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Shtykova EV, Dubrovin EV, Ksenofontov AL, Gifer PK, Petoukhov MV, Tokhtar VK, Sapozhnikova IM, Stavrianidi AN, Kordyukova LV, Batishchev OV. Structural Insights into Plant Viruses Revealed by Small-Angle X-ray Scattering and Atomic Force Microscopy. Viruses 2024; 16:427. [PMID: 38543792 PMCID: PMC10975137 DOI: 10.3390/v16030427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 05/23/2024] Open
Abstract
The structural study of plant viruses is of great importance to reduce the damage caused by these agricultural pathogens and to support their biotechnological applications. Nowadays, X-ray crystallography, NMR spectroscopy and cryo-electron microscopy are well accepted methods to obtain the 3D protein structure with the best resolution. However, for large and complex supramolecular structures such as plant viruses, especially flexible filamentous ones, there are a number of technical limitations to resolving their native structure in solution. In addition, they do not allow us to obtain structural information about dynamics and interactions with physiological partners. For these purposes, small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) are well established. In this review, we have outlined the main principles of these two methods and demonstrated their advantages for structural studies of plant viruses of different shapes with relatively high spatial resolution. In addition, we have demonstrated the ability of AFM to obtain information on the mechanical properties of the virus particles that are inaccessible to other experimental techniques. We believe that these under-appreciated approaches, especially when used in combination, are valuable tools for studying a wide variety of helical plant viruses, many of which cannot be resolved by classical structural methods.
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Affiliation(s)
- Eleonora V. Shtykova
- National Research Centre, “Kurchatov Institute”, Moscow 123098, Russia; (E.V.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Evgeniy V. Dubrovin
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Polina K. Gifer
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Maxim V. Petoukhov
- National Research Centre, “Kurchatov Institute”, Moscow 123098, Russia; (E.V.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Valeriy K. Tokhtar
- Scientific and Educational Center, Botanical Garden of the National Research University “BelSU”, Belgorod 308033, Russia;
| | - Irina M. Sapozhnikova
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Ekaterinburg 620002, Russia;
| | - Andrey N. Stavrianidi
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Larisa V. Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Oleg V. Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
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Ksenofontov AL, Petoukhov MV, Matveev VV, Fedorova NV, Semenyuk PI, Arutyunyan AM, Manukhova TI, Evtushenko EA, Nikitin NA, Karpova OV, Shtykova EV. Effect of the Coat Protein N-Terminal Domain Structure on the Structure and Physicochemical Properties of Virions of Potato Virus X and Alternanthera Mosaic Virus. BIOCHEMISTRY (MOSCOW) 2023; 88:119-130. [PMID: 37068873 DOI: 10.1134/s0006297923010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The amino acid sequences of the coat proteins (CPs) of the potexviruses potato virus X (PVX) and alternanthera mosaic virus (AltMV) share ~40% identity. The N-terminal domains of these proteins differ in the amino acid sequence and the presence of the N-terminal fragment of 28 residues (ΔN peptide) in the PVX CP. Here, we determined the effect of the N-terminal domain on the structure and physicochemical properties of PVX and AltMV virions. The circular dichroism spectra of these viruses differed significantly, and the melting point of PVX virions was 10-12°C higher than that of AltMV virions. Alignment of the existing high-resolution 3D structures of the potexviral CPs showed that the RMSD value between the Cα-atoms was the largest for the N-terminal domains of the two compared models. Based on the computer modeling, the ΔN peptide of the PVX CP is fully disordered. According to the synchrotron small-angle X-ray scattering (SAXS) data, the structure of CPs from the PVX and AltMV virions differ; in particular, the PVX CP has a larger portion of crystalline regions and, therefore, is more ordered. Based on the SAXS data, the diameters of the PVX and AltMV virions and helix parameters in solution were calculated. The influence of the conformation of the PVX CP N-terminal domain and its position relative to the virion surface on the virion structure was investigated. Presumably, an increased thermal stability of PVX virions vs. AltMV is provided by the extended N-terminal domain (ΔN peptide, 28 amino acid residues), which forms additional contacts between the adjacent CP subunits in the PVX virion.
