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Sheibani N, Arab SS, Kamalvand M. The coat protein of tobacco mosaic virus as an anti-tobacco mosaic virus: a molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:13792-13797. [PMID: 36856083 DOI: 10.1080/07391102.2023.2183036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
The Coat Protein (CP) of the Tobacco Mosaic Virus (TMV) executes an important duty in the protection of virus RNA. The interaction between the virus CP and host plant proteins induces infection in the host and creates dark and light green mosaics on crops, which disturb the growth and function of the plant. The interaction between the virus CP and the modified CP, expressed in transgenic plants, causes Coat Protein-Mediated Resistance (CP-MR), which reduces virus infection in transgenic plants. In this study, a model is suggested for resistance as "stop assembly of CP" in the virus. It is based on the fact that the CP, when mutated, acts as a dead-end in virus assembly. For evaluation of the model, we investigated the effect of four mutants including CBT28I, ABT42W, ABD77R, and ABT89W complexes on plant resistance against TMV infection by molecular dynamics simulation. Previous studies had shown the influence of such mutations on the CP-MR. The MD results of in the present study further confirmed the mentioned effect and demonstrated how the mutations could be the cause of CP-MR. The results are calculated by the RMSD, Rg, H-bond, and g-MMPBSA scripts. The change in binding energy between two chains is consistent with CP-MR such that with increase in binding energy, the affinity between two chains was reduced and the CP-MR increased. Based on this model, it is possible to design mutants with a high level of efficiency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Narjes Sheibani
- Department of Chemistry, Faculty of Science, Yazd University, Yazd, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Kamalvand
- Department of Chemistry, Faculty of Science, Yazd University, Yazd, Iran
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The Plant Viruses and Molecular Farming: How Beneficial They Might Be for Human and Animal Health? Int J Mol Sci 2023; 24:ijms24021533. [PMID: 36675043 PMCID: PMC9863966 DOI: 10.3390/ijms24021533] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Plant viruses have traditionally been studied as pathogens in the context of understanding the molecular and cellular mechanisms of a particular disease affecting crops. In recent years, viruses have emerged as a new alternative for producing biological nanomaterials and chimeric vaccines. Plant viruses were also used to generate highly efficient expression vectors, revolutionizing plant molecular farming (PMF). Several biological products, including recombinant vaccines, monoclonal antibodies, diagnostic reagents, and other pharmaceutical products produced in plants, have passed their clinical trials and are in their market implementation stage. PMF offers opportunities for fast, adaptive, and low-cost technology to meet ever-growing and critical global health needs. In this review, we summarized the advancements in the virus-like particles-based (VLPs-based) nanotechnologies and the role they played in the production of advanced vaccines, drugs, diagnostic bio-nanomaterials, and other bioactive cargos. We also highlighted various applications and advantages plant-produced vaccines have and their relevance for treating human and animal illnesses. Furthermore, we summarized the plant-based biologics that have passed through clinical trials, the unique challenges they faced, and the challenges they will face to qualify, become available, and succeed on the market.
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Kondakova OA, Evtushenko EA, Baranov OA, Nikitin NA, Karpova OV. Structurally Modified Plant Viruses and Bacteriophages with Helical Structure. Properties and Applications. BIOCHEMISTRY (MOSCOW) 2022; 87:548-558. [PMID: 35790410 PMCID: PMC9201271 DOI: 10.1134/s0006297922060062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Structurally modified virus particles can be obtained from the rod-shaped or filamentous virions of plant viruses and bacteriophages by thermal or chemical treatment. They have recently attracted attention of the researchers as promising biogenic platforms for the development of new biotechnologies. This review presents data on preparation, structure, and properties of the structurally modified virus particles. In addition, their biosafety for animals is considered, as well as the areas of application of such particles in biomedicine. A separate section is devoted to one of the most relevant and promising areas for the use of structurally modified plant viruses – design of vaccine candidates based on them.
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Affiliation(s)
- Olga A Kondakova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | | | - Oleg A Baranov
- 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
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Vaidya AJ, Solomon KV. Surface Functionalization of Rod-Shaped Viral Particles for Biomedical Applications. ACS APPLIED BIO MATERIALS 2022; 5:1980-1989. [PMID: 35148077 DOI: 10.1021/acsabm.1c01204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While synthetic nanoparticles play a very important role in modern medicine, concerns regarding toxicity, sustainability, stability, and dispersity are drawing increasing attention to naturally derived alternatives. Rod-shaped plant viruses and virus-like particles (VLPs) are biological nanoparticles with powerful advantages such as biocompatibility, tunable size and aspect ratio, monodispersity, and multivalency. These properties facilitate controlled biodistribution and tissue targeting for powerful applications in medicine. Ongoing research efforts focus on functionalizing or otherwise engineering these structures for a myriad of applications, including vaccines, imaging, and drug delivery. These include chemical and biological strategies for conjugation to small molecule chemical dyes, drugs, metals, polymers, peptides, proteins, carbohydrates, and nucleic acids. Many strategies are available and vary greatly in efficiency, modularity, selectivity, and simplicity. This review provides a comprehensive summary of VLP functionalization approaches while highlighting biomedically relevant examples. Limitations of current strategies and opportunities for further advancement will also be discussed.
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Affiliation(s)
- Akash J Vaidya
- Department of Chemical & Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, Delaware 19716, United States
| | - Kevin V Solomon
- Department of Chemical & Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, Delaware 19716, United States
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Paiva TO, Schneider A, Bataille L, Chovin A, Anne A, Michon T, Wege C, Demaille C. Enzymatic activity of individual bioelectrocatalytic viral nanoparticles: dependence of catalysis on the viral scaffold and its length. NANOSCALE 2022; 14:875-889. [PMID: 34985473 DOI: 10.1039/d1nr07445h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The enzymatic activity of tobacco mosaic virus (TMV) nanorod particles decorated with an integrated electro-catalytic system, comprising the quinoprotein glucose-dehydrogenase (PQQ-GDH) enzyme and ferrocenylated PEG chains as redox mediators, is probed at the individual virion scale by atomic force microscopy-scanning electrochemical atomic force microscopy (AFM-SECM). A marked dependence of the catalytic activity on the particle length is observed. This finding can be explained by electron propagation along the viral backbone, resulting from electron exchange between ferrocene moieties, coupled with enzymatic catalysis. Thus, the use of a simple 1D diffusion/reaction model allows the determination of the kinetic parameters of the virus-supported enzyme. Comparative analysis of the catalytic behavior of the Fc-PEG/PQQ-GDH system assembled on two differing viral scaffolds, TMV (this work) and bacteriophage-fd (previous work), reveals two distinct kinetic effects of scaffolding: An enhancement of catalysis that does not depend on the virus type and a modulation of substrate inhibition that depends on the virus type. AFM-SECM detection of the enzymatic activity of a few tens of PQQ-GDH molecules, decorating a 40 nm-long viral domain, is also demonstrated, a record in terms of the lowest number of enzyme molecules interrogated by an electrochemical imaging technique.
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Affiliation(s)
- Telmo O Paiva
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, CNRS UMR 7591, F-75013 Paris, France.
| | - Angela Schneider
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Research Unit Molecular and Synthetic Plant Virology, 70569 Stuttgart, Germany.
| | - Laure Bataille
- Université de Bordeaux, Biologie du Fruit et Pathologie, INRA UMR 1332, F-33140 Villenave d'Ornon, France.
| | - Arnaud Chovin
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, CNRS UMR 7591, F-75013 Paris, France.
| | - Agnès Anne
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, CNRS UMR 7591, F-75013 Paris, France.
| | - Thierry Michon
- Université de Bordeaux, Biologie du Fruit et Pathologie, INRA UMR 1332, F-33140 Villenave d'Ornon, France.
| | - Christina Wege
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Research Unit Molecular and Synthetic Plant Virology, 70569 Stuttgart, Germany.
| | - Christophe Demaille
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, CNRS UMR 7591, F-75013 Paris, France.
