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Lorenz UJ. Microsecond time-resolved cryo-electron microscopy. Curr Opin Struct Biol 2024; 87:102840. [PMID: 38810313 DOI: 10.1016/j.sbi.2024.102840] [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: 02/13/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
Abstract
Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics that were previously inaccessible and therefore, to significantly advance our understanding of protein function. This review summarizes the properties of the laser melting and revitrification process that underlies the technique and describes different experimental implementations. Strategies for initiating and probing dynamics are discussed. Finally, the microsecond time-resolved observation of the capsid dynamics of cowpea chlorotic mottle virus, an icosahedral plant virus, is reviewed, which illustrates important features of the technique as well as its potential.
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Affiliation(s)
- Ulrich J Lorenz
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015 Lausanne, Switzerland.
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2
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Michalski J, Kalwarczyk T, Kwapiszewska K, Enderlein J, Poniewierski A, Karpińska A, Kucharska K, Hołyst R. Rotational and translational diffusion of biomolecules in complex liquids and HeLa cells. SOFT MATTER 2024; 20:5810-5821. [PMID: 38995242 DOI: 10.1039/d4sm00422a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Diffusive motion accompanies many physical and biological processes. The Stokes-Sutherland-Einstein relation for the translational diffusion coefficient, DT, agrees with experiments done in simple fluids but fails for complex fluids. Moreover, the interdependence between DT and rotational diffusion coefficient, DR, also deviates in complex fluids from the classical relation of DT/DR = 4r2/3 known in simple fluids. Makuch et al. Soft Matter, 2020, 16, 114-124 presented a generalization of the classical translational and rotational diffusion theory for complex fluids. In this work, we empirically verify this model based on simultaneous translational and rotational diffusion measurements. We use fluorescently stained cowpea chlorotic mottle virus (CCMV) particles as monodisperse probes and aqueous polyethylene glycol (PEG) solutions as a model complex fluid. The theory and experimental data obtained from fluorescence correlation spectroscopy (FCS) measurements agreed. Finally, we used the same model and analyzed the diffusion of Yo-Pro-1 stained large ribosomal subunits (LSU) in the cytoplasm and nucleus of living HeLa cells.
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Affiliation(s)
- Jarosław Michalski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Karina Kwapiszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Andrzej Poniewierski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Aneta Karpińska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Karolina Kucharska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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3
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Martínez A, Porras A, Pastor AR, Palomares LA, Ramírez OT. One-Step Purification Strategy for Cowpea Chlorotic Mottle Virus-Like Particles Produced by the IC-BEVS. Methods Mol Biol 2024; 2829:237-246. [PMID: 38951339 DOI: 10.1007/978-1-0716-3961-0_17] [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] [Indexed: 07/03/2024]
Abstract
Virus-like particles (VLP) of the cowpea chlorotic mottle virus (CCMV), a plant virus, have been shown to be safe and noncytotoxic vehicles for delivering various cargos, including nucleic acids and peptides, and as scaffolds for presenting epitopes. Thus, CCMV-VLP have acquired increasing attention to be used in fields such as gene therapy, drug delivery, and vaccine development. Regardless of their production method, most reports purify CCMV-VLP through a series of ultracentrifugation steps using sucrose density gradient ultracentrifugation, which is a complex and time-consuming process. Here, the use of anion exchange chromatography is described as a one-step protocol for purification of CCMV-VLP produced by the insect cell-baculovirus expression vector system (IC-BEVS).
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Affiliation(s)
- Anayeli Martínez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Alberto Porras
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Ana Ruth Pastor
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Laura A Palomares
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Octavio T Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico.
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4
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Ramirez-Acosta K, Loredo-García E, Herrera-Hernandez MM, Cadena-Nava RD. Plant Virus-Like Particles for RNA Delivery. Methods Mol Biol 2024; 2822:387-410. [PMID: 38907930 DOI: 10.1007/978-1-0716-3918-4_24] [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] [Indexed: 06/24/2024]
Abstract
Plant viruses such as brome mosaic virus and cowpea chlorotic mottle virus are effectively purified through PEG precipitation and sucrose cushion ultracentrifugation. Increasing ionic strength and an alkaline pH cause the viruses to swell and disassemble into coat protein subunits. The coat proteins can be reassembled into stable virus-like particles (VLPs) that carry anionic molecules at low ionic strength and through two-step dialysis from neutral pH to acidic buffer. VLPs have been extensively studied due to their ability to protect and deliver cargo, particularly RNA, while avoiding degradation under physiological conditions. Furthermore, chemical functionalization of the surface of VLPs allows for the targeted drug delivery. VLPs derived from plants have demonstrated great potential in nanomedicine by offering a versatile platform for drug delivery, imaging, and therapeutic applications.
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Affiliation(s)
- Kendra Ramirez-Acosta
- Centro de Nanociencias y Nanotecnología-Universidad Nacional Autónoma de México (UNAM), Ensenada, Baja California, Mexico
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, Mexico
| | - Elizabeth Loredo-García
- Centro de Nanociencias y Nanotecnología-Universidad Nacional Autónoma de México (UNAM), Ensenada, Baja California, Mexico
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, Mexico
| | - M Mariana Herrera-Hernandez
- Centro de Nanociencias y Nanotecnología-Universidad Nacional Autónoma de México (UNAM), Ensenada, Baja California, Mexico
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, Mexico
| | - Ruben D Cadena-Nava
- Centro de Nanociencias y Nanotecnología-Universidad Nacional Autónoma de México (UNAM), Ensenada, Baja California, Mexico.
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5
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Torres-Salgado JF, Villagrana-Escareño MV, Duran-Meza AL, Segovia-Gonzalez XF, Cadena-Nava RD, Gelbart WM, Knobler CM, Ruiz-García J. Spontaneous bilayer wrapping of virus particles by a phospholipid Langmuir monolayer. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:118. [PMID: 38051443 PMCID: PMC10697897 DOI: 10.1140/epje/s10189-023-00366-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/27/2023] [Indexed: 12/07/2023]
Abstract
We report here the spontaneous formation of lipid-bilayer-wrapped virus particles, following the injection of "naked" virus particles into the subphase of a Langmuir trough with a liquid monolayer of lipids at its air-water interface. The virus particles are those of the well-studied cowpea chlorotic mottle virus, CCMV, which are negatively charged at the pH 6 of the subphase; the lipids are a 9:1 mix of neutral DMPC and cationic CTAB molecules. Before adding CCMV particles to the subphase we establish the mixed lipid monolayer in its liquid-expanded state at a fixed pressure (17.5 mN/m) and average area-per-molecule of (41Å2). Keeping the total area fixed, the surface pressure is observed to decrease at about 15 h after adding the virus particles in the subphase; by 37 h it has dropped to zero, corresponding to essentially all the lipid molecules having been removed from the air-water interface. By collecting particles from the subphase and measuring their sizes by atomic force microscopy, we show that the virus particles have been wrapped by lipid bilayers (or by two lipid bilayers). These results can be understood in terms of thermal fluctuations and electrostatic interactions driving the wrapping of the anionic virus particles by the cationic lipids. Spontaneous acquisition by a virus particle of, first, a hydrophobic lipid monolayer envelope and, then, a hydrophilic lipid bilayer envelope, as it interacts from the subphase with an oppositely charged Langmuir monolayer.
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Affiliation(s)
- J F Torres-Salgado
- Biological Physics Laboratory, Institute of Physics, Universidad Autónoma de San Luis Potosí, San Luis/dF Potosí, 78000, San Luis Potosí, México
| | - M V Villagrana-Escareño
- Biological Physics Laboratory, Institute of Physics, Universidad Autónoma de San Luis Potosí, San Luis/dF Potosí, 78000, San Luis Potosí, México
| | - A L Duran-Meza
- Biological Physics Laboratory, Institute of Physics, Universidad Autónoma de San Luis Potosí, San Luis/dF Potosí, 78000, San Luis Potosí, México
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - X F Segovia-Gonzalez
- Biological Physics Laboratory, Institute of Physics, Universidad Autónoma de San Luis Potosí, San Luis/dF Potosí, 78000, San Luis Potosí, México
| | - R D Cadena-Nava
- Biological Physics Laboratory, Institute of Physics, Universidad Autónoma de San Luis Potosí, San Luis/dF Potosí, 78000, San Luis Potosí, México
- Present Address: Center of Nanosciences and Nanotechnology-UNAM, Km 107 Carretera Tijuana-Ensenada, 22800, Ensenada, BC, México
| | - W M Gelbart
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569, USA.
| | - C M Knobler
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - J Ruiz-García
- Biological Physics Laboratory, Institute of Physics, Universidad Autónoma de San Luis Potosí, San Luis/dF Potosí, 78000, San Luis Potosí, México
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6
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Nonappa. Precision nanoengineering for functional self-assemblies across length scales. Chem Commun (Camb) 2023; 59:13800-13819. [PMID: 37902292 DOI: 10.1039/d3cc02205f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
As nanotechnology continues to push the boundaries across disciplines, there is an increasing need for engineering nanomaterials with atomic-level precision for self-assembly across length scales, i.e., from the nanoscale to the macroscale. Although molecular self-assembly allows atomic precision, extending it beyond certain length scales presents a challenge. Therefore, the attention has turned to size and shape-controlled metal nanoparticles as building blocks for multifunctional colloidal self-assemblies. However, traditionally, metal nanoparticles suffer from polydispersity, uncontrolled aggregation, and inhomogeneous ligand distribution, resulting in heterogeneous end products. In this feature article, I will discuss how virus capsids provide clues for designing subunit-based, precise, efficient, and error-free self-assembly of colloidal molecules. The atomically precise nanoscale proteinic subunits of capsids display rigidity (conformational and structural) and patchy distribution of interacting sites. Recent experimental evidence suggests that atomically precise noble metal nanoclusters display an anisotropic distribution of ligands and patchy ligand bundles. This enables symmetry breaking, consequently offering a facile route for two-dimensional colloidal crystals, bilayers, and elastic monolayer membranes. Furthermore, inter-nanocluster interactions mediated via the ligand functional groups are versatile, offering routes for discrete supracolloidal capsids, composite cages, toroids, and macroscopic hierarchically porous frameworks. Therefore, engineered nanoparticles with atomically precise structures have the potential to overcome the limitations of molecular self-assembly and large colloidal particles. Self-assembly allows the emergence of new optical properties, mechanical strength, photothermal stability, catalytic efficiency, quantum yield, and biological properties. The self-assembled structures allow reproducible optoelectronic properties, mechanical performance, and accurate sensing. More importantly, the intrinsic properties of individual nanoclusters are retained across length scales. The atomically precise nanoparticles offer enormous potential for next-generation functional materials, optoelectronics, precision sensors, and photonic devices.
