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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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2
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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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3
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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4
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Duran-Meza AL, Villagrana-Escareño MV, Ruiz-García J, Knobler CM, Gelbart WM. Controlling the surface charge of simple viruses. PLoS One 2021; 16:e0255820. [PMID: 34506491 PMCID: PMC8432797 DOI: 10.1371/journal.pone.0255820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/25/2021] [Indexed: 12/28/2022] Open
Abstract
The vast majority of plant viruses are unenveloped, i.e., they lack a lipid bilayer that is characteristic of most animal viruses. The interactions between plant viruses, and between viruses and surfaces, properties that are essential for understanding their infectivity and to their use as bionanomaterials, are largely controlled by their surface charge, which depends on pH and ionic strength. They may also depend on the charge of their contents, i.e., of their genes or-in the instance of virus-like particles-encapsidated cargo such as nucleic acid molecules, nanoparticles or drugs. In the case of enveloped viruses, the surface charge of the capsid is equally important for controlling its interaction with the lipid bilayer that it acquires and loses upon leaving and entering host cells. We have previously investigated the charge on the unenveloped plant virus Cowpea Chlorotic Mottle Virus (CCMV) by measurements of its electrophoretic mobility. Here we examine the electrophoretic properties of a structurally and genetically closely related bromovirus, Brome Mosaic Virus (BMV), of its capsid protein, and of its empty viral shells, as functions of pH and ionic strength, and compare them with those of CCMV. From measurements of both solution and gel electrophoretic mobilities (EMs) we find that the isoelectric point (pI) of BMV (5.2) is significantly higher than that of CCMV (3.7), that virion EMs are essentially the same as those of the corresponding empty capsids, and that the same is true for the pIs of the virions and of their cleaved protein subunits. We discuss these results in terms of current theories of charged colloidal particles and relate them to biological processes and the role of surface charge in the design of new classes of drug and gene delivery systems.
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Affiliation(s)
- A. L. Duran-Meza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
| | - M. V. Villagrana-Escareño
- Laboratorio de Física Biológica, Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México
| | - J. Ruiz-García
- Laboratorio de Física Biológica, Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México
| | - C. M. Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
| | - W. M. Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
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5
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Isaacs A, Li Z, Cheung STM, Wijesundara DK, McMillan CLD, Modhiran N, Young PR, Ranasinghe C, Watterson D, Chappell KJ. Adjuvant Selection for Influenza and RSV Prefusion Subunit Vaccines. Vaccines (Basel) 2021; 9:vaccines9020071. [PMID: 33498370 PMCID: PMC7909420 DOI: 10.3390/vaccines9020071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 12/18/2022] Open
Abstract
Subunit vaccines exhibit favorable safety and immunogenicity profiles and can be designed to mimic native antigen structures. However, pairing with an appropriate adjuvant is imperative in order to elicit effective humoral and cellular immune responses. In this study, we aimed to determine an optimal adjuvant pairing with the prefusion form of influenza haemagglutinin (HA) or respiratory syncytial virus (RSV) fusion (F) subunit vaccines in BALB/c mice in order to inform future subunit vaccine adjuvant selection. We tested a panel of adjuvants, including aluminum hydroxide (alhydrogel), QS21, Addavax, Addavax with QS21 (AdQS21), and Army Liposome Formulation 55 with monophosphoryl lipid A and QS21 (ALF55). We found that all adjuvants elicited robust humoral responses in comparison to placebo, with the induction of potent neutralizing antibodies observed in all adjuvanted groups against influenza and in AdQS21, alhydrogel, and ALF55 against RSV. Upon HA vaccination, we observed that none of the adjuvants were able to significantly increase the frequency of CD4+ and CD8+ IFN-γ+ cells when compared to unadjuvanted antigen. The varying responses to antigens with each adjuvant highlights that those adjuvants most suited for pairing purposes can vary depending on the antigen used and/or the desired immune response. We therefore suggest that an adjuvant trial for different subunit vaccines in development would likely be necessary in preclinical studies.