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Lee KZ, Basnayake Pussepitiyalage V, Lee YH, Loesch-Fries LS, Harris MT, Hemmati S, Solomon KV. Engineering Tobacco Mosaic Virus and Its Virus-Like-Particles for Synthesis of Biotemplated Nanomaterials. Biotechnol J 2021; 16:e2000311. [PMID: 33135368 DOI: 10.1002/biot.202000311] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Indexed: 12/12/2022]
Abstract
Biomolecules are increasingly attractive templates for the synthesis of functional nanomaterials. Chief among them is the plant tobacco mosaic virus (TMV) due to its high aspect ratio, narrow size distribution, diverse biochemical functionalities presented on the surface, and compatibility with a number of chemical conjugations. These properties are also easily manipulated by genetic modification to enable the synthesis of a range of metallic and non-metallic nanomaterials for diverse applications. This article reviews the characteristics of TMV and related viruses, and their virus-like particle (VLP) derivatives, and how these may be manipulated to extend their use and function. A focus of recent efforts has been on greater understanding and control of the self-assembly processes that drive biotemplate formation. How these features have been exploited in engineering applications such as, sensing, catalysis, and energy storage are briefly outlined. While control of VLP surface features is well-established, fewer tools exist to control VLP self-assembly, which limits efforts to control template uniformity and synthesis of certain templated nanomaterials. However, emerging advances in synthetic biology, machine learning, and other fields promise to accelerate efforts to control template uniformity and nanomaterial synthesis enabling more widescale industrial use of VLP-based biotemplates.
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Affiliation(s)
- Kok Zhi Lee
- Agricultural & Biological Engineering, Purdue University, 225 S University St, West Lafayette, IN, 47907, USA
| | | | - Yu-Hsuan Lee
- School of Chemical Engineering, Purdue University, 480 W Stadium Ave, West Lafayette, IN, 47907, USA
| | - L Sue Loesch-Fries
- Department of Botany and Plant Pathology, Purdue University, 915 W State St, West Lafayette, IN, 47907, USA
| | - Michael T Harris
- School of Chemical Engineering, Purdue University, 480 W Stadium Ave, West Lafayette, IN, 47907, USA
| | - Shohreh Hemmati
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK, 74078, USA
| | - Kevin V Solomon
- Agricultural & Biological Engineering, Purdue University, 225 S University St, West Lafayette, IN, 47907, USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN, 47907, USA
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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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8
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Synthesis and applications of anisotropic nanoparticles with precisely defined dimensions. Nat Rev Chem 2020; 5:21-45. [PMID: 37118104 DOI: 10.1038/s41570-020-00232-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
Shape and size play powerful roles in determining the properties of a material; controlling these aspects with precision is therefore an important, fundamental goal of the chemical sciences. In particular, the introduction of shape anisotropy at the nanoscale has emerged as a potent way to access new properties and functionality, enabling the exploration of complex nanomaterials across a range of applications. Recent advances in DNA and protein nanotechnology, inorganic crystallization techniques, and precision polymer self-assembly are now enabling unprecedented control over the synthesis of anisotropic nanoparticles with a variety of shapes, encompassing one-dimensional rods, dumbbells and wires, two-dimensional and three-dimensional platelets, rings, polyhedra, stars, and more. This has, in turn, enabled much progress to be made in our understanding of how anisotropy and particle dimensions can be tuned to produce materials with unique and optimized properties. In this Review, we bring these recent developments together to critically appraise the different methods for the bottom-up synthesis of anisotropic nanoparticles enabling exquisite control over morphology and dimensions. We highlight the unique properties of these materials in arenas as diverse as electron transport and biological processing, illustrating how they can be leveraged to produce devices and materials with otherwise inaccessible functionality. By making size and shape our focus, we aim to identify potential synergies between different disciplines and produce a road map for future research in this crucial area.
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Zhou K, Zhou Y, Pan V, Wang Q, Ke Y. Programming Dynamic Assembly of Viral Proteins with DNA Origami. J Am Chem Soc 2020; 142:5929-5932. [PMID: 32191463 DOI: 10.1021/jacs.9b13773] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biomolecular assembly in biological systems is typically a complex dynamic process regulated by the exchange of molecular information between biomolecules such as proteins and nucleic acids. Here, we demonstrate a nucleic-acid-based system that can program the dynamic assembly process of viral proteins. Tobacco mosaic virus (TMV) genome-mimicking RNA is anchored on DNA origami nanostructures via hybridization with a series of DNA strands which also function as locks that prevent the packaging of RNA by the TMV proteins. The selective, sequential releasing of the RNA via toehold-mediated strand displacement allows us to program the availability of RNA and subsequently the TMV growth in situ. Furthermore, the programmable dynamic assembly of TMV on DNA templates also enables the production of new DNA-protein hybrid nanostructures, which are not attainable by using previous assembly methods.
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Affiliation(s)
- Kun Zhou
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Yihao Zhou
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Qiangbin Wang
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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Fejer SN. Minimalistic coarse-grained modeling of viral capsid assembly. COMPUTATIONAL APPROACHES FOR UNDERSTANDING DYNAMICAL SYSTEMS: PROTEIN FOLDING AND ASSEMBLY 2020; 170:405-434. [DOI: 10.1016/bs.pmbts.2019.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Gamper C, Spenlé C, Boscá S, van der Heyden M, Erhardt M, Orend G, Bagnard D, Heinlein M. Functionalized Tobacco Mosaic Virus Coat Protein Monomers and Oligomers as Nanocarriers for Anti-Cancer Peptides. Cancers (Basel) 2019; 11:cancers11101609. [PMID: 31652529 PMCID: PMC6826726 DOI: 10.3390/cancers11101609] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 01/13/2023] Open
Abstract
Components with self-assembly properties derived from plant viruses provide the opportunity to design biological nanoscaffolds for the ordered display of agents of diverse nature and with complementing functions. With the aim of designing a functionalized nanoscaffold to target cancer, the coat protein (CP) of Tobacco mosaic virus (TMV) was tested as nanocarrier for an insoluble, highly hydrophobic peptide that targets the transmembrane domain of the Neuropilin-1 (NRP1) receptor in cancer cells. The resulting construct CPL-K (CP-linker-“Kill”) binds to NRP1 in cancer cells and disrupts NRP1 complex formation with PlexA1 as well as downstream Akt survival signaling. The application of CPL-K also inhibits angiogenesis and cell migration. CP was also fused to a peptide that targets the extracellular domain of NRP1 and this fusion protein (CPL-F, CP-Linker-“Find”) is shown to bind to cultured cancer cells and to inhibit NRP1-dependent angiogenesis as well. CPL-K and CPL-F maintain their anti-angiogenic properties upon co-assembly to oligomers/nanoparticles together with CPL. The observations show that the CP of TMV can be employed to generate a functionalized nanoparticle with biological activity. Remarkably, fusion to CPL allowed us to solubilize the highly insoluble transmembrane NRP1 peptide and to retain its anti-angiogenic effect.
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Affiliation(s)
- Coralie Gamper
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), Université de Strasbourg, 67000 Strasbourg, France.
- INSERM 1119, BMNST Laboratory, Université de Strasbourg, 67000 Strasbourg, France.
- Labex Medalis, Université de Strasbourg, 67000 Strasbourg, France.
- Fédération de Médecine Translationnelle de Strasbourg, FMTS, Université de Strasbourg, 67000 Strasbourg, France.
- INSERM 1109, MN3T, The Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Université de Strasbourg, 67000 Strasbourg, France.
| | - Caroline Spenlé
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), Université de Strasbourg, 67000 Strasbourg, France.
- INSERM 1119, BMNST Laboratory, Université de Strasbourg, 67000 Strasbourg, France.
- Labex Medalis, Université de Strasbourg, 67000 Strasbourg, France.
- Fédération de Médecine Translationnelle de Strasbourg, FMTS, Université de Strasbourg, 67000 Strasbourg, France.
- INSERM 1109, MN3T, The Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Université de Strasbourg, 67000 Strasbourg, France.
| | - Sonia Boscá
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), Université de Strasbourg, 67000 Strasbourg, France.
| | - Michael van der Heyden
- INSERM 1119, BMNST Laboratory, Université de Strasbourg, 67000 Strasbourg, France.
- Labex Medalis, Université de Strasbourg, 67000 Strasbourg, France.
- Fédération de Médecine Translationnelle de Strasbourg, FMTS, Université de Strasbourg, 67000 Strasbourg, France.
- INSERM 1109, MN3T, The Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Université de Strasbourg, 67000 Strasbourg, France.
| | - Mathieu Erhardt
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), Université de Strasbourg, 67000 Strasbourg, France.
| | - Gertraud Orend
- Labex Medalis, Université de Strasbourg, 67000 Strasbourg, France.
- Fédération de Médecine Translationnelle de Strasbourg, FMTS, Université de Strasbourg, 67000 Strasbourg, France.
- INSERM 1109, MN3T, The Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Université de Strasbourg, 67000 Strasbourg, France.
- INSERM 1109, The Tumor Microenvironment Laboratory, Université de Strasbourg, 67000 Strasbourg, France.
| | - Dominique Bagnard
- INSERM 1119, BMNST Laboratory, Université de Strasbourg, 67000 Strasbourg, France.
