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Kaniyala Melanthota S, Banik S, Chakraborty I, Pallen S, Gopal D, Chakrabarti S, Mazumder N. Elucidating the microscopic and computational techniques to study the structure and pathology of SARS-CoVs. Microsc Res Tech 2020; 83:1623-1638. [PMID: 32770582 PMCID: PMC7436590 DOI: 10.1002/jemt.23551] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/11/2022]
Abstract
Severe Acute Respiratory Syndrome Coronaviruses (SARS‐CoVs), causative of major outbreaks in the past two decades, has claimed many lives all over the world. The virus effectively spreads through saliva aerosols or nasal discharge from an infected person. Currently, no specific vaccines or treatments exist for coronavirus; however, several attempts are being made to develop possible treatments. Hence, it is important to study the viral structure and life cycle to understand its functionality, activity, and infectious nature. Further, such studies can aid in the development of vaccinations against this virus. Microscopy plays an important role in examining the structure and topology of the virus as well as pathogenesis in infected host cells. This review deals with different microscopy techniques including electron microscopy, atomic force microscopy, fluorescence microscopy as well as computational methods to elucidate various prospects of this life‐threatening virus. Structural analysis of SARS‐CoVs aids in understanding its nature, activity, and pathophysiology Revealing the surface morphology of SARS‐CoVs using scanning electron microscope and atomic force microscopy Computational methods help to understand the structure of SARS‐CoVs and their interactions with various inhibitors
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Affiliation(s)
- Sindhoora Kaniyala Melanthota
- Department of Biophysics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Soumyabrata Banik
- Department of Biophysics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Ishita Chakraborty
- Department of Biophysics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Sparsha Pallen
- Department of Bioinformatics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Dharshini Gopal
- Department of Bioinformatics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Shweta Chakrabarti
- Department of Bioinformatics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
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2
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Evans CT, Payton O, Picco L, Allen MJ. Algal Viruses: The (Atomic) Shape of Things to Come. Viruses 2018; 10:E490. [PMID: 30213102 PMCID: PMC6165301 DOI: 10.3390/v10090490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 01/15/2023] Open
Abstract
Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.
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Affiliation(s)
- Christopher T Evans
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK.
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
| | - Oliver Payton
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
| | - Loren Picco
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Michael J Allen
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK.
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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3
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Leclercq L, Dewilde A, Aubry JM, Nardello-Rataj V. Supramolecular assistance between cyclodextrins and didecyldimethylammonium chloride against enveloped viruses: Toward eco-biocidal formulations. Int J Pharm 2016; 512:273-281. [PMID: 27576667 DOI: 10.1016/j.ijpharm.2016.08.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
Nosocomial infections have emerged as important causes of morbidity and mortality in immunocompromised individuals. In this respect, biocides are widely used in hospitals leading to resistant microorganisms. We show here that cyclodextrins can remarkably boost the virucidal activity of di-n-decyldimethylammonium chloride. These oligosaccharides synergistically work with the biocide affording a noticeable reduction of the active virucide concentration between 40 and 85%. Partial replacement of a significant amount of the biocide by eco- and bio-compatible cyclodextrins whilst maintaining the same activity is of great interest as it allows the reduction of the toxicological drawbacks of classical biocide mixtures.
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Affiliation(s)
- Loïc Leclercq
- Univ. Lille, CNRS, ENSCL, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide-Equipe CÏSCO, F-59000 Lille, France.
| | - Anny Dewilde
- Univ. Lille, Faculté de Médecine, UPRES EA 3610, Institut de Microbiologie, Laboratoire de Virologie, CHRU Lille, F-59037 Lille Cedex, France
| | - Jean-Marie Aubry
- Univ. Lille, CNRS, ENSCL, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide-Equipe CÏSCO, F-59000 Lille, France
| | - Véronique Nardello-Rataj
- Univ. Lille, CNRS, ENSCL, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide-Equipe CÏSCO, F-59000 Lille, France.
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4
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Physical interaction and assembly of Bacillus subtilis spore coat proteins CotE and CotZ studied by atomic force microscopy. J Struct Biol 2016; 195:245-251. [DOI: 10.1016/j.jsb.2016.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/12/2016] [Accepted: 06/14/2016] [Indexed: 11/19/2022]
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5
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Nardello-Rataj V, Leclercq L. Aqueous solutions of didecyldimethylammonium chloride and octaethylene glycol monododecyl ether: Toward synergistic formulations against enveloped viruses. Int J Pharm 2016; 511:550-559. [PMID: 27452423 DOI: 10.1016/j.ijpharm.2016.07.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 11/25/2022]
Abstract
Micellization of di-n-decyldimethylammonium chloride, [DiC10][Cl], and octaethylene glycol monododecyl ether, C12E8, mixtures have been investigated by surface tension and conductivity measurements. From these results, various physicochemical and thermodynamic key parameters (e.g. micellar mole fraction of [DiC10][Cl], interaction parameter, free energy of micellization, etc.) have been evaluated and discussed in detail. The results prove high synergistic effect between the two surfactants. Based on these results, the virucidal activity of an equimolar mixture of [DiC10][Cl] and C12E8 has been investigated. A marked synergism was observed on lipid-containing deoxyribonucleic and ribonucleic acid viruses, such as herpes virus, respiratory syncytial virus, and vaccinia viruses. In contrast, Coxsackievirus (non-enveloped virus) was not inactivated. These results support that the mechanism is based on the extraction of lipids and/or proteins from the envelope inside the mixed micelles. This extraction creates "holes" the size of which increases with concentration up to a specific value which triggers the virus inactivation. Such a mixture could be used to extend the spectrum of virucidal activity of the amphiphiles virucides commonly employed in numerous disinfectant solutions.
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Affiliation(s)
| | - Loïc Leclercq
- Univ. Lille, CNRS, ENSCL, UMR 8181UCCS Equipe CÿSCO, F-59000 Lille, France.
