sacha De Carlo
- Department of Chemistry, and Institute for Macro Molecular Assemblies, The City College of CUNY, 160 Convent Ave, New York, NY, USA.
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Harris JR, Palmer M. Cholesterol specificity of some heptameric beta-barrel pore-forming bacterial toxins: structural and functional aspects. Subcell Biochem 2010; 51:579-596. [PMID: 20213559 DOI: 10.1007/978-90-481-8622-8_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Apart from the thiol-specific/cholesterol-dependent cytolysin family of toxins (see Chapter 20) there are a number of other unrelated bacterial toxins that also have an affinity for plasma membrane cholesterol. Emphasis is given here on the Vibrio cholerae cytolysin (VCC) and the cytolysins from related Vibrio species. The inhibition of the cytolytic activity of these toxins by prior incubation with extracellular cholesterol or low density lipoprotein emerges as a unifying feature, as does plasma membrane cholesterol depletion. Incubation of VCC with cholesterol produces a heptameric oligomer, which is not equivalent to the pre-pore since it is unable to penetrate the plasma membrane. In structural terms, the precise sequence of VCC monomer binding to membrane, oligomer formation and pore insertion through the bilayer has yet to be fully defined. Several other bacterial toxins have a dependency for cholesterol, although the available data is limited in most cases.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, Mainz, D-55099, Germany.
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Abstract
Cryoelectron microscopy (cryo-EM) combined with single-particle reconstruction methods is a powerful technique to study the structure of biological assemblies at molecular resolution (i.e., 3-10 Å). Since electron micrographs of frozen-hydrated biological particles are usually very noisy, improvement of the signal-to-noise ratio (SNR) is necessary and is usually achieved by image processing. We propose an alternative method to improve the contrast at the specimen preparation stage: cryonegative staining. Cryonegative staining aims to increase the SNR while preserving the biological samples in the frozen-hydrated state. Here, we present two alternative procedures to efficiently perform cryonegative staining on macromolecular assemblies. The first is very similar to conventional cryo-EM, the main difference being that the samples are observed in the presence of an additional contrasting agent, ammonium molybdate. The second is based on a carbon-sandwich method and is typically used with uranyl formate or acetate. Compared to air-dried negative staining at room temperature, the advantage of both cryonegative-staining procedures presented here is that the sample is kept hydrated at all steps and observed at liquid nitrogen temperature in the electron microscope. The advantage over conventional cryo-EM is that the SNR is improved by at least a factor of three. For each of these approaches, a few examples of attainable data are given. We cover the technical background to cryonegative staining of macromolecular assemblies, and then expand upon the different possibilities and limitations.
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Affiliation(s)
- Sacha De Carlo
- Department of Chemistry, Institute for Macromolecular Assemblies, City University of New York, City College Campus, New York, USA
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19
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Alatorre-Meda M, González-Pérez A, Rodríguez JR. DNA–METAFECTENE™ PRO complexation: a physical chemistry study. Phys Chem Chem Phys 2010; 12:7464-72. [DOI: 10.1039/b920900j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Weston AE, Armer HEJ, Collinson LM. Towards native-state imaging in biological context in the electron microscope. J Chem Biol 2009; 3:101-12. [PMID: 19916039 DOI: 10.1007/s12154-009-0033-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 10/22/2009] [Indexed: 12/11/2022] Open
Abstract
Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context.
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Affiliation(s)
- Anne E Weston
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3PX UK
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21
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Lorber B, Adrian M, Witz J, Erhardt M, Harris JR. Formation of two-dimensional crystals of icosahedral RNA viruses. Micron 2008; 39:431-46. [PMID: 17466523 DOI: 10.1016/j.micron.2007.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 02/08/2007] [Accepted: 02/08/2007] [Indexed: 11/28/2022]
Abstract
UNLABELLED The formation of 2D arrays of three small icosahedral RNA viruses with known 3D structures (tomato bushy stunt virus, turnip yellow mosaic virus and bromegrass mosaic virus) has been investigated to determine the role of each component of a negative staining solution containing ammonium molybdate and polyethylene glycol. Virion association was monitored by dynamic light scattering (DLS) and virus array formation was visualised by conventional transmission electron microscopy and cryo-electron microscopy after negative staining. The structural properties of viral arrays prepared in vitro were compared to those of microcrystals found in the leaves of infected plants. A novel form of macroscopic 3D crystals of turnip yellow mosaic virus has been grown in the negative staining solution. On the basis of the experimental results, the hypothesis is advanced that microscopic arrays might be planar crystallisation nuclei. The formation of 2D crystals and the enhancing effect of polyethylene glycol on the self-organisation of virions at the air/water interface are discussed. SYNOPSIS The formation of 2D arrays of icosahedral viruses was investigated by spectroscopic and transmission electron microscopic methods.
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Affiliation(s)
- Bernard Lorber
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France.
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22
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Small capsid protein pORF65 is essential for assembly of Kaposi's sarcoma-associated herpesvirus capsids. J Virol 2008; 82:7201-11. [PMID: 18463150 DOI: 10.1128/jvi.00423-08] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent for KS tumors, multicentric Castleman's disease, and primary effusion lymphomas. Like other herpesvirus capsids, the KSHV capsid is an icosahedral structure composed of six proteins. The capsid shell is made up of the major capsid protein, two triplex proteins, and the small capsid protein. The scaffold protein and the protease occupy the internal space. The assembly of KSHV capsids is thought to occur in a manner similar to that determined for herpes simplex virus type 1 (HSV-1). Our goal was to assemble KSHV capsids in insect cells using the baculovirus expression vector system. Six KSHV capsid open reading frames were cloned and the proteins expressed in Sf9 cells: pORF25 (major capsid protein), pORF62 (triplex 1), pORF26 (triplex 2), pORF17 (protease), pORF17.5 (scaffold protein), and also pORF65 (small capsid protein). When insect cells were coinfected with these baculoviruses, angular capsids that contained internal core structures were readily observed by conventional electron microscopy of the infected cells. Capsids were also readily isolated from infected cells by using rate velocity sedimentation. With immuno-electron microscopy methods, these capsids were seen to be reactive to antisera to pORF65 as well as to KSHV-positive human sera, indicating the correct conformation of pORF65 in these capsids. When either virus expressing the triplex proteins was omitted from the coinfection, capsids did not assemble; similar to observations made in HSV-1-infected cells. If the virus expressing the scaffold protein was excluded, large open shells that did not attain icosahedral structure were seen in the nuclei of infected cells. The presence of pORF65 was required for capsid assembly, in that capsids did not form if this protein was absent as judged by both by ultrastructural analysis of infected cells and rate velocity sedimentation experiments. Thus, a novel outcome of this study is the finding that the small capsid protein of KSHV, like the major capsid and triplex proteins, is essential for capsid shell assembly.