- Labex Medalis, Université de Strasbourg, 67000 Strasbourg, France.
- Fédération de Médecine Translationnelle de Strasbourg, FMTS, Université de Strasbourg, 67000 Strasbourg, France.
- INSERM 1109, MN3T, The Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Université de Strasbourg, 67000 Strasbourg, France.
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), Université de Strasbourg, 67000 Strasbourg, France.
- University of Strasbourg Institute of Advanced Study (USIAS), 67000 Strasbourg, France.
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Wege C, Koch C. From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1591. [PMID: 31631528 DOI: 10.1002/wnan.1591] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/04/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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13
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Wang B, Zhang J, Wu Y. A Multiscale Model for the Self-Assembly of Coat Proteins in Bacteriophage MS2. J Chem Inf Model 2019; 59:3899-3909. [PMID: 31411466 PMCID: PMC7273741 DOI: 10.1021/acs.jcim.9b00514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The self-assembly of viral capsids is an essential step to the formation of infectious viruses. Elucidating the kinetic mechanisms of how a capsid or virus-like particle assembles could advance our knowledge about the viral lifecycle, as well as the general principles in self-assembly of biomaterials. However, current understanding of capsid assembly remains incomplete for many viruses due to the fact that the transient intermediates along the assembling pathways are experimentally difficult to be detected. In this paper, we constructed a new multiscale computational framework to simulate the self-assembly of virus-like particles. We applied our method to the coat proteins of bacteriophage MS2 as a specific model system. This virus-like particle of bacteriophage MS2 has a unique feature that its 90 sequence-identical dimers can be classified into two structurally various groups: one is the symmetric CC dimer, and the other is the asymmetric AB dimer. The homotypic interactions between AB dimers result in a 5-fold symmetric contact, while the heterotypic interactions between AB and CC dimers result in 6-fold symmetric contact. We found that the assembly can be described as a physical process of phase transition that is regulated by various factors such as concentration and specific stoichiometry between AB and CC dimers. Our simulations also demonstrate that heterotypic and homotypic interfaces play distinctive roles in modulating the assembling kinetics. The interaction between AB and CC dimers is much more dynamic than that between two AB dimers. We therefore suggest that the alternate growth of viral capsid through the heterotypic dimer interactions dominates the assembling pathways. This is, to the best of our knowledge, the first multiscale model to simulate the assembling process of coat proteins in bacteriophage MS2. The generality of this approach opens the door to its further applications in assembly of other viral capsids, virus-like particles, and novel drug delivery systems.
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Affiliation(s)
- Bo Wang
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX 77843
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
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14
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Wang H, Chen Y, Zhang W. A single-molecule atomic force microscopy study reveals the antiviral mechanism of tannin and its derivatives. NANOSCALE 2019; 11:16368-16376. [PMID: 31436278 DOI: 10.1039/c9nr05410c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antiviral agents work by stopping or intervening the virus replication. Virus replication is a fast and multi-step process while effective antiviral intervention requires agents to interact with the protein coat, genetic RNA/DNA or both during virus replication. Thus, quantifying these interactions at the molecular level, although it is quite challenging, is very important for an understanding of the underlying molecular mechanism of antiviral intervention. Here, at the single molecule level, we employ single molecule force spectroscopy (SMFS) in combination with AFM imaging and choose tobacco mosaic virus (TMV)/tannin as a model system of tubular virus to directly study how the inhibitor influences the interactions of RNA and coat protein. We illustrated the antiviral mechanism of tannin during the three main stages of TMV infection, i.e., before the entry of cells, the disassembly of genetic RNA and reassembly of genetic RNA, respectively. Our SMFS results show that tannin and its derivatives can stabilize the TMV complex by enhancing the interactions between RNA and coat protein via weak interactions, such as hydrogen bonding and hydrophobic interactions. In addition, the stabilization effect showed molecular weight dependence, i.e., for higher molecular weight tannin the stabilization occurs after genetic RNA gets partially disassembled from the protein coat, while the lower molecular weight tannin hydrolyte starts experiencing the stabilization effect before the RNA disassembly. Furthermore, the cycling stretching-relaxation experiments in the presence/absence of tannin proved that tannin can prevent the assembling of RNA and coat protein. In addition, the AFM imaging results demonstrate that tannin can cause the aggregation of TMV particles in a concentration-dependent manner; a higher concentration of tannin will cause more severe aggregations. These results deepen our understanding of the antiviral mechanism of tannin and its derivatives, which facilitate the rational design of efficient agents for antiviral therapy.
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Affiliation(s)
- Huijie Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China.
| | - Ying Chen
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China.
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China.
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15
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Plant virus-based materials for biomedical applications: Trends and prospects. Adv Drug Deliv Rev 2019; 145:96-118. [PMID: 30176280 DOI: 10.1016/j.addr.2018.08.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 12/14/2022]
Abstract
Nanomaterials composed of plant viral components are finding their way into medical technology and health care, as they offer singular properties. Precisely shaped, tailored virus nanoparticles (VNPs) with multivalent protein surfaces are efficiently loaded with functional compounds such as contrast agents and drugs, and serve as carrier templates and targeting vehicles displaying e.g. peptides and synthetic molecules. Multiple modifications enable uses including vaccination, biosensing, tissue engineering, intravital delivery and theranostics. Novel concepts exploit self-organization capacities of viral building blocks into hierarchical 2D and 3D structures, and their conversion into biocompatible, biodegradable units. High yields of VNPs and proteins can be harvested from plants after a few days so that various products have reached or are close to commercialization. The article delineates potentials and limitations of biomedical plant VNP uses, integrating perspectives of chemistry, biomaterials sciences, molecular plant virology and process engineering.
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16
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Autonomous helical propagation of active toroids with mechanical action. Nat Commun 2019; 10:1080. [PMID: 30842429 PMCID: PMC6403424 DOI: 10.1038/s41467-019-09099-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/21/2019] [Indexed: 01/25/2023] Open
Abstract
Self-assembly in nature is fundamentally dynamic, existing in out-of-equilibrium state in which the systems have the ability to autonomously respond to environmental changes. However, artificial systems exist in a global minimum state, which are incapable of conducting such complex functions. Here we report that input of thermal energy can trigger fixed, artificial toroids to spontaneously nucleate helical growth. The helical polymerization undergoes reversible and repeatable cycles with subsequent energy input. When the toroids are located inside lipid vesicles, the polymerization-depolymerization cycle is accompanied by reversible elongation of spherical vesicles. Such liberation from a global minimum state will pave the way to create emergent structures with functions as complex as those of living systems. Self-assembly in nature is dynamic and exists in out-of-equilibrium state and thus systems have the ability to autonomously respond to environmental changes. Here the authors report that input of thermal energy can trigger fixed, artificial toroids to spontaneously nucleate helical growth.
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17
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Altintoprak K, Farajollahi F, Seidenstücker A, Ullrich T, Wenz NL, Krolla P, Plettl A, Ziemann P, Marti O, Walther P, Exner D, Schwaiger R, Gliemann H, Wege C. Improved manufacture of hybrid membranes with bionanopore adapters capable of self-luting. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2019. [DOI: 10.1680/jbibn.18.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Farid Farajollahi
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Timo Ullrich
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Peter Krolla
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Alfred Plettl
- Institute of Solid State Physics, University of Ulm, Ulm, Germany
| | - Paul Ziemann
- Institute of Solid State Physics, University of Ulm, Ulm, Germany
| | - Othmar Marti
- Institute of Experimental Physics, University of Ulm, Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, University of Ulm, Ulm, Germany
| | - Daniela Exner
- Institute for Applied Materials – Materials and Biomechanics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany; Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Ruth Schwaiger
- Institute for Applied Materials – Materials and Biomechanics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany; Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Hartmut Gliemann
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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18
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Ibrahim A, Odon V, Kormelink R. Plant Viruses in Plant Molecular Pharming: Toward the Use of Enveloped Viruses. FRONTIERS IN PLANT SCIENCE 2019; 10:803. [PMID: 31275344 PMCID: PMC6594412 DOI: 10.3389/fpls.2019.00803] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/04/2019] [Indexed: 05/03/2023]
Abstract
Plant molecular pharming has emerged as a reliable platform for recombinant protein expression providing a safe and low-cost alternative to bacterial and mammalian cells-based systems. Simultaneously, plant viruses have evolved from pathogens to molecular tools for recombinant protein expression, chimaeric viral vaccine production, and lately, as nanoagents for drug delivery. This review summarizes the genesis of viral vectors and agroinfection, the development of non-enveloped viruses for various biotechnological applications, and the on-going research on enveloped plant viruses.