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6
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Kämmer E, Götz I, Bocklitz T, Stöckel S, Dellith A, Cialla-May D, Weber K, Zell R, Dellith J, Deckert V, Popp J. Single particle analysis of herpes simplex virus: comparing the dimensions of one and the same virions via atomic force and scanning electron microscopy. Anal Bioanal Chem 2016; 408:4035-41. [PMID: 27052775 DOI: 10.1007/s00216-016-9492-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/12/2016] [Accepted: 03/15/2016] [Indexed: 10/22/2022]
Abstract
Currently, two types of direct methods to characterize and identify single virions are available: electron microscopy (EM) and scanning probe techniques, especially atomic force microscopy (AFM). AFM in particular provides morphologic information even of the ultrastructure of viral specimens without the need to cultivate the virus and to invasively alter the sample prior to the measurements. Thus, AFM can play a critical role as a frontline method in diagnostic virology. Interestingly, varying morphological parameters for virions of the same type can be found in the literature, depending on whether AFM or EM was employed and according to the respective experimental conditions during the AFM measurements. Here, an inter-methodological proof of principle is presented, in which the same single virions of herpes simplex virus 1 were probed by AFM previously and after they were measured by scanning electron microscopy (SEM). Sophisticated chemometric analyses then allowed a calculation of morphological parameters of the ensemble of single virions and a comparison thereof. A distinct decrease in the virions' dimensions was found during as well as after the SEM analyses and could be attributed to the sample preparation for the SEM measurements. Graphical abstract The herpes simplex virus is investigated with scanning electron and atomic force microscopy in view of varying dimensions.
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Affiliation(s)
- Evelyn Kämmer
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany.,InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany
| | - Isabell Götz
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany.,InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany
| | - Thomas Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany. .,Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany. .,InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany.
| | - Stephan Stöckel
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany
| | - Andrea Dellith
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Dana Cialla-May
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany.,InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany
| | - Karina Weber
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany.,InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany
| | - Roland Zell
- Department of Virology and Antiviral Therapy, Jena University Hospital, Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Jan Dellith
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Volker Deckert
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany.,InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745, Jena, Germany.,InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany
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7
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Chen SWW, Teulon JM, Godon C, Pellequer JL. Atomic force microscope, molecular imaging, and analysis. J Mol Recognit 2015. [PMID: 26224520 DOI: 10.1002/jmr.2491] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Image visibility is a central issue in analyzing all kinds of microscopic images. An increase of intensity contrast helps to raise the image visibility, thereby to reveal fine image features. Accordingly, a proper evaluation of results with current imaging parameters can be used for feedback on future imaging experiments. In this work, we have applied the Laplacian function of image intensity as either an additive component (Laplacian mask) or a multiplying factor (Laplacian weight) for enhancing image contrast of high-resolution AFM images of two molecular systems, an unknown protein imaged in air, provided by AFM COST Action TD1002 (http://www.afm4nanomedbio.eu/), and tobacco mosaic virus (TMV) particles imaged in liquid. Based on both visual inspection and quantitative representation of contrast measurements, we found that the Laplacian weight is more effective than the Laplacian mask for the unknown protein, whereas for the TMV system the strengthened Laplacian mask is superior to the Laplacian weight. The present results indicate that a mathematical function, as exemplified by the Laplacian function, may yield varied processing effects with different operations. To interpret the diversity of molecular structure and topology in images, an explicit expression for processing procedures should be included in scientific reports alongside instrumental setups.
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Affiliation(s)
| | - Jean-Marie Teulon
- CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire, F-30207, Bagnols sur Cèze, France.,CEA, IBS, Univ. Grenoble Alpes/CNRS/CEA, 71 avenue des Martyrs CS 10090, F-38044, Grenoble cedex 9, France
| | - Christian Godon
- CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire, F-30207, Bagnols sur Cèze, France.,CEA, iBEB, Service de Biologie Végétale et Microbiologie Environnementale/LBDP, F-13108, Saint-Paul-Lez-Durance, France
| | - Jean-Luc Pellequer
- CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire, F-30207, Bagnols sur Cèze, France.,CEA, IBS, Univ. Grenoble Alpes/CNRS/CEA, 71 avenue des Martyrs CS 10090, F-38044, Grenoble cedex 9, France
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8
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Bernaud J, Castelnovo M, Muriaux D, Faivre-Moskalenko C. [Atomic force microscopy: a tool to analyze the viral cycle]. Med Sci (Paris) 2015; 31:522-8. [PMID: 26059303 DOI: 10.1051/medsci/20153105014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Each step of the HIV-1 life cycle frequently involves a change in the morphology and/or mechanical properties of the viral particle or core. The atomic force microscope (AFM) constitutes a powerful tool for characterizing these physical changes at the scale of a single virus. Indeed, AFM enables the visualization of viral capsids in a controlled physiological environment and to probe their mechanical properties by nano-indentation. Finally, AFM force spectroscopy allows to characterize the affinities between viral envelope proteins and cell receptors at the single molecule level.
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Affiliation(s)
- Julien Bernaud
- Laboratoire de physique, CNRS UMR 5672, Ecole normale supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Martin Castelnovo
- Laboratoire de physique, CNRS UMR 5672, Ecole normale supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Delphine Muriaux
- Centre d'étude d'agents pathogènes et biotechnologie pour la santé, CNRS UMR 5236, 1919, route de Mende, 34 293 Montpellier Cedex 5, France
| | - Cendrine Faivre-Moskalenko
- Laboratoire de physique, CNRS UMR 5672, Ecole normale supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
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9
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de Pablo PJ, Carrión-Vázquez M. Imaging biological samples with atomic force microscopy. Cold Spring Harb Protoc 2014; 2014:167-77. [PMID: 24492779 DOI: 10.1101/pdb.top080473] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Atomic force microscopy (AFM) is an invaluable tool both for obtaining high-resolution topographical images and for determining the values of mechanical and structural properties of specimens adsorbed onto a surface. AFM is useful in an array of fields and applications, from materials science to biology. It is an extremely versatile technique that can be applied to almost any surface-mounted sample and can be operated in ambient air, ultrahigh vacuum, and, most importantly for biology, liquids. AFM can be used to explore samples ranging in size from atoms to molecules, molecular aggregates, and cells. Individual biomolecules can be viewed and manipulated at the nanoscale, providing fundamental biological information. In particular, the study of the mechanical properties of biomolecular aggregates at the nanoscale constitutes an important source of data to elaborate mechanochemical structure/function models of single-particle biomachines, expanding and complementing the information obtained from bulk experiments.
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Abstract
Atomic force microscopy (AFM) is a helpful tool to acquire nanometric-resolution images, and also to perform a certain physical characterization of specimens, including their stiffness and mechanical resilience. Besides of the wide range of applications, from materials science to biology, this technique works in a variety of conditions as long as the sample is supported on a solid surface, in air, ultra high vacuum or, most importantly for virus research, in liquids. The adaptability of this technique is also fostered by the variety of sizes of the specimens that it can dealt with, such as atoms, molecules, molecular complexes including viruses and cells, and the possibility to observe dynamic processes in real time. Indeed, AFM facilitates single molecule experiments enabling not only to see but also to touch the material under study (i.e., to undertake mechanical manipulations), and constitutes a fundamental source of information for material characterization. In particular, the study of the mechanical properties at the nanoscale of viruses and other biomolecular aggregates, is providing an important set of data which help to elaborate mechano-chemical structure/function models of molecular biomachines, expanding and complementing the information obtained by other structural techniques.
