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Villanueva Valencia JR, Tsimtsirakis E, Krueger S, Evilevitch A. Temperature-induced DNA density transition in phage λ capsid revealed with contrast-matching SANS. Proc Natl Acad Sci U S A 2023; 120:e2220518120. [PMID: 37903276 PMCID: PMC10636372 DOI: 10.1073/pnas.2220518120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 09/25/2023] [Indexed: 11/01/2023] Open
Abstract
Structural details of a genome packaged in a viral capsid are essential for understanding how the structural arrangement of a viral genome in a capsid controls its release dynamics during infection, which critically affects viral replication. We previously found a temperature-induced, solid-like to fluid-like mechanical transition of packaged λ-genome that leads to rapid DNA ejection. However, an understanding of the structural origin of this transition was lacking. Here, we use small-angle neutron scattering (SANS) to reveal the scattering form factor of dsDNA packaged in phage λ capsid by contrast matching the scattering signal from the viral capsid with deuterated buffer. We used small-angle X-ray scattering and cryoelectron microscopy reconstructions to determine the initial structural input parameters for intracapsid DNA, which allows accurate modeling of our SANS data. As result, we show a temperature-dependent density transition of intracapsid DNA occurring between two coexisting phases-a hexagonally ordered high-density DNA phase in the capsid periphery and a low-density, less-ordered DNA phase in the core. As the temperature is increased from 20 °C to 40 °C, we found that the core-DNA phase undergoes a density and volume transition close to the physiological temperature of infection (~37 °C). The transition yields a lower energy state of DNA in the capsid core due to lower density and reduced packing defects. This increases DNA mobility, which is required to initiate rapid genome ejection from the virus capsid into a host cell, causing infection. These data reconcile our earlier findings of mechanical DNA transition in phage.
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Affiliation(s)
| | - Efthymios Tsimtsirakis
- Department of Experimental Medical Science and NanoLund, Lund University, Lund22184, Sweden
| | - Susan Krueger
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD20899-6102
| | - Alex Evilevitch
- Department of Experimental Medical Science and NanoLund, Lund University, Lund22184, Sweden
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2
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Lapinaite A, Carlomagno T, Gabel F. Small-Angle Neutron Scattering of RNA-Protein Complexes. Methods Mol Biol 2020; 2113:165-188. [PMID: 32006315 DOI: 10.1007/978-1-0716-0278-2_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Small-angle neutron scattering (SANS) provides structural information on biomacromolecules and their complexes in dilute solutions at the nanometer length scale. The overall dimensions, shapes, and interactions can be probed and compared to information obtained by complementary structural biology techniques such as crystallography, NMR, and EM. SANS, in combination with solvent H2O/D2O exchange and/or deuteration, is particularly well suited to probe the internal structure of RNA-protein (RNP) complexes since neutrons are more sensitive than X-rays to the difference in scattering length densities of proteins and RNA, with respect to an aqueous solvent. In this book chapter we provide a practical guide on how to carry out SANS experiments on RNP complexes, as well as possibilities of data analysis and interpretation.
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Affiliation(s)
- Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research, Leibniz University Hannover, Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Braunschweig, Germany
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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3
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Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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4
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Gabel F. Small-Angle Neutron Scattering for Structural Biology of Protein–RNA Complexes. Methods Enzymol 2015; 558:391-415. [DOI: 10.1016/bs.mie.2015.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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5
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Tresset G, Tatou M, Le Cœur C, Zeghal M, Bailleux V, Lecchi A, Brach K, Klekotko M, Porcar L. Weighing polyelectrolytes packaged in viruslike particles. PHYSICAL REVIEW LETTERS 2014; 113:128305. [PMID: 25279650 DOI: 10.1103/physrevlett.113.128305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 06/03/2023]
Abstract
This Letter reports on the remarkable selectivity of capsid proteins for packaging synthetic polyelectrolytes in viruslike particles. By applying the contrast variation method in small-angle neutron scattering, we accurately estimated the mean mass of packaged polyelectrolytes ⟨Mp⟩ and that of the surrounding capsid ⟨Mcap⟩. Remarkably, the mass ratio ⟨Mp⟩/⟨Mcap⟩ was invariant for polyelectrolyte molecular weights spanning more than 2 orders of magnitude. To do so, capsids either packaged several chains simultaneously or selectively retained the shortest chains that could fit the capsid interior. Our data are in qualitative agreement with theoretical predictions based on free energy minimization and emphasize the importance of protein self-energy. These findings may give new insights into the nonspecific origin of genome selectivity for a number of viral systems.
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Affiliation(s)
- Guillaume Tresset
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Mouna Tatou
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Clémence Le Cœur
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Mehdi Zeghal
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Virginie Bailleux
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Amélie Lecchi
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Katarzyna Brach
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, 27 Wybrzeże Wyspiańskiego, 50-370 Wrocław, Poland
| | - Magdalena Klekotko
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, 27 Wybrzeże Wyspiańskiego, 50-370 Wrocław, Poland
| | - Lionel Porcar
- Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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6
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Jung B, Anvari B. Virus-mimicking optical nanomaterials: near infrared absorption and fluorescence characteristics and physical stability in biological environments. ACS APPLIED MATERIALS & INTERFACES 2013; 5:7492-7500. [PMID: 23875529 DOI: 10.1021/am401800w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The use of viruses as platforms for the development of optical imaging materials has received increasing attention in recent years. We have engineered a hybrid nanomaterial composed of the capsid proteins of genome-depleted plant-infecting Brome mosaic virus that encapsulates the near-infrared (NIR) dye indocyanine green. Herein, we investigate the NIR absorption and fluorescence characteristics of these nanomaterials in biological environments consisting of cell culture media with and without serum proteins. Our results demonstrate that the NIR absorption and fluorescence emission of the constructs are enhanced in the presence of serum proteins. The constructs remain physically stable and maintain their NIR absorption and fluorescence properties for at least 79 days. The presence of serum proteins also reduces the aggregation of the constructs. These findings have relevance for the further development of optical imaging and phototherapeutic methods on the basis of such virus-mimicking nanomaterials as well as the expected optical and physical characteristics of these nanomaterials in vivo.