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Mishra A, Panda JJ, Basu A, Chauhan VS. Nanovesicles based on self-assembly of conformationally constrained aromatic residue containing amphiphilic dipeptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:4571-6. [PMID: 18358051 DOI: 10.1021/la7034533] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Peptide-based vesicular structures have been the focus of research in the past decade for their potential application as drug delivery agents. We here report the self-assembly of amphiphilic dipeptides containing conformation-constraining alpha,beta-dehydrophenylalanine into nanovesicles. The vesicles can encapsulate small drug molecules such as riboflavin and vitamin B(12), bioactive peptides, and small protein molecules. The nanovesicles are resistant to treatment of a nonspecific protease, proteinase K, and are stable at low concentrations of monovalent and divalent cations. The vesicles are effectively taken up by actively growing cells in culture and show no observable cytopathic effects. These peptide-based nanostructures can be considered as models for further development as delivery agents for different biomolecules.
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Affiliation(s)
- Aseem Mishra
- International Centre for Genetic Engineering and Biotechnology, New Delhi, and National Institute of Virology, Pune, India
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24
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Massover WH. On the experimental use of light metal salts for negative staining. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2008; 14:126-137. [PMID: 18312717 DOI: 10.1017/s1431927608080033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 07/21/2007] [Indexed: 05/26/2023]
Abstract
All common negative stains are salts of heavy metals. To remedy several technical defects inherent in the use of heavy metal compounds, this study investigates whether salts of the light metals sodium, magnesium, and aluminum can function as negative stains. Screening criteria require aqueous solubility at pH 7.0, formation of a smooth amorphous layer upon drying, and transmission electron microscope imaging of the 87-A (8.7-nm) lattice periodicity in thin catalase crystals. Six of 23 salts evaluated pass all three screens; detection of the protein shell in ferritin macromolecules indicates that light metal salts also provide negative staining of single particle specimens. Appositional contrast is less than that given by heavy metal negative stains; image density can be raised by increasing electron phase contrast and by selecting salts with phosphate or sulfate anions, thereby adding strong scattering from P or S atoms. Low-dose electron diffraction of catalase crystals negatively stained with 200 mM magnesium sulfate shows Bragg spots extending out to 4.4 A. Future experimental use of sodium phosphate buffer and magnesium sulfate for negative staining is anticipated, particularly in designing new cocktail (multicomponent) negative stains able to support and protect protein structure to higher resolution levels than are currently achieved.
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Affiliation(s)
- William H Massover
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA.
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25
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Simon P, Lichte H, Formanek P, Lehmann M, Huhle R, Carrillo-Cabrera W, Harscher A, Ehrlich H. Electron holography of biological samples. Micron 2008; 39:229-56. [PMID: 17374487 DOI: 10.1016/j.micron.2006.11.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 11/28/2006] [Accepted: 11/29/2006] [Indexed: 11/20/2022]
Abstract
In this paper, we summarise the development of off-axis electron holography on biological samples starting in 1986 with the first results on ferritin from the group of Tonomura. In the middle of the 1990s strong interest was evoked, but then stagnation took place because the results obtained at that stage did not reach the contrast and the resolution achieved by conventional electron microscopy. To date, there exist only a few ( approximately 12) publications on electron holography of biological objects, thus this topic is quite small and concise. The reason for this could be that holography is mostly established in materials science by physicists. Therefore, applications for off-axis holography were powerfully pushed forward in the area of imaging, e.g. electric or magnetic micro- and nanofields. Unstained biological systems investigated by means of off-axis electron holography up to now are ferritin, tobacco mosaic virus, a bacterial flagellum, T5 bacteriophage virus, hexagonal packed intermediate layer of bacteria and the Semliki Forest virus. New results of the authors on collagen fibres and surface layer of bacteria, the so-called S-layer 2D crystal lattice are presented in this review. For the sake of completeness, we will shortly discuss in-line holography of biological samples and off-axis holography of materials related to biological systems, such as biomaterial composites or magnetotactic bacteria.
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Affiliation(s)
- P Simon
- Max-Planck-Institut für Chemische Physik fester Stoffe, Nöthnitzer Strasse 40, 01187 Dresden, Germany.
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26
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Schmidt CD, Böttcher C, Hirsch A. Synthesis and Aggregation Properties of Water-Soluble Newkome-Dendronized Perylenetetracarboxdiimides. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700567] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Kim YM, Kang JS, Kim JS, Jeung JM, Lee JY, Kim YJ. Ultrathin carbon support films for high-resolution electron microscopy of nanoparticles. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2007; 13:285-90. [PMID: 17637077 DOI: 10.1017/s1431927607070250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 01/16/2007] [Indexed: 05/16/2023]
Abstract
We introduce a simple preparation method for ultrathin carbon support films that is especially useful for high-resolution electron microscopy (HREM) of nanoparticles. Oxidized iron nanoparticles were used as a test sample in a demonstration of this method. The film qualities are discussed on the basis of electron-energy-loss spectroscopy (EELS) and image analysis techniques such as thickness maps and histograms. We carried out a comparison between the homemade and commercial film qualities. The relative thickness of the homemade support films was 0.6 times less than that of the commercial films, which was calculated from the EELS analysis, whereas the thicknesses of both carbon support films varied within about 3%. The percentage of the observable area was about 67 +/- 7.6% of the support film. This was about twice as large as the commercial film (32 +/- 9.3%). The HREM image of the sample prepared with our support film improved 9% in brightness and 15% in contrast compared with images obtained with the commercial support.