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Affiliation(s)
- Nonappa
- Facutly of Engineering and Natural Sciences, Tampere University, FI-33720, Tampere, Finland.
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7
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Segovia-González XF, Villagrana-Escareño MV, Ríos-Ramírez M, de la Cruz VS, Mejía-Hernández JN, Cuellar-Camacho JL, Patrón-Soberano A, Sportsman R, Ruiz-García J. An Observation of a Very High Swelling of Bromovirus Members at Specific Ionic Strengths and pH. Viruses 2023; 15:2046. [PMID: 37896823 PMCID: PMC10612077 DOI: 10.3390/v15102046] [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: 07/31/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Cowpea chlorotic mottle virus (CCMV) and brome mosaic virus (BMV) are naked plant viruses with similar characteristics; both form a T = 3 icosahedral protein capsid and are members of the bromoviridae family. It is well known that these viruses completely disassemble and liberate their genome at a pH around 7.2 and 1 M ionic strength. However, the 1 M ionic strength condition is not present inside cells, so an important question is how these viruses deliver their genome inside cells for their viral replication. There are some studies reporting the swelling of the CCMV virus using different techniques. For example, it is reported that at a pH~7.2 and low ionic strength, the swelling observed is about 10% of the initial diameter of the virus. Furthermore, different regions within the cell are known to have different pH levels and ionic strengths. In this work, we performed several experiments at low ionic strengths of 0.1, 0.2, and 0.3 and systematically increased the pH in 0.2 increments from 4.6 to 7.4. To determine the change in virus size at the different pHs and ionic strengths, we first used dynamic light scattering (DLS). Most of the experiments agree with a 10% capsid swelling under the conditions reported in previous works, but surprisingly, we found that at some particular conditions, the virus capsid swelling could be as big as 20 to 35% of the original size. These measurements were corroborated by atomic force microscopy (AFM) and transmission electron microscopy (TEM) around the conditions where the big swelling was determined by DLS. Therefore, this big swelling could be an easier mechanism that viruses use inside the cell to deliver their genome to the cell machinery for viral replication.
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Affiliation(s)
- Xochitl Fabiola Segovia-González
- Biologycal Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78000, Mexico; (X.F.S.-G.); (M.V.V.-E.); (M.R.-R.); (V.S.d.l.C.); (J.N.M.-H.); (J.L.C.-C.)
| | - Maria Veronica Villagrana-Escareño
- Biologycal Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78000, Mexico; (X.F.S.-G.); (M.V.V.-E.); (M.R.-R.); (V.S.d.l.C.); (J.N.M.-H.); (J.L.C.-C.)
| | - Maricarmen Ríos-Ramírez
- Biologycal Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78000, Mexico; (X.F.S.-G.); (M.V.V.-E.); (M.R.-R.); (V.S.d.l.C.); (J.N.M.-H.); (J.L.C.-C.)
| | - Vianey Santiago de la Cruz
- Biologycal Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78000, Mexico; (X.F.S.-G.); (M.V.V.-E.); (M.R.-R.); (V.S.d.l.C.); (J.N.M.-H.); (J.L.C.-C.)
| | - Jessica Nathaly Mejía-Hernández
- Biologycal Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78000, Mexico; (X.F.S.-G.); (M.V.V.-E.); (M.R.-R.); (V.S.d.l.C.); (J.N.M.-H.); (J.L.C.-C.)
| | - Jose Luis Cuellar-Camacho
- Biologycal Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78000, Mexico; (X.F.S.-G.); (M.V.V.-E.); (M.R.-R.); (V.S.d.l.C.); (J.N.M.-H.); (J.L.C.-C.)
| | - Araceli Patrón-Soberano
- Molecular Biology Division, IPICYT, Instituto Potosino de Investigación Científica y Tecnológica A.C., San Luis Potosí 78216, Mexico;
| | - Richard Sportsman
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, USA;
| | - Jaime Ruiz-García
- Biologycal Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78000, Mexico; (X.F.S.-G.); (M.V.V.-E.); (M.R.-R.); (V.S.d.l.C.); (J.N.M.-H.); (J.L.C.-C.)
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8
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Seitz I, Saarinen S, Kumpula EP, McNeale D, Anaya-Plaza E, Lampinen V, Hytönen VP, Sainsbury F, Cornelissen JJLM, Linko V, Huiskonen JT, Kostiainen MA. DNA-origami-directed virus capsid polymorphism. NATURE NANOTECHNOLOGY 2023; 18:1205-1212. [PMID: 37460794 PMCID: PMC10575778 DOI: 10.1038/s41565-023-01443-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/06/2023] [Indexed: 10/15/2023]
Abstract
Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have advantages in the development of new vaccines and delivery systems. However, current tools to direct the assembly process in a programmable manner are exceedingly elusive. Here we introduce a modular approach by demonstrating DNA-origami-directed polymorphism of single-protein subunit capsids. We achieve control over the capsid shape, size and topology by employing user-defined DNA origami nanostructures as binding and assembly platforms, which are efficiently encapsulated within the capsid. Furthermore, the obtained viral capsid coatings can shield the encapsulated DNA origami from degradation. Our approach is, moreover, not limited to a single type of capsomers and can also be applied to RNA-DNA origami structures to pave way for next-generation cargo protection and targeting strategies.
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Affiliation(s)
- Iris Seitz
- Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Sharon Saarinen
- Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Donna McNeale
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | | | - Vili Lampinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Jeroen J L M Cornelissen
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, Enschede, Netherlands
| | - Veikko Linko
- Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
- LIBER Center of Excellence, Aalto University, Aalto, Finland
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Mauri A Kostiainen
- Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, Aalto, Finland.
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9
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Harder OF, Barrass SV, Drabbels M, Lorenz UJ. Fast viral dynamics revealed by microsecond time-resolved cryo-EM. Nat Commun 2023; 14:5649. [PMID: 37704664 PMCID: PMC10499870 DOI: 10.1038/s41467-023-41444-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incomplete. To enable such observations, we have recently proposed a technique that improves the time resolution of cryo-electron microscopy (cryo-EM) to microseconds. Here, we demonstrate that microsecond time-resolved cryo-EM enables observations of fast protein dynamics. We use our approach to elucidate the mechanics of the capsid of cowpea chlorotic mottle virus (CCMV), whose large-amplitude motions play a crucial role in the viral life cycle. We observe that a pH jump causes the extended configuration of the capsid to contract on the microsecond timescale. While this is a concerted process, the motions of the capsid proteins involve different timescales, leading to a curved reaction path. It is difficult to conceive how such a detailed picture of the dynamics could have been obtained with any other method, which highlights the potential of our technique. Crucially, our experiments pave the way for microsecond time-resolved cryo-EM to be applied to a broad range of protein dynamics that previously could not have been observed. This promises to fundamentally advance our understanding of protein function.
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Affiliation(s)
- Oliver F Harder
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland
| | - Sarah V Barrass
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland
| | - Marcel Drabbels
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland
| | - Ulrich J Lorenz
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland.
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10
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Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
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11
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Chakravarty A, Rao ALN. Modulation of Capsid Dynamics in Bromoviruses by the Host and Heterologous Viral Replicase. J Virol 2023; 97:e0128422. [PMID: 36786601 PMCID: PMC10062129 DOI: 10.1128/jvi.01284-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
The three genomic and a single subgenomic RNA of Cowpea chlorotic mottle virus (CCMV), which is pathogenic to plants, is packaged into three morphologically indistinguishable icosahedral virions with T=3 symmetry. The two virion types, C1V and C2V, package genomic RNAs 1 (C1) and 2 (C2), respectively. The third virion type, C3+4V, copackages genomic RNA3 and its subgenomic RNA (RNA4). In this study, we sought to evaluate how the alteration of native capsid dynamics by the host and viral replicase modulate the general biology of the virus. The application of a series of biochemical, molecular, and biological assays revealed the following. (i) Proteolytic analysis of the three virion types of CCMV assembled individually in planta revealed that, while retaining the structural integrity, C1V and C2V virions released peptide regions encompassing the N-terminal arginine-rich RNA binding motif. In contrast, a minor population of the C3+4V virion type was sensitive to trypsin-releasing peptides encompassing the entire capsid protein region. (ii) The wild-type CCMV virions purified from cowpea are highly susceptible to trypsin digestion, while those from Nicotiana benthamiana remained resistant, and (iii) finally, the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis evaluated the relative dynamics of C3+4V and B3+4V virions assembled under the control of the homologous versus heterologous replicase. The role of viral replicase in modulating the capsid dynamics was evident by the differential sensitivity to protease exhibited by B3+4V and C3+4V virions assembled under the homologous versus heterologous replicase. Our results collectively conclude that constant modulation of capsid dynamics by the host and viral replicase is obligatory for successful infection. IMPORTANCE Infectious virus particles or virions are considered static structures and undergo various conformational transitions to replicate and infect many eukaryotic cells. In viruses, conformational changes are essential for establishing infection and evolution. Although viral capsid fluctuations, referred to as dynamics or breathing, have been well studied in RNA viruses pathogenic to animals, such information is limited among plant viruses. The primary focus of this study is to address how capsid dynamics of plant-pathogenic RNA viruses, namely, Cowpea chlorotic mottle (CCMV) and Brome mosaic virus (BMV), are modulated by the host and viral replicase. The results presented have improved and transformed our understanding of the functional relationship between capsid dynamics and the general biology of the virus. They are likely to provide stimulus to extend similar studies to viruses pathogenic to eukaryotic organisms.