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Affiliation(s)
- Bongsu Jung
- Department of Bioengineering, University of California-Riverside, Riverside, California 92521, United States
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7
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Ankner JF, Heller WT, Herwig KW, Meilleur F, Myles DAA. Neutron scattering techniques and applications in structural biology. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.16. [PMID: 23546619 DOI: 10.1002/0471140864.ps1716s72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neutron scattering is exquisitely sensitive to the position, concentration, and dynamics of hydrogen atoms in materials and is a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, nondestructive suite of instruments for biophysical characterization that provides spatial and dynamic information spanning from Ångstroms to microns and from picoseconds to microseconds, respectively. Applications in structural biology range from the atomic-resolution analysis of individual hydrogen atoms in enzymes through to meso- and macro-scale analysis of complex biological structures, membranes, and assemblies. The large difference in neutron scattering length between hydrogen and deuterium allows contrast variation experiments to be performed and enables H/D isotopic labeling to be used for selective and systematic analysis of the local structure, dynamics, and interactions of multi-component systems. This overview describes the available techniques and summarizes their practical application to the study of biomolecular systems.
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Affiliation(s)
- John F Ankner
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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8
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Straight lines of neutron scattering in biology: a review of basic controls in SANS and EINS. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:781-7. [DOI: 10.1007/s00249-012-0825-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/27/2012] [Accepted: 05/13/2012] [Indexed: 10/28/2022]
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9
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Gopal A, Zhou ZH, Knobler CM, Gelbart WM. Visualizing large RNA molecules in solution. RNA (NEW YORK, N.Y.) 2012; 18:284-99. [PMID: 22190747 PMCID: PMC3264915 DOI: 10.1261/rna.027557.111] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 11/12/2011] [Indexed: 05/24/2023]
Abstract
Single-stranded RNAs (ssRNAs) longer than a few hundred nucleotides do not have a unique structure in solution. Their equilibrium properties therefore reflect the average of an ensemble of structures. We use cryo-electron microscopy to image projections of individual long ssRNA molecules and characterize the anisotropy of their ensembles in solution. A flattened prolate volume is found to best represent the shapes of these ensembles. The measured sizes and anisotropies are in good agreement with complementary determinations using small-angle X-ray scattering and coarse-grained molecular dynamics simulations. A long viral ssRNA is compared with shorter noncoding transcripts to demonstrate that prolate geometry and flatness are generic properties independent of sequence length and origin. The anisotropy persists under physiological as well as low-ionic-strength conditions, revealing a direct correlation between secondary structure asymmetry and 3D shape and size. We discuss the physical origin of the generic anisotropy and its biological implications.
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Affiliation(s)
- Ajaykumar Gopal
- Department of Chemistry and Biochemistry, University of California-Los Angeles, CA 90095, USA.
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10
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He L, Piper A, Meilleur F, Hernandez R, Heller WT, Brown DT. Conformational changes in Sindbis virus induced by decreased pH are revealed by small-angle neutron scattering. J Virol 2012; 86:1982-7. [PMID: 22156534 PMCID: PMC3302394 DOI: 10.1128/jvi.06569-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 11/26/2011] [Indexed: 01/30/2023] Open
Abstract
Alphaviruses, such as Sindbis virus, undergo dramatic changes in three-dimensional structure upon exposure to low pH, and such exposure can establish conditions allowing fusion of the virus membrane with a cell plasma membrane upon return to neutral pH. While exposure to low pH is not required for entry of Sindbis virus into vertebrate or invertebrate cells, the conformational changes occurring at low pH may mimic those occurring upon virus-receptor interaction. Here, we employed small-angle neutron scattering with contrast variation to probe how the structure of a mammalian-grown Sindbis virus responds to moderately acidic pH. Several changes took place throughout the virion structure when the pH decreased from 7.2 to 6.4. Specifically, the RNA in the virion core underwent a conformational change. Additionally, the protein was redistributed. A significant amount of protein moved from the layer containing the lipid bilayer to the exterior of the virion. The results improve our understanding of the pH-driven alteration of Sindbis virus structure.
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Affiliation(s)
- Lilin He
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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11
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Kao CC, Ni P, Hema M, Huang X, Dragnea B. The coat protein leads the way: an update on basic and applied studies with the Brome mosaic virus coat protein. MOLECULAR PLANT PATHOLOGY 2011; 12:403-12. [PMID: 21453435 PMCID: PMC6640235 DOI: 10.1111/j.1364-3703.2010.00678.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The Brome mosaic virus (BMV) coat protein (CP) accompanies the three BMV genomic RNAs and the subgenomic RNA into and out of cells in an infection cycle. In addition to serving as a protective shell for all of the BMV RNAs, CP plays regulatory roles during the infection process that are mediated through specific binding of RNA elements in the BMV genome. One regulatory RNA element is the B box present in the 5' untranslated region (UTR) of BMV RNA1 and RNA2 that play important roles in the formation of the BMV replication factory, as well as the regulation of translation. A second element is within the tRNA-like 3' UTR of all BMV RNAs that is required for efficient RNA replication. The BMV CP can also encapsidate ligand-coated metal nanoparticles to form virus-like particles (VLPs). This update summarizes the interaction between the BMV CP and RNAs that can regulate RNA synthesis, translation and RNA encapsidation, as well as the formation of VLPs.