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Vignali V, S. Miranda B, Lodoso-Torrecilla I, van Nisselroy CAJ, Hoogenberg BJ, Dantuma S, Hollmann F, de Vries JW, Warszawik EM, Fischer R, Commandeur U, van Rijn P. Biocatalytically induced surface modification of the tobacco mosaic virus and the bacteriophage M13. Chem Commun (Camb) 2019; 55:51-54. [DOI: 10.1039/c8cc08042a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A one-step laccase induced free radical oxidation of the tobacco mosaic virus and bacteriophage M13 led to acrylate-functionalized viruses with customizable properties.
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20
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Lah NAC, Trigueros S. Synthesis and modelling of the mechanical properties of Ag, Au and Cu nanowires. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2019; 20:225-261. [PMID: 30956731 PMCID: PMC6442207 DOI: 10.1080/14686996.2019.1585145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 02/16/2019] [Accepted: 02/16/2019] [Indexed: 05/04/2023]
Abstract
The recent interest to nanotechnology aims not only at device miniaturisation, but also at understanding the effects of quantised structure in materials of reduced dimensions, which exhibit different properties from their bulk counterparts. In particular, quantised metal nanowires made of silver, gold or copper have attracted much attention owing to their unique intrinsic and extrinsic length-dependent mechanical properties. Here we review the current state of art and developments in these nanowires from synthesis to mechanical properties, which make them leading contenders for next-generation nanoelectromechanical systems. We also present theories of interatomic interaction in metallic nanowires, as well as challenges in their synthesis and simulation.
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Affiliation(s)
- Nurul Akmal Che Lah
- Innovative Manufacturing, Mechatronics and Sports Lab (iMAMS), Faculty of Manufacturing Engineering, Universiti Malaysia Pahang, Pekan, Malaysia
- CONTACT Nurul Akmal Che Lah
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21
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Mickoleit F, Altintoprak K, Wenz NL, Richter R, Wege C, Schüler D. Precise Assembly of Genetically Functionalized Magnetosomes and Tobacco Mosaic Virus Particles Generates a Magnetic Biocomposite. ACS APPLIED MATERIALS & INTERFACES 2018; 10:37898-37910. [PMID: 30360046 DOI: 10.1021/acsami.8b16355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Magnetosomes represent magnetic nanoparticles with unprecedented characteristics. Both their crystal morphology and the composition of the enveloping membrane can be manipulated by genetic means, allowing the display of functional moieties on the particle surface. In this study, we explore the generation of a new biomaterial assembly by coupling magnetosomes with tobacco mosaic virus (TMV) particles, both functionalized with complementary recognition sites. TMV consists of single-stranded RNA encapsidated by more than 2100 coat proteins, which enable chemical modification via functional groups. Incubation of EmGFP- or biotin-decorated TMV particles with magnetosomes genetically functionalized with GFP-binding nanobodies or streptavidin, respectively, results in the formation of magnetic, mesoscopic, strand-like biocomposites. TMV facilitates the agglomeration of magnetosomes by providing a scaffold. The size of the TMV-magnetosome mesostrands can be adjusted by varying the TMV-magnetosome particle ratios. The versatility of this novel material combination is furthermore demonstrated by coupling magnetosomes and terminal, 5'-functionalized TMV particles with high molecular precision, which results in "drumstick"-like TMV-magnetosome complexes. In summary, our approaches provide promising strategies for the generation of new biomaterial assemblies that could be used as scaffold for the introduction of further functionalities, and we foresee a broad application potential in the biomedical and biotechnological field.
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Affiliation(s)
| | - Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems , University of Stuttgart , D-70569 Stuttgart , Germany
| | - Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems , University of Stuttgart , D-70569 Stuttgart , Germany
| | | | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems , University of Stuttgart , D-70569 Stuttgart , Germany
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22
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Lomonossoff GP, Wege C. TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications. Adv Virus Res 2018; 102:149-176. [PMID: 30266172 PMCID: PMC7112118 DOI: 10.1016/bs.aivir.2018.06.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ever since its initial characterization in the 19th century, tobacco mosaic virus (TMV) has played a prominent role in the development of modern virology and molecular biology. In particular, research on the three-dimensional structure of the virus particles and the mechanism by which these assemble from their constituent protein and RNA components has made TMV a paradigm for our current view of the morphogenesis of self-assembling structures, including viral particles. More recently, this knowledge has been applied to the development of novel reagents and structures for applications in biomedicine and bionanotechnology. In this article, we review how fundamental science has led to TMV being at the vanguard of these new technologies.
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Affiliation(s)
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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23
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Zhou K, Ke Y, Wang Q. Selective in Situ Assembly of Viral Protein onto DNA Origami. J Am Chem Soc 2018; 140:8074-8077. [PMID: 29932333 DOI: 10.1021/jacs.8b03914] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Engineering hybrid protein-DNA assemblies in a controlled manner has attracted particular attention, for their potential applications in biomedicine and nanotechnology due to their intricate folding properties and important physiological roles. Although DNA origami has served as a powerful platform for spatially arranging functional molecules, in situ assembly of proteins onto DNA origami is still challenging, especially in a precisely controlled and facile manner. Here, we demonstrate in situ assembly of tobacco mosaic virus (TMV) coat proteins onto DNA origami to generate programmable assembly of hybrid DNA origami-protein nanoarchitectures. The protein nanotubes of controlled length are precisely anchored on the DNA origami at selected locations using TMV genome-mimicking RNA strands. This study opens a new route to the organization of protein and DNA into sophisticated protein-DNA nanoarchitectures by harnessing the viral encapsidation mechanism and the programmability of DNA origami.
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Affiliation(s)
- Kun Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics , Chinese Academy of Sciences , Suzhou 215123 , China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics , Chinese Academy of Sciences , Suzhou 215123 , China.,School of Nano-Tech and Nano-Bionics , University of Science and Technology of China , Hefei 230026 , China
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24
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Abstract
Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.
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Affiliation(s)
- William M Aumiller
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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25
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Electrochemically-Driven Insertion of Biological Nanodiscs into Solid State Membrane Pores as a Basis for "Pore-In-Pore" Membranes. NANOMATERIALS 2018; 8:nano8040237. [PMID: 29652841 PMCID: PMC5923567 DOI: 10.3390/nano8040237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022]
Abstract
Nanoporous membranes are of increasing interest for many applications, such as molecular filters, biosensors, nanofluidic logic and energy conversion devices. To meet high-quality standards, e.g., in molecular separation processes, membranes with well-defined pores in terms of pore diameter and chemical properties are required. However, the preparation of membranes with narrow pore diameter distributions is still challenging. In the work presented here, we demonstrate a strategy, a "pore-in-pore" approach, where the conical pores of a solid state membrane produced by a multi-step top-down lithography procedure are used as a template to insert precisely-formed biomolecular nanodiscs with exactly defined inner and outer diameters. These nanodiscs, which are the building blocks of tobacco mosaic virus-deduced particles, consist of coat proteins, which self-assemble under defined experimental conditions with a stabilizing short RNA. We demonstrate that the insertion of the nanodiscs can be driven either by diffusion due to a concentration gradient or by applying an electric field along the cross-section of the solid state membrane. It is found that the electrophoresis-driven insertion is significantly more effective than the insertion via the concentration gradient.
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26
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Wenz NL, Piasecka S, Kalinowski M, Schneider A, Richert C, Wege C. Building expanded structures from tetrahedral DNA branching elements, RNA and TMV protein. NANOSCALE 2018; 10:6496-6510. [PMID: 29569670 DOI: 10.1039/c7nr07743b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
By combining both chemical and enzymatic ligation with procedures guiding the self-assembly of nanotubular tobacco mosaic virus (TMV)-like particles (TLPs), novel nucleoprotein structures based on DNA-terminated branching elements, RNA scaffolds and TMV coat protein (CP) are made accessible. Tetrahedral tetrakis(hydroxybiphenyl)adamantane cores with four 5'-phosphorylated dinucleotide arms were coupled to DNA linkers by chemical ligation. The resulting three-dimensional (3D) branching elements were enzymatically ligated to the 3' termini of RNA scaffolds either prior to or after the RNAs' incorporation into TLPs. Thus, architectures with interconnected nanotube domains in two different length classes were generated, each containing 70 CP subunits per 10 nm length. Short TMV origin-of-assembly-containing RNA scaffolds ligated to the DNA allowed the growth of protein-coated 34 nm tubes on the terminal RNA strands in situ. Alternatively, 290 nm pre-fabricated tubes with accessible RNA 3' termini, attained by DNA blocking elements hybridized to the RNAs, were ligated with the branched cores. Both approaches resulted in four-armed nanoobjects, demonstrating a so far unique combination of organic synthesis of branching elements, enzymatic modifications, nucleic acid-based scaffolding and RNA-guided and DNA-controlled assembly of tubular RNA-encapsidating protein domains, yielding a novel class of 3D nucleoprotein architectures with polyvalent protein elements. In the long term, the production route might give rise to supramolecular systems with complex functionalities, installed via the orthogonal coupling of effector molecules to TLP domains.