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Affiliation(s)
- Antara Chakravarty
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
| | - A. L. N. Rao
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
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12
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Tscheuschner G, Ponader M, Raab C, Weider PS, Hartfiel R, Kaufmann JO, Völzke JL, Bosc-Bierne G, Prinz C, Schwaar T, Andrle P, Bäßler H, Nguyen K, Zhu Y, Mey ASJS, Mostafa A, Bald I, Weller MG. Efficient Purification of Cowpea Chlorotic Mottle Virus by a Novel Peptide Aptamer. Viruses 2023; 15:v15030697. [PMID: 36992405 PMCID: PMC10051510 DOI: 10.3390/v15030697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/31/2023] Open
Abstract
The cowpea chlorotic mottle virus (CCMV) is a plant virus explored as a nanotechnological platform. The robust self-assembly mechanism of its capsid protein allows for drug encapsulation and targeted delivery. Additionally, the capsid nanoparticle can be used as a programmable platform to display different molecular moieties. In view of future applications, efficient production and purification of plant viruses are key steps. In established protocols, the need for ultracentrifugation is a significant limitation due to cost, difficult scalability, and safety issues. In addition, the purity of the final virus isolate often remains unclear. Here, an advanced protocol for the purification of the CCMV from infected plant tissue was developed, focusing on efficiency, economy, and final purity. The protocol involves precipitation with PEG 8000, followed by affinity extraction using a novel peptide aptamer. The efficiency of the protocol was validated using size exclusion chromatography, MALDI-TOF mass spectrometry, reversed-phase HPLC, and sandwich immunoassay. Furthermore, it was demonstrated that the final eluate of the affinity column is of exceptional purity (98.4%) determined by HPLC and detection at 220 nm. The scale-up of our proposed method seems to be straightforward, which opens the way to the large-scale production of such nanomaterials. This highly improved protocol may facilitate the use and implementation of plant viruses as nanotechnological platforms for in vitro and in vivo applications.
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Affiliation(s)
- Georg Tscheuschner
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Marco Ponader
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Christopher Raab
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Prisca S Weider
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Reni Hartfiel
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Jan Ole Kaufmann
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- Department of Diagnostic and Interventional Radiology, Technical University of Munich, 81675 Munich, Germany
| | - Jule L Völzke
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Gaby Bosc-Bierne
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Carsten Prinz
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | | | - Paul Andrle
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Henriette Bäßler
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Khoa Nguyen
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Yanchen Zhu
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Antonia S J S Mey
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Amr Mostafa
- Institute of Chemistry-Physical Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Michael G Weller
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
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13
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Liu Q, Yang S, Seitz I, Pistikou AMM, de Greef TFA, Kostiainen MA. A Synthetic Protocell-Based Heparin Scavenger. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2201790. [PMID: 35570377 DOI: 10.1002/smll.202201790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Heparin is a commonly applied blood anticoagulant agent in clinical use. After treatment, excess heparin needs to be removed to circumvent side effects and recover the blood-clotting cascade. Most existing heparin antidotes rely on direct heparin binding and complexation, yet selective compartmentalization and sequestration of heparin would be beneficial for safety and efficiency. However, such systems have remained elusive. Herein, a semipermeable protein-based microcompartment (proteinosome) is loaded with a highly positively charged chitosan derivative, which can induce electrostatics-driven internalization of anionic guest molecules inside the compartment. Chitosan-loaded proteinosomes are subsequently employed to capture heparin, and an excellent heparin-scavenging performance is demonstrated under physiologically relevant conditions. Both the highly positive scavenger and the polyelectrolyte complex are confined and shielded by the protein compartment in a time-dependent manner. Moreover, selective heparin-scavenging behavior over serum albumin is realized through adjusting the localized scavenger or surrounding salt concentrations at application-relevant circumstances. In vitro studies reveal that the cytotoxicity of the cationic scavenger and the produced polyelectrolyte complex is reduced by protocell shielding. Therefore, the proteinosome-based systems may present a novel polyelectrolyte-scavenging method for biomedical applications.
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Affiliation(s)
- Qing Liu
- Wenzhou Institute, University of Chinese Academy of Sciences (WIUCAS), Wenzhou, Zhejiang, 325001, China
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, 02150, Finland
| | - Shuo Yang
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Computational Biology Group, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB, 5600, The Netherlands
| | - Iris Seitz
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, 02150, Finland
| | - Anna-Maria Makri Pistikou
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Computational Biology Group, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB, 5600, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Computational Biology Group, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB, 5600, The Netherlands
- Institute for Molecules and Materials, Radboud University, Nijmegen, MB, 6525, The Netherlands
- Center for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, CB 3584, The Netherlands
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, 02150, Finland
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14
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Chan SK, Steinmetz NF. microRNA-181a silencing by antisense oligonucleotides delivered by virus-like particles. J Mater Chem B 2023; 11:816-825. [PMID: 36597907 PMCID: PMC9898218 DOI: 10.1039/d2tb02199d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cowpea chlorotic mottle virus (CCMV) is a positive-sense RNA virus that can be repurposed for gene delivery applications. Understanding the self-assembly process of the virus enabled to remove its genome and replace it with desired nucleic acids, and we and others have previously reported using CCMV virus-like particle (VLP) to encapsulate siRNA, mRNA, as well as CpG oligodeoxynucleotides. In this study, the CCMV VLP was applied to encapsulate two different formats of anti-miR-181a oligonucleotides: naked RNA and chemically stabilized RNA to knockdown highly regulated miR-181a in ovarian cancer cells. miR-181a expression in ovarian tumors is associated with high aggressiveness, invasiveness, resistance to chemotherapy, and overall poor prognosis. Therefore, miR-181a is an important target for ovarian cancer therapy. qPCR data and cancer cell migration assays demonstrated higher knockdown efficacy when anti-miR-181a oligonucleotides were encapsulated and delivered using the VLPs resulting in reduced cancer cell invasiveness. Importantly, delivery of anti-miR-181a oligonucleotide into cells could be achieved without the aid of a transfection agent or surface modification. These results highlight the opportunity of plant-derived VLPs as nucleic acid carriers.
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Affiliation(s)
- Soo Khim Chan
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.
| | - Nicole F. Steinmetz
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA,Department of Radiology, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA,Center for Nano-ImmunoEngineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA,Center for Engineering in Cancer, Institute for Engineering in Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA,Moores Cancer Center, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA,Institute for Materials Discovery and Design, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
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15
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Kim KR, Lee AS, Kim SM, Heo HR, Kim CS. Virus-like nanoparticles as a theranostic platform for cancer. Front Bioeng Biotechnol 2023; 10:1106767. [PMID: 36714624 PMCID: PMC9878189 DOI: 10.3389/fbioe.2022.1106767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
Virus-like nanoparticles (VLPs) are natural polymer-based nanomaterials that mimic viral structures through the hierarchical assembly of viral coat proteins, while lacking viral genomes. VLPs have received enormous attention in a wide range of nanotechnology-based medical diagnostics and therapies, including cancer therapy, imaging, and theranostics. VLPs are biocompatible and biodegradable and have a uniform structure and controllable assembly. They can encapsulate a wide range of therapeutic and diagnostic agents, and can be genetically or chemically modified. These properties have led to sophisticated multifunctional theranostic platforms. This article reviews the current progress in developing and applying engineered VLPs for molecular imaging, drug delivery, and multifunctional theranostics in cancer research.
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Affiliation(s)
- Kyeong Rok Kim
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, South Korea
| | - Ae Sol Lee
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, South Korea
| | - Su Min Kim
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, South Korea
| | - Hye Ryoung Heo
- Senotherapy-Based Metabolic Disease Control Research Center, Yeungnam University, Gyeongsan, South Korea,*Correspondence: Chang Sup Kim, ; Hye Ryoung Heo,
| | - Chang Sup Kim
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, South Korea,School of Chemistry and Biochemistry, Yeungnam University, Gyeongsan, South Korea,*Correspondence: Chang Sup Kim, ; Hye Ryoung Heo,
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16
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Shen L, Cao S, Wang Y, Zhou P, Wang S, Zhao Y, Meng L, Zhang Q, Li Y, Xu X, Yuan Q, Li J. Self-Adaptive Antibacterial Scaffold with Programmed Delivery of Osteogenic Peptide and Lysozyme for Infected Bone Defect Treatment. ACS APPLIED MATERIALS & INTERFACES 2023; 15:626-637. [PMID: 36541416 DOI: 10.1021/acsami.2c19026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bone defects caused by disease or trauma are often accompanied by infection, which severely disrupts the normal function of bone tissue at the defect site. Biomaterials that can simultaneously reduce inflammation and promote osteogenesis are effective tools for addressing this problem. In this study, we set up a programmed delivery platform based on a chitosan scaffold to enhance its osteogenic activity and prevent implant-related infections. In brief, the osteogenic peptide sequence (YGFGG) was modified onto the surface of cowpea chlorotic mottle virus (CCMV) to form CCMV-YGFGG nanoparticles. CCMV-YGFGG exhibited good biocompatibility and osteogenic ability in vitro. Then, CCMV-YGFGG and lysozyme were loaded on the chitosan scaffold, which exhibited a good antibacterial effect and promoted bone regeneration for infected bone defect treatment. As a delivery platform, the scaffold showed staged release of lysozyme and CCMV-YGFGG, which facilitates the regeneration of infected bone defects. Our study provides a novel and promising strategy for the treatment of infected bone defects.
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Affiliation(s)
- Luxuan Shen
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Shuqin Cao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Yuemin Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Pei Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Shuaibing Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Yao Zhao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Lingzhuang Meng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Quan Zhang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Yanyan Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Xinyuan Xu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Jianshu Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
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17
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Timmermans SBPE, Mesman R, Blezer KJR, van Niftrik L, van Hest JCM. Cargo-loading of hybrid cowpea chlorotic mottle virus capsids via a co-expression approach. Virology 2022; 577:99-104. [PMID: 36335770 DOI: 10.1016/j.virol.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/12/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Capsids of the cowpea chlorotic mottle virus (CCMV) are great candidates for the development into in vivo catalytic or therapeutic nanocarriers. However, due to their limited intrinsic stability at physiological pH, thus far no methods exist for incorporating cargo into these nanoparticles in cellulo. Here, we employ a stabilized VW1-VW8 ELP-CCMV variant for the development of a co-expression-based cargo-loading approach. Co-expression of the non-functionalized VW1-VW8 ELP-CCMV coat protein with fusion proteins with enhanced green fluorescent protein (mEGFP) and pyrrolysine synthase D (PylD) in E. coli enabled the purification of cargo-loaded capsids from the bacteria directly either via affinity chromatography or PEG-precipitation and subsequent size exclusion chromatography. Microscopy results indicated that the co-expression does not harm the E. coli cells and that proper folding of the mEGFP domain is not hampered by the co-assembly. Our co-expression strategy is thus a suitable approach to produce cargo-loaded CCMV nanoparticles.