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Affiliation(s)
- Ariel Isaacs
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.I.); (S.T.M.C.); (C.L.D.M.); (N.M.); (P.R.Y.); (D.W.)
| | - Zheyi Li
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; (Z.L.); (C.R.)
| | - Stacey T. M. Cheung
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.I.); (S.T.M.C.); (C.L.D.M.); (N.M.); (P.R.Y.); (D.W.)
| | - Danushka K. Wijesundara
- The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia;
| | - Christopher L. D. McMillan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.I.); (S.T.M.C.); (C.L.D.M.); (N.M.); (P.R.Y.); (D.W.)
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.I.); (S.T.M.C.); (C.L.D.M.); (N.M.); (P.R.Y.); (D.W.)
| | - Paul R. Young
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.I.); (S.T.M.C.); (C.L.D.M.); (N.M.); (P.R.Y.); (D.W.)
- The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia;
- Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Charani Ranasinghe
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; (Z.L.); (C.R.)
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.I.); (S.T.M.C.); (C.L.D.M.); (N.M.); (P.R.Y.); (D.W.)
- Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Keith J. Chappell
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.I.); (S.T.M.C.); (C.L.D.M.); (N.M.); (P.R.Y.); (D.W.)
- The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia;
- Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia
- Correspondence:
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6
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Ashaolu TJ. Nanoemulsions for health, food, and cosmetics: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2021; 19:3381-3395. [PMID: 33746662 PMCID: PMC7956871 DOI: 10.1007/s10311-021-01216-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/03/2021] [Indexed: 05/03/2023]
Abstract
Nanoemulsions are gaining importance in healthcare and cosmetics sectors as a result of the unique properties of nanosized droplets, such as high surface area. Here we review nanotechnology and nanoemulsions with focus on emulsifiers and nanoemulsifiers, and applications for drugs and vaccines delivery, cancer therapy, inflammation treatment, cosmetics, perfumes, polymers, and food. We discuss nanoemulsion safety and properties, e.g., stability, emulsification, solubility, molecular number and arrangements, ionic strength, pH and temperature.
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Affiliation(s)
- Tolulope Joshua Ashaolu
- Institute of Research and Development, Faculty of Environmental and Chemical Engineering, Duy Tan University, Da Nang, 550000 Vietnam
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7
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Edwardson TGW, Tetter S, Hilvert D. Two-tier supramolecular encapsulation of small molecules in a protein cage. Nat Commun 2020; 11:5410. [PMID: 33106476 PMCID: PMC7588467 DOI: 10.1038/s41467-020-19112-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Expanding protein design to include other molecular building blocks has the potential to increase structural complexity and practical utility. Nature often employs hybrid systems, such as clathrin-coated vesicles, lipid droplets, and lipoproteins, which combine biopolymers and lipids to transport a broader range of cargo molecules. To recapitulate the structure and function of such composite compartments, we devised a supramolecular strategy that enables porous protein cages to encapsulate poorly water-soluble small molecule cargo through templated formation of a hydrophobic surfactant-based core. These lipoprotein-like complexes protect their cargo from sequestration by serum proteins and enhance the cellular uptake of fluorescent probes and cytotoxic drugs. This design concept could be applied to other protein cages, surfactant mixtures, and cargo molecules to generate unique hybrid architectures and functional capabilities.
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Affiliation(s)
| | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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8
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Encapsidation of Different Plasmonic Gold Nanoparticles by the CCMV CP. Molecules 2020; 25:molecules25112628. [PMID: 32516956 PMCID: PMC7321416 DOI: 10.3390/molecules25112628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022] Open
Abstract
Different types of gold nanoparticles have been synthesized that show great potential in medical applications such as medical imaging, bio-analytical sensing and photothermal cancer therapy. However, their stability, polydispersity and biocompatibility are major issues of concern. For example, the synthesis of gold nanorods, obtained through the elongated micelle process, produce them with a high positive surface charge that is cytotoxic, while gold nanoshells are unstable and break down in a few weeks due to the Ostwald ripening process. In this work, we report the self-assembly of the capsid protein (CP) of cowpea chlorotic mottle virus (CCMV) around spherical gold nanoparticles, gold nanorods and gold nanoshells to form virus-like particles (VLPs). All gold nanoparticles were synthesized or treated to give them a negative surface charge, so they can interact with the positive N-terminus of the CP leading to the formation of the VLPs. To induce the protein self-assembly around the negative gold nanoparticles, we use different pH and ionic strength conditions determined from a CP phase diagram. The encapsidation with the viral CP will provide the nanoparticles better biocompatibility, stability, monodispersity and a new biological substrate on which can be introduced ligands toward specific cells, broadening the possibilities for medical applications.