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Affiliation(s)
- Pedro J de Pablo
- Department of Physics of the Condensed Matter, C03, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain,
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Castellanos M, Pérez R, Carrillo PJP, de Pablo PJ, Mateu MG. Mechanical disassembly of single virus particles reveals kinetic intermediates predicted by theory. Biophys J 2012; 102:2615-24. [PMID: 22713577 DOI: 10.1016/j.bpj.2012.04.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/30/2012] [Accepted: 04/17/2012] [Indexed: 01/22/2023] Open
Abstract
New experimental approaches are required to detect the elusive transient intermediates predicted by simulations of virus assembly or disassembly. Here, an atomic force microscope (AFM) was used to mechanically induce partial disassembly of single icosahedral T=1 capsids and virions of the minute virus of mice. The kinetic intermediates formed were imaged by AFM. The results revealed that induced disassembly of single minute-virus-of-mice particles is frequently initiated by loss of one of the 20 equivalent capsomers (trimers of capsid protein subunits) leading to a stable, nearly complete particle that does not readily lose further capsomers. With lower frequency, a fairly stable, three-fourths-complete capsid lacking one pentamer of capsomers and a free, stable pentamer were obtained. The intermediates most frequently identified (capsids missing one capsomer, capsids missing one pentamer of capsomers, and free pentamers of capsomers) had been predicted in theoretical studies of reversible capsid assembly based on thermodynamic-kinetic models, molecular dynamics, or oligomerization energies. We conclude that mechanical manipulation and imaging of simple virus particles by AFM can be used to experimentally identify kinetic intermediates predicted by simulations of assembly or disassembly.
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Affiliation(s)
- Milagros Castellanos
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Departamento de Física de la Materia Condensada C-III, Universidad Autónoma de Madrid, Madrid, Spain
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12
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Abstract
Atomic force microscopy (AFM) has proven to be a valuable approach to delineate the architectures and detailed structural features of a wide variety of viruses. These have ranged from small plant satellite viruses of only 17 nm to the giant mimivirus of 750 nm diameter, and they have included diverse morphologies such as those represented by HIV, icosahedral particles, vaccinia, and bacteriophages. Because it is a surface technique, it provides images and information that are distinct from those obtained by electron microscopy, and in some cases, at even higher resolution. By enzymatic and chemical dissection of virions, internal structures can be revealed, as well as DNA and RNA. The method is relatively rapid and can be carried out on both fixed and unfixed samples in either air or fluids, including culture media. It is nondestructive and even non-perturbing. It can be applied to individual isolated virus, as well as to infected cells. AFM is still in its early development and holds great promise for further investigation of biological systems at the nanometer scale.
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Affiliation(s)
- Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
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13
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Kuznetsov YG, McPherson A. Atomic force microscopy in imaging of viruses and virus-infected cells. Microbiol Mol Biol Rev 2011; 75:268-85. [PMID: 21646429 PMCID: PMC3122623 DOI: 10.1128/mmbr.00041-10] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Atomic force microscopy (AFM) can visualize almost everything pertinent to structural virology and at resolutions that approach those for electron microscopy (EM). Membranes have been identified, RNA and DNA have been visualized, and large protein assemblies have been resolved into component substructures. Capsids of icosahedral viruses and the icosahedral capsids of enveloped viruses have been seen at high resolution, in some cases sufficiently high to deduce the arrangement of proteins in the capsomeres as well as the triangulation number (T). Viruses have been recorded budding from infected cells and suffering the consequences of a variety of stresses. Mutant viruses have been examined and phenotypes described. Unusual structural features have appeared, and the unexpectedly great amount of structural nonconformity within populations of particles has been documented. Samples may be imaged in air or in fluids (including culture medium or buffer), in situ on cell surfaces, or after histological procedures. AFM is nonintrusive and nondestructive, and it can be applied to soft biological samples, particularly when the tapping mode is employed. In principle, only a single cell or virion need be imaged to learn of its structure, though normally images of as many as is practical are collected. While lateral resolution, limited by the width of the cantilever tip, is a few nanometers, height resolution is exceptional, at approximately 0.5 nm. AFM produces three-dimensional, topological images that accurately depict the surface features of the virus or cell under study. The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM.
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Affiliation(s)
- Yurii G. Kuznetsov
- University of California, Irvine, Department of Molecular Biology and Biochemistry, 560 Steinhaus Hall, Irvine, California 92697-3900
| | - Alexander McPherson
- University of California, Irvine, Department of Molecular Biology and Biochemistry, 560 Steinhaus Hall, Irvine, California 92697-3900
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14
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Coelho-Dos-Reis JGA, Gomes OA, Bortolini DE, Martins ML, Almeida MR, Martins CS, Carvalho LD, Souza JG, Vilela JMC, Andrade MS, Barbosa-Stancioli EF. Evaluation of the effects of Quercetin and Kaempherol on the surface of MT-2 cells visualized by atomic force microscopy. J Virol Methods 2011; 174:47-52. [PMID: 21507333 DOI: 10.1016/j.jviromet.2011.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/10/2011] [Accepted: 03/15/2011] [Indexed: 02/08/2023]
Abstract
This study investigated the anti-viral effects of the polyphenolic compounds Quercetin and Kaempherol on the release of HTLV-1 from the surface of MT-2 cells. Atomic force microscopy (AFM) was used to scan the surface of the MT-2 cells. MT-2 cells were fixed with 100% methanol on round glass lamina or cleaved mica and dried under UV light and laminar flow. The images were captured on a Multimode equipment monitored by a NanoScope IIId controller from Veeco Instruments Inc operated in tapping mode and equipped with phase-imaging hardware. The images demonstrated viral budding structures 131 ± 57 nm in size, indicating profuse viral budding. Interestingly, cell-free viruses and budding structures visualized on the surface of cells were less common when MT-2 was incubated with Quercetin, and no particles were seen on the surface of cells incubated with Kaempherol. In summary, these data indicate that HTLV-1 is budding constantly from the MT-2 cell surface and that polyphenolic compounds were able to reduce this viral release. Biological samples were analyzed with crude cell preparations just after cultivation in the presence of Quercetin and Kaempherol, showing that the AFM technique is a rapid and powerful tool for analysis of antiviral activity of new biological compounds.