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Affiliation(s)
- C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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12
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Timmins PA. Neutron scattering studies of the structure and assembly of spherical viruses. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/masy.19880150124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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He L, Piper A, Meilleur F, Myles DAA, Hernandez R, Brown DT, Heller WT. The structure of Sindbis virus produced from vertebrate and invertebrate hosts as determined by small-angle neutron scattering. J Virol 2010; 84:5270-6. [PMID: 20219936 PMCID: PMC2863847 DOI: 10.1128/jvi.00044-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 02/25/2010] [Indexed: 01/14/2023] Open
Abstract
The complex natural cycle of vectored viruses that transition between host species, such as between insects and mammals, makes understanding the full life cycle of the virus an incredibly complex problem. Sindbis virus, an arbovirus and prototypic alphavirus having an inner protein shell and an outer glycoprotein coat separated by a lipid membrane, is one example of a vectored virus that transitions between vertebrate and insect hosts. While evidence of host-specific differences in Sindbis virus has been observed, no work has been performed to characterize the impact of the host species on the structure of the virus. Here, we report the first study of the structural differences between Sindbis viruses grown in mammalian and insect cells, which were determined by small-angle neutron scattering (SANS), a nondestructive technique that did not decrease the infectivity of the Sindbis virus particles studied. The scattering data and modeling showed that, while the radial position of the lipid bilayer did not change significantly, it was possible to conclude that it did have significantly more cholesterol when the virus was grown in mammalian cells. Additionally, the outer protein coat was found to be more extended in the mammalian Sindbis virus. The SANS data also demonstrated that the RNA and nucleocapsid protein share a closer interaction in the mammalian-cell-grown virus than in the virus from insect cells.
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Affiliation(s)
- Lilin He
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Amanda Piper
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Flora Meilleur
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Dean A. A. Myles
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Raquel Hernandez
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Dennis T. Brown
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - William T. Heller
- Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, Neutron Scattering Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
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14
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Nuzzaci M, Bochicchio I, De Stradis A, Vitti A, Natilla A, Piazzolla P, Tamburro AM. Structural and biological properties of Cucumber mosaic virus particles carrying hepatitis C virus-derived epitopes. J Virol Methods 2009; 155:118-21. [PMID: 18992770 DOI: 10.1016/j.jviromet.2008.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 10/02/2008] [Accepted: 10/07/2008] [Indexed: 11/26/2022]
Abstract
The Cucumber mosaic virus (CMV) is a three-component isodiametric plant virus with an extremely wide host range, present worldwide. A pseudorecombinant form has been described, deriving from the RNA3 component of the CMV-S strain, carrying the coat protein (CP) gene, and the RNA 1, 2 components of the CMV-D strain. The CP gene was then engineered to express one or two copies of a synthetic peptide derived from many hypervariable region 1 (HVR1) sequences of the Hepatitis C virus (HCV) envelope protein E2 (the so-called R9 mimotope). Study of the symptoms pattern displayed in tobacco by these chimeric CMV particles, together with determination of their structural characteristics, assessed by circular dichroism (CD) spectroscopy and electron microscopy, revealed a possible relationship between the biological behavior and the structural properties of virus components.
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Affiliation(s)
- M Nuzzaci
- Department of Biology, Plant Protection and Agrobiotechnology, University of Basilicata, Viale dell'Ateneo Lucano, 10, 85100 Potenza, Italy
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15
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Virudachalam R, Sitaraman K, Heuss KL, Markley JL, Argos P. Evidence for pH-induced release of RNA from belladonna mottle virus and the stabilizing effect of polyamines and cations. Virology 2008; 130:351-9. [PMID: 18639151 DOI: 10.1016/0042-6822(83)90089-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/1983] [Accepted: 07/18/1983] [Indexed: 11/29/2022]
Abstract
The RNA of belladonna mottle virus (BDMV) is released from virions by increasing the pH to neutrality or above, leaving behind intact protein shells. In contrast, much harsher conditions are required to release the RNA from the closely related turnip yellow mosaic virus (TYMV). The heat-induced or pH-dependent escape of RNA from BDMV has been investigated by 31P NMR spectroscopy and ultracentrifugation. The methods show a transition pH near 6.8 at which the RNA undergoes a structural alteration probably caused by disruption of protein-RNA linkages. Addition of cations or polyamines to BDMV prevents the RNA loss at alkaline pH; the virions become stable to pH values up to 11.5 as observed for TYMV. We suggest that repulsion of the negatively charged phosphate groups of the nucleic acid provides the driving force for RNA release at pH values above the threshold point where protein-RNA interactions are broken. The polyamines effectively counter the phosphate charge in BDMV and thereby prevent RNA loss. Since TYMV is packaged with polyamines and BDMV is not (R. Virudachalam, K. Sitaraman, K. L. Heuss, P. Argos, and J. L. Markley, Virology 130, 360-371, 1983), the different conditions required for RNA escape from the two viruses are explained. Heating of BDMV virions at pH 7.0 to 40 degrees resulted in their partial disruption; the product some intact particles, empty capsids, and RNA fragments with a sedimentation coefficient of 5S.