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Affiliation(s)
- Suzanne B P E Timmermans
- Bio-Organic Chemistry Research Group Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513 (STO3.41), 5600, MB, Eindhoven, the Netherlands
| | - Rob Mesman
- Microbial Cell Biology & Biochemistry Research Group, Department of Microbiology, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Kim J R Blezer
- Bio-Organic Chemistry Research Group Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513 (STO3.41), 5600, MB, Eindhoven, the Netherlands
| | - Laura van Niftrik
- Microbial Cell Biology & Biochemistry Research Group, Department of Microbiology, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Jan C M van Hest
- Bio-Organic Chemistry Research Group Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513 (STO3.41), 5600, MB, Eindhoven, the Netherlands.
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18
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Unravelling viral dynamics through molecular dynamics simulations - A brief overview. Biophys Chem 2022; 291:106908. [DOI: 10.1016/j.bpc.2022.106908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022]
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19
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Prakash DL, Gosavi S. The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids. Front Mol Biosci 2022; 9:967877. [PMID: 36339706 PMCID: PMC9631432 DOI: 10.3389/fmolb.2022.967877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Some non-enveloped virus capsids assemble from multiple copies of a single type of coat-protein (CP). The comparative energetics of the diverse CP-CP interfaces present in such capsids likely govern virus assembly-disassembly mechanisms. The T = 3 icosahedral capsids comprise 180 CP copies arranged about two-, three-, five- and six-fold axes of (quasi-)rotation symmetry. Structurally diverse CPs can assemble into T = 3 capsids. Specifically, the Leviviridae CPs are structurally distinct from the Bromoviridae, Tombusviridae and Tymoviridae CPs which fold into the classic “jelly-roll” fold. However, capsids from across the four families are known to disassemble into dimers. To understand whether the overall symmetry of the capsid or the structural details of the CP determine virus assembly-disassembly mechanisms, we analyze the different CP-CP interfaces that occur in the four virus families. Previous work studied protein homodimer interfaces using interface size (relative to the monomer) and hydrophobicity. Here, we analyze all CP-CP interfaces using these two parameters and find that the dimerization interface (present between two CPs congruent through a two-fold axis of rotation) has a larger relative size in the Leviviridae than in the other viruses. The relative sizes of the other Leviviridae interfaces and all the jelly-roll interfaces are similar. However, the dimerization interfaces across families have slightly higher hydrophobicity, potentially making them stronger than other interfaces. Finally, although the CP-monomers of the jelly-roll viruses are structurally similar, differences in their dimerization interfaces leads to varied dimer flexibility. Overall, differences in CP-structures may induce different modes of swelling and assembly-disassembly in the T = 3 viruses.
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20
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Hajebi S, Yousefiasl S, Rahimmanesh I, Dahim A, Ahmadi S, Kadumudi FB, Rahgozar N, Amani S, Kumar A, Kamrani E, Rabiee M, Borzacchiello A, Wang X, Rabiee N, Dolatshahi-Pirouz A, Makvandi P. Genetically Engineered Viral Vectors and Organic-Based Non-Viral Nanocarriers for Drug Delivery Applications. Adv Healthc Mater 2022; 11:e2201583. [PMID: 35916145 DOI: 10.1002/adhm.202201583] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 01/28/2023]
Abstract
Conventional drug delivery systems are challenged by concerns related to systemic toxicity, repetitive doses, drug concentrations fluctuation, and adverse effects. Various drug delivery systems are developed to overcome these limitations. Nanomaterials are employed in a variety of biomedical applications such as therapeutics delivery, cancer therapy, and tissue engineering. Physiochemical nanoparticle assembly techniques involve the application of solvents and potentially harmful chemicals, commonly at high temperatures. Genetically engineered organisms have the potential to be used as promising candidates for greener, efficient, and more adaptable platforms for the synthesis and assembly of nanomaterials. Genetically engineered carriers are precisely designed and constructed in shape and size, enabling precise control over drug attachment sites. The high accuracy of these novel advanced materials, biocompatibility, and stimuli-responsiveness, elucidate their emerging application in controlled drug delivery. The current article represents the research progress in developing various genetically engineered carriers. Organic-based nanoparticles including cellulose, collagen, silk-like polymers, elastin-like protein, silk-elastin-like protein, and inorganic-based nanoparticles are discussed in detail. Afterward, viral-based carriers are classified, and their potential for targeted therapeutics delivery is highlighted. Finally, the challenges and prospects of these delivery systems are concluded.
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Affiliation(s)
- Sakineh Hajebi
- Department of Polymer Engineering, Sahand University of Technology, Tabriz, 51335-1996, Iran
- Institute of Polymeric Materials, Sahand University of Technology, Tabriz, 51335-1996, Iran
| | - Satar Yousefiasl
- School of Dentistry, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran
| | - Ilnaz Rahimmanesh
- Applied Physiology Research Center, Isfahan Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, 8174673461, Iran
| | - Alireza Dahim
- Department of Anesthesia, Jundishapur University of Medical Sciences, Ahvaz, 61357-15794, Iran
| | - Sepideh Ahmadi
- Department of Biology, Faculty of Sciences, University of Zabol, Sistan and Baluchestan, Zabol, 98613-35856, Iran
| | - Firoz Babu Kadumudi
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Nikta Rahgozar
- Department of Chemistry, Amirkabir University of Technology, Tehran, 15875-4413, Iran
| | - Sanaz Amani
- Department of Chemical Engineering, Sahand University of Technology, Tabriz, 51335-1996, Iran
| | - Arun Kumar
- Chitkara College of Pharmacy, Chitkara University, Himachal Pradesh, 174 103, India
| | - Ehsan Kamrani
- Harvard-MIT Health Science and Technology, Cambridge, MA, 02139, USA
- Wellman Center for Photomedicine, Harvard Medical School, Boston, MA, 02139, USA
| | - Mohammad Rabiee
- Biomaterials Group, Department of Biomedical Engineering, Amirkabir University of Technology, Tehran, 15875-4413, Iran
| | - Assunta Borzacchiello
- Institute for Polymers, Composites and Biomaterials, National Research Council, IPCB-CNR, Naples, 80125, Italy
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | | | - Pooyan Makvandi
- Centre for Materials Interfaces, Istituto Italiano di Tecnologia, Pontedera, Pisa, 56025, Italy
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, Zhejiang, 324000, China
- School of Chemistry, Damghan University, Damghan, 36716-41167, Iran
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21
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Single-particle studies of the effects of RNA-protein interactions on the self-assembly of RNA virus particles. Proc Natl Acad Sci U S A 2022; 119:e2206292119. [PMID: 36122222 PMCID: PMC9522328 DOI: 10.1073/pnas.2206292119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Understanding the pathways by which simple RNA viruses self-assemble from their coat proteins and RNA is of practical and fundamental interest. Although RNA-protein interactions are thought to play a critical role in the assembly, our understanding of their effects is limited because the assembly process is difficult to observe directly. We address this problem by using interferometric scattering microscopy, a sensitive optical technique with high dynamic range, to follow the in vitro assembly kinetics of more than 500 individual particles of brome mosaic virus (BMV)-for which RNA-protein interactions can be controlled by varying the ionic strength of the buffer. We find that when RNA-protein interactions are weak, BMV assembles by a nucleation-and-growth pathway in which a small cluster of RNA-bound proteins must exceed a critical size before additional proteins can bind. As the strength of RNA-protein interactions increases, the nucleation time becomes shorter and more narrowly distributed, but the time to grow a capsid after nucleation is largely unaffected. These results suggest that the nucleation rate is controlled by RNA-protein interactions, while the growth process is driven less by RNA-protein interactions and more by protein-protein interactions and intraprotein forces. The nucleated pathway observed with the plant virus BMV is strikingly similar to that previously observed with bacteriophage MS2, a phylogenetically distinct virus with a different host kingdom. These results raise the possibility that nucleated assembly pathways might be common to other RNA viruses.
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22
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Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers. Sci Rep 2022; 12:14251. [PMID: 35995818 PMCID: PMC9395436 DOI: 10.1038/s41598-022-18019-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Intermediates of the self-assembly process of the salt stable cowpea chlorotic mottle virus (ss-CCMV) capsid can be modelled atomistically on realistic computational timescales either by studying oligomers in equilibrium or by focusing on their dissociation instead of their association. Our previous studies showed that among the three possible dimer interfaces in the icosahedral capsid, two are thermodynamically relevant for capsid formation. The aim of the current study is to evaluate the relative structural stabilities of the three different ss-CCMV dimers and to find and understand the conditions that lead to their dissociation. Long timescale molecular dynamics simulations at 300 K of the various dimers and of the pentamer of dimers underscore the importance of large contact surfaces on stabilizing the capsid subunits within an oligomer. Simulations in implicit solvent show that at higher temperature (350 K), the N-terminal tails of the protein units act as tethers, delaying dissociation for all but the most stable interface. The pentamer of dimers is also found to be stable on long timescales at 300 K, with an inherent flexibility of the outer protein chains.
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23
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Almendárez-Rodriguez C, Solis-Andrade KI, Govea-Alonso DO, Comas-Garcia M, Rosales-Mendoza S. Production and characterization of chimeric SARS-CoV-2 antigens based on the capsid protein of cowpea chlorotic mottle virus. Int J Biol Macromol 2022; 213:1007-1017. [PMID: 35690161 PMCID: PMC9174154 DOI: 10.1016/j.ijbiomac.2022.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 11/17/2022]
Abstract
The COVID-19 pandemic has highlighted the need for new vaccine platforms to rapidly develop solutions against emerging pathogens. In particular, some plant viruses offer several advantages for developing subunit vaccines, such as high expression rates in E. coli, high immunogenicity and safety, and absence of pre-immunity that could interfere with the vaccine's efficacy. Cowpea chlorotic mottle virus (CCMV) is a model system that has been extensively characterized, with key advantages for its use as an epitope carrier. In the present study, three relevant epitopes from the SARS-CoV-2 Spike protein were genetically inserted into the CCMV CP and expressed in E. coli cultures, resulting in the CCMV1, CCMV2, and CCMV3 chimeras. The recombinant CP mutants were purified from the formed inclusion bodies and refolded, and their immunogenicity as a subunit vaccine was assessed in BALB/c mice. The three mutants are immunogenic as they induce high IgG antibody titers that recognize the recombinant full-length S protein. This study supports the application of CCMV CP as an attractive carrier for the clinical evaluation of vaccine candidates against SARS-CoV-2. Furthermore, it suggests that VLPs assembled from these chimeric proteins could result in antigens with better immunogenicity.