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15
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Abstract
Atomic force microscopy (AFM) is an invaluable tool not only to obtain high-resolution topographical images, but also to determine certain physical properties of specimens, such as their mechanical properties and composition. In addition to the wide range of applications, from materials science to biology, this technique can be operated in a number of environments as long as the specimen is attached to a surface, including ambient air, ultra high vacuum (UHV), and most importantly for biology, in liquids. The versatility of this technique is also reflected by the wide range of sizes of the sample that can dealt with, such as atoms, molecules, molecular aggregates, and cells. Indeed, this technique enables biological problems to be tackled from the single-molecule point of view and it allows not only to see but also to touch the material under study (i.e., mechanical manipulation at the nanoscale), a fundamental source of information for its characterization. In particular, the study of the mechanical properties at the nanoscale of biomolecular aggregates constitute an important source of data to elaborate mechano-chemical structure/function models of single-particle biomachines, expanding and complementing the information obtained from bulk experiments.
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Affiliation(s)
- Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.
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16
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Hermann P, Hermelink A, Lausch V, Holland G, Möller L, Bannert N, Naumann D. Evaluation of tip-enhanced Raman spectroscopy for characterizing different virus strains. Analyst 2011; 136:1148-52. [DOI: 10.1039/c0an00531b] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Archakov AI, Ivanov YD. Application of AFM and optical biosensor for investigation of complexes formed in P450-containing monooxygenase systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:102-10. [PMID: 20832504 DOI: 10.1016/j.bbapap.2010.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/20/2010] [Accepted: 08/29/2010] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) allows to visualize and count the individual protein molecules and their complexes within multiprotein systems. On the other hand, optical biosensor (OB) provides information on complex formation kinetics as well as complex lifetime (τ(LT)) and affinity. Comparison of complex lifetime τ(LT) with the time required for enzyme's catalytic cycle (τ(cat)) enables to characterize productive complexes and distinguish them from non-productive ones. Both these approaches were applied for the analysis of the three cytochrome P450-containing monooxygenase systems: cytochrome P450 101, cytochrome P450 11A1 and cytochrome P450 2B4. By using AFM, the formation of binary and ternary protein complexes was registered in all the three systems. OB analysis enabled to kinetically characterize these binary and ternary complexes. It was shown that the binary complexes putidaredoxin reductase (PdR)/putidaredoxin (Pd) and Pd/cytochrome P450 101 (P450 101) formed within the P450 101 system and, also, the binary complexes adrenodoxin reductase (AdR)/adrenodoxin (Ad) and Ad/cytochrome P450 11A1 (P450 11A1) formed within the P450 11A1 system are non-productive (deadlock). At the same time, the ternary PdR/Pd/P450 101 and AdR/Ad/P450 11A1 complexes proved to be productive. The binary cytochrome P450 reductase (Fp)/cytochrome P450 2B4 (2B4) complexes and the ternary Fp/2B4/cytochrome b5 (b5) complexes formed within P450 2B4 system were productive.
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Affiliation(s)
- A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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18
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Kuznetsov YG, Martiny JBH, McPherson A. Structural analysis of a Synechococcus myovirus S-CAM4 and infected cells by atomic force microscopy. J Gen Virol 2010; 91:3095-104. [PMID: 20739271 DOI: 10.1099/vir.0.025254-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A tailed cyanophage, S-CAM4 (family Myoviridae) from California coastal waters that infects Synechococcus, was characterized by atomic force microscopy. Capsomeric clusters of protein composing the 85 nm diameter icosahedral head were resolved and indicated a triangulation number of T=16. The 140 nm tail assembly, exhibiting a helical appearance with a 13 nm pitch, was seen in both extended and contracted states, the latter exposing the injection tube within. Attached below the base plate were six 50 nm long fibres, and six fibres 275-300 nm in length protruded from the periphery of the base plate. Protein-free DNA was abundant from ruptured heads. Virus attached en masse, in clusters and individually to cells, and cell fragments were recorded, as were perforated cells lysed by the phages. The capsid structure appears most closely related to that of the cyanophage Syn9 and the Bacillus subtilis phage SPO1, which may, in turn, be evolutionarily related to herpesvirus.
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Affiliation(s)
- Yuri G Kuznetsov
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
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19
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Zink M, Grubmüller H. Primary changes of the mechanical properties of Southern Bean Mosaic Virus upon calcium removal. Biophys J 2010; 98:687-95. [PMID: 20159165 DOI: 10.1016/j.bpj.2009.10.047] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 10/29/2009] [Accepted: 10/30/2009] [Indexed: 01/21/2023] Open
Abstract
The mechanical properties of viral shells are crucial determinates for the pathway and mechanism by which the genetic material leaves the capsid during infection and have therefore been studied by atomic force microscopy as well as by atomistic simulations. The mechanical response to forces from inside the capsid are found to be relevant, especially after ion removal from the shell structure, which is generally assumed to be essential during viral infection; however, atomic force microscopy measurements are restricted to probing the capsids from outside, and the primary effect of ion removal is still inaccessible. To bridge this gap, we performed atomistic force-probe molecular dynamics simulations of the complete solvated icosahedral shell of Southern Bean Mosaic Virus and compared the distribution of elastic constants and yielding forces on the icosahedral shell for probing from inside with the distribution of outside mechanical properties obtained previously. Further, the primary effect of calcium removal on the mechanical properties on both sides, as well as on their spatial distribution, is quantified. Marked differences are seen particularly at the pentamer centers, although only small structural changes occur on the short timescales of the simulation. This unexpected primary effect, hence, precedes subsequent effects due to capsid swelling. In particular, assuming that genome release is preceded by an opening of capsomers instead of a complete capsid bursting, our observed weakening along the fivefold symmetry axes let us suggest pentamers as possible exit ports for RNA release.
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Affiliation(s)
- Mareike Zink
- Max-Planck-Institute for Biophysical Chemistry, Department of Theoretical and Computational Biophysics, Göttingen, Germany.