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Affiliation(s)
- R Virudachalam
- Purdue University Biochemical Magnetic Resonance Laboratory, Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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16
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Lee SI, Nguyen TT. Radial distribution of RNA genomes packaged inside spherical viruses. PHYSICAL REVIEW LETTERS 2008; 100:198102. [PMID: 18518491 DOI: 10.1103/physrevlett.100.198102] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Indexed: 05/26/2023]
Abstract
The problem of RNA genomes packaged inside spherical viruses is studied. The RNA-capsid attraction is assumed to be nonspecific and occurs at the inner capsid surface only. For weak attraction, RNA concentration is maximum at the center of the capsid to maximize their configurational entropy. For stronger attraction, RNA concentration peaks near the capsid surface. In the latter case, the competition between the branching of RNA secondary structure and its adsorption to the inner capsid results in the formation of a dense layer of RNA near capsid surface. The layer thickness is a slowly varying (logarithmic) function of the capsid inner radius. Consequently, the amount of RNA packaged is proportional to the capsid area (or the number of proteins) instead of its volume. The numerical profiles describe reasonably well the observed RNA concentration profiles of various viruses.
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Affiliation(s)
- Se Il Lee
- Georgia Institute of Technology, School of Physics, Atlanta, GA 30332-0430, USA
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17
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Packaging of a polymer by a viral capsid: the interplay between polymer length and capsid size. Biophys J 2007; 94:1428-36. [PMID: 17981893 DOI: 10.1529/biophysj.107.117473] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report a study of the in vitro self-assembly of virus-like particles formed by the capsid protein of cowpea chlorotic mottle virus and the anionic polymer poly(styrene sulfonate) (PSS) for five molecular masses ranging from 400 kDa to 3.4 MDa. The goal is to explore the effect on capsid size of the competition between the preferred curvature of the protein and the molecular mass of the packaged cargo. The capsid size distribution for each polymer was unimodal, but two distinct sizes were observed: 22 nm for the lower molecular masses, jumping to 27 nm at a molecular mass of 2 MDa. A model is provided for the formation of the virus-like particles that accounts for both the PSS and capsid protein self-interactions and the interactions between the protein and PSS. Our study suggests that the size of the encapsidated polymer cargo is the deciding factor for the selection of one distinct capsid size from several possible sizes with the same inherent symmetry.
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18
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Nguyen TT, Bruinsma RF. RNA condensation and the wetting transition. PHYSICAL REVIEW LETTERS 2006; 97:108102. [PMID: 17025857 DOI: 10.1103/physrevlett.97.108102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Indexed: 05/12/2023]
Abstract
We present a continuum theory for the condensation of large, soluble, single-stranded RNA molecules on attractive substrates. In the mean-field approximation, the theory reduces to the Cahn-de Gennes description of wetting fluids and offers a natural explanation for the development of a sharply defined density profile following a prewetting surface phase transition. This mapping onto the wetting problem can break down because of a capillary instability where the adsorbed film decomposes into a collection of segregated, nonoverlapping molecules.
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Affiliation(s)
- Toan T Nguyen
- Department of Physics and Astronomy, University of California-Los Angeles, 475 Portola Plaza, Los Angeles, California 90095, USA
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19
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Pacios LF, García-Arenal F. Comparison of properties of particles of Cucumber mosaic virus and Tomato aspermy virus based on the analysis of molecular surfaces of capsids. J Gen Virol 2006; 87:2073-2083. [PMID: 16760411 DOI: 10.1099/vir.0.81621-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The plant RNA viruses Cucumber mosaic virus (CMV) and Tomato aspermy virus (TAV) (genus Cucumovirus) have similar icosahedral particles, the crystal structures of which have been reported recently. Similarity in particle structure agrees with reports of stable capsids assembled from their capsid proteins and of viable recombinant viruses with chimeric capsid proteins derived from CMV and TAV. However, differences between the cucumoviruses have been reported for physicochemical properties. Here, structural and electrostatic features of the molecular surfaces are studied to investigate their relationship with these observations. Two coat-protein recombinants with structures modelled by taking CMV and TAV as templates were also included in the analysis. Results show that there exists an external region of negative electrostatic potential that has arisen from strictly conserved charged residues situated near the external HI loop of the subunits in the capsomers. This negative domain surrounds the fivefold and quasi-sixfold axes and locates above regions of positive potential that extend to cover, nearly homogeneously, the inner surface of capsids, where interaction with encapsidated RNA occurs. Differences between the outer electrostatic distributions in CMV and TAV explain the distinct response of both viruses to variations in physicochemical conditions required for particle stability and are essential to rationalize the biological activity of the coat-protein recombinants, in spite of their seemingly distinct electrostatic characteristics.
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Affiliation(s)
- Luis F Pacios
- Departamento de Biotecnología, ETSI Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Fernando García-Arenal
- Departamento de Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Larson SB, Lucas RW, Greenwood A, McPherson A. The RNA of turnip yellow mosaic virus exhibits icosahedral order. Virology 2005; 334:245-54. [PMID: 15780874 DOI: 10.1016/j.virol.2005.01.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Revised: 12/22/2004] [Accepted: 01/14/2005] [Indexed: 11/16/2022]
Abstract
Difference electron density maps, based on structure factor amplitudes and experimental phases from crystals of wild-type turnip yellow mosaic virus and those of empty capsids prepared by freeze-thawing, show a large portion of the encapsidated RNA to have an icosahedral distribution. Four unique segments of base-paired, double-helical RNA, one to two turns in length, lie between 33-A and 101-A radius and are organized about either 2-fold or 5-fold icosahedral axes. In addition, single-stranded loops of RNA invade the pentameric and hexameric capsomeres where they contact the interior capsid surface. The remaining RNA, not seen in electron density maps, must serve as connecting links between these secondary structural elements and is likely icosahedrally disordered. The distribution of RNA observed crystallographically appears to be in agreement with models based on biochemical data and secondary structural analyses.