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Affiliation(s)
- Alexander L Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Vladimir V Matveev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
| | - Natalia V Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Pavel I Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tatiana I Manukhova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | | | - Nikolai A Nikitin
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Olga V Karpova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Eleonora V Shtykova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia
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De S, Nguyen HM, Liljeström V, Mäkinen K, Kostiainen MA, Vapaavuori J. Potato virus A particles - A versatile material for self-assembled nanopatterned surfaces. Virology 2023; 578:103-110. [PMID: 36493505 DOI: 10.1016/j.virol.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Potato virus A (PVA) is a plant-infecting RNA virus that produces flexible particles with a high aspect ratio. PVA has been investigated extensively for its infection biology, however, its potential to serve as a nanopatterning platform remains unexplored. Here, we study the liquid crystal and interfacial self-assembly behavior of PVA particles. Furthermore, we generate nanopatterned surfaces using self-assembled PVA particles through three different coating techniques: drop-casting, drop-top deposition and flow-coating. The liquid crystal phase of PVA solution visualized by polarized optical microscopy revealed a chiral nematic phase in water, while in pH 8 buffer it produced a nematic phase. This allowed us to produce thin films with either randomly or anisotropically oriented cylindrical nanopatterns using drop-top and flow-coating methods. Overall, this study explores the self-assembly process of PVA in different conditions, establishing a starting point for PVA self-assembly research and contributing a virus-assisted fabrication technique for nanopatterned surfaces.
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Affiliation(s)
- Swarnalok De
- Department of Chemistry and Materials Science, Aalto University, 00076, Espoo, Finland
| | - Hoang M Nguyen
- Department of Chemistry and Materials Science, Aalto University, 00076, Espoo, Finland
| | - Ville Liljeström
- Nanomicroscopy Center, OtaNano, Aalto University, 00076, Espoo, Finland
| | - Kristiina Mäkinen
- Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland
| | - Mauri A Kostiainen
- Department of Bioproducts and Biosystems, Aalto University, 00076, Espoo, Finland.
| | - Jaana Vapaavuori
- Department of Chemistry and Materials Science, Aalto University, 00076, Espoo, Finland.
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Shtykova EV, Petoukhov MV, Fedorova NV, Arutyunyan AM, Skurat EV, Kordyukova LV, Moiseenko AV, Ksenofontov AL. The Structure of the Potato Virus A Particles Elucidated by Small Angle X-Ray Scattering and Complementary Techniques. BIOCHEMISTRY (MOSCOW) 2021; 86:230-240. [PMID: 33832421 DOI: 10.1134/s0006297921020115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Potato virus A (PVA) protein coat contains on its surface partially unstructured N-terminal domain of the viral coat protein (CP), whose structural and functional characteristics are important for understanding the mechanism of plant infection with this virus. In this work, we investigated the properties and the structure of intact PVA and partially trypsinized PVAΔ32 virions using small-angle X-ray scattering (SAXS) and complimentary methods. It was shown that after the removal of 32 N-terminal amino acids of the CP, the virion did not disintegrate and remained compact, but the helical pitch of the CP packing changed. To determine the nature of these changes, we performed ab initio modeling, including the multiphase procedure, with the geometric bodies (helices) and restoration of the PVA structure in solution using available high-resolution structures of the homologous CP from the PVY potyvirus, based on the SAXS data. As a result, for the first time, a low-resolution structure of the filamentous PVA virus, both intact and partially degraded, was elucidated under conditions close to natural. The far-UV circular dichroism spectra of the PVA and PVAΔ32 samples differed significantly in the amplitude and position of the main negative maximum. The extent of thermal denaturation of these samples in the temperature range of 20-55°C was also different. The data of transmission electron microscopy showed that the PVAΔ32 virions were mostly rod-shaped, in contrast to the flexible filamentous particles typical of the intact virus, which correlated well with the SAXS results. In general, structural analysis indicates an importance of the CP N-terminal domain for the vital functions of PVA, which can be used to develop a strategy for combating this plant pathogen.
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Affiliation(s)
- Eleonora V Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, 119333, Russia.