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20
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Wark AW, Lee J, Kim S, Faisal SN, Lee HJ. Bioaffinity detection of pathogens on surfaces. J IND ENG CHEM 2010; 16:169-177. [PMID: 32288511 PMCID: PMC7129010 DOI: 10.1016/j.jiec.2010.01.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 12/04/2009] [Indexed: 01/12/2023]
Abstract
The demand for improved technologies capable of rapidly detecting pathogens with high sensitivity and selectivity in complex environments continues to be a significant challenge that helps drive the development of new analytical techniques. Surface-based detection platforms are particularly attractive as multiple bioaffinity interactions between different targets and corresponding probe molecules can be monitored simultaneously in a single measurement. Furthermore, the possibilities for developing new signal transduction mechanisms alongside novel signal amplification strategies are much more varied. In this article, we describe some of the latest advances in the use of surface bioaffinity detection of pathogens. Three major sections will be discussed: (i) a brief overview on the choice of probe molecules such as antibodies, proteins and aptamers specific to pathogens and surface attachment chemistries to immobilize those probes onto various substrates, (ii) highlighting examples among the current generation of surface biosensors, and (iii) exploring emerging technologies that are highly promising and likely to form the basis of the next generation of pathogenic sensors.
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Affiliation(s)
- Alastair W. Wark
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, UK
| | - Jaeyoung Lee
- Electrochemical Reaction and Technology Laboratory, Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, Republic of Korea
| | - Suhee Kim
- Department of Chemistry, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Republic of Korea
| | - Shaikh Nayeem Faisal
- Department of Chemistry, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Republic of Korea
| | - Hye Jin Lee
- Department of Chemistry, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Republic of Korea
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21
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Zink M, Grubmüller H. Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study. Biophys J 2009; 96:1350-63. [PMID: 19217853 PMCID: PMC2717248 DOI: 10.1016/j.bpj.2008.11.028] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Accepted: 11/19/2008] [Indexed: 12/16/2022] Open
Abstract
The mechanical properties of viral shells are crucial for viral assembly and infection. To study their distribution and heterogeneity on the viral surface, we performed atomistic force-probe molecular dynamics simulations of the complete shell of southern bean mosaic virus, a prototypical T = 3 virus, in explicit solvent. The simulation system comprised more than 4,500,000 atoms. To facilitate direct comparison with atomic-force microscopy (AFM) measurements, a Lennard-Jones sphere was used as a model of the AFM tip, and was pushed with different velocities toward the capsid protein at 19 different positions on the viral surface. A detailed picture of the spatial distribution of elastic constants and yielding forces was obtained that can explain corresponding heterogeneities observed in previous AFM experiments. Our simulations reveal three different deformation regimes: a prelinear regime of outer surface atom rearrangements, a linear regime of elastic capsid deformation, and a rearrangement regime that describes irreversible structural changes and the transition from elastic to plastic deformation. For both yielding forces and elastic constants, a logarithmic velocity dependency is evident over nearly two decades, the explanation for which requires including nonequilibrium effects within the established theory of enforced barrier crossing.
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Affiliation(s)
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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22
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Abstract
The term "biological complexes" broadly encompasses particles as diverse as multisubunit enzymes, viral capsids, transport cages, molecular nets, ribosomes, nucleosomes, biological membrane components and amyloids. The complexes represent a broad range of stability and composition. Atomic force microscopy offers a wealth of structural and functional data about such assemblies. For this review, we choose to comment on the significance of AFM to study various aspects of biology of selected nonmembrane protein assemblies. Such particles are large enough to reveal many structural details under the AFM probe. Importantly, the specific advantages of the method allow for gathering dynamic information about their formation, stability or allosteric structural changes critical for their function. Some of them have already found their way to nanomedical or nanotechnological applications. Here we present examples of studies where the AFM provided pioneering information about the biology of complexes, and examples of studies where the simplicity of the method is used toward the development of potential diagnostic applications.
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23
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Abstract
Vaccinia virus was treated in a controlled manner with various combinations of nonionic detergents, reducing agents, and proteolytic enzymes, and successive products of the reactions were visualized using atomic force microscopy (AFM). Following removal of the outer lipid/protein membrane, a layer 20 to 40 nm in thickness was encountered that was composed of fibrous elements which, under reducing conditions, rapidly decomposed into individual monomers on the substrate. Beneath this layer was the virus core and its prominent lateral bodies, which could be dissociated or degraded with proteases. The core, in addition to the lateral bodies, was composed of a thick, multilayered shell of proteins of diverse sizes and shapes. The shell, which was readily etched with proteases, was thoroughly permeated with pores, or channels. Prolonged exposure to proteases and reductants produced disgorgement of the viral DNA from the remainders of the cores and also left residual, flattened, protease-resistant sacs on the imaging substrate. The DNA was readily visualized by AFM, which revealed some regions to be "soldered" by proteins, others to be heavily complexed with protein, and yet other parts to apparently exist as bundled, naked DNA. Prolonged exposure to proteases deproteinized the DNA, leaving masses of extended, free DNA. Estimates of the interior core volume suggest moderate but not extreme compaction of the genome.
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24
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Arduino PG, Porter SR. Herpes Simplex Virus Type 1 infection: overview on relevant clinico-pathological features. J Oral Pathol Med 2008; 37:107-21. [PMID: 18197856 DOI: 10.1111/j.1600-0714.2007.00586.x] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herpes Simplex Virus Type 1 (HSV-1) is a nuclear replicating enveloped virus, usually acquired through direct contact with infected lesions or body fluids (typically saliva). The prevalence of HSV-1 infection increases progressively from childhood, the seroprevalence being inversely related to socioeconomic background. Primary HSV-1 infections in children are either asymptomatic or following an incubation period of about 1 week gives rise to mucocutaneous vesicular eruptions. Herpetic gingivostomatitis typically affects the tongue, lips, gingival, buccal mucosa and the hard and soft palate. Most primary oro-facial HSV infection is caused by HSV-1, infection by HSV-2 is increasingly common. Recurrent infections, which occur at variable intervals, typically give rise to vesiculo-ulcerative lesions at mucocutaneous junctions particularly the lips (herpes labialis). Recurrent HSV-1 infection within the mouth is uncommon in otherwise healthy patients, although in immunocompromised patients, recurrent infection can be more extensive and/or aggressive. The diagnosis of common herpetic infection can usually be based upon the clinical history and presenting features. Confirmatory laboratory diagnosis is, however, required when patients are, or may be, immunocompromised.
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Affiliation(s)
- Paolo G Arduino
- Department of Biomedical Sciences and Human Oncology, Oral Medicine Section, University of Turin, Turin, Italy.
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25
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Roos WH, Ivanovska IL, Evilevitch A, Wuite GJL. Viral capsids: mechanical characteristics, genome packaging and delivery mechanisms. Cell Mol Life Sci 2007; 64:1484-97. [PMID: 17440680 PMCID: PMC2771126 DOI: 10.1007/s00018-007-6451-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The main functions of viral capsids are to protect, transport and deliver their genome. The mechanical properties of capsids are supposed to be adapted to these tasks. Bacteriophage capsids also need to withstand the high pressures the DNA is exerting onto it as a result of the DNA packaging and its consequent confinement within the capsid. It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. DNA packaging and ejection strategies are obviously dependent on the mechanical properties of the capsid. This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular.