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Affiliation(s)
- Young-Min Kim
- Division of Electron Microscopic Research, Korea Basic Science Institute, 52 Yeoeun-dong, Yuseong-gu, Daejeon 305-333, Korea
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28
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Harris JR. Negative staining across holes: application to fibril and tubular structures. Micron 2007; 39:168-76. [PMID: 17804247 DOI: 10.1016/j.micron.2007.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 07/19/2007] [Accepted: 07/19/2007] [Indexed: 10/23/2022]
Abstract
The negative staining technique, when used with holey carbon support films, presents superior imaging conditions than is the case when samples are adsorbed to continuous carbon films. A demonstration of this negative staining approach is presented, using ammonium molybdate in combination with trehalose, applied to several fibrillar and tubular samples. Fibrils formed from the amyloid-beta peptide and the protease inhibitor pepstain A spread very well unsupported across holes and the different polymorphic fibril forms can be readily assessed. However, tubular forms of amyloid-beta have a tendency to be flattened, due to surface tension forces prior to and during specimen drying. Sub-fibril assembly forms and D-banded rat tail type 1 collagen fibres are presented. The air-dried collagen images produced are shown to contain almost as much detail as those obtainable by cryo-negative staining. Fragile DNA and DNA-protein nanotubes are also shown to yield superior quality images to those produced on continuous carbon films. The iron-storage protein, frataxin, creates elongated oligomeric assemblies, containing bound ferrihydrite microcrystals. The iron particles within these flexuous oligomers can be defined in the presence of ammonium molybdate, but they are more readily demonstrated if the frataxin is spread across holes in the presence of trehalose alone. The samples used here serve to show the likely benefit obtainable from negative staining across holes for a range of other fibrillar and tubular samples in biology, medicine and nanobiotechnology.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, D-55099 Mainz, Germany.
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29
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Gaillard C, Fuchs G, Plummer CJG, Stadelmann PA. The morphology of submicronsized core–shell latex particles: An electron microscopy study. Micron 2007; 38:522-35. [PMID: 17045482 DOI: 10.1016/j.micron.2006.07.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 07/19/2006] [Indexed: 10/24/2022]
Abstract
The core-shell structure of a range of acrylic-acrylic latexes has been investigated by combining different specimen preparation methods with transmission electron microscopy (TEM), dark-field scanning transmission electron microscopy (DSTEM) and low-voltage scanning electron microscopy (LV-SEM), including the first reported use of LV-SEM to observe composite latex particles at ambient and subambient temperatures. Spin-coating of liquid latex dispersions directly onto TEM grids or SEM stubs is shown to be a relatively straightforward mean of avoiding film formation during specimen preparation. In conjunction with double staining techniques, it has been found to be particularly convenient for characterizing the fine structure of particles with diameters down to below 100 nm.
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Affiliation(s)
- Cédric Gaillard
- Centre Interdisciplinaire de Microscopie Electronique (CIME), EPFL, CH-1015 Lausanne, Switzerland.
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30
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Meissner U, Schröder E, Scheffler D, Martin AG, Harris JR. Formation, TEM study and 3D reconstruction of the human erythrocyte peroxiredoxin-2 dodecahedral higher-order assembly. Micron 2007; 38:29-39. [PMID: 16839769 DOI: 10.1016/j.micron.2006.04.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2004] [Revised: 04/11/2006] [Accepted: 04/12/2006] [Indexed: 11/27/2022]
Abstract
The production of a higher-order assembly of peroxiredoxin-2 (Prx-2) from human erythrocytes has been achieved during specimen preparation on holey carbon support films, in the presence of ammonium molybdate and polyethylene glycol. TEM study suggested that this assembly is a regular dodecahedron, containing 12 Prx-2 decamers (Mr 2.62 MDa, external diameter approximately 20 nm). This interpretation has been supported by production of a approximately 1.6 nm 3D reconstruction from the negative stain TEM data, with automated docking of the available X-ray data of the Prx-2 decamer. Comparison with other known protein dodecahedral and viral icosahedral structures indicates that this arrangement of protein molecules is one of the fundamental macromolecular higher-order assemblies found in biology. Widespread biotechnological interest in macromolecular "cage" structures is relevant to the production of the Prx-2 dodecahedron.
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Affiliation(s)
- Ulrich Meissner
- Institute of Zoology, University of Mainz, D-55099 Mainz, Germany
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31
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Abstract
Negative staining is widely applicable to isolated viruses, protein molecules, macro-molecular assemblies and fibrils, subcellular membrane fractions, liposomes and artificial membranes, synthetic DNA arrays, and also to polymer solutions. In this chapter, techniques are provided for the preparation of the necessary support films (continuous carbon and holey/perforated carbon). The range of suitable negative stains is presented, with some emphasis on the benefit of using ammonium molybdate and of negative stain-trehalose combinations. Protocols are provided for the single-droplet negative staining technique (on continuous and holey carbon support films), the negative staining-carbon film technique, for randomly dispersed fragile molecules, 2D crystallization of proteins, and for cleavage of cells and organelles. The newly developed cryonegative staining procedure also is included. Immunonegative staining and negative staining of affinity labeled complexes (e.g., biotin-streptavidin) are discussed in some detail. The formation of immune complexes in solution for droplet negative staining is presented, as is the use of carbon-plastic support films as an adsorption surface on which to perform immunolabeling or affinity experiments, before negative staining. Dynamic biological systems can be investigated by negative staining, where the time period is in excess of a few minutes, but there are possibilities to greatly reduce the time by rapid stabilization of molecular systems with uranyl acetate or tannic acid.