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9
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Song Y, Yang Y, Lin X, Li X, Zhang X, Ma G, Su Z, Zhang S. In-situ and sensitive stability study of emulsion and aluminum adjuvanted inactivated foot-and-mouth disease virus vaccine by differential scanning fluorimetry analysis. Vaccine 2020; 38:2904-2912. [DOI: 10.1016/j.vaccine.2020.02.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/20/2022]
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10
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Sasaki E, Dragoman RM, Mantri S, Dirin DN, Kovalenko MV, Hilvert D. Self‐Assembly of Proteinaceous Shells around Positively Charged Gold Nanomaterials Enhances Colloidal Stability in High‐Ionic‐Strength Buffers. Chembiochem 2019; 21:74-79. [DOI: 10.1002/cbic.201900469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Eita Sasaki
- Laboratory of Organic ChemistryETH Zürich Vladimir-Prelog-Weg, 1-5/10 8093 Zürich Switzerland
- Present address: Graduate School of Agricultural and Life SciencesThe University of Tokyo 1-1-1 Yayoi Bunkyo-ku Tokyo 113–8657 Japan
| | - Ryan M. Dragoman
- Laboratory of Inorganic ChemistryETH Zürich Vladimir-Prelog-Weg, 1-5/10 8093 Zürich Switzerland
- Empa-Swiss Federal Laboratories for Materials Science and Technology Überland Strasse 129 8600 Dübendorf Switzerland
| | - Shiksha Mantri
- Laboratory of Organic ChemistryETH Zürich Vladimir-Prelog-Weg, 1-5/10 8093 Zürich Switzerland
| | - Dmitry N. Dirin
- Laboratory of Inorganic ChemistryETH Zürich Vladimir-Prelog-Weg, 1-5/10 8093 Zürich Switzerland
- Empa-Swiss Federal Laboratories for Materials Science and Technology Überland Strasse 129 8600 Dübendorf Switzerland
| | - Maksym V. Kovalenko
- Laboratory of Inorganic ChemistryETH Zürich Vladimir-Prelog-Weg, 1-5/10 8093 Zürich Switzerland
- Empa-Swiss Federal Laboratories for Materials Science and Technology Überland Strasse 129 8600 Dübendorf Switzerland
| | - Donald Hilvert
- Laboratory of Organic ChemistryETH Zürich Vladimir-Prelog-Weg, 1-5/10 8093 Zürich Switzerland
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11
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Thurm AR, Beren C, Duran-Meza AL, Knobler CM, Gelbart WM. RNA Homopolymers Form Higher-Curvature Virus-like Particles Than Do Normal-Composition RNAs. Biophys J 2019; 117:1331-1341. [PMID: 31514968 PMCID: PMC6818174 DOI: 10.1016/j.bpj.2019.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/17/2019] [Accepted: 08/07/2019] [Indexed: 11/15/2022] Open
Abstract
Unlike double-stranded DNA, single-stranded RNA can be spontaneously packaged into spherical capsids by viral capsid protein (CP) because it is a more compact and flexible polymer. Many systematic investigations of this self-assembly process have been carried out using CP from cowpea chlorotic mottle virus, with a wide range of sequences and lengths of single-stranded RNA. Among these studies are measurements of the relative packaging efficiencies of these RNAs into spherical capsids. In this work, we address a fundamental issue that has received very little attention, namely the question of the preferred curvature of the capsid formed around different RNA molecules. We show in particular that homopolymers of RNA-polyribouridylic acid and polyriboadenylic acid-form exclusively T = 2-sized (∼22-nm diameter) virus-like particles (VLPs) when mixed with cowpea chlorotic mottle virus CP, independent of their length, ranging from 500 to more than 4000 nucleotides. This is in contrast to "normal-composition" RNAs (i.e., molecules with comparable numbers of each of the four nucleotides and hence capable of developing a large amount of secondary structure because of intramolecular complementarity/basepairing); a curvature corresponding to T = 3-size (∼28 nm in diameter) is preferred for the VLPs formed with such RNAs. Our work is consistent with the preferred curvature of VLPs being a consequence of interaction of CP with RNA-in particular, the presence or absence of short RNA duplexes-and suggests that the equilibrium size of the capsid results from a trade-off between this optimum size and the cost of confinement.