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Affiliation(s)
- Claudia Almendárez-Rodriguez
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico
| | - Karla I Solis-Andrade
- Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico
| | - Dania O Govea-Alonso
- Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico
| | - Mauricio Comas-Garcia
- Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico; Sección de Microscopía de Alta Resolución, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico; Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Parque Chapultepec 1570, 78210 San Luis, S.L.P., San Luis Potosí 78210, Mexico.
| | - Sergio Rosales-Mendoza
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico.
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24
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Shrestha N, Duvall MR, Bujarski JJ. Variability among the Isolates of Broad Bean Mottle Virus and Encapsidation of Host RNAs. Pathogens 2022; 11:pathogens11070817. [PMID: 35890061 PMCID: PMC9321246 DOI: 10.3390/pathogens11070817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/03/2022] [Accepted: 07/18/2022] [Indexed: 02/05/2023] Open
Abstract
Broad bean mottle bromovirus infects legume plants and is transmissible by insects. Several broad bean mottle virus (BBMV) isolates have been identified, including one in England (isolate Ba) and five in the Mediterranean countries: Libya (LyV), Morocco (MV), Syria (SV), Sudan (TU) and Tunisia (TV). Previously, we analyzed the nucleotide sequence of the Ba RNA and here we report on and compare it with another five Mediterranean variants. The RNA segments in the latter ones were extensively homologous, with some SNPs, single nucleotide deletions and insertions, while the number of mutations was higher in isolate Ba. Both the 5′ and 3′ untranslated terminal regions (UTRs) among the corresponding RNAs are highly conserved, reflecting their functionality in virus replication. The AUG initiation codons are within suboptimal contexts, possibly to adjust/regulate translation. The proteins 1a, 2a, 3a and coat protein (CP) are almost identical among the five isolates, but in Ba they have more amino acid (aa) substitutions. Phylogenetic analysis revealed the isolates from Morocco and Syria clustering with the isolate from England, while the variants from Libya, Tunisia and Sudan created a different clade. The BBMV isolates encapsidate a high content of host (ribosomal and messenger) RNAs. Our studies present BBMV as a useful model for bromoviruses infecting legumes.
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Affiliation(s)
- Nipin Shrestha
- Correspondence: (N.S.); (J.J.B.); Tel.: +1-305-684-2589 (N.S.); +1-815-753-0601 (J.J.B.); Fax: +1-815-753-7855 (J.J.B.)
| | | | - Jozef J. Bujarski
- Correspondence: (N.S.); (J.J.B.); Tel.: +1-305-684-2589 (N.S.); +1-815-753-0601 (J.J.B.); Fax: +1-815-753-7855 (J.J.B.)
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25
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Harder OF, Voss JM, Olshin PK, Drabbels M, Lorenz UJ. Microsecond melting and revitrification of cryo samples: protein structure and beam-induced motion. Acta Crystallogr D Struct Biol 2022; 78:883-889. [PMID: 35775987 PMCID: PMC9248841 DOI: 10.1107/s205979832200554x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/21/2022] [Indexed: 11/10/2022] Open
Abstract
A novel approach to time-resolved cryo-electron microscopy (cryo-EM) has recently been introduced that involves melting a cryo sample with a laser beam to allow protein dynamics to briefly occur in the liquid, before trapping the particles in their transient configurations by rapidly revitrifying the sample. With a time resolution of just a few microseconds, this approach is notably fast enough to study the domain motions that are typically associated with the activity of proteins but which have previously remained inaccessible. Here, crucial details are added to the characterization of the method. It is shown that single-particle reconstructions of apoferritin and Cowpea chlorotic mottle virus from revitrified samples are indistinguishable from those from conventional samples, demonstrating that melting and revitrification leaves the particles intact and that they do not undergo structural changes within the spatial resolution afforded by the instrument. How rapid revitrification affects the properties of the ice is also characterized, showing that revitrified samples exhibit comparable amounts of beam-induced motion. The results pave the way for microsecond time-resolved studies of the conformational dynamics of proteins and open up new avenues to study the vitrification process and to address beam-induced specimen movement.
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26
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Tsidilkovski L, Mohajerani F, Hagan MF. Microcompartment assembly around multicomponent fluid cargoes. J Chem Phys 2022; 156:245104. [PMID: 35778087 PMCID: PMC9249432 DOI: 10.1063/5.0089556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a complex of enzymes and other components involved in certain metabolic processes. The simulations demonstrate that the relative interaction strengths among the different cargo species play a key role in determining the amount of each species that is encapsulated, their spatial organization, and the nature of the shell assembly pathways. However, the shell protein–shell protein and shell protein–cargo component interactions that help drive assembly and encapsulation also influence cargo composition within certain parameter regimes. These behaviors are governed by a combination of thermodynamic and kinetic effects. In addition to elucidating how natural microcompartments encapsulate multiple components involved within reaction cascades, these results have implications for efforts in synthetic biology to colocalize alternative sets of molecules within microcompartments to accelerate specific reactions. More broadly, the results suggest that coupling between self-assembly and multicomponent liquid–liquid phase separation may play a role in the organization of the cellular cytoplasm.
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Affiliation(s)
- Lev Tsidilkovski
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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27
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Tasneem N, Szyszka TN, Jenner EN, Lau YH. How Pore Architecture Regulates the Function of Nanoscale Protein Compartments. ACS NANO 2022; 16:8540-8556. [PMID: 35583458 DOI: 10.1021/acsnano.2c02178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Self-assembling proteins can form porous compartments that adopt well-defined architectures at the nanoscale. In nature, protein compartments act as semipermeable barriers to enable spatial separation and organization of complex biochemical processes. The compartment pores play a key role in their overall function by selectively controlling the influx and efflux of important biomolecular species. By engineering the pores, the functionality of compartments can be tuned to facilitate non-native applications, such as artificial nanoreactors for catalysis. In this review, we analyze how protein structure determines the porosity and impacts the function of both native and engineered compartments, highlighting the wealth of structural data recently obtained by cryo-EM and X-ray crystallography. Through this analysis, we offer perspectives on how current structural insights can inform future studies into the design of artificial protein compartments as nanoreactors with tunable porosity and function.
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Affiliation(s)
- Nuren Tasneem
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
| | - Eric N Jenner
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
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28
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Yaraki MT, Zahed Nasab S, Zare I, Dahri M, Moein Sadeghi M, Koohi M, Tan YN. Biomimetic Metallic Nanostructures for Biomedical Applications, Catalysis, and Beyond. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c00285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Shima Zahed Nasab
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 143951561, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz 7178795844, Iran
| | - Mohammad Dahri
- Student Research Committee, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345, Iran
| | - Mohammad Moein Sadeghi
- Student Research Committee, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345, Iran
| | - Maedeh Koohi
- Department of Chemistry, Faculty of Science, University of Zanjan, Zanjan 45371-38791, Islamic Republic of Iran
| | - Yen Nee Tan
- Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K
- Newcastle Research and Innovation Institute, Newcastle University in Singapore, 80 Jurong East Street 21, No. 05-04, 609607, Singapore
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29
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Abstract
There is increasing interest in two-dimensional and quasi-two-dimensional materials and metamaterials for applications in chemistry, physics and engineering. Some of these applications are driven by the possible auxetic properties of such materials. Auxetic frameworks expand along one direction when subjected to a perpendicular stretching force. An equiauxetic framework has a unique mechanism of expansion (an equiauxetic mode) where the symmetry forces a Poisson’s ratio of −1. Hinged tilings offer opportunities for the design of auxetic and equiauxetic frameworks in 2D, and generic auxetic behaviour can often be detected using a symmetry extension of the scalar counting rule for mobility of periodic body-bar systems. Hinged frameworks based on Archimedean tilings of the plane are considered here. It is known that the regular hexagonal tiling, {63}, leads to an equiauxetic framework for both single-link and double-link connections between the tiles. For single-link connections, three Archimedean tilings considered as hinged body-bar frameworks are found here to be equiauxetic: these are {3.122}, {4.6.12}, and {4.82}. For double-link connections, three Archimedean tilings considered as hinged body-bar frameworks are found to be equiauxetic: these are {34.6}, {32.4.3.4}, and {3.6.3.6}.
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30
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Li Z, Maity B, Hishikawa Y, Ueno T, Lu D. Importance of the Subunit-Subunit Interface in Ferritin Disassembly: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1106-1113. [PMID: 35015545 DOI: 10.1021/acs.langmuir.1c02753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ferritin is a spherical cage-like protein that is useful for loading large functional particles for various applications. To our knowledge, how pH affects the interfaces inside ferritin and the mechanism of ferritin disassembly is far from complete. For this article, we conducted a series of molecular dynamics simulations (MD) at different pH values to study how interfaces affect ferritins' stability. It is shown that dimers are stable even at extremely low pH (pH 2.0), indicating that the dimer is the essential subunit for disassembly, and the slight swelling of the dimer resulting from monomer rotation inside a dimer is what triggers disassembly. During ferritin disassembly, there are two types of interfaces involved, and the interface between dimers is crucial. We also found that the driving forces for maintaining dimer stability are different when a dimer is inside ferritin and in an acidic solution. At low pH, the protonation of residues can lead to the loss of the salt bridge and the hydrogen bond between dimers, resulting in the disassembly of ferritin in an acidic environment. The above simulations reveal the possible mechanism of ferritin disassembly in an acidic solution, which can help us to design innovative and functional ferritin cages for different applications.
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Affiliation(s)
- Zhipeng Li
- Ministry of Education Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yuki Hishikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Diannan Lu
- Ministry of Education Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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31
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Kim NH, Choi H, Shahzad ZM, Ki H, Lee J, Chae H, Kim YH. Supramolecular assembly of protein building blocks: from folding to function. NANO CONVERGENCE 2022; 9:4. [PMID: 35024976 PMCID: PMC8755899 DOI: 10.1186/s40580-021-00294-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.
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Affiliation(s)
- Nam Hyeong Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hojae Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Zafar Muhammad Shahzad
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heesoo Ki
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyoung Lee
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heeyeop Chae
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea.