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Affiliation(s)
- J Robin Harris
- Instiute of Zoology, University of Mainz, Mainz, Germany
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32
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Kroeger A, Deimede V, Belack J, Lieberwirth I, Fytas G, Wegner G. Equilibrium Length and Shape of Rodlike Polyelectrolyte Micelles in Dilute Aqueous Solutions. Macromolecules 2006. [DOI: 10.1021/ma061966j] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anja Kroeger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Department of Materials Science and Technology, University of Crete and F.O.R.T.H., P.O. Box 1527, 71110 Heraklion, Greece
| | - Valadoula Deimede
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Department of Materials Science and Technology, University of Crete and F.O.R.T.H., P.O. Box 1527, 71110 Heraklion, Greece
| | - Joerg Belack
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Department of Materials Science and Technology, University of Crete and F.O.R.T.H., P.O. Box 1527, 71110 Heraklion, Greece
| | - Ingo Lieberwirth
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Department of Materials Science and Technology, University of Crete and F.O.R.T.H., P.O. Box 1527, 71110 Heraklion, Greece
| | - George Fytas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Department of Materials Science and Technology, University of Crete and F.O.R.T.H., P.O. Box 1527, 71110 Heraklion, Greece
| | - Gerhard Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Department of Materials Science and Technology, University of Crete and F.O.R.T.H., P.O. Box 1527, 71110 Heraklion, Greece
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Rousselot M, Jaenicke E, Lamkemeyer T, Harris JR, Pirow R. Native and subunit molecular mass and quarternary structure of the hemoglobin from the primitive branchiopod crustacean Triops cancriformis. FEBS J 2006; 273:4055-71. [PMID: 16899051 DOI: 10.1111/j.1742-4658.2006.05408.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many branchiopod crustaceans are endowed with extracellular, high-molecular-weight hemoglobins whose exact structural characteristics have remained a matter of conjecture. By using a broad spectrum of techniques, we provide precise and coherent information on the hemoglobin of one of the phylogenetically 'oldest' extant branchiopods, the tadpole shrimp Triops cancriformis. The hemoglobin dissociated under reducing conditions into two subunits, designated TcHbA and TcHbB, with masses of 35,775+/-4 and 36,055+/-4 Da, respectively, determined by ESI-MS. Nonreducing conditions showed only two disulfide-bridged dimers, a homodimer of TcHbA, designated D1 (71,548+/-5 Da), and the heterodimer D2 (71,828+/-5 Da). Carbamidomethylation of free SH groups revealed the presence of three cysteines per subunit and indicated one intrasubunit and one intersubunit disulfide bridge. Ultracentrifugation and light-scattering experiments under nondenaturating conditions yielded mass estimates that suggested an uneven number of 17 subunits forming the native hemoglobin. This unrealistic number resulted from the presence of two size classes (16-mer and 18-mer), which were recognized by native PAGE and Ferguson plot analysis. ESI-MS revealed three hemoglobin isoforms with masses of 588.1 kDa, 662.0 kDa, and 665.0 kDa. The 16-mer and the smaller 18-mer species are supposed to be composed of TcHbA only, given the dominance of this subunit type in SDS/PAGE. Transmission electron microscopy of negatively stained specimens showed a population of compact molecules with geometrical extensions of 14, 16 and 9 nm. The proposed stoichiometric model of quarternary structure provides the missing link to achieve a mechanistic understanding of the structure-function relationships among the multimeric arthropodan hemoglobins.
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Affiliation(s)
- Morgane Rousselot
- Equipe Ecophysiologie: Adaptation et Evolutions Moléculaires, Station Biologique, Roscoff, France
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Lamkemeyer T, Zeis B, Decker H, Jaenicke E, Waschbüsch D, Gebauer W, Markl J, Meissner U, Rousselot M, Zal F, Nicholson GJ, Paul RJ. Molecular mass of macromolecules and subunits and the quaternary structure of hemoglobin from the microcrustacean Daphnia magna. FEBS J 2006; 273:3393-410. [PMID: 16857019 DOI: 10.1111/j.1742-4658.2006.05346.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular masses of macromolecules and subunits of the extracellular hemoglobin from the fresh-water crustacean Daphnia magna were determined by analytical ultracentrifugation, multiangle laser light scattering and electrospray ionization mass spectrometry. The hemoglobins from hypoxia-incubated, hemoglobin-rich and normoxia-incubated, hemoglobin-poor Daphnia magna were analyzed separately. The sedimentation coefficient of the macromolecule was 17.4 +/- 0.1 S, and its molecular mass was 583 kDa (hemoglobin-rich animals) determined by AUC and 590.4 +/- 11.1 kDa (hemoglobin-rich animals) and 597.5 +/- 49 kDa (hemoglobin-poor animals), respectively, determined by multiangle laser light scattering. Measurements of the hemoglobin subunit mass of hemoglobin-rich animals by electrospray ionization mass spectrometry revealed a significant peak at 36.482 +/- 0.0015 kDa, i.e. 37.715 kDa including two heme groups. The hemoglobin subunits are modified by O-linked glycosylation in the pre-A segments of domains 1. No evidence for phosphorylation of hemoglobin subunits was found. The subunit migration behavior during SDS/PAGE was shown to be influenced by the buffer system used (Tris versus phosphate). The subunit mass heterogeneity found using Tris buffering can be explained by glycosylation of hemoglobin subunits. Based on molecular mass information, Daphnia magna hemoglobin is demonstrated to consist of 16 subunits. The quaternary structure of the Daphnia magna hemoglobin macromolecule was assessed by three-dimensional reconstructions via single-particle analysis based on negatively stained electron microscopic specimens. It turned out to be much more complex than hitherto proposed: it displays D4 symmetry with a diameter of approximately 12 nm and a height of about 8 nm.
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Affiliation(s)
- Tobias Lamkemeyer
- Institut für Zoophysiologie, Westfälische Wilhelms-Universität, Münster, Germany.