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Affiliation(s)
- W. H. Roos
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - I. L. Ivanovska
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - A. Evilevitch
- Department of Biochemistry, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - G. J. L. Wuite
- Fysica van complexe systemen, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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26
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Trindade G, Vilela J, Ferreira J, Aguiar P, Leite J, Guedes M, Lobato Z, Madureira M, da Silva M, da Fonseca F, Kroon E, Andrade M. Use of atomic force microscopy as a diagnostic tool to identify orthopoxvirus. J Virol Methods 2007; 141:198-204. [DOI: 10.1016/j.jviromet.2006.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 12/08/2006] [Accepted: 12/12/2006] [Indexed: 11/30/2022]
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27
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Kuznetsov YG, Ulbrich P, Haubova S, Ruml T, McPherson A. Atomic force microscopy investigation of Mason-Pfizer monkey virus and human immunodeficiency virus type 1 reassembled particles. Virology 2006; 360:434-46. [PMID: 17123565 DOI: 10.1016/j.virol.2006.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2006] [Revised: 09/18/2006] [Accepted: 10/06/2006] [Indexed: 11/22/2022]
Abstract
Particles of DeltaProCANC, a fusion of capsid (CA) and nucleocapsid (NC) protein of Mason-Pfizer monkey virus (M-PMV), which lacks the amino terminal proline, were reassembled in vitro and visualized by atomic force microscopy (AFM). The particles, of 83-84 nm diameter, exhibited ordered domains based on trigonal arrays of prominent rings with center to center distances of 8.7 nm. Imperfect closure of the lattice on the spherical surface was affected by formation of discontinuities. The lattice is consistent only with plane group p3 where one molecule is shared between contiguous rings. There are no pentameric clusters nor evidence that the particles are icosahedral. Tubular structures were also reassembled, in vitro, from two HIV fusion proteins, DeltaProCANC and CANC. The tubes were uniform in diameter, 40 nm, but varied in length to a maximum of 600 nm. They exhibited left handed helical symmetry based on a p6 hexagonal net. The organization of HIV fusion proteins in the tubes is significantly different than for the protein units in the particles of M-PMV DeltaProCANC.
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Affiliation(s)
- Yu G Kuznetsov
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 560 SH, Irvine, CA 92697-3900, USA
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28
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Kuznetsov YG, McPherson A. Identification of DNA and RNA from retroviruses using ribonuclease A. SCANNING 2006; 28:278-81. [PMID: 17063767 DOI: 10.1002/sca.4950280506] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Retroviruses, such as human immunodeficiency virus (HIV), can be disrupted with chemical agents and made to disgorge their encapsidated nucleic acid. The products can be visualized by atomic force microscopy (AFM). Retroviruses may contain both viral genomic RNA and reverse transcribed DNA produced prior to integration into the host cell genome. It is necessary to know which molecules are RNA and which are DNA in order to interpret the events that transpire during infection. DNA, when imaged by AFM, is generally between one and two nanometers in thickness, more regular in its contours, and it is relatively uniform in height over its entire length; RNA, on the other hand, is less than a nanometer in thickness within single stranded regions, but varies dramatically in height over its length due to the presence of secondary structural domains. These observations, however, are often not definitive. Nonetheless, we have been able to tell one from the other using AFM, by exposing the molecules, in buffer, to moderate concentrations of RNase A. Upon exposure to the enzyme, the DNA, which cannot be cleaved, becomes coated with the protein, and the nucleic acid-protein complex exhibits a height of about three times that of the native molecule, appearing as thick cords. RNA, however, is degraded by the single strand specific RNase A into short, stable, presumably double-stranded segments, reflecting its pattern of secondary structure. Using this approach, we obtained evidence that reverse transcription of RNA into DNA may occur within the retroviral capsid.
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Affiliation(s)
- Yuri G Kuznetsov
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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29
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Jensen HL. Herpes simplex virus type 1 morphogenesis and virus-cell interactions: significance of cytoskeleton and methodological aspects. APMIS 2006:7-55. [PMID: 16930175 DOI: 10.1111/j.1600-0463.2006.apm_v114_s119.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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30
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Shahin V, Hafezi W, Oberleithner H, Ludwig Y, Windoffer B, Schillers H, Kühn JE. The genome of HSV-1 translocates through the nuclear pore as a condensed rod-like structure. J Cell Sci 2005; 119:23-30. [PMID: 16339172 DOI: 10.1242/jcs.02705] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Incoming herpes simplex virus type-1 (HSV-1) capsids are known to dock to the nuclear pore complex (NPC) and release their genome. It has remained elusive, however, how the huge viral DNA translocates through the comparatively small NPC channel. In the present study, the interaction of HSV-1 with NPCs was analyzed by atomic force microscopy. In addition to capsids, smaller subviral structures--most with a diameter of 35-40 nm and a length of 130-160 nm--were visualized at the cytoplasmic side of the NPC. These components differed from capsids in their adhesion and stiffness properties, and were the sole subviral structures translocated through dilated NPCs towards the nucleus. It is presumed that they are the HSV-1 genome, and that a change in NPC conformation allows translocation of this genome as a densely packaged, rodlike structure.
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Affiliation(s)
- Victor Shahin
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, 48149 Münster, Germany.
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31
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Plomp M, Leighton TJ, Wheeler KE, Pitesky ME, Malkin AJ. Bacillus atrophaeus outer spore coat assembly and ultrastructure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:10710-6. [PMID: 16262341 DOI: 10.1021/la0517437] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Our previous atomic force microscopy (AFM) studies successfully visualized native Bacillus atrophaeus spore coat ultrastructure and surface morphology. We have shown that the outer spore coat surface is formed by a crystalline array of approximately 11 nm thick rodlets, having a periodicity of approximately 8 nm. We present here further AFM ultrastructural investigations of air-dried and fully hydrated spore surface architecture. In the rodlet layer planar and point defects as well as domain boundaries similar to those described for inorganic and macromolecular crystals were identified. For several Bacillus species rodlet structure assembly and architectural variation appear to be a consequence of species-specific nucleation and crystallization mechanisms that regulate the formation of the outer spore coat. We propose a unifying mechanism for nucleation and self-assembly of this crystalline layer on the outer spore coat surface.