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Affiliation(s)
- Steven B Larson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
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21
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van Roon AMM, Bink HHJ, Plaisier JR, Pleij CWA, Abrahams JP, Pannu NS. Crystal Structure of an Empty Capsid of Turnip Yellow Mosaic Virus. J Mol Biol 2004; 341:1205-14. [PMID: 15321716 DOI: 10.1016/j.jmb.2004.06.085] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 06/24/2004] [Accepted: 06/30/2004] [Indexed: 11/26/2022]
Abstract
Empty capsids (artificial top component) of turnip yellow mosaic virus were co-crystallized with an encapsidation initiator RNA hairpin. No clear density was observed for the RNA, but there were clear differences in the conformation of a loop of the coat protein at the opening of the pentameric capsomer (formed by five A-subunits) protruding from the capsid, compared to the corresponding loop in the intact virus. Further differences were found at the N terminus of the A-subunit. These differences have implications for the mechanism of decapsidation of the virus, required for infection.
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Affiliation(s)
- Anne-Marie M van Roon
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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22
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Gilbert RJ, Grimes JM, Stuart DI. Hybrid vigor: hybrid methods in viral structure determination. ADVANCES IN PROTEIN CHEMISTRY 2003; 64:37-91. [PMID: 13677045 DOI: 10.1016/s0065-3233(03)01002-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Affiliation(s)
- Robert J Gilbert
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
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23
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Abstract
The structure of brome mosaic virus (BMV), the type member of the bromoviridae family, has been determined from a single rhombohedral crystal by X-ray diffraction, and refined to an R value of 0.237 for data in the range 3.4-40.0 A. The structure, which represents the native, compact form at pH 5.2 in the presence of 0.1 M Mg(2+), was solved by molecular replacement using the model of cowpea chlorotic mottle virus (CCMV), which BMV closely resembles. The BMV model contains amino acid residues 41-189 for the pentameric capsid A subunits, and residues 25-189 and 1-189 for the B and C subunits, respectively, which compose the hexameric capsomeres. In the model there are two Mg ions and one molecule of polyethylene glycol (PEG). The first 25 amino acid residues of the C subunit are modeled as polyalanine. The coat protein has the canonical "jellyroll" beta-barrel topology with extended amino-terminal polypeptides as seen in other icosahedral plant viruses. Mass spectrometry shows that in native BMV virions, a significant fraction of the amino-terminal peptides are apparently cleaved. No recognizable nucleic acid residue is visible in the electron density maps except at low resolution where it appears to exhibit a layered arrangement in the virion interior. It is juxtaposed closely with the interior surface of the capsid but does not interpenetrate. The protein subunits forming hexameric capsomeres, and particularly dimers, appear to interact extensively, but the subunits otherwise contact one another sparsely about the 5-fold and quasi 3-fold axes. Thus, the virion appears to be an assembly of loosely associated hexameric capsomeres, which may be the basis for the swelling and dissociation that occurs at neutral pH and elevated salt concentration. A Mg ion is observed to lie exactly on the quasi-3-fold axis and is closely coordinated by side-chains of three quasi-symmetry-related residues glutamates 84, with possible participation of side-chains from threonines 145, and asparagines 148. A presumptive Mg(2+) is also present on the 5-fold axis where there is a concentration of negatively charged side-chains, but the precise coordination is unclear. In both cases these cations appear to be essential for maintenance of virion stability. Density that is contiguous with the viral interior is present on the 3-fold axis at the center of the hexameric capsomere, where there is a pore of about 6 A diameter. The density cannot be attributed to cations and it was modeled as a PEG molecule.
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Affiliation(s)
- Robert W Lucas
- University of California-Irvine, 560 Steinhaus Hall, Irvine, CA 92697-3900, USA
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24
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Canady MA, Larson SB, Day J, McPherson A. Crystal structure of turnip yellow mosaic virus. NATURE STRUCTURAL BIOLOGY 1996; 3:771-81. [PMID: 8784351 DOI: 10.1038/nsb0996-771] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The structure of turnip yellow mosaic virus (TYMV) has been solved to 3.2 A resolution and an R-value of 18.7%. The structure is consistent with models based on low resolution X-ray and electron microscopy studies, with pentameric and hexameric protein aggregates protruding from the surface and forming deep valleys at the quasi three-fold axes. The N-terminal 26 residues of the A-subunit are disordered, while those of the B- and C-subunits are seen to interact around the interior of the quasi six-fold cluster where they form an annulus. The three histidine residues of each protein subunit are located in the interior and accessible for interaction with the RNA genome. The appearance of the interior surface of the virus capsid, along with buried surface area calculations, suggest that a pentameric unit is lost during decapsidation.
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Affiliation(s)
- M A Canady
- Department of Biochemistry, University of California, Riverside 92521, USA
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25
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Böttcher B, Crowther RA. Difference imaging reveals ordered regions of RNA in turnip yellow mosaic virus. Structure 1996; 4:387-94. [PMID: 8740361 DOI: 10.1016/s0969-2126(96)00044-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Turnip yellow mosaic virus (TYMV) is a small icosahedral plant virus with a capsid containing 180 subunits arranged with hexamer-pentamer clustering. Cross-linking studies have indicated extensive contacts between RNA and coat protein, suggesting that substantial parts of the RNA might be icosahedrally ordered. RESULTS Comparison of maps computed to a Fourier cut-off of 1.5 nm from electron micrographs of ice-embedded specimens of TYMV and of empty capsids produced by freeze-thawing reveals strong inner features around the threefold axes in the virus but not in the empty capsid. Internal features of subunit packing indicate that interhexamer contacts are closer than those between pentamers and hexamers and that pentamer density in the empty capsid is reduced relative to that in the virus. CONCLUSIONS The differences between virus and empty capsid indicate that substantial parts of the RNA are icosahedrally ordered and that the exit of RNA on freeze-thawing is accompanied by the loss of at least one pentamer unit.