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35
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Sun J, Duffy KE, Ranjith-Kumar CT, Xiong J, Lamb RJ, Santos J, Masarapu H, Cunningham M, Holzenburg A, Sarisky RT, Mbow ML, Kao C. Structural and Functional Analyses of the Human Toll-like Receptor 3. J Biol Chem 2006; 281:11144-51. [PMID: 16533755 DOI: 10.1074/jbc.m510442200] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Toll-like receptors (TLRs) play critical roles in bridging the innate and adaptive immune responses. The human TLR3 recognizes foreign-derived double-stranded RNA and endogenous necrotic cell RNA as ligands. Herein we characterized the contribution of glycosylation to TLR3 structure and function. Exogenous addition of purified extracellular domain of TLR3 (hTLR3 ECD) expressed in human embryonic kidney cells was found to inhibit TLR3-dependent signaling, thus providing a reagent for structural and functional characterization. Approximately 35% of the mass of the hTLR3 ECD was due to posttranslational modification, with N-linked glycosyl groups contributing substantially to the additional mass. Cells treated with tunicamycin, an inhibitor of glycosylation, prevented TLR3-induced NF-kappaB activation, confirming that N-linked glycosylation is required for bioactivity of this receptor. Further, mutations in two of these predicted glycosylation sites impaired TLR3 signaling without obviously affecting the expression of the protein. Single-particle structures reconstructed from electron microscopy images and two-dimensional crystallization revealed that hTLR3 ECD forms a horseshoe structure similar to the recently elucidated x-ray structure of the protein expressed in insect cells using baculovirus vectors (Choe, J., Kelker, M. S., and Wilson, I. A. (2005) Science 309, 581-585 and Bell, J. K., Botos, I., Hall, P. R., Askins, J., Shiloach, J., Segal, D. M., and Davies, D. R. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 10976-10980). There are, however, notable differences between the human cell-derived and insect cell-derived structures, including features attributable to glycosylation.
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Affiliation(s)
- Jingchuan Sun
- Department of Biology, Texas A&M University, College Station 77843, USA
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36
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O'Hara SP, Huang BQ, Chen XM, Nelson J, LaRusso NF. DISTRIBUTION OF CRYPTOSPORIDIUM PARVUM SPOROZOITE APICAL ORGANELLES DURING ATTACHMENT TO AND INTERNALIZATION BY CULTURED BILIARY EPITHELIAL CELLS. J Parasitol 2005; 91:995-9. [PMID: 16419739 DOI: 10.1645/ge-495r.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Although accumulating evidence supports an active role for host cells during Cryptosporidium parvum invasion of epithelia, our knowledge of the underlying parasite-specific processes triggering such events is limited. In an effort to better understand the invasion strategy of C. parvum, we characterized the presence and distribution of the apical organelles (micronemes, dense granules, and rhoptry) through the stages of attachment to, and internalization by, human biliary epithelia, using serial-section electron microscopy. Novel findings include an apparent organized rearrangement of micronemes upon host cell attachment. The apically segregated micronemes were apposed to a central microtubule-like filamentous structure, and the more distal micronemes localized to the periphery and apical region of the parasite during internalization, coinciding with the formation of the anterior vacuole. The morphological observations presented here extend our understanding of parasite-specific processes that occur during attachment to, and internalization by, host epithelial cells.
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Affiliation(s)
- Steven P O'Hara
- The Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Medical School, Clinic, and Foundation, Rochester, Minnesota 55905, USA
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37
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Vacha F, Bumba L, Kaftan D, Vacha M. Microscopy and single molecule detection in photosynthesis. Micron 2005; 36:483-502. [PMID: 15951188 DOI: 10.1016/j.micron.2005.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 04/18/2005] [Accepted: 04/19/2005] [Indexed: 11/30/2022]
Abstract
Progress in various fields of microscopy techniques brought up enormous possibilities to study the photosynthesis down to the level of individual pigment-protein complexes. The aim of this review is to present recent developments in the photosynthesis research obtained using such highly advanced techniques. Three areas of microscopy techniques covering optical microscopy, electron microscopy and scanning probe microscopy are reviewed. Whereas the electron microscopy and scanning probe microscopy are used in photosynthesis mainly for structural studies of photosynthetic pigment-protein complexes, the optical microscopy is used also for functional studies.
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Affiliation(s)
- Frantisek Vacha
- Institute of Physical Biology, University of South Bohemia, Budejovice, Czech Republic.
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38
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Gaudiano MC, Colone M, Bombelli C, Chistolini P, Valvo L, Diociaiuti M. Early stages of salmon calcitonin aggregation: effect induced by ageing and oxidation processes in water and in the presence of model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1750:134-45. [PMID: 15964788 DOI: 10.1016/j.bbapap.2005.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 03/29/2005] [Accepted: 04/14/2005] [Indexed: 10/25/2022]
Abstract
The natural ageing- and hydrogen peroxide-induced aggregation of salmon calcitonin were studied in water and in the presence of dipalmitoylphosphatidylcholine (DPPC) liposomes. The early stages of the aggregation process at low protein concentration were investigated by means of Circular Dichroism spectroscopy (CD) and conventional and immunogold labelling Transmission Electron Microscopy (TEM). In buffered water solution, salmon calcitonin showed a two-stage conformational variation related to fibril formation and phase-separation of larger aggregates. A first stage, characterised by small conformational changes but a decrease in dichroic band intensity, was followed by a second stage, 6 days after, leading to higher conformational variations and aggregations. Salmon calcitonin showed a distinct modification in the secondary structure and aggregate morphology in the presence of hydrogen peroxide with respect to natural ageing, indicating that the two aggregation processes (natural and chemical-induced) followed a distinct mechanism. The oxidised forms of the peptide were separated by liquid chromatography. The same study was performed in the presence of DPPC liposomes. The results obtained by conventional and immunogold labelling TEM evidenced that salmon calcitonin in buffered water solution essentially does not enter the liposomes but forms around them a fibril network characterised by the same conformational changes after 6 days. The oxidised sample in the presence of liposomes showed a "fibrils hank", separated from liposomes. The presence of liposomes did not affect either the aggregation or the conformational modifications yet observed by TEM and CD in water solution.