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, 119333, Russia
| | - Natalia V Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexander M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Eugene V Skurat
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Andrey V Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexander L Ksenofontov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, 119333, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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Ksenofontov AL, Petoukhov MV, Prusov AN, Fedorova NV, Shtykova EV. Characterization of Tobacco Mosaic Virus Virions and Repolymerized Coat Protein Aggregates in Solution by Small-Angle X-Ray Scattering. BIOCHEMISTRY (MOSCOW) 2021; 85:310-317. [PMID: 32564735 DOI: 10.1134/s0006297920030062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The structure of tobacco mosaic virus (TMV) virions and stacked disk aggregates of TMV coat protein (CP) in solution was analyzed by synchrotron-based small-angle X-ray scattering (SAXS) and negative contrast transmission electron microscopy (TEM). TMV CP aggregates had a unique stability but did not have helical symmetry. According to the TEM data, they were stacked disks associated into transversely striated rod-shaped structures 300 to 800 Å long. According to modeling based on the crystallographic model of the 4-layer TMV CP aggregate (PDB: 1EI7), the stacked disks represented hollow cylinders. The calculated SAXS pattern for the disks was compared to the experimental one over the entire measured range. The best correlation with the SAXS data was found for the model with the repeating central pair of discs; the SAXS curves for the stacked disks were virtually identical irrespectively of the protein isolation method. The positions of maxima on the scatter curves could be used as characteristic features of the studied samples; some of the peaks were assigned to the existing elements of the quaternary structure (periodicity of aggregate structure, virion helix pitch). Low-resolution structural data for the repolymerized TMV CP aggregates in solution under conditions similar to natural were produced for the first time. Analysis of such nano-size objects is essential for their application in biomedicine and biotechnology.
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Affiliation(s)
- A L Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - M V Petoukhov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia. .,Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - A N Prusov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - N V Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - E V Shtykova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia.
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Martínez-Turiño S, García JA. Potyviral coat protein and genomic RNA: A striking partnership leading virion assembly and more. Adv Virus Res 2020; 108:165-211. [PMID: 33837716 DOI: 10.1016/bs.aivir.2020.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Potyvirus genus clusters a significant and expanding number of widely distributed plant viruses, responsible for large losses impacting most crops of economic interest. The potyviral genome is a single-stranded, linear, positive-sense RNA of around 10kb that is encapsidated in flexuous rod-shaped filaments, mostly made up of a helically arranged coat protein (CP). Beyond its structural role of protecting the viral genome, the potyviral CP is a multitasking protein intervening in practically all steps of the virus life cycle. In particular, interactions between the CP and the viral RNA must be tightly controlled to allow the correct assignment of the RNA to each of its functions through the infection process. This review attempts to bring together the most relevant available information regarding the architecture and modus operandi of potyviral CP and virus particles, highlighting significant discoveries, but also substantial gaps in the existing knowledge on mechanisms orchestrating virion assembly and disassembly. Biotechnological applications based on potyvirus nanoparticles is another important topic addressed here.
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Ksenofontov AL, Fedorova NV, Badun GA, Serebryakova MV, Nikitin NA, Evtushenko EA, Chernysheva MG, Bogacheva EN, Dobrov EN, Baratova LA, Atabekov JG, Karpova OV. Surface characterization of the thermal remodeling helical plant virus. PLoS One 2019; 14:e0216905. [PMID: 31150411 PMCID: PMC6544241 DOI: 10.1371/journal.pone.0216905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/30/2019] [Indexed: 01/19/2023] Open
Abstract
Previously, we have reported that spherical particles (SPs) are formed by the thermal remodeling of rigid helical virions of native tobacco mosaic virus (TMV) at 94°C. SPs have remarkable features: stability, unique adsorption properties and immunostimulation potential. Here we performed a comparative study of the amino acid composition of the SPs and virions surface to characterize their properties and take an important step to understanding the structure of SPs. The results of tritium planigraphy showed that thermal transformation of TMV leads to a significant increase in tritium label incorporation into the following sites of SPs protein: 41-71 а.a. and 93-122 a.a. At the same time, there was a decrease in tritium label incorporation into the N- and C- terminal region (1-15 a.a., 142-158 a.a). The use of complementary physico-chemical methods allowed us to carry out a detailed structural analysis of the surface and to determine the most likely surface areas of SPs. The obtained data make it possible to consider viral protein thermal rearrangements, and to open new opportunities for biologically active complex design using information about SPs surface amino acid composition and methods of non-specific adsorption and bioconjugation.
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Affiliation(s)
- Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia V. Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Gennady A. Badun
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Nikolai A. Nikitin
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Elena N. Bogacheva
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Eugeny N. Dobrov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ludmila A. Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Joseph G. Atabekov
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V. Karpova
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia
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Ksenofontov AL, Dobrov EN, Fedorova NV, Arutyunyan AM, Golanikov AE, Järvekülg L, Shtykova EV. Structure of Potato Virus A Coat Protein Particles and Their Dissociation. Mol Biol 2018. [DOI: 10.1134/s0026893318060109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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