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Affiliation(s)
- B Böttcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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26
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Canady MA, Leja CA, Day J, McPherson A. Preliminary X-ray diffraction analysis of crystals of tomato aspermy virus (TAV). Proteins 1995; 21:265-7. [PMID: 7784430 DOI: 10.1002/prot.340210310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Tomato aspermy virus (TAV) is a member of the T = 3 cucumovirus group, and the chrysanthemum strain (C-TAV) has been crystallized in a form suitable for X-ray structural analysis. The crystals, which grow in 14-17% ethanol at pH 8.5, are of orthorhombic space group I222 with unit cell dimensions of a = 295.1 A, b = 320.5 A, and c = 383.6 A. There are two T = 3 virus particles in the unit cell, which means that they must be centered at 0,0,0 and 1/2, 1/2, 1/2 with icosahedral 222 symmetry elements coincident with crystallographic symmetry operators. The asymmetric unit of the crystals, therefore, contains one quarter of a virus particle, or 45 capsid subunits. Native diffraction data to 4 A resolution have been collected using synchrotron radiation, though data appear to be present beyond that resolution.
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Affiliation(s)
- M A Canady
- Department of Biochemistry, University of California, Riverside 92521, USA
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27
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Witz J, Timmins PA, Adrian M. Organization of turnip yellow mosaic virus investigated by neutron small angle scattering at 80 K: an intermediate state preceding decapsidation of the virion? Proteins 1993; 17:223-31. [PMID: 8272422 DOI: 10.1002/prot.340170302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The organization of turnip yellow mosaic virus has been investigated by neutron small angle scattering at 300 K and 80 K in buffers containing various amounts of D2O. We confirm that in native virions, no substantial part of the RNA is located at a radius larger than ca. 100-110 A, i.e., that there is very little interpretation of the RNA into the capsid. At 80 K, scattering curves do not depend much upon contrast, from 40% D2O to 100% D2O buffers, but are strongly affected by interparticle interference. We could, however, show that it is not the case for the subsidiary intensity maximum at q approximately 0.06 A-1. From the position of this maximum, we conclude that upon freezing, the radius of the capsid expands by c.a. 3.5% and the RNA penetrates deeply into the protein shell. Biological implications of this conformational change immediately preceding decapsidation are discussed.
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Affiliation(s)
- J Witz
- Département d'Immunochimie des Peptides et Virus, Institut de Biologie Moléculaire et Cellulaire du C.N.R.S., Strasbourg, France
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28
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Affiliation(s)
- P Palukaitis
- Department of Plant Pathology, Cornell University, Ithaca, New York 14853
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29
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The thermal stability of turnip yellow mosaic virus under hydrostatic pressure. EUROPEAN BIOPHYSICS JOURNAL: EBJ 1991. [DOI: 10.1007/bf01561137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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31
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Bentley GA, Lewit-Bentley A, Liljas L, Skoglund U, Roth M, Unge T. Structure of RNA in satellite tobacco necrosis virus. A low resolution neutron diffraction study using 1H2O/2H2O solvent contrast variation. J Mol Biol 1987; 194:129-41. [PMID: 3612799 DOI: 10.1016/0022-2836(87)90722-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The crystal structure of satellite tobacco necrosis virus has been studied by neutron diffraction at 16 A resolution using the technique of 1H2O/2H2O solvent contrast variation to distinguish between the regions of protein and nucleic acid. The RNA density is essentially localized in a region just inside the protein coat, leading to a significant interaction between the two components. From the appearance of the RNA density we conclude that the protein coat imposes partial icosahedral symmetry on a significant proportion of the nucleic acid. The shape and dimensions of the major part of this density suggests that about 72% of the total RNA could be double-helical in structure. The most important interaction between the two components of the virus occurs between the N-terminal triple-helical arms of the protein subunits and those regions of the RNA density that could have a double-helical secondary structure.
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32
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Sgro JY, Jacrot B, Chroboczek J. Identification of regions of brome mosaic virus coat protein chemically cross-linked in situ to viral RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1986; 154:69-76. [PMID: 3943527 DOI: 10.1111/j.1432-1033.1986.tb09360.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RNA-protein cross-links were introduced into brome mosaic virus in situ by using the heterobifunctional agent p-azidophenylglyoxal. An improved RNA isolation method, without phenol extraction, was used to isolate RNA cross-linked with protein. RNA of the covalently linked complex was acid-digested and the oligonucleotides still attached to protein were 5'-end-labelled with 32P. The complexes were digested with trypsin and the tryptic peptides were purified by reversed-phase high-performance liquid chromatography. Amino acid analyses of cross-linked tryptic peptides revealed that out of the total 188 amino acids of brome mosaic virus coat protein only the 80 N-terminal amino acids are involved in the interaction with viral RNA. These results are discussed in connection with a predicted secondary structure of the coat protein. Both alpha helix (for amino acids 11-19) and other structures (between amino acids 20 and 80) are implicated in the coat protein-viral RNA interactions.