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Affiliation(s)
- Maria Cristina Gaudiano
- Dipartimento del Farmaco, Istituto Superiore di Sanità, viale Regina Elena, 299-00161 Roma, Italy
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39
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Ubbink J, Schär-Zammaretti P. Probing bacterial interactions: integrated approaches combining atomic force microscopy, electron microscopy and biophysical techniques. Micron 2005; 36:293-320. [PMID: 15857770 DOI: 10.1016/j.micron.2004.11.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 11/24/2004] [Accepted: 11/25/2004] [Indexed: 11/27/2022]
Abstract
Recent developments in the application of Atomic Force Microscopy (AFM) and other biophysical techniques for the study of bacterial interactions and adhesion are discussed in the light of established biological and microscopic approaches. Whereas molecular-biological techniques combined with electron microscopy allow the identification and localization of surface constituents mediating bacterial interactions, with AFM it has become possible to actually measure the forces involved in bacterial interactions. Combined with the flexibility of AFM in probing various types of physical interactions, such as electrostatic interactions, specific ligand-receptor interactions and the elastic forces of deformation and extension of bacterial surface polymers and cell wall, this provides prospects for the elucidation of the biophysical mechanism of bacterial interaction. However, because of the biochemical and a biophysical complexity of the bacterial cell wall, integrated approaches combining AFM with electron microscopy and biophysical techniques are needed to elucidate the mechanism by which a bacterium interacts with a host or material surface. The literature on electron microscopy of the bacterial cell wall is reviewed, with particular emphasis on the staining of specific classes of cell-wall constituents. The application of AFM in the analysis of bacterial surfaces is discussed, including AFM operating modes, sample preparation methods and results obtained on various strains. For various bacterial strains, the integration of EM and AFM data is discussed. Various biophysical aspects of the analysis of bacterial surface structure and interactions are discussed, including the theory of colloidal interactions and Bell's theory of cell-to-cell adhesion. An overview is given of biophysical techniques used in the analysis of the properties of bacterial surfaces and bacterial surface constituents and their integration with AFM. Finally, we discuss recent progress in the understanding of the role of bacterial interactions in medicine within the framework of the techniques and concepts discussed in the paper.
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Affiliation(s)
- Job Ubbink
- Nestlé Research Center, Vers-chez-les-Blanc, P.O. Box 44, CH-1000 Lausanne 26, Switzerland.
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40
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Harris JR. The contribution of microscopy to the study of Alzheimer's disease, amyloid plaques and Abeta fibrillogenesis. Subcell Biochem 2005; 38:1-44. [PMID: 15709471 DOI: 10.1007/0-387-23226-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
A broad survey is presented in this chapter, dealing with the impact that microscopy has made to the study of Alzheimer's disease, amyloid plaques and amyloid-beta fibrillogenesis. This includes classical light microscopy and the modem immunolabelling and confocal microscopies, together with the contribution of transmission electron microscopy and atomic force microscopy. Whilst usefully standing alone, the individual microscopies often contribute most effectively when they are integrated with cellular, biophysical and molecular approaches.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, D-55099 Mainz, Germany
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41
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Harris JR, Adrian M, Petry F. Amylopectin: a major component of the residual body in Cryptosporidium parvum oocysts. Parasitology 2004; 128:269-82. [PMID: 15074876 DOI: 10.1017/s003118200300458x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Amylopectin is used for carbohydrate storage in different life-stages of a number of apicomplexan parasites. We have performed an ultrastructural analysis of amylopectin granules from the oocyst residual body and sporozoites of Cryptosporidium parvum. Amylopectin granules were studied in situ and after isolation from 'French' press disrupted parasites, by conventional transmission electron microscopy (TEM) of sectioned oocysts and various negative staining and cryoelectron microscopy techniques. Within the membrane-enclosed oocyst residuum large amylopectin granules (0.1-0.3 microm) can be found besides a characteristic large lipid body and a crystalline protein inclusion. Smaller granules were detected in sectioned sporozoites. Negative staining of isolated amylopectin granules revealed some ultrastructural features not readily visible in sectioned material. The large amylopectin granules had a smooth surface with a 'ball of string'-like inner structure. Granules isolated from sporozoites were more irregularly shaped and showed a rod-like particulate composition. With the exception of alpha-amylase, which led to some degree of damage of the surface of the particles, treatment of amylopectin granules with other glycohydrolases had little effect on the overall structure. However, granules adhered to one another. Only when the granules were boiled did the 'ball of string' structure gradually dissolve.
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Affiliation(s)
- J R Harris
- Institute of Zoology, Johannes Gutenberg-University, D-55099 Mainz, Germany
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42
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Massover WH. A low-dose electron diffraction assay for protection of protein structure against damage from drying. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2004; 10:261-269. [PMID: 15306051 DOI: 10.1017/s1431927604040073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2002] [Indexed: 05/24/2023]
Abstract
A new assay using low-dose electron diffraction to measure the protection of protein structure against damage from drying is described. When thin single crystals of catalase are dried within water alone, low-dose electron diffraction yields no Bragg spots. Drying within an experimental aqueous solution that permits detection of diffraction spots thereby indicates a positive result, and the extent of these Bragg reflections into the high angle range gives a quantitative measure of the degree of protection. Bragg spots out to 3.73.9 are recorded for drying within 100 mM solutions of the known structure-preserving sugars, sucrose, tannin, and trehalose. The ability of trehalose to maintain native protein structure during drying starts between 10 and 25 mM, and changes only slightly at concentrations above this threshold; with drying in 150-mM trehalose, catalase crystals yield diffraction spots out to 3.7. Drying within the organic nonsugar polymer polyvinylpyrrolidone gives Bragg spots to 4.0. This new assay should be useful to measure the unexamined structure-preserving capabilities of modified sugars, other nonsugars, and mixtures to identify which protective matrix maintains native protein structure to the greatest extent during drying; electron crystallography using that optimal matrix should yield protein structure at improved levels of high resolution.