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Affiliation(s)
- Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Sylwia Piasecka
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Matthäus Kalinowski
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Angela Schneider
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
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27
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Abstract
Virus-like particle (VLP) technologies are based on virus-inspired artificial structures and the intrinsic ability of viral proteins to self-assemble at controlled conditions. Therefore, the basic knowledge about the mechanisms of viral particle formation is highly important for designing of industrial applications. As an alternative to genetic and chemical processes, different physical methods are frequently used for VLP construction, including well characterized protein complexes for introduction of foreign molecules in VLP structures.This chapter shortly discusses the mechanisms how the viruses form their perfectly ordered structures as well as the principles and most interesting application examples, how to exploit the structural and assembly/disassembly properties of viral structures for creation of new nanomaterials.
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Affiliation(s)
- Andris Zeltins
- Latvian Biomedical Research and Study Centre, Riga, Latvia.
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28
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Abstract
RNA-guided self-assembly of tobacco mosaic virus (TMV)-like nucleoprotein nanotubes is possible using 3'-terminally surface-linked scaffold RNAs containing the viral origin of assembly (OAS). In combination with TMV coat protein (CP) preparations, these scaffold RNAs can direct the growth of selectively addressable multivalent carrier particles directly at sites of interest on demand. Serving as adapter templates for the installation of functional molecules, they may promote an integration of active units into miniaturized technical devices, or enable their presentation on soft-matter nanotube systems at high surface densities advantageous for, for example, biodetection or purification applications. This chapter describes all procedures essential for the bottom-up fabrication of "nanostar" colloids with gold cores and multiple TMV-like arms, immobilized in a programmable manner by way of hybridization of the RNA scaffolds to oligodeoxynucleotides exposed on the gold beads.
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Affiliation(s)
- Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany.
| | - Fabian J Eber
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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29
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Dickmeis C, Altintoprak K, van Rijn P, Wege C, Commandeur U. Bioinspired Silica Mineralization on Viral Templates. Methods Mol Biol 2018; 1776:337-362. [PMID: 29869253 DOI: 10.1007/978-1-4939-7808-3_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant virus capsids are attractive entities for nanotechnological applications because of their variation in shape and natural assembly ability. This chapter describes the production and modification of three differently shaped plant virus capsids for silica mineralization purposes. The chosen plant viruses exhibit either an icosahedral (cowpea mosaic virus, CPMV), or a flexuous rod-like structure (potato virus X, PVX), or a rigid rod-like shape (tobacco mosaic virus, TMV), and are well-known and frequently used plant viruses for biotechnological applications. We describe the production (including genetic or chemical modification) and purification of the plant viruses or of empty virus-like particles in the case of CPMV, as well as the characterization of these harvested templates. The mineralization procedures and differences in the protocols specific to the distinct viruses are described, and the analyses of the mineralization results are explained.
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Affiliation(s)
- Christina Dickmeis
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Patrick van Rijn
- Faculty of Medical Sciences, University of Groningen, AV, Groningen, The Netherlands
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany.
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30
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Abstract
Plant viruses are emerging as versatile tools for nanotechnology applications since it is possible to modify their multivalent protein surfaces and thereby introduce and display new functionalities. In this chapter, we describe a tobacco mosaic virus (TMV) variant that exposes two selectively addressable amino acid moieties on each of its 2130 coat protein (CP) subunits. A lysine as well as a cysteine introduced at accessible sites of every CP can be modified with amino- and/or thiol-reactive chemistry such as N-hydroxysuccinimide esters (NHS ester) and maleimide containing reagents alone or simultaneously. This enables the pairwise immobilization of distinct molecules in close vicinity to each other on the TMV surface by simple standard conjugation protocols. We describe the generation of the mutations, the virus propagation and isolation as well as the dual functionalization of the TMV variant with two fluorescent dyes. The labeling is evaluated by SDS-PAGE and spectrophotometry and the degree of labeling (DOL) calculated.
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Affiliation(s)
- Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Fania Geiger
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Heidelberg, Germany.
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31
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Eiben S. RNA-Directed Assembly of Tobacco Mosaic Virus (TMV)-Like Carriers with Tunable Fractions of Differently Addressable Coat Proteins. Methods Mol Biol 2018; 1776:35-50. [PMID: 29869233 DOI: 10.1007/978-1-4939-7808-3_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Taking advantage of the ability for in vitro assembly of the plant-infecting virus tobacco mosaic virus (TMV), rod-shaped nanoscale scaffolds presenting different addressable groups can be obtained. We have established procedures resulting in virus-like particles with randomly distributed functional groups, with different groups arranged in striped but randomized structures, and even with distinct groups clustered in adjacent, better-defined domains. The TMV coat protein (CP) variants combined in these approaches can either originate all from TMV mutants propagated in planta, or be mixed with CP expressed in E. coli (CPEc). Protocols for expression and purification of a CPEc-His6 mutant in E. coli as well as the different methods for in vitro assembly and the visualization by decoration of one CP type are explained in detail.
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Affiliation(s)
- Sabine Eiben
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany.
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Altintoprak K, Seidenstücker A, Krolla-Sidenstein P, Plettl A, Jeske H, Gliemann H, Wege C. RNA-stabilized protein nanorings: high-precision adapters for biohybrid design. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2017. [DOI: 10.1680/jbibn.16.00047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | | | - Peter Krolla-Sidenstein
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Alfred Plettl
- Institute of Solid State Physics, University of Ulm, Ulm, Germany
| | - Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Hartmut Gliemann
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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Gan X, Hu D, Chen Z, Wang Y, Song B. Synthesis and antiviral evaluation of novel 1,3,4-oxadiazole/thiadiazole-chalcone conjugates. Bioorg Med Chem Lett 2017; 27:4298-4301. [PMID: 28838690 DOI: 10.1016/j.bmcl.2017.08.038] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/21/2017] [Accepted: 08/17/2017] [Indexed: 11/27/2022]
Abstract
A series of novel 1,3,4-oxadiazole/thiadiazole-chalcone conjugates were synthesized and their in vitro and in vivo antiviral activities were evaluated via microscale thermophoresis method and half-leaf method, respectively. The in vitro results indicated that compounds 7g, 7l, 8h, and 8l displayed good antiviral activity against TMV, with the binding constant values of 5.93, 6.15, 6.02, and 5.04μM, respectively, which were comparable to that of Ninnanmycin (6.78μM) and even better than that of Ribavirin (99.25μM). The in vivo results demonstrated that compounds 7g, 7l, 8h, and 8l exhibited remarkable anti-TMV activity with the EC50 values of 33.66, 33.97, 33.87 and 30.57µg/mL, respectively, which were comparable to that of Ningnanmycin (36.85µg/mL) and superior to that of Ribavirin (88.52µg/mL). Interestingly, the trend of antiviral activity in vivo was consistent with the in vitro results.
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Affiliation(s)
- Xiuhai Gan
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research, and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China; College of Chemistry and Life Science, Guizhou Education University, Guiyang 550018, China
| | - Deyu Hu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research, and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China.
| | - Zhuo Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research, and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Yanjiao Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research, and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research, and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China.