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Affiliation(s)
- Marco Plomp
- BioSecurity and NanoSciences Laboratory, Department of Chemistry and Materials Science, Lawrence Livermore National Laboratory, California 94551, USA
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32
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Plomp M, Leighton TJ, Wheeler KE, Malkin AJ. Architecture and high-resolution structure of Bacillus thuringiensis and Bacillus cereus spore coat surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:7892-8. [PMID: 16089397 DOI: 10.1021/la050412r] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We have utilized atomic force microscopy (AFM) to visualize the native surface topography and ultrastructure of Bacillus thuringiensis and Bacillus cereus spores in water and in air. AFM was able to resolve the nanostructure of the exosporium and three distinctive classes of appendages. Removal of the exosporium exposed either a hexagonal honeycomb layer (B. thuringiensis) or a rodlet outer spore coat layer (B. cereus). Removal of the rodlet structure from B. cereus spores revealed an underlying honeycomb layer similar to that observed with B. thuringiensis spores. The periodicity of the rodlet structure on the outer spore coat of B. cereus was approximately 8 nm, and the length of the rodlets was limited to the cross-patched domain structure of this layer to approximately 200 nm. The lattice constant of the honeycomb structures was approximately 9 nm for both B. cereus and B. thuringiensis spores. Both honeycomb structures were composed of multiple, disoriented domains with distinct boundaries. Our results demonstrate that variations in storage and preparation procedures result in architectural changes in individual spore surfaces, which establish AFM as a useful tool for evaluation of preparation and processing "fingerprints" of bacterial spores. These results establish that high-resolution AFM has the capacity to reveal species-specific assembly and nanometer scale structure of spore surfaces. These species-specific spore surface structural variations are correlated with sequence divergences in a spore core structural protein SspE.
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Affiliation(s)
- Marco Plomp
- BioSecurity and NanoSciences Laboratory, Department of Chemistry and Materials Science, Lawrence Livermore National Laboratory, L-234, Livermore, California 94551, USA
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33
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Plomp M, Leighton TJ, Wheeler KE, Malkin AJ. The high-resolution architecture and structural dynamics of Bacillus spores. Biophys J 2005; 88:603-8. [PMID: 15501940 PMCID: PMC1305037 DOI: 10.1529/biophysj.104.049312] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Accepted: 10/13/2004] [Indexed: 12/28/2022] Open
Abstract
The capability to image single microbial cell surfaces at nanometer scale under native conditions would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, environmental resistance, and biotransformation. Here, using in vitro atomic force microscopy, we have directly visualized high-resolution native structures of bacterial endospores, including the exosporium and spore coats of four Bacillus species in air and water environments. Our results demonstrate that the mechanisms of spore coat self-assembly are similar to those described for inorganic and macromolecular crystallization. The dimensions of individual Bacillus atrophaeus spores decrease reversibly by 12% in response to a change in the environment from fully hydrated to air-dried state, establishing that the dormant spore is a dynamic physical structure. The interspecies distributions of spore length and width were determined for four species of Bacillus spores in water and air environments. The dimensions of individual spores differ significantly depending upon species, growth regimes, and environmental conditions. These findings may be useful in the reconstruction of environmental and physiological conditions during spore formation and for modeling the inhalation and dispersal of spores. This study provides a direct insight into molecular architecture and structural variability of bacterial endospores as a function of spatial and developmental organizational scales.
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Affiliation(s)
- Marco Plomp
- BioSecurity and Nanosciences Laboratory, Lawrence Livermore National Laboratory, Livermore, California; and Children's Hospital Oakland Research Institute, Oakland, California
| | - Terrance J. Leighton
- BioSecurity and Nanosciences Laboratory, Lawrence Livermore National Laboratory, Livermore, California; and Children's Hospital Oakland Research Institute, Oakland, California
| | - Katherine E. Wheeler
- BioSecurity and Nanosciences Laboratory, Lawrence Livermore National Laboratory, Livermore, California; and Children's Hospital Oakland Research Institute, Oakland, California
| | - Alexander J. Malkin
- BioSecurity and Nanosciences Laboratory, Lawrence Livermore National Laboratory, Livermore, California; and Children's Hospital Oakland Research Institute, Oakland, California
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34
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Kuznetsov YG, Victoria JG, Low A, Robinson WE, Fan H, McPherson A. Atomic force microscopy imaging of retroviruses: human immunodeficiency virus and murine leukemia virus. SCANNING 2004; 26:209-216. [PMID: 15536976 DOI: 10.1002/sca.4950260409] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Retroviruses are membrane-enveloped, RNA-containing viruses that produce a wide range of threatening diseases in higher animals. Among these are human immunodeficiency virus (HIV), which produces acquired immune deficiency syndrome (AIDS) in humans, and murine leukemia virus (MuLV), which produces leukemias in rodents. We have obtained the first atomic force microscopy (AFM) images of these two retroviruses, both isolated from culture media and emerging from infected cell surfaces. The HIV virions are 127 nm diameter on average, and those of MuLV are 145 nm, although there are wide distributions about the means. The AFM images show the arrangement of the envelope protein, responsible for host cell entry, on the surfaces of both virions. Disruption of the viruses using detergents or physical means allowed us to visualize interior structures, including the outer shells of both MuLV and HIV, the cores of MuLV, and the nucleic acid of HIV complexed with core proteins. Using immunolabeling techniques borrowed from electron microscopy, we were able to demonstrate the binding of gold-labeled antibodies directed against the envelope protein of MuLV. The AFM images are revealing, not only in terms of surface topology, but in terms of interior features as well, and they reveal the eccentricities and uniqueness of individual virus particles rather than yielding the average member of the population. Further application of AFM to viruses associated with other pathologies may ultimately have a significant impact on the diagnosis and treatment of virus-promoted diseases.
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Affiliation(s)
- Yu G Kuznetsov
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-4800, USA
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Kuznetsov YG, Low A, Fan H, McPherson A. Atomic force microscopy investigation of wild-type Moloney murine leukemia virus particles and virus particles lacking the envelope protein. Virology 2004; 323:189-96. [PMID: 15193915 DOI: 10.1016/j.virol.2004.02.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Accepted: 02/16/2004] [Indexed: 10/26/2022]
Abstract
Moloney murine leukemia virus (M-MuLV) lacking the gene for the envelope glycoprotein (env(-)) was produced in NIH 3T3 cells and investigated using atomic force microscopy (AFM). The particles were compared with similarly produced wild-type virions, some of which had been exposed to a monoclonal antibody against the surface component of the envelope protein (SU protein). The env(-) particles generally exhibit a distinctly different external appearance suggesting only a low density of associated proteins that have an almost fluid, mechanically unstable character. The weakly associated proteins may be host cell membrane proteins that are incorporated into the viral membrane in place of or in addition to virus envelope protein. The amount of this non-viral protein on virion surfaces appears to vary from negligible in most cases to a substantial complement in others. It seems clear that the presence of the envelope protein, in a mechanical sense, significantly strengthens and stabilizes the virion envelope. Binding of monoclonal antibody to wild-type virions indicates that some particles expose a significant amount of antigen while adjacent virions may not. This suggests that the conformation of the envelope glycoprotein or the disposition of oligosaccharides may be different among particles, on some virions exposing the specific epitope, and others little or none.