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Affiliation(s)
- William H Massover
- Department of Cell Biology and Molecular Medicine, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, NJ 07101-1709, USA.
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43
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Chen CC, Lewis RJ, Harris R, Yudkin MD, Delumeau O. A supramolecular complex in the environmental stress signalling pathway of Bacillus subtilis. Mol Microbiol 2003; 49:1657-69. [PMID: 12950928 DOI: 10.1046/j.1365-2958.2003.03663.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SigmaB, an alternative sigma-factor of Bacillus subtilis, mediates the response of the cell to a variety of physical insults. Within the environmental stress signalling pathway RsbU, a protein phosphatase, is stimulated by its interaction with the protein kinase RsbT. In the absence of stress RsbT is expected to be trapped by an alternative binding partner, RsbS. Here, we have demonstrated that RsbS alone cannot act as an alternative partner for RsbT, but instead requires the presence of RsbR to create a high molecular mass RsbR:RsbS complex (approximately 1 MDa) able to capture RsbT. In this complex the phosphorylation state of RsbS, and not that of RsbR, controlled the binding to RsbT, whose kinase activity towards RsbS could be counterbalanced by the activity of RsbX, the phosphatase for RsbS-P. The RsbR:RsbS complex recruited RsbT from a mixture of RsbT and RsbU. The phosphorylated form of RsbR in the complex enhanced the kinase activity of RsbT towards RsbS. This supramolecular complex thus has the functional properties of an alternative partner for RsbT. Electron micrographs of this complex are presented, and the purification of the RsbR:RsbS complex from cellular extracts provides evidence for the existence of such a complex in vivo.
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Affiliation(s)
- Chien-Cheng Chen
- Microbiology Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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Harris JR, Adrian M, Petry F. Structure of the Cryptosporidium parvum microneme: a metabolically and osmotically labile apicomplexan organelle. Micron 2003; 34:65-78. [PMID: 12801539 DOI: 10.1016/s0968-4328(03)00020-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
From an EM study of thin sections, the rod-like microneme organelles within conventionally glutaraldehyde fixed Cryptosporidium parvum sporozoites have been shown to undergo a shape change to a more spherical structure when the sporozoites age in vitro for a period of approximately 12 to 24 h. This correlates with the shape change of intact sporozoites, from motile hence viable thin banana-shaped cells to swollen pear-shaped cells, shown by differential interference contrast light microscopy of unstained unfixed and glutaraldehyde-fixed samples, as well as by thin section EM of fixed sporozoites. From negatively stained EM specimens of unfixed and fixed sporozoites the cellular shape change has been confirmed as has the rod to sphere micronemal shape change. Intact micronemes released directly from sporozoites exclude negative stain and appear as smooth-surfaced electron transparent particles. Biochemically purified rod-shaped C. parvum micronemes are shown to be fragile organelles that inevitably undergo variable damage during isolation, storage and subsequent specimen preparation for EM study. In the absence of glutaraldehyde fixation, damaged micronemes allow the negative stain to enter and loose their contents and during storage undergo a rod-to-sphere shape transformation. Glutaraldehyde-fixed micronemes maintain the rod shape; intact fixed micronemes still exclude negative stain but damaged micronemes reveal a complex quasi-helical arrangement of internal protein within the rod-like micronemes. Loss of this internal organized structure appears to be responsible for the micronemal shape change. This interpretation has been advanced from mutually supportive data obtained from cryoelectron microscopy of unstained vitrified samples, conventional air-dry negative staining and cryo-negative staining. Attempts to biochemically solubilize the micronemal content by lysis and ultrasonication, and separate it from the micronemal membranes, have so far met with limited success as the internal material tends to remain as a disorganized cluster of particles upon release.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, D-55099 Mainz, Germany
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45
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Becker C, Kruse MN, Slotty KA, Köhler D, Harris JR, Rösmann S, Sterchi EE, Stöcker W. Differences in the activation mechanism between the alpha and beta subunits of human meprin. Biol Chem 2003; 384:825-31. [PMID: 12817480 DOI: 10.1515/bc.2003.092] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Meprins are zinc-endopeptidases of the astacin family, which are expressed as membrane-bound or secreted forms in renal and intestinal brush-border membranes of mouse, rat and man. There are two types of meprin subunits, alpha and beta, which form disulfide-bonded homo- and heterodimers; further oligomerization is mediated by non-covalent interactions. Both subunits are translated as proenzymes that have to be activated by removal of an N-terminal propeptide. In the gut, the most probable activator is trypsin. In addition, plasmin has been shown to activate the human alpha subunit in colorectal cancer tissue. In the present study we have overexpressed the human meprin alpha subunit and a His-tagged soluble tail-switch-mutant of meprin beta in Baculovirus-infected insect cells. The recombinant homo-oligomeric proteins were purified by gel filtration and affinity chromatography with yields of up to 10 mg/l cell culture medium and analyzed with regard to their activation mechanism. While both alpha and beta homo-oligomers are activated by trypsin, only meprin alpha homo-oligomers are processed to their mature form by plasmin. These results indicate a different accessibility of the propeptide in meprin homo-oligomers and suggest an explanation for the appearance of meprin hetero-oligomers consisting of active alpha, but latent beta subunits.