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Affiliation(s)
- Abby R Thurm
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California
| | - Christian Beren
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California
| | - Ana Luisa Duran-Meza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California; Molecular Biology Institute, University of California, Los Angeles, California; California NanoSystems Institute, University of California, Los Angeles, California.
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12
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Jefferys EE, Sansom MSP. Computational Virology: Molecular Simulations of Virus Dynamics and Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:201-233. [DOI: 10.1007/978-3-030-14741-9_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Zhao K, Mason TG. Assembly of colloidal particles in solution. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:126601. [PMID: 29978830 DOI: 10.1088/1361-6633/aad1a7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Advances in both top-down and bottom-up syntheses of a wide variety of complex colloidal building blocks and also in methods of controlling their assembly in solution have led to new and interesting forms of highly controlled soft matter. In particular, top-down lithographic methods of producing monodisperse colloids now provide precise human-designed control over their sub-particle features, opening up a wide range of new possibilities for assembly structures that had been previously limited by the range of shapes available through bottom-up methods. Moreover, an increasing level of control over anisotropic interactions between these colloidal building blocks, which can be tailored through local geometries of sub-particle features as well as site-specific surface modifications, is giving rise to new demonstrations of massively parallel off-chip self-assembly of specific target structures with low defect rates. In particular, new experimental realizations of hierarchical self-assembly and control over the chiral purity of resulting assembly structures have been achieved. Increasingly, shape-dependent, shape-complementary, and roughness-controlled depletion attractions between non-spherical colloids are being used in novel ways to create assemblies that go far beyond early examples, such as fractal clusters formed by diffusion-limited and reaction-limited aggregation of spheres. As self-assembly methods have progressed, a wide variety of advanced directed assembly methods have also been developed; approaches based on microfluidic control and applying structured electromagnetic fields are particularly promising.
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Affiliation(s)
- Kun Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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14
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Formulation of nanoemulsion from leaves essential oil of Ocimum basilicum L. and its antibacterial, antioxidant and larvicidal activities (Culex quinquefasciatus). Microb Pathog 2018; 125:475-485. [DOI: 10.1016/j.micpath.2018.10.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023]
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15
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Tasker A, Sainsbury F, Puttick S. Particle-Stabilized Fluid-Fluid Interfaces: The Impact of Core Composition on Interfacial Structure. Front Chem 2018; 6:383. [PMID: 30214900 PMCID: PMC6125302 DOI: 10.3389/fchem.2018.00383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/09/2018] [Indexed: 12/18/2022] Open
Abstract
The encapsulation of small molecule drugs in nanomaterials has become an increasingly popular approach to the delivery of therapeutics. The use of emulsions as templates for the synthesis of drug impregnated nanomaterials is an exciting area of research, and a great deal of progress has been made in understanding the interfacial chemistry that is critical to controlling the physicochemical properties of both the encapsulated material and the templated material. For example, control of the interfacial tension between an oil and aqueous phase is a fundamental concern when designing drug delivery vehicles that are stabilized by particulate surfactants at the fluid interface. Particles in general are capable of self-assembly at a fluid interface, with a preference for one or the other of the phases, and much work has focussed on modification of the particle properties to optimize formation and stability of the emulsion. An issue arises however when a model, single oil system is translated into more complex, real-world scenarios, which are often multi-component, with the incorporation of charged active ingredients and other excipients. The result is potentially a huge change in the properties of the dispersed phase which can lead to a failure in the capability of particles to continue to stabilize the interface. In this mini-review, we will focus on two encapsulation strategies based on the selective deposition of particles or proteins on a fluid-fluid interface: virus-like particles and polymer microcapsules formed from particle-stabilized emulsion templates. The similarity between these colloidal systems lies in the fact that particulate entities are used to stabilize fluid cores. We will focus on those studies that have described the effect of subtle changes in core composition on the self-assembly of particles at the fluid-fluid interface and how this influences the resulting capsule structure.
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Affiliation(s)
- Alison Tasker
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- Commonwealth Scientific