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Affiliation(s)
- Y G Kuznetsov
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA 92697-3900, USA
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Abstract
Spores produced by bacilli are encased in a proteinaceous multilayered coat and, in some species (including Bacillus anthracis), further surrounded by a glycoprotein-containing exosporium. To characterize bacillus spore surface morphology and to identify proteins that direct formation of coat surface features, we used atomic-force microscopy (AFM) to image the surfaces of wild-type and mutant spores of Bacillus subtilis, as well as the spore surfaces of Bacillus cereus 569 and the Sterne strain of Bacillus anthracis. This analysis revealed that the coat surfaces in these strains are populated by a series of bumps ranging between 7 and 40 nm in diameter, depending on the species. Furthermore, a series of ridges encircled the spore, most of which were oriented along the long axis of the spore. The structures of these ridges differ sufficiently between species to permit species-specific identification. We propose that ridges are formed early in spore formation, when the spore volume likely decreases, and that when the spore swells during germination the ridges unfold. AFM analysis of a set of B. subtilis coat protein gene mutants revealed three coat proteins with roles in coat surface morphology: CotA, CotB, and CotE. Our data indicate novel roles for CotA and CotB in ridge pattern formation. Taken together, these results are consistent with the view that the coat is not inert. Rather, the coat is a dynamic structure that accommodates changes in spore volume.
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Affiliation(s)
- Venkata G R Chada
- Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, USA
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Kuznetsov YG, Victoria JG, Robinson WE, McPherson A. Atomic force microscopy investigation of human immunodeficiency virus (HIV) and HIV-infected lymphocytes. J Virol 2003; 77:11896-909. [PMID: 14581526 PMCID: PMC254268 DOI: 10.1128/jvi.77.22.11896-11909.2003] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Accepted: 08/18/2003] [Indexed: 01/11/2023] Open
Abstract
Isolated human immunodeficiency virus (HIV) and HIV-infected human lymphocytes in culture have been imaged for the first time by atomic force microscopy (AFM). Purified virus particles spread on glass substrates are roughly spherical, reasonably uniform, though pleomorphic in appearance, and have diameters of about 120 nm. Similar particles are also seen on infected cell surfaces, but morphologies and sizes are considerably more varied, possibly a reflection of the budding process. The surfaces of HIV particles exhibit "tufts" of protein, presumably gp120, which do not physically resemble spikes. The protein tufts, which number about 100 per particle, have average diameters of about 200 A, but with a large variance. They likely consist of arbitrary associations of small numbers of gp120 monomers on the surface. In examining several hundred virus particles, we found no evidence that the gp120 monomers form threefold symmetric trimers. Although >95% of HIV-infected H9 lymphocytic cells were producing HIV antigens by immunofluorescent assay, most lymphocytes displayed few or no virus on their surfaces, while others were almost covered by a hundred or more viruses, suggesting a dependence on cell cycle or physiology. HIV-infected cells treated with a viral protease inhibitor and their progeny viruses were also imaged by AFM and were indistinguishable from untreated virions. Isolated HIV virions were disrupted by exposure to mild neutral detergents (Tween 20 and CHAPS) at concentrations from 0.25 to 2.0%. Among the products observed were intact virions, the remnants of completely degraded virions, and partially disrupted particles that lacked sectors of surface proteins as well as virions that were split or broken open to reveal their empty interiors. Capsids containing nucleic acid were not seen, suggesting that the capsids were even more fragile than the envelope and were totally degraded and lost. From these images, a good estimate of the thickness of the envelope protein-membrane-matrix protein outer shell of the virion was obtained. Treatment with even low concentrations (<0.1%) of sodium dodecyl sulfate completely destroyed all virions but produced many interesting products, including aggregates of viral proteins with strands of nucleic acid.
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Affiliation(s)
- Y G Kuznetsov
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, California 92697-3900, USA
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Malkin AJ, McPherson A, Gershon PD. Structure of intracellular mature vaccinia virus visualized by in situ atomic force microscopy. J Virol 2003; 77:6332-40. [PMID: 12743290 PMCID: PMC155008 DOI: 10.1128/jvi.77.11.6332-6340.2003] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2002] [Accepted: 03/04/2003] [Indexed: 11/20/2022] Open
Abstract
Vaccinia virus, the basis of the smallpox vaccine, is one of the largest viruses to replicate in humans. We have used in situ atomic force microscopy (AFM) to directly visualize fully hydrated, intact intracellular mature vaccinia virus (IMV) virions and chemical and enzymatic treatment products thereof. The latter included virion cores, core-enveloping coats, and core substructures. The isolated coats appeared to be composed of a highly cross-linked protein array. AFM imaging of core substructures indicated association of the linear viral DNA genome with a segmented protein sheath forming an extended approximately 16-nm-diameter filament with helical surface topography; enclosure of this filament within a 30- to 40-nm-diameter tubule which also shows helical topography; and enclosure of the folded, condensed 30- to 40-nm-diameter tubule within the core by a wall covered with peg-like projections. Proteins observed attached to the 30- to 40-nm-diameter tubules may mediate folding and/or compaction of the tubules and/or represent vestiges of the core wall and/or pegs. An accessory "satellite domain" was observed protruding from the intact core. This corresponded in size to isolated 70- to 100-nm-diameter particles that were imaged independently and might represent detached accessory domains. AFM imaging of intact virions indicated that IMV underwent a reversible shrinkage upon dehydration (as much as 2.2- to 2.5-fold in the height dimension), accompanied by topological and topographical changes, including protrusion of the satellite domain. As shown here, the chemical and enzymatic dissection of large, asymmetrical virus particles in combination with in situ AFM provides an informative complement to other structure determination techniques.
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Affiliation(s)
- A J Malkin
- BioSecurity and NanoSciences Laboratory, Department of Chemistry and Materials Science, Lawrence Livermore National Laboratory, California 94551, USA.
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