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32
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Adams MC, Schiltz CJ, Heck ML, Chappie JS. Crystal structure of the potato leafroll virus coat protein and implications for viral assembly. J Struct Biol 2021; 214:107811. [PMID: 34813955 DOI: 10.1016/j.jsb.2021.107811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/04/2021] [Accepted: 11/13/2021] [Indexed: 10/19/2022]
Abstract
Luteoviruses, poleroviruses, and enamoviruses are insect-transmitted, agricultural pathogens that infect a wide array of plants, including staple food crops. Previous cryo-electron microscopy studies of virus-like particles show that luteovirid viral capsids are built from a structural coat protein that organizes with T = 3 icosahedral symmetry. Here, we present the crystal structure of a truncated version of the coat protein monomer from potato leafroll virus at 1.80-Å resolution. In the crystal lattice, monomers pack into flat sheets that preserve the two-fold and three-fold axes of icosahedral symmetry and show minimal structural deviations when compared to the full-length subunits of the assembled virus-like particle. These observations have important implications in viral assembly and maturation and suggest that the CP N-terminus and its interactions with RNA play an important role in generating capsid curvature.
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Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Michelle L Heck
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; Boyce Thompson Institute, Ithaca, NY 14853, USA; Robert W. Holley Center for Agriculture and Health, Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.
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33
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Martín-Bravo M, Llorente JMG, Hernández-Rojas J, Wales DJ. Minimal Design Principles for Icosahedral Virus Capsids. ACS NANO 2021; 15:14873-14884. [PMID: 34492194 PMCID: PMC8939845 DOI: 10.1021/acsnano.1c04952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 06/13/2023]
Abstract
The geometrical structures of single- and multiple-shell icosahedral virus capsids are reproduced as the targets that minimize the cost corresponding to relatively simple design functions. Capsid subunits are first identified as building blocks at a given coarse-grained scale and then represented in these functions as point particles located on an appropriate number of concentric spherical surfaces. Minimal design cost is assigned to optimal spherical packings of the particles. The cost functions are inspired by the packings favored for the Thomson problem, which minimize the electrostatic potential energy between identical charged particles. In some cases, icosahedral symmetry constraints are incorporated as external fields acting on the particles. The simplest cost functions can be obtained by separating particles in disjoint nonequivalent sets with distinct interactions, or by introducing interacting holes (the absence of particles). These functions can be adapted to reproduce any capsid structure found in real viruses. Structures absent in Nature require significantly more complex designs. Measures of information content and complexity are assigned to both the cost functions and the capsid geometries. In terms of these measures, icosahedral structures and the corresponding cost functions are the simplest solutions.
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Affiliation(s)
- Manuel Martín-Bravo
- Departamento
de Física and IUdEA, Universidad
de La Laguna, 38205 Tenerife, Spain
| | | | | | - David J. Wales
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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34
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Liu Q, Shaukat A, Kyllönen D, Kostiainen MA. Polyelectrolyte Encapsulation and Confinement within Protein Cage-Inspired Nanocompartments. Pharmaceutics 2021; 13:1551. [PMID: 34683843 PMCID: PMC8537137 DOI: 10.3390/pharmaceutics13101551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/17/2022] Open
Abstract
Protein cages are nanocompartments with a well-defined structure and monodisperse size. They are composed of several individual subunits and can be categorized as viral and non-viral protein cages. Native viral cages often exhibit a cationic interior, which binds the anionic nucleic acid genome through electrostatic interactions leading to efficient encapsulation. Non-viral cages can carry various cargo, ranging from small molecules to inorganic nanoparticles. Both cage types can be functionalized at targeted locations through genetic engineering or chemical modification to entrap materials through interactions that are inaccessible to wild-type cages. Moreover, the limited number of constitutional subunits ease the modification efforts, because a single modification on the subunit can lead to multiple functional sites on the cage surface. Increasing efforts have also been dedicated to the assembly of protein cage-mimicking structures or templated protein coatings. This review focuses on native and modified protein cages that have been used to encapsulate and package polyelectrolyte cargos and on the electrostatic interactions that are the driving force for the assembly of such structures. Selective encapsulation can protect the payload from the surroundings, shield the potential toxicity or even enhance the intended performance of the payload, which is appealing in drug or gene delivery and imaging.
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Affiliation(s)
- Qing Liu
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland; (Q.L.); (A.S.); (D.K.)
| | - Ahmed Shaukat
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland; (Q.L.); (A.S.); (D.K.)
| | - Daniella Kyllönen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland; (Q.L.); (A.S.); (D.K.)
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland; (Q.L.); (A.S.); (D.K.)
- HYBER Center, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
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35
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Anil Sushma A, Zhao B, Tsvetkova IB, Pérez-Segura C, Hadden-Perilla JA, Reilly JP, Dragnea B. Subset of Fluorophores Is Responsible for Radiation Brightening in Viromimetic Particles. J Phys Chem B 2021; 125:10494-10505. [PMID: 34507491 DOI: 10.1021/acs.jpcb.1c06395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In certain conditions, dye-conjugated icosahedral virus shells exhibit suppression of concentration quenching. The recently observed radiation brightening at high fluorophore densities has been attributed to coherent emission, i.e., to a cooperative process occurring within a subset of the virus-supported fluorophores. Until now, the distribution of fluorophores among potential conjugation sites and the nature of the active subset remained unknown. With the help of mass spectrometry and molecular dynamics simulations, we found which conjugation sites in the brome mosaic virus capsid are accessible to fluorophores. Reactive external surface lysines but also those at the lumenal interface where the coat protein N-termini are located showed virtually unrestricted access to dyes. The third type of labeled lysines was situated at the intercapsomeric interfaces. Through limited proteolysis of flexible N-termini, it was determined that dyes bound to them are unlikely to be involved in the radiation brightening effect. At the same time, specific labeling of genetically inserted cysteines on the exterior capsid surface alone did not lead to radiation brightening. The results suggest that lysines situated within the more rigid structural part of the coat protein provide the chemical environments conducive to radiation brightening, and we discuss some of the characteristics of these environments.
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Affiliation(s)
- Arathi Anil Sushma
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Bingqing Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Irina B Tsvetkova
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - James P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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36
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Exploiting Complex Fluorophore Interactions to Monitor Virus Capsid Disassembly. Molecules 2021; 26:molecules26195750. [PMID: 34641294 PMCID: PMC8510433 DOI: 10.3390/molecules26195750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 02/06/2023] Open
Abstract
Supramolecular protein complexes are the corner stone of biological processes; they are essential for many biological functions. Unraveling the interactions responsible for the (dis)assembly of these complexes is required to understand nature and to exploit such systems in future applications. Virus capsids are well-defined assemblies of hundreds of proteins and form the outer shell of non-enveloped viruses. Due to their potential as a drug carriers or nano-reactors and the need for virus inactivation strategies, assessing the intactness of virus capsids is of great interest. Current methods to evaluate the (dis)assembly of these protein assemblies are experimentally demanding in terms of instrumentation, expertise and time. Here we investigate a new strategy to monitor the disassembly of fluorescently labeled virus capsids. To monitor surfactant-induced capsid disassembly, we exploit the complex photophysical interplay between multiple fluorophores conjugated to capsid proteins. The disassembly of the capsid changes the photophysical interactions between the fluorophores, and this can be spectrally monitored. The presented data show that this low complexity method can be used to study and monitor the disassembly of supramolecular protein complexes like virus capsids. However, the range of labeling densities that is suitable for this assay is surprisingly narrow.
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Marichal L, Gargowitsch L, Rubim RL, Sizun C, Kra K, Bressanelli S, Dong Y, Panahandeh S, Zandi R, Tresset G. Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus. Biophys J 2021; 120:3925-3936. [PMID: 34418368 PMCID: PMC8511167 DOI: 10.1016/j.bpj.2021.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/21/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022] Open
Abstract
The process of genome packaging in most of viruses is poorly understood, notably the role of the genome itself in the nucleocapsid structure. For simple icosahedral single-stranded RNA viruses, the branched topology due to the RNA secondary structure is thought to lower the free energy required to complete a virion. We investigate the structure of nucleocapsids packaging RNA segments with various degrees of compactness by small-angle x-ray scattering and cryotransmission electron microscopy. The structural differences are mild even though compact RNA segments lead on average to better-ordered and more uniform particles across the sample. Numerical calculations confirm that the free energy is lowered for the RNA segments displaying the larger number of branch points. The effect is, however, opposite with synthetic polyelectrolytes, in which a star topology gives rise to more disorder in the capsids than a linear topology. If RNA compactness and size account in part for the proper assembly of the nucleocapsid and the genome selectivity, other factors most likely related to the host cell environment during viral assembly must come into play as well.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Laetitia Gargowitsch
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Rafael Leite Rubim
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Christina Sizun
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Kalouna Kra
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Yinan Dong
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Sanaz Panahandeh
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France.
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38
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Abstract
The disassembly of a viral capsid leading to the release of its genetic material into the host cell is a fundamental step in viral infection. In hepatitis B virus (HBV), the capsid consists of identical protein monomers that dimerize and then arrange themselves into pentamers or hexamers on the capsid surface. By applying atomistic molecular dynamics simulation to an entire solvated HBV capsid subjected to a uniform mechanical stress protocol, we monitor the capsid-disassembly process and analyze the process down to the level of individual amino acids in 20 independent simulation replicas. The strain of an isotropic external force, combined with structural fluctuations, causes structurally heterogeneous cracks to appear in the HBV capsid. Analysis of the monomer-monomer interfaces reveals that, in contrast to the expectation from purely mechanical considerations, the cracks mainly occur within hexameric sites, whereas pentameric sites remain largely intact. Only a small subset of the capsid protein monomers, different in each simulation, are engaged in each instance of disassembly. We identify specific residues whose interactions are most readily lost during disassembly; R127, I139, Y132, N136, A137, and V149 are among the hot spots at the interfaces between dimers that lie within hexamers, leading to disassembly. The majority of these hot-spot residues are conserved by evolution, hinting to their importance for disassembly by avoiding overstabilization of capsids.