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Steele JFC, Peyret H, Saunders K, Castells‐Graells R, Marsian J, Meshcheriakova Y, Lomonossoff GP. Synthetic plant virology for nanobiotechnology and nanomedicine. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2017; 9:e1447. [PMID: 28078770 PMCID: PMC5484280 DOI: 10.1002/wnan.1447] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/12/2016] [Accepted: 11/23/2016] [Indexed: 12/12/2022]
Abstract
Nanotechnology is a rapidly expanding field seeking to utilize nano-scale structures for a wide range of applications. Biologically derived nanostructures, such as viruses and virus-like particles (VLPs), provide excellent platforms for functionalization due to their physical and chemical properties. Plant viruses, and VLPs derived from them, have been used extensively in biotechnology. They have been characterized in detail over several decades and have desirable properties including high yields, robustness, and ease of purification. Through modifications to viral surfaces, either interior or exterior, plant-virus-derived nanoparticles have been shown to support a range of functions of potential interest to medicine and nano-technology. In this review we highlight recent and influential achievements in the use of plant virus particles as vehicles for diverse functions: from delivery of anticancer compounds, to targeted bioimaging, vaccine production to nanowire formation. WIREs Nanomed Nanobiotechnol 2017, 9:e1447. doi: 10.1002/wnan.1447 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
| | - Hadrien Peyret
- Department of Biology ChemistryJohn Innes CentreNorwichUK
| | - Keith Saunders
- Department of Biology ChemistryJohn Innes CentreNorwichUK
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Kim Y, Li H, He Y, Chen X, Ma X, Lee M. Collective helicity switching of a DNA-coat assembly. NATURE NANOTECHNOLOGY 2017; 12:551-556. [PMID: 28346455 DOI: 10.1038/nnano.2017.42] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
Hierarchical assemblies of biomolecular subunits can carry out versatile tasks at the cellular level with remarkable spatial and temporal precision. As an example, the collective motion and mutual cooperation between complex protein machines mediate essential functions for life, such as replication, synthesis, degradation, repair and transport. Nucleic acid molecules are far less dynamic than proteins and need to bind to specific proteins to form hierarchical structures. The simplest example of these nucleic acid-based structures is provided by a rod-shaped tobacco mosaic virus, which consists of genetic material surrounded by coat proteins. Inspired by the complexity and hierarchical assembly of viruses, a great deal of effort has been devoted to design similarly constructed artificial viruses. However, such a wrapping approach makes nucleic acid dynamics insensitive to environmental changes. This limitation generally restricts, for example, the amplification of the conformational dynamics between the right-handed B form to the left-handed Z form of double-stranded deoxyribonucleic acid (DNA). Here we report a virus-like hierarchical assembly in which the native DNA and a synthetic coat undergo repeated collective helicity switching triggered by pH change under physiological conditions. We also show that this collective helicity inversion occurs during translocation of the DNA-coat assembly into intracellular compartments. Translating DNA conformational dynamics into a higher level of hierarchical dynamics may provide an approach to create DNA-based nanomachines.
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Affiliation(s)
- Yongju Kim
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Huichang Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Ying He
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xi Chen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xiaoteng Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Myongsoo Lee
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
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Kolliopoulou A, Taning CNT, Smagghe G, Swevers L. Viral Delivery of dsRNA for Control of Insect Agricultural Pests and Vectors of Human Disease: Prospects and Challenges. Front Physiol 2017; 8:399. [PMID: 28659820 PMCID: PMC5469917 DOI: 10.3389/fphys.2017.00399] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/26/2017] [Indexed: 12/12/2022] Open
Abstract
RNAi is applied as a new and safe method for pest control in agriculture but efficiency and specificity of delivery of dsRNA trigger remains a critical issue. Various agents have been proposed to augment dsRNA delivery, such as engineered micro-organisms and synthetic nanoparticles, but the use of viruses has received relatively little attention. Here we present a critical view of the potential of the use of recombinant viruses for efficient and specific delivery of dsRNA. First of all, it requires the availability of plasmid-based reverse genetics systems for virus production, of which an overview is presented. For RNA viruses, their application seems to be straightforward since dsRNA is produced as an intermediate molecule during viral replication, but DNA viruses also have potential through the production of RNA hairpins after transcription. However, application of recombinant virus for dsRNA delivery may not be straightforward in many cases, since viruses can encode RNAi suppressors, and virus-induced silencing effects can be determined by the properties of the encoded RNAi suppressor. An alternative is virus-like particles that retain the efficiency and specificity determinants of natural virions but have encapsidated non-replicating RNA. Finally, the use of viruses raises important safety issues which need to be addressed before application can proceed.
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Affiliation(s)
- Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology Research Group, Institute of Biosciences and Applications, NCSR “Demokritos,”Aghia Paraskevi, Greece
| | - Clauvis N. T. Taning
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology Research Group, Institute of Biosciences and Applications, NCSR “Demokritos,”Aghia Paraskevi, Greece
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Ksenofontov AL, Dobrov EN, Fedorova NV, Serebryakova MV, Prusov AN, Baratova LA, Paalme V, Järvekülg L, Shtykova EV. Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles. J Biomol Struct Dyn 2017; 36:1728-1738. [DOI: 10.1080/07391102.2017.1333457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Eugeny N. Dobrov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Natalia V. Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Andrei N. Prusov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Ludmila A. Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Viiu Paalme
- Department of Chemistry and Biotechnology, Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618, Estonia
| | - Lilian Järvekülg
- Department of Chemistry and Biotechnology, Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618, Estonia
| | - Eleonora V. Shtykova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences , Moscow, Russia
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Lemloh ML, Altintoprak K, Wege C, Weiss IM, Rothenstein D. Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization. MATERIALS (BASEL, SWITZERLAND) 2017; 10:E119. [PMID: 28772478 PMCID: PMC5459154 DOI: 10.3390/ma10020119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/18/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022]
Abstract
Proteins regulate diverse biological processes by the specific interaction with, e.g., nucleic acids, proteins and inorganic molecules. The generation of inorganic hybrid materials, such as shell formation in mollusks, is a protein-controlled mineralization process. Moreover, inorganic-binding peptides are attractive for the bioinspired mineralization of non-natural inorganic functional materials for technical applications. However, it is still challenging to identify mineral-binding peptide motifs from biological systems as well as for technical systems. Here, three complementary approaches were combined to analyze protein motifs consisting of alternating positively and negatively charged amino acids: (i) the screening of natural biomineralization proteins; (ii) the selection of inorganic-binding peptides derived from phage display; and (iii) the mineralization of tobacco mosaic virus (TMV)-based templates. A respective peptide motif displayed on the TMV surface had a major impact on the SiO₂ mineralization. In addition, similar motifs were found in zinc oxide- and zirconia-binding peptides indicating a general binding feature. The comparative analysis presented here raises new questions regarding whether or not there is a common design principle based on acidic and basic amino acids for peptides interacting with minerals.
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Affiliation(s)
- Marie-Louise Lemloh
- Institute of Biomaterials and Biomolecular Systems (IBBS), Biobased Materials, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Klara Altintoprak
- Institute of Biomaterials and Biomolecular Systems (IBBS), Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems (IBBS), Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
- Projekthaus NanoBioMater, Allmandring 5B, 70569 Stuttgart, Germany.
| | - Ingrid M Weiss
- Institute of Biomaterials and Biomolecular Systems (IBBS), Biobased Materials, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
- Projekthaus NanoBioMater, Allmandring 5B, 70569 Stuttgart, Germany.
| | - Dirk Rothenstein
- Projekthaus NanoBioMater, Allmandring 5B, 70569 Stuttgart, Germany.
- Institute for Materials Science, Chair of Chemical Materials Synthesis, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
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Schneider A, Eber FJ, Wenz NL, Altintoprak K, Jeske H, Eiben S, Wege C. Dynamic DNA-controlled "stop-and-go" assembly of well-defined protein domains on RNA-scaffolded TMV-like nanotubes. NANOSCALE 2016; 8:19853-19866. [PMID: 27878174 DOI: 10.1039/c6nr03897b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A DNA-based approach allows external control over the self-assembly process of tobacco mosaic virus (TMV)-like ribonucleoprotein nanotubes: their growth from viral coat protein (CP) subunits on five distinct RNA scaffolds containing the TMV origin of assembly (OAs) could be temporarily blocked by a stopper DNA oligomer hybridized downstream (3') of the OAs. At two upstream (5') sites tested, simple hybridization was not sufficient for stable stalling, which correlates with previous findings on a non-symmetric assembly of TMV. The growth of DNA-arrested particles could be restarted efficiently by displacement of the stopper via its toehold by using a release DNA oligomer, even after storage for twelve days. This novel strategy for growing proteinaceous tubes under tight kinetic and spatial control combines RNA guidance and its site-specific but reversible interruption by DNA blocking elements. As three of the RNA scaffolds contained long heterologous non-TMV sequence portions that included the stopping sites, this method is applicable to all RNAs amenable to TMV CP encapsidation, albeit with variable efficiency most likely depending on the scaffolds' secondary structures. The use of two distinct, selectively addressable CP variants during the serial assembly stages finally enabled an externally configured fabrication of nanotubes with highly defined subdomains. The "stop-and-go" strategy thus might pave the way towards production routines of TMV-like particles with variable aspect ratios from a single RNA scaffold, and of nanotubes with two or even more adjacent protein domains of tightly pre-defined lengths.