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33
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34
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The structure of rice dwarf virus determined by small-angle neutron scattering measurements. Virology 1985; 147:214-6. [DOI: 10.1016/0042-6822(85)90242-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/1985] [Accepted: 08/09/1985] [Indexed: 11/19/2022]
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35
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Virudachalam R, Low PS, Argos P, Markley JL. Turnip yellow mosaic virus and its capsid have thermal stabilities with opposite pH dependence: studies by differential scanning calorimetry and 31P nuclear magnetic resonance spectroscopy. Virology 1985; 146:213-20. [PMID: 4049734 DOI: 10.1016/0042-6822(85)90005-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In the differential scanning calorimetry (DSC) scans of turnip yellow mosaic virus (TYMV) or its capsid a single endotherm was observed. The endotherm was attributed to disruption of the virion or capsid structure with accompanying protein denaturation. At pH 4.5 the thermal stabilities of the TYMV virion and capsid were similar. With increasing pH, the capsid stability increased while the virion stability decreased. At neutral pH the capsid disrupted at 83.5 degrees, and the virion disrupted at 69 degrees. Our results suggest that packaging of viral RNA in the TYMV capsid imparts instability. The pHmid for disruption of the TYMV capsid is 5.7, which is in the pKa range expected for histidine side chains. Hence repulsive interactions involving one or more of the three histidines of the TYMV coat protein may explain the decreased stability of the TYMV capsid at low pH. This conclusion is supported further by the observation that belladonna mottle virus (BDMV) capsid (BDMV and TYMV belong to the tymo virus group), which contains no histidine in its coat protein, did not exhibit pH-dependent stability. The size of the cooperative unit in the disruption of TYMV capsid was estimated to be approximately that of a dimer of the coat protein, at pH 7.0, but a larger oligomer at low pH. Several reports implicate pH-dependent protein-RNA interactions with a pHmid near 7 as important in stabilizing tymovirus virions. Both DSC and 31P nuclear magnetic resonance linewidth analyses of the TYMV virion showed a transition midpoint at pH 7.0.
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36
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Katouzian-Safadi M, Charlier M, Maurizot JC. A circular dichroism study of the Turnip yellow mosaic virus-RNA. Biochimie 1985; 67:1007-13. [PMID: 4084608 DOI: 10.1016/s0300-9084(85)80295-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We examined the circular dichroism spectra of intact Turnip yellow mosaic virus, freezed/thawed virus, empty capsid particles, and phenol extracted RNA. The circular dichroism signal of the empty capsid was found to contribute for less than 1% to the circular dichroism of the virus. Differences in the circular dichroism spectra indicate that TYMV-RNA exhibits different conformations when it is in situ in the virus, when it has been ejected by freezing/thawing and when it has been phenol extracted. Increase of the ionic strength up to 0.1 M NaCl led to conformational change of the RNA either freezed/thawed ejected or phenol extracted but not in situ in the capsid. Addition of spermidine (3 mM) induced a conformational change only for the phenol extracted RNA. These results are discussed with respect to the origin of the various conformational states of viral RNA.
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37
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Gogol EP, Engelman DM. Neutron scattering shows that cytochrome b5 penetrates deeply into the lipid bilayer. Biophys J 1984; 46:491-5. [PMID: 6498267 PMCID: PMC1435021 DOI: 10.1016/s0006-3495(84)84046-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Cytochrome b5 was asymmetrically reconstituted into small lipid vesicles made of a highly deuterated phospholipid. Small-angle neutron diffraction patterns were collected in a series of H2O-D2O mixtures from vesicles consisting of lipid and native or trypsinized cytochrome b5. The second moment of the radial distribution of scattering density in the vesicles was derived from these data and was compared to values calculated from three proposed models, which differ by the degree that cytochrome b5 penetrates the lipid bilayer. The model in which the hydrophobic domain of the protein is distributed across the bilayer agreed most closely with the data.
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38
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Katouzian-Safadi M, Berthet-Colominas C. Evidence for the presence of a hole in the capsid of turnip yellow mosaic virus after RNA release by freezing and thawing. Decapsidation of turnip yellow mosaic virus in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1983; 137:47-53. [PMID: 6653559 DOI: 10.1111/j.1432-1033.1983.tb07793.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Turnip yellow mosaic virus (TYMV) RNA escapes from viral capsids after freezing and thawing the virus, and the remaining capsids look very similar to natural capsids in the electron microscope after negative staining [Katouzian-Safadi, M., Favre, A., and Haenni, A. L. (1980) Eur. J. Biochem. 112, 478-486]. In order to understand how an RNA of 2 X 10(6) Da (33% virus by weight) can escape from a compact protein shell we have compared artificial capsids formed after freezing TYMV and natural capsids produced in vivo in infected plants. We have used various physicochemical techniques including analytical ultracentrifugation, X-ray scattering, X-ray diffraction and orientation in a magnetic field. From the combination of these results we conclude that the escape of the RNA is accompanied by the formation of a hole in the capsid surface. The size of such a hole is estimated to 5-9 coat protein subunits.