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Jo CH, Voronina N, Sun YK, Myung ST. Gifts from Nature: Bio-Inspired Materials for Rechargeable Secondary Batteries. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2006019. [PMID: 34337779 DOI: 10.1002/adma.202006019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/29/2021] [Indexed: 06/13/2023]
Abstract
Materials in nature have evolved to the most efficient forms and have adapted to various environmental conditions over tens of thousands of years. Because of their versatile functionalities and environmental friendliness, numerous attempts have been made to use bio-inspired materials for industrial applications, establishing the importance of biomimetics. Biomimetics have become pivotal to the search for technological breakthroughs in the area of rechargeable secondary batteries. Here, the characteristics of bio-inspired materials that are useful for secondary batteries as well as their benefits for application as the main components of batteries (e.g., electrodes, separators, and binders) are discussed. The use of bio-inspired materials for the synthesis of nanomaterials with complex structures, low-cost electrode materials prepared from biomass, and biomolecular organic electrodes for lithium-ion batteries are also introduced. In addition, nature-derived separators and binders are discussed, including their effects on enhancing battery performance and safety. Recent developments toward next-generation secondary batteries including sodium-ion batteries, zinc-ion batteries, and flexible batteries are also mentioned to understand the feasibility of using bio-inspired materials in these new battery systems. Finally, current research trends are covered and future directions are proposed to provide important insights into scientific and practical issues in the development of biomimetics technologies for secondary batteries.
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Affiliation(s)
- Chang-Heum Jo
- Hybrid Materials Research Center, Department of Nano Technology and Advanced Materials Engineering & Sejong Battery Institute, Sejong University, Gunja-dong, Gwangjin-gu, Seoul, 05006, South Korea
| | - Natalia Voronina
- Hybrid Materials Research Center, Department of Nano Technology and Advanced Materials Engineering & Sejong Battery Institute, Sejong University, Gunja-dong, Gwangjin-gu, Seoul, 05006, South Korea
| | - Yang-Kook Sun
- Department of Energy Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Seung-Taek Myung
- Hybrid Materials Research Center, Department of Nano Technology and Advanced Materials Engineering & Sejong Battery Institute, Sejong University, Gunja-dong, Gwangjin-gu, Seoul, 05006, South Korea
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40
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Wu Y, Cao S, Alam MNA, Raabe M, Michel-Souzy S, Wang Z, Wagner M, Ermakova A, Cornelissen JJLM, Weil T. Fluorescent nanodiamonds encapsulated by Cowpea Chlorotic Mottle Virus (CCMV) proteins for intracellular 3D-trajectory analysis. J Mater Chem B 2021; 9:5621-5627. [PMID: 34184014 PMCID: PMC8292973 DOI: 10.1039/d1tb00890k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/20/2021] [Indexed: 02/05/2023]
Abstract
Long-term tracking of nanoparticles to resolve intracellular structures and motions is essential to elucidate fundamental parameters as well as transport processes within living cells. Fluorescent nanodiamond (ND) emitters provide cell compatibility and very high photostability. However, high stability, biocompatibility, and cellular uptake of these fluorescent NDs under physiological conditions are required for intracellular applications. Herein, highly stable NDs encapsulated with Cowpea chlorotic mottle virus capsid proteins (ND-CP) are prepared. A thin capsid protein layer is obtained around the NDs, which imparts reactive groups and high colloidal stability, while retaining the opto-magnetic properties of the coated NDs as well as the secondary structure of CPs adsorbed on the surface of NDs. In addition, the ND-CP shows excellent biocompatibility both in vitro and in vivo. Long-term 3D trajectories of the ND-CP with fine spatiotemporal resolutions are recorded; their intracellular motions are analyzed by different models, and the diffusion coefficients are calculated. The ND-CP with its brilliant optical properties and stability under physiological conditions provides us with a new tool to advance the understanding of cell biology, e.g., endocytosis, exocytosis, and active transport processes in living cells as well as intracellular dynamic parameters.
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Affiliation(s)
- Yingke Wu
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany.
| | - Shuqin Cao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China and Department of Molecules & Materials, MESA+Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands.
| | - Md Noor A Alam
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany. and Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Marco Raabe
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany. and Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Sandra Michel-Souzy
- Department of Molecules & Materials, MESA+Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands.
| | - Zuyuan Wang
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany. and Institute for Measurement and Automation, Division of Sensor Technology and Measurement Systems, Bundeswehr University Munich, Werner-Heisenberg-Weg 39, Neubiberg 85579, Germany
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany.
| | - Anna Ermakova
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany. and Institute for Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, Mainz 55128, Germany
| | - Jeroen J L M Cornelissen
- Department of Molecules & Materials, MESA+Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands.
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany. and Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
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41
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Pretto C, Tang M, Chen M, Xu H, Subrizi A, Urtti A, van Hest JCM. Cowpea Chlorotic Mottle Virus-Like Particles as Potential Platform for Antisense Oligonucleotide Delivery in Posterior Segment Ocular Diseases. Macromol Biosci 2021; 21:e2100095. [PMID: 34031995 DOI: 10.1002/mabi.202100095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/06/2021] [Indexed: 01/08/2023]
Abstract
Due to its small size, easy accessibility and immune privileged environment, the eye represents an ideal target for therapeutic nucleic acids in the treatment of posterior segment ocular diseases, such as age-related macular degeneration (AMD). Among nanocarriers that can be used to achieve nucleic acid delivery, virus-like particles (VLPs) obtained from the Cowpea chlorotic mottle virus (CCMV) are an appealing platform, because of their loading capacity, ease of manufacture and amenability for functionalization. Herein, antisense oligonucleotide-loaded CCMV nanoparticles, intended for intravitreal injection, are evaluated for selective silencing of miR-23, an important target in AMD. CCMV nanoparticles loaded with anti-miR-23 locked nucleic acid and stabilized using the 3,3'-dithiobis(sulfosuccinimidyl propionate) (DTSSP) cross-linker, are assembled in vitro with a loading efficiency up to 80%. VLPs are found to be stable at 37 °C in the vitreous humor up to 24 hours. Nanoparticle cytotoxicity, cellular uptake and transfection efficacy are evaluated in endothelial cells. Selective miRNA down-regulation is achieved by the loaded CCMV VLPs both in absence and presence of Lipofectamine, with efficacies of ≈40% and more than 80%, respectively. The authors' findings pave the way for the future development of CCMV nanoparticles as oligonucleotide delivery platform to treat posterior segment ocular diseases.
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Affiliation(s)
- Chiara Pretto
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Miao Tang
- The Welcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Mei Chen
- The Welcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Heping Xu
- The Welcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Astrid Subrizi
- School of Pharmacy, University of Eastern Finland, Kuopio, 70210, Finland
| | - Arto Urtti
- School of Pharmacy, University of Eastern Finland, Kuopio, 70210, Finland
| | - Jan C M van Hest
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, The Netherlands
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42
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Vervoort DF, Heiringhoff R, Timmermans SBPE, van Stevendaal MHME, van Hest JCM. Dual Site-Selective Presentation of Functional Handles on Protein-Engineered Cowpea Chlorotic Mottle Virus-Like Particles. Bioconjug Chem 2021; 32:958-963. [PMID: 33861931 PMCID: PMC8154214 DOI: 10.1021/acs.bioconjchem.1c00108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/29/2021] [Indexed: 01/14/2023]
Abstract
Protein cages hold much promise as carrier systems in nanomedicine, due to their well-defined size, cargo-loading capacity, and inherent biodegradability. In order to make them suitable for drug delivery, they have to be stable under physiological conditions. In addition, often surface modifications are required, for example, to improve cell targeting or reduce the particle immunogenicity by PEGylation. For this purpose, we investigated the functionalization capacity of the capsid of cowpea chlorotic mottle virus (CCMV), modified at the interior with a stabilizing elastin-like polypeptide (ELP) tag, by employing a combination of protein engineering and bio-orthogonal chemistry. We first demonstrated the accessibility of the native cysteine residue in ELP-CCMV as a site-selective surface-exposed functional handle, which was not available in the native CCMV capsid. An additional bio-orthogonal functional handle was introduced by incorporation of the noncanonical amino acid, azido-phenylalanine (AzF), using the amber suppression mechanism. Dual site-selective presentation of both a cell-penetrating TAT peptide and a fluorophore to track the particles was demonstrated successfully in HeLa cell uptake studies.
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Affiliation(s)
- Daan F.
M. Vervoort
- Eindhoven University of Technology, Institute for Complex Molecular Systems, PO Box 513 (STO 3.41), 5600 MB Eindhoven, The Netherlands
| | - Robin Heiringhoff
- Eindhoven University of Technology, Institute for Complex Molecular Systems, PO Box 513 (STO 3.41), 5600 MB Eindhoven, The Netherlands
| | - Suzanne B. P. E. Timmermans
- Eindhoven University of Technology, Institute for Complex Molecular Systems, PO Box 513 (STO 3.41), 5600 MB Eindhoven, The Netherlands
| | - Marleen H. M. E. van Stevendaal
- Eindhoven University of Technology, Institute for Complex Molecular Systems, PO Box 513 (STO 3.41), 5600 MB Eindhoven, The Netherlands
| | - Jan C. M. van Hest
- Eindhoven University of Technology, Institute for Complex Molecular Systems, PO Box 513 (STO 3.41), 5600 MB Eindhoven, The Netherlands
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43
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Lv C, Zhang X, Liu Y, Zhang T, Chen H, Zang J, Zheng B, Zhao G. Redesign of protein nanocages: the way from 0D, 1D, 2D to 3D assembly. Chem Soc Rev 2021; 50:3957-3989. [PMID: 33587075 DOI: 10.1039/d0cs01349h] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Compartmentalization is a hallmark of living systems. Through compartmentalization, ubiquitous protein nanocages such as viral capsids, ferritin, small heat shock proteins, and DNA-binding proteins from starved cells fulfill a variety of functions, while their shell-like structures hold great promise for various applications in the field of nanomedicine and nanotechnology. However, the number and structure of natural protein nanocages are limited, and these natural protein nanocages may not be suited for a given application, which might impede their further application as nanovehicles, biotemplates or building blocks. To overcome these shortcomings, different strategies have been developed by scientists to construct artificial protein nanocages, and 1D, 2D and 3D protein arrays with protein nanocages as building blocks through genetic and chemical modification to rival the size and functionality of natural protein nanocages. This review outlines the recent advances in the field of the design and construction of artificial protein nanocages and their assemblies with higher order, summarizes the strategies for creating the assembly of protein nanocages from zero-dimension to three dimensions, and introduces their corresponding applications in the preparation of nanomaterials, electrochemistry, and drug delivery. The review will highlight the roles of both the inter-subunit/intermolecular interactions at the key interface and the protein symmetry in constructing and controlling protein nanocage assemblies with different dimensions.