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Affiliation(s)
- Angela Schneider
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Fabian J Eber
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Klara Altintoprak
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Sabine Eiben
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
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40
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Papillomavirus assembly: An overview and perspectives. Virus Res 2016; 231:103-107. [PMID: 27840111 DOI: 10.1016/j.virusres.2016.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 11/20/2022]
Abstract
Papillomavirus life cycle is tightly coupled to epithelial cell differentiation, which has hindered the investigation of many aspects of papillomavirus biology, including virion assembly. The development of in vitro production methods of papillomavirus pseudoviruses, and the production of "native" virus in raft cultures have facilitated the study of some aspects of the assembly process. In this paper we review the current knowledge of papillomavirus assembly, directions for future research, and the implications of these studies on new therapeutic interventions.
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Abstract
During the life cycle of a virus, viral proteins and other components self-assemble to form an ordered protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article, we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly and thus should be taken into account in models that are used to estimate interaction parameters from experimental data.
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Affiliation(s)
- Guillermo R Lazaro
- Martin Fisher School of Physics, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University , Waltham, Massachusetts 02454, United States
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Koch C, Eber FJ, Azucena C, Förste A, Walheim S, Schimmel T, Bittner AM, Jeske H, Gliemann H, Eiben S, Geiger FC, Wege C. Novel roles for well-known players: from tobacco mosaic virus pests to enzymatically active assemblies. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:613-29. [PMID: 27335751 PMCID: PMC4901926 DOI: 10.3762/bjnano.7.54] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/03/2016] [Indexed: 05/22/2023]
Abstract
The rod-shaped nanoparticles of the widespread plant pathogen tobacco mosaic virus (TMV) have been a matter of intense debates and cutting-edge research for more than a hundred years. During the late 19th century, their behavior in filtration tests applied to the agent causing the 'plant mosaic disease' eventually led to the discrimination of viruses from bacteria. Thereafter, they promoted the development of biophysical cornerstone techniques such as electron microscopy and ultracentrifugation. Since the 1950s, the robust, helically arranged nucleoprotein complexes consisting of a single RNA and more than 2100 identical coat protein subunits have enabled molecular studies which have pioneered the understanding of viral replication and self-assembly, and elucidated major aspects of virus-host interplay, which can lead to agronomically relevant diseases. However, during the last decades, TMV has acquired a new reputation as a well-defined high-yield nanotemplate with multivalent protein surfaces, allowing for an ordered high-density presentation of multiple active molecules or synthetic compounds. Amino acid side chains exposed on the viral coat may be tailored genetically or biochemically to meet the demands for selective conjugation reactions, or to directly engineer novel functionality on TMV-derived nanosticks. The natural TMV size (length: 300 nm) in combination with functional ligands such as peptides, enzymes, dyes, drugs or inorganic materials is advantageous for applications ranging from biomedical imaging and therapy approaches over surface enlargement of battery electrodes to the immobilization of enzymes. TMV building blocks are also amenable to external control of in vitro assembly and re-organization into technically expedient new shapes or arrays, which bears a unique potential for the development of 'smart' functional 3D structures. Among those, materials designed for enzyme-based biodetection layouts, which are routinely applied, e.g., for monitoring blood sugar concentrations, might profit particularly from the presence of TMV rods: Their surfaces were recently shown to stabilize enzymatic activities upon repeated consecutive uses and over several weeks. This review gives the reader a ride through strikingly diverse achievements obtained with TMV-based particles, compares them to the progress with related viruses, and focuses on latest results revealing special advantages for enzyme-based biosensing formats, which might be of high interest for diagnostics employing 'systems-on-a-chip'.
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Affiliation(s)
- Claudia Koch
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, D-70550, Germany
| | - Fabian J Eber
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, D-70550, Germany
| | - Carlos Azucena
- Institute of Functional Interfaces (IFG), Chemistry of Oxidic and Organic Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, Karlsruhe, D-76344, Germany
| | - Alexander Förste
- Institute of Nanotechnology (INT) and Karlsruhe Institute of Applied Physics (IAP) and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), INT: Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, D-76344, Germany, and IAP/CFN: Wolfgang-Gaede-Straße 1, Karlsruhe, D-76131 Germany
| | - Stefan Walheim
- Institute of Nanotechnology (INT) and Karlsruhe Institute of Applied Physics (IAP) and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), INT: Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, D-76344, Germany, and IAP/CFN: Wolfgang-Gaede-Straße 1, Karlsruhe, D-76131 Germany
| | - Thomas Schimmel
- Institute of Nanotechnology (INT) and Karlsruhe Institute of Applied Physics (IAP) and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), INT: Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, D-76344, Germany, and IAP/CFN: Wolfgang-Gaede-Straße 1, Karlsruhe, D-76131 Germany
| | - Alexander M Bittner
- CIC Nanogune, Tolosa Hiribidea 76, E-20018 Donostia-San Sebastián, Spain, and Ikerbasque, Maria Díaz de Haro 3, E-48013 Bilbao, Spain
| | - Holger Jeske
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, D-70550, Germany
| | - Hartmut Gliemann
- Institute of Functional Interfaces (IFG), Chemistry of Oxidic and Organic Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, Karlsruhe, D-76344, Germany
| | - Sabine Eiben
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, D-70550, Germany
| | - Fania C Geiger
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, D-70550, Germany
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, D-70550, Germany
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Zhang J, Ferré-DAmaré AR. Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers. Biomolecules 2016; 6:biom6020018. [PMID: 27043647 PMCID: PMC4919913 DOI: 10.3390/biom6020018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 12/27/2022] Open
Abstract
Length determination is a fundamental problem in biology and chemistry. Numerous proteins measure distances on linear biopolymers to exert effects with remarkable spatial precision. Recently, ruler-like devices made of noncoding RNAs have been structurally and biochemically characterized. Two prominent examples are the RNase P ribozyme and the T-box riboswitch. Both act as molecular calipers. The two RNAs clamp onto the elbow of tRNA (or pre-tRNA) and make distance measurements orthogonal to each other. Here, we compare and contrast the molecular ruler characteristics of these RNAs. RNase P appears pre-configured to measure a fixed distance on pre-tRNA to ensure the fidelity of its maturation. RNase P is a multiple-turnover ribozyme, and its rigid structure efficiently selects pre-tRNAs, cleaves, and releases them. In contrast, the T-box is flexible and segmented, an architecture that adapts to the intrinsically flexible tRNA. The tripartite T-box inspects the overall shape, anticodon sequence, and aminoacylation status of an incoming tRNA while it folds co-transcriptionally, leading to a singular, conditional genetic switching event. The elucidation of the structures and mechanisms of action of these two RNA molecular rulers may augur the discovery of new RNA measuring devices in noncoding and viral transcriptomes, and inform the design of artificial RNA rulers.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA.
| | - Adrian R Ferré-DAmaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA.
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Multifrequency Force Microscopy of Helical Protein Assembly on a Virus. Sci Rep 2016; 6:21899. [PMID: 26915629 PMCID: PMC4768132 DOI: 10.1038/srep21899] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/01/2016] [Indexed: 01/09/2023] Open
Abstract
High-resolution microscopy techniques have been extensively used to investigate the structure of soft, biological matter at the nanoscale, from very thin membranes to small objects, like viruses. Electron microscopy techniques allow for obtaining extraordinary resolution by averaging signals from multiple identical structures. In contrast, atomic force microscopy (AFM) collects data from single entities. Here, it is possible to finely modulate the interaction with the samples, in order to be sensitive to their top surface, avoiding mechanical deformations. However, most biological surfaces are highly curved, such as fibers or tubes, and ultimate details of their surface are in the vicinity of steep height variations. This limits lateral resolution, even when sharp probes are used. We overcome this problem by using multifrequency force microscopy on a textbook example, the Tobacco Mosaic Virus (TMV). We achieved unprecedented resolution in local maps of amplitude and phase shift of the second excited mode, recorded together with sample topography. Our data, which combine multifrequency imaging and Fourier analysis, confirm the structure deduced from averaging techniques (XRD, cryoEM) for surface features of single virus particles, down to the helical pitch of the coat protein subunits, 2.3 nm. Remarkably, multifrequency AFM images do not require any image postprocessing.