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Affiliation(s)
- Christoph Becker
- Institut für Zoophysiologie, Molekulare Physiologie, Westfälische Wilhelms-Universität Münster, Hindenburgplatz 55, D-48143 Münster, Germany
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Harris JR. In vitro fibrillogenesis of the amyloid beta 1-42 peptide: cholesterol potentiation and aspirin inhibition. Micron 2003; 33:609-26. [PMID: 12475558 DOI: 10.1016/s0968-4328(02)00029-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the formation of extracellular amyloid neurofibrillar bundles/senile plaques and their role in the development of Alzheimer's disease is of considerable interest to neuroscientists and clinicians. Major components of the extracellular neurofibrillar bundles are polymerized amyloid beta (Abeta) peptides (1-40), (1-42) and (1-43), derived in vivo from the soluble amyloid precursor protein (sAPP) by proteolytic (beta- and gamma-secretase) cleavage. The Abeta(1-42) peptide is widely considered to be of greatest significance in relation to the pathogenesis of Alzheimer's disease. A well-defined ultrastructural characteristic within Alzheimer dense plaques is the presence of helical fibrils that are believed to consist of polymerized amyloid beta, together with other associated proteins such as the serum amyloid P protein, apolipoprotein E isoform epsilon 4, alpha1-anti-chymotrypsin, catalase, glycoproteins, proteoglycans, cholesterol and other lipids. The spontaneous in vitro fibrillogenesis of chemically synthesized Abeta(1-42) peptide (rat sequence), following 20h incubation at 37 degrees C, has been assessed from uranyl acetate negatively stained specimens studied by transmission electron microscopy (TEM). Amyloid beta(1-42) peptide fibrillogenesis in the presence of cholesterol has been investigated using aqueous suspensions of microcrystalline cholesterol and cholesteryl acetate, globular particles of cholesteryl oleate, a soluble (micellar) cholesterol derivative (polyoxyethyl cholesteryl sebacate/cholesteryl PEG 600 sebacate), cholesterol-sphingomyelin liposomes and sphingomyelin liposomes. In all these cases, with the exception of cholesteryl oleate, considerable potentiation of long smooth helical fibril formation occurred, compared to 20h 37 degrees C control samples containing the Abeta(1-42) peptide alone. The binding of polyoxyethyl cholesteryl sebacate micelles to helical Abeta fibrils/filaments and the binding of fibrils to the surface of cholesterol and cholesteryl acetate microcrystals, and to a lesser extent on cholesteryl oleate globules, indicates an affinity of the Abeta peptide for cholesterol. This potentiation of Abeta(1-42) polymerization is likely to be mediated at the molecular level via hydrophobic interaction between the amino acid side chains of the peptide and the tetracyclic sterol nucleus. Addition of cupric sulphate (0.1mM) to the Abeta solution produced large disorganized fibril aggregates. Inclusion of 1mM aspirin (sodium acetylsalicylate) in the Abeta peptide alone and as an addition to Abeta peptide solution containing cholesterol, cholesteryl acetate, soluble cholesterol, sphingomyelin and sphingomyelin-cholesterol liposomes, and to 0.1mM cupric sulphate solution, completely inhibited fibrillogenesis. Instead, only non-crystalline diffuse, non-filamentous microaggregates of insoluble Abeta particles were found, free and attached to the sterol particles. The in vitro system presented here provides a way to rapidly monitor at the structural/TEM level other compounds (e.g. chelating agents, drugs, beta-sheet breaking peptides and anti-oxidants) for their effects on amyloid beta peptide fibrillogenesis (and on preformed fibril disassembly) in parallel with in vitro biochemical studies and in vivo studies using animal models of Alzheimer's disease as well as studies on man.
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Affiliation(s)
- J R Harris
- Institute of Zoology, University of Mainz, D-55099 Mainz, Germany.
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Abstract
Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerization states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidized to a sulfenic acid by the peroxide substrate. The recycling of the sulfenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity.
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Affiliation(s)
- Zachary A Wood
- Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA
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48
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Harris JR, Bhakdi S, Meissner U, Scheffler D, Bittman R, Li G, Zitzer A, Palmer M. Interaction of the Vibrio cholerae cytolysin (VCC) with cholesterol, some cholesterol esters, and cholesterol derivatives: a TEM study. J Struct Biol 2002; 139:122-35. [PMID: 12406694 DOI: 10.1016/s1047-8477(02)00563-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Vibrio cholerae cytolysin (VCC) 63-kDa monomer has been shown to interact in aqueous suspension with cholesterol microcystals to produce a ring/pore-like heptameric oligomer approximately 8 nm in outer diameter. Transmission electron microscopy data were produced from cholesterol samples adsorbed to carbon support films, spread across the holes of holey carbon films, and negatively stained with ammonium molybdate. The VCC oligomers initially attach to the edge of the stacked cholesterol bilayers and with increasing time cover the two planar surfaces. VCC oligomers are also released into solution, with some tendency to cluster, possibly via the hydrophobic membrane-spanning domain. At the air/water interface, the VCC oligomers are likely to be selectively oriented with the hydrophobic domain facing the air. Despite some molecular disorder/plasticity within the oligomers, multivariate statistical analysis and rotational self-correlation using IMAGIC-5 strongly suggest the presence of sevenfold rotational symmetry. To correlate the electron microscopy data with on-going biochemical and permeability studies using liposomes of varying lipid composition, the direct interaction of VCC with several cholesterol derivatives and other steroids has been examined. 19-Hydroxycholesterol and 7 beta-hydroxycholesterol both induce VCC oligomerization. beta-Estradiol, which does not possess an aliphatic side chain, also efficiently induces VCC oligomer formation, as does cholesteryl acetate. Cholesteryl stearate and oleate and the C22 (2-trifluoroacetyl)naphthyloxy analogue of cholesterol fail to induce VCC oligomerization, but binding of the monomer to the surface of these steroids does occur. Stigmasterol has little tendency to induce oligomer formation, and oligomers are largely confined to the edge of the bilayers; ergosterol has even less oligomerization ability. Attempts to solubilize and stabilize the VCC oligomers from cholesterol suspensions have been pursued using the neutral surfactant octylglucoside. Although individual solubilized oligomers have been defined which exhibit a characteristic cytolysin channel conformation in the side-on orientation, a tendency remains for the oligomers to cluster via their hydrophobic domains.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, 55099 Mainz, Germany.
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