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Affiliation(s)
- Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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44
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Possible Action of Transition Divalent Metal Ions at the Inter-Pentameric Interface of Inactivated Foot-and-Mouth Disease Virus Provide A Simple but Effective Approach to Enhance Stability. J Virol 2021; 95:JVI.02431-20. [PMID: 33441340 PMCID: PMC8092711 DOI: 10.1128/jvi.02431-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The structural instability of inactivated foot-and-mouth disease virus (FMDV) hinders the development of vaccine industry. Here we found that some transition metal ions like Cu2+ and Ni2+ could specifically bind to FMDV capsids at capacities about 7089 and 3448 metal ions per capsid, respectively. These values are about 33- and 16-folds of the binding capacity of non-transition metal ion Ca2+ (about 214 per capsid). Further thermodynamic studies indicated that all these three metal ions bound to the capsids in spontaneous enthalpy driving manners (ΔG<0, ΔH<0, ΔS<0), and the Cu2+ binding had the highest affinity. The binding of Cu2+ and Ni2+ could enhance both the thermostability and acid-resistant stability of capsids, while the binding of Ca2+ was helpful only to the thermostability of the capsids. Animal experiments showed that the immunization of FMDV bound with Cu2+ induced the highest specific antibody titers in mice. Coincidently, the FMDV bound with Cu2+ exhibited significantly enhanced affinities to integrin β6 and heparin sulfate, both of which are important cell surface receptors for FMDV attaching. Finally, the specific interaction between capsids and Cu2+ or Ni2+ was applied to direct purification of FMDV from crude cell culture feedstock by the immobilized metal affinity chromatography. Based on our new findings and structural analysis of the FMDV capsid, a "transition metal ion bridges" mechanism that describes linkage between adjacent histidine and other amino acids at the inter-pentameric interface of the capsids by transition metal ions coordination action was proposed to explain their stabilizing effect imposed on the capsid.IMPORTANCE How to stabilize the inactivated FMDV without affecting virus infectivity and immunogenicity is a big challenge in vaccine industry. The electrostatic repulsion induced by protonation of a large amount of histidine residues at the inter-pentameric interface of viral capsids is one of the major mechanisms causing the dissociation of capsids. In the present work, this structural disadvantage inspired us to stabilize the capsids through coordinating transition metal ions with the adjacent histidine residues in FMDV capsid, instead of removing or substituting them. This approach was proved effective to enhance not only the stability of FMDV, but also enhance the specific antibody responses; thus, providing a new guideline for designing an easy-to-use strategy suitable for large-scale production of FMDV vaccine antigen.
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45
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Li R, Chen H, Choi JH. Topological Assembly of a Deployable Hoberman Flight Ring from DNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007069. [PMID: 33615664 DOI: 10.1002/smll.202007069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Deployable geometries are finite auxetic structures that preserve their overall shapes during expansion and contraction. The topological behaviors emerge from intricately arranged elements and their connections. Despite the considerable utility of such configurations in nature and in engineering, deployable nanostructures have never been demonstrated. Here a deployable flight ring, a simplified planar structure of Hoberman sphere is shown, using DNA origami. The DNA flight ring consists of topologically assembled six triangles in two layers that can slide against each other, thereby switching between two distinct (open and closed) states. The origami topology is a trefoil knot, and its auxetic reconfiguration results in negative Poisson's ratios. This work shows the feasibility of deployable nanostructures, providing a versatile platform for topological studies and opening new opportunities for bioengineering.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Haorong Chen
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
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46
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Gama P, Cadena-Nava RD, Juarez-Moreno K, Pérez-Robles J, Vazquez-Duhalt R. Virus-Based Nanoreactors with GALT Activity for Classic Galactosemia Therapy. ChemMedChem 2021; 16:1438-1445. [PMID: 33595183 DOI: 10.1002/cmdc.202000999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Indexed: 12/30/2022]
Abstract
Enzymatic nanoreactors were obtained by galactose-1-phosphate uridylyl-transferase (GALT) encapsulation into plant virus capsids by a molecular self-assembly strategy. The aim of this work was to produce virus-like nanoparticles containing GALT for an enzyme-replacement therapy for classic galactosemia. The encapsulation efficiency and the catalytic constants of bio-nanoreactors were determined by using different GALT and virus coat protein ratios. The substrate affinity of nanoreactors was slightly lower than that of the free enzyme; the activity rate was 16 % of the GALT free enzyme. The enzymatic nanoreactors without functionalization were internalized into different cell lines including fibroblast and kidney cells, but especially into hepatocytes. The enzymatic nanoreactors are an innovative enzyme preparation with potential use for the treatment of classic galactosemia.
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Affiliation(s)
- Pedro Gama
- Department of Bionanotechnology, Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Ruben D Cadena-Nava
- Department of Bionanotechnology, Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Karla Juarez-Moreno
- Department of Bionanotechnology, Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Javier Pérez-Robles
- Department of Bionanotechnology, Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Rafael Vazquez-Duhalt
- Department of Bionanotechnology, Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
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47
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Wu Y, Li J, Shin HJ. Self-assembled Viral Nanoparticles as Targeted Anticancer Vehicles. BIOTECHNOL BIOPROC E 2021; 26:25-38. [PMID: 33584104 PMCID: PMC7872722 DOI: 10.1007/s12257-020-0383-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 12/31/2022]
Abstract
Viral nanoparticles (VNPs) comprise a variety of mammalian viruses, plant viruses, and bacteriophages, that have been adopted as building blocks and supra-molecular templates in nanotechnology. VNPs demonstrate the dynamic, monodisperse, polyvalent, and symmetrical architectures which represent examples of such biological templates. These programmable scaffolds have been exploited for genetic and chemical manipulation for displaying of targeted moieties together with encapsulation of various payloads for diagnosis or therapeutic intervention. The drug delivery system based on VNPs offer diverse advantages over synthetic nanoparticles, including biocompatibility, biodegradability, water solubility, and high uptake capability. Here we summarize the recent progress of VNPs especially as targeted anticancer vehicles from the encapsulation and surface modification mechanisms, involved viruses and VNPs, to their application potentials.
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Affiliation(s)
- Yuanzheng Wu
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, Jinan, 250103 China
| | - Jishun Li
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, Jinan, 250103 China
| | - Hyun-Jae Shin
- Department of Biochemical and Polymer Engineering, Chosun University, Gwangju, 61452 Korea
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48
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Chakravarty A, Rao AL. The interplay between capsid dynamics and pathogenesis in tripartite bromoviruses. Curr Opin Virol 2021; 47:45-51. [PMID: 33517133 DOI: 10.1016/j.coviro.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 11/18/2022]
Abstract
Infectious virus capsids or virions are considered static structures and undergo various conformational transitions to replicate and infect a wide range of eukaryotic cells. Therefore, virus capsids must be stable enough to overcome the physicochemical environment and flexible enough to reorganize their biologically relevant surface peptides for optimal interaction with the host machinery. Although viral capsid fluctuations, referred to as dynamics or breathing, have been well studied in RNA viruses pathogenic to animals, such information is limited among plant viruses. However, more recent attempts have been made in characterizing the capsid dynamics in the plant virus genus bromovirus characterized by having a tripartite, positive-sense RNA genome. Using the available research data on the genus bromovirus members, this review is focused on updating the readers on the interrelationships between the viral capsid dynamics and host-pathogen interactions.
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Affiliation(s)
- Antara Chakravarty
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521-0122, United States
| | - Ayala Ln Rao
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521-0122, United States.
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49
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Chan SK, Du P, Ignacio C, Mehta S, Newton IG, Steinmetz NF. Biomimetic Virus-Like Particles as Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostic Tools. ACS NANO 2021; 15:1259-1272. [PMID: 33237727 PMCID: PMC7724985 DOI: 10.1021/acsnano.0c08430] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/19/2020] [Indexed: 05/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly transmissible disease that has affected more than 90% of the countries worldwide. At least 17 million individuals have been infected, and some countries are still battling first or second waves of the pandemic. Nucleic acid tests, especially reverse transcription polymerase chain reaction (RT-PCR), have become the workhorse for early detection of COVID-19 infection. Positive controls for the molecular assays have been developed to validate each test and to provide high accuracy. However, most available positive controls require cold-chain distribution and cannot serve as full-process control. To overcome these shortcomings, we report the production of biomimetic virus-like particles (VLPs) as SARS-CoV-2 positive controls. A SARS-CoV-2 detection module for RT-PCR was encapsidated into VLPs from a bacteriophage and a plant virus. The chimeric VLPs were obtained either by in vivo reconstitution and coexpression of the target detection module and coat proteins or by in vitro assembly of purified detection module RNA sequences and coat proteins. These VLP-based positive controls mimic SARS-CoV-2 packaged ribonucleic acid (RNA) while being noninfectious. Most importantly, we demonstrated that the positive controls are scalable, stable, and can serve broadly as controls, from RNA extraction to PCR in clinical settings.
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Affiliation(s)
- Soo Khim Chan
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Pinyi Du
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Caroline Ignacio
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Sanjay Mehta
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Isabel G. Newton
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Nicole F. Steinmetz
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
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50
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Chatterjee S, Molenaar R, Tromp L, Wagterveld RM, Roesink HDW, Cornelissen JJLM, Claessens MMAE, Blum C. Optimizing fluorophore density for single virus counting: a photophysical approach. Methods Appl Fluoresc 2021; 9:025001. [PMID: 33480360 DOI: 10.1088/2050-6120/abd8e4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In health and environmental research, it is often necessary to quantify the concentrations of single (bio) nanoparticles present at very low concentrations. Suitable quantification approaches that rely on counting and tracking of single fluorescently labelled (bio) nanoparticles are often challenging since fluorophore self-quenching limits the maximum particle brightness. Here we study how the number of labels per nanoparticle influences the total brightness of fluorescently labelled cowpea chlorotic mottle virus (CCMV). We analyze in detail the photophysical interplay between the fluorophores on the virus particles. We deduce that the formation of dark aggregates and energy transfer towards these aggregates limits the total particle brightness that can be achieved. We show that by carefully selecting the number of fluorescent labels per CCMV, and thus minimizing the negative effects on particle brightness, it is possible to quantify fluorescently labelled CCMV concentrations down to fM concentrations in single particle counting experiments.
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Affiliation(s)
- Swarupa Chatterjee
- Nanobiophysics (NBP), MESA + Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands. Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911MA, Leeuwarden, The Netherlands
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