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Niehl A, Appaix F, Boscá S, van der Sanden B, Nicoud JF, Bolze F, Heinlein M. Fluorescent Tobacco mosaic virus-Derived Bio-Nanoparticles for Intravital Two-Photon Imaging. FRONTIERS IN PLANT SCIENCE 2016; 6:1244. [PMID: 26793221 PMCID: PMC4710741 DOI: 10.3389/fpls.2015.01244] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/21/2015] [Indexed: 05/20/2023]
Abstract
Multi-photon intravital imaging has become a powerful tool to investigate the healthy and diseased brain vasculature in living animals. Although agents for multi-photon fluorescence microscopy of the microvasculature are available, issues related to stability, bioavailability, toxicity, cost or chemical adaptability remain to be solved. In particular, there is a need for highly fluorescent dyes linked to particles that do not cross the blood brain barrier (BBB) in brain diseases like tumor or stroke to estimate the functional blood supply. Plant virus particles possess a number of distinct advantages over other particles, the most important being the multi-valency of chemically addressable sites on the particle surface. This multi-valency, together with biological compatibility and inert nature, makes plant viruses ideal carriers for in vivo imaging agents. Here, we show that the well-known Tobacco mosaic virus is a suitable nanocarrier for two-photon dyes and for intravital imaging of the mouse brain vasculature.
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Affiliation(s)
- Annette Niehl
- Institut de Biologie Moléculaire des Plantes (IBMP-UPR2357), Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Florence Appaix
- Two-Photon Microscopy Platform, Grenoble Institut des Neurosciences, Institut National de la Santé et de la Recherche Médicale U836, Université Grenoble AlpesGrenoble, France
| | - Sonia Boscá
- Institut de Biologie Moléculaire des Plantes (IBMP-UPR2357), Centre National de la Recherche ScientifiqueStrasbourg, France
| | | | - Jean-François Nicoud
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 Centre National de la Recherche Scientifique-Université de StrasbourgIllkirch, France
| | - Frédéric Bolze
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 Centre National de la Recherche Scientifique-Université de StrasbourgIllkirch, France
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes (IBMP-UPR2357), Centre National de la Recherche ScientifiqueStrasbourg, France
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Koch C, Wabbel K, Eber FJ, Krolla-Sidenstein P, Azucena C, Gliemann H, Eiben S, Geiger F, Wege C. Modified TMV Particles as Beneficial Scaffolds to Present Sensor Enzymes. FRONTIERS IN PLANT SCIENCE 2015; 6:1137. [PMID: 26734040 PMCID: PMC4689848 DOI: 10.3389/fpls.2015.01137] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/30/2015] [Indexed: 05/22/2023]
Abstract
Tobacco mosaic virus (TMV) is a robust nanotubular nucleoprotein scaffold increasingly employed for the high density presentation of functional molecules such as peptides, fluorescent dyes, and antibodies. We report on its use as advantageous carrier for sensor enzymes. A TMV mutant with a cysteine residue exposed on every coat protein (CP) subunit (TMVCys) enabled the coupling of bifunctional maleimide-polyethylene glycol (PEG)-biotin linkers (TMVCys/Bio). Its surface was equipped with two streptavidin [SA]-conjugated enzymes: glucose oxidase ([SA]-GOx) and horseradish peroxidase ([SA]-HRP). At least 50% of the CPs were decorated with a linker molecule, and all thereof with active enzymes. Upon use as adapter scaffolds in conventional "high-binding" microtiter plates, TMV sticks allowed the immobilization of up to 45-fold higher catalytic activities than control samples with the same input of enzymes. Moreover, they increased storage stability and reusability in relation to enzymes applied directly to microtiter plate wells. The functionalized TMV adsorbed to solid supports showed a homogeneous distribution of the conjugated enzymes and structural integrity of the nanorods upon transmission electron and atomic force microscopy. The high surface-increase and steric accessibility of the viral scaffolds in combination with the biochemical environment provided by the plant viral coat may explain the beneficial effects. TMV can, thus, serve as a favorable multivalent nanoscale platform for the ordered presentation of bioactive proteins.
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Affiliation(s)
- Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Katrin Wabbel
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Fabian J. Eber
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Peter Krolla-Sidenstein
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Carlos Azucena
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Hartmut Gliemann
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Sabine Eiben
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Fania Geiger
- Department of New Materials and Biosystems, Max-Planck-Institute for Intelligent SystemsStuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
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47
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Chen Z, Li N, Li S, Dharmarwardana M, Schlimme A, Gassensmith JJ. Viral chemistry: the chemical functionalization of viral architectures to create new technology. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2015; 8:512-34. [DOI: 10.1002/wnan.1379] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/31/2015] [Accepted: 09/15/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Zhuo Chen
- Department of Chemistry and BiochemistryThe University of Texas at DallasRichardsonTXUSA
| | - Na Li
- Department of Chemistry and BiochemistryThe University of Texas at DallasRichardsonTXUSA
| | - Shaobo Li
- Department of Chemistry and BiochemistryThe University of Texas at DallasRichardsonTXUSA
| | | | - Anna Schlimme
- Department of Chemistry and BiochemistryThe University of Texas at DallasRichardsonTXUSA
| | - Jeremiah J Gassensmith
- Department of Chemistry and BiochemistryThe University of Texas at DallasRichardsonTXUSA
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48
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Clare DK, Pechnikova EV, Skurat EV, Makarov VV, Sokolova OS, Solovyev AG, Orlova EV. Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy. Structure 2015; 23:1815-1826. [PMID: 26278173 PMCID: PMC4597109 DOI: 10.1016/j.str.2015.06.028] [Citation(s) in RCA: 21] [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: 02/10/2015] [Revised: 05/27/2015] [Accepted: 06/21/2015] [Indexed: 11/30/2022]
Abstract
Barley stripe mosaic virus (BSMV, genus Hordeivirus) is a rod-shaped single-stranded RNA virus similar to viruses of the structurally characterized and well-studied genus Tobamovirus. Here we report the first high-resolution structure of BSMV at 4.1 Å obtained by cryo-electron microscopy. We discovered that BSMV forms two types of virion that differ in the number of coat protein (CP) subunits per turn and interactions between the CP subunits. While BSMV and tobacco mosaic virus CP subunits have a similar fold and interact with RNA using conserved residues, the axial contacts between the CP of these two viral groups are considerably different. BSMV CP subunits lack substantial axial contacts and are held together by a previously unobserved lateral contact formed at the virion surface via an interacting loop, which protrudes from the CP hydrophobic core to the adjacent CP subunit. These data provide an insight into diversity in structural organization of helical viruses.
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Affiliation(s)
- Daniel Kofi Clare
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Eugenia V Pechnikova
- A.V. Shubnikov Institute of Crystallography RAS, 59 Leninsky Avenue, 119333 Moscow, Russia
| | - Eugene V Skurat
- Department of Biology, Moscow State University, 1 Leninskie Gory, Building 12, 119991 Moscow, Russia
| | - Valentin V Makarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Olga S Sokolova
- A.V. Shubnikov Institute of Crystallography RAS, 59 Leninsky Avenue, 119333 Moscow, Russia; Department of Biology, Moscow State University, 1 Leninskie Gory, Building 12, 119991 Moscow, Russia
| | - Andrey G Solovyev
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Elena V Orlova
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London WC1E 7HX, UK.
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49
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Vilona D, Di Lorenzo R, Carraro M, Licini G, Trainotti L, Bonchio M. Viral nano-hybrids for innovative energy conversion and storage schemes. J Mater Chem B 2015; 3:6718-6730. [PMID: 32262464 DOI: 10.1039/c5tb00924c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Typical rod-like viruses (the Tobacco Mosaic Virus (TMV) and the Bacteriophage M13) are biological nanostructures that couple a 1D mono-dispersed morphology with a precisely defined topology of surface spaced and orthogonal reactive domains. These biogenic scaffolds offer a unique alternative to synthetic nano-platforms for the assembly of functional molecules and materials. Spatially resolved 1D arrays of inorganic-organic hybrid domains can thus be obtained on viral nano-templates resulting in the functional arrangement of photo-triggers and catalytic sites with applications in light energy conversion and storage. Different synthetic strategies are herein highlighted depending on the building blocks and with a particular emphasis on the molecular design of viral-templated nano-interfaces holding great potential for the dream-goal of artificial photosynthesis.
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Affiliation(s)
- D Vilona
- CNR-ITM and Department of Chemical Sciences, University of Padova, via F. Marzolo 1, 35131 Padova, Italy.
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50
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Plant virus directed fabrication of nanoscale materials and devices. Virology 2015; 479-480:200-12. [DOI: 10.1016/j.virol.2015.03.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/24/2015] [Accepted: 03/02/2015] [Indexed: 11/21/2022]
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