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39
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Rossmann MG, Abad-Zapatero C, Erickson JW, Savithri HS. RNA-protein interactions in some small plant viruses. J Biomol Struct Dyn 1983; 1:565-79. [PMID: 6401119 DOI: 10.1080/07391102.1983.10507462] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The structure of the three quasi-equivalent protein subunits A, B and C of the spherical, T = 3 southern bean mosaic virus (SBMV) have been carefully built in accordance with a refined electron density map of the complete virus. The lower electron density in the RNA portion of the map could not be explicitly interpreted in terms of a preferred RNA structure on which some icosahedral symmetry might have been imposed. However, the extremely basic nature of the interior surface of the coat protein must be associated with the binding and organization of the RNA. Comparison with the small spherical, T = 1 satellite tobacco necrosis virus (STNV; Liljas et al., J. Mol. Biol. 159, 93-108, 1982) and the T = 1 aggregate of alfalfa mosaic virus (AMV) protein (Fukuyama et al., J. Mol. Biol. 150, 33-41, 1981) showed similar results. The pattern of basic residues on the SBMV coat protein surface facing the RNA is able to dock a 9 base pair double-helical A-RNA structure with surprising accuracy. The basic residues are each associated with a different phosphate and the protein can make interactions with five bases in the minor groove. This may be one of a small number of ways in which the RNA interacts with SBMV coat protein. The self-assembly of SBMV has been studied in relation to the presence of the 63 basic amino-terminal coat protein sequence, pH, Ca2+ and Mg2+ ions and RNA. These results have led to a two-state model where the "relaxed" dimers initially self-assemble into 10-mer caps which nucleate the assembly of T = 1 or T = 3 capsids depending on the charge state of the carboxyl group clusters in the subunit contact region. The two-state condition of dimers in a viral coat protein extends the range of structures originally envisaged by Caspar and Klug (Cold Spring Harbor Symp. Quant. Biol. 27, 1-24, 1962).
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Affiliation(s)
- M G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
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40
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Moras D, Lorber B, Romby P, Ebel JP, Giegé R, Lewit-Bentley A, Roth M. Yeast tRNAAsp-aspartyl-tRNA synthetase: the crystalline complex. J Biomol Struct Dyn 1983; 1:209-23. [PMID: 6401112 DOI: 10.1080/07391102.1983.10507435] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Aspartyl-tRNA synthetase from yeast, a dimer of molecular weight 125,000 and its cognate tRNA (Mr = 24,160) were co-crystallized using ammonium sulfate as precipitant agent. The presence in the crystals of both components in the two-to-one stoichiometric ratio was demonstrated by electrophoresis, biological activity assays and crystallographic data. Crystals belong to the cubic space group I432 with cell parameter of 354 A and one complex particle per asymmetric unit. The solvent content of about 78% is favorable for a low resolution structural investigation. By exchanging H2O for D2O in mother liquors, advantage can be taken from contrast variation techniques with neutron radiations. Diffraction data to 20 A resolution were measured at five different contrasts, two of them being close to the theoretical matching point of RNA and protein in the presence of ammonium sulfate. The experimental extinction of the diffracted signal was observed to be close to 36% D2O, significantly different from the predicted value of 41%. The phenomenon can be explained by the existence of a large interface region between the two tRNAs and the enzyme. These parts of the molecules are hidden from the solvent and their protons are less easily exchangeable. Accessibility studies toward chemicals of tRNAAsp in solution and in the presence of synthetase are in agreement with such a model.
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Affiliation(s)
- D Moras
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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41
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Rossmann MG, Chandrasekaran R, Abad-Zapatero C, Erickson JW, Arnott S. RNA-protein binding in southern bean mosaic virus. J Mol Biol 1983; 166:73-80. [PMID: 6854634 DOI: 10.1016/s0022-2836(83)80050-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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42
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Schmidt T, Johnson JE, Phillips WE. Tje spherically averaged structures of cowpea mosaic virus components by X-ray solution scattering. Virology 1983; 127:65-73. [DOI: 10.1016/0042-6822(83)90371-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/1982] [Accepted: 02/02/1986] [Indexed: 10/26/2022]
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43
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Cuillel M, Berthet-Colominas C, Krop B, Tardieu A, Vachette P, Jacrot B. Self-assembly of brome mosaic virus capsids. Kinetic study using neutron and X-ray solution scattering. J Mol Biol 1983; 164:645-50. [PMID: 6842602 DOI: 10.1016/0022-2836(83)90055-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The self-assembly of brome mosaic virus capsid has been studied kinetically by means of X-ray and neutron scattering. It appears to be a very fast process: for the concentrations used (5 to 8 mg/ml) the forward scattering reaches 50% of its maximal value in less than one second. Further, the assembly seems to proceed through intermediate states whose nature is still speculative.
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44
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45
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krüse J, Timmins P, Witz J. A neutron scattering study of the structure of compact and swollen forms of southern bean mosaic virus. Virology 1982; 119:42-50. [DOI: 10.1016/0042-6822(82)90063-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/1981] [Accepted: 01/05/1982] [Indexed: 10/26/2022]
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46
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Moore PB. 8. Small-Angle Scattering Techniques for the Study of Biological Macromolecules and Macromolecular Aggregates. METHODS IN EXPERIMENTAL PHYSICS 1982. [DOI: 10.1016/s0076-695x(08)60157-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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48
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Rybicki EP, Von Wechmar M. The serology of the bromoviruses I. Serological interrelationships of the bromoviruses. Virology 1981; 109:391-402. [DOI: 10.1016/0042-6822(81)90509-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/1980] [Indexed: 11/30/2022]
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49
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Bentley GA, Finch JT, Lewit-Bentley A. Neutron diffraction studies on crystals of nucleosome cores using contrast variation. J Mol Biol 1981; 145:771-84. [PMID: 7265220 DOI: 10.1016/0022-2836(81)90314-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Hatta T, Francki RI. Identification of small polyhedral virus particles in thin sections of plant cells by an enzyme cytochemical technique. JOURNAL OF ULTRASTRUCTURE RESEARCH 1981; 74:116-29. [PMID: 7017158 DOI: 10.1016/s0022-5320(81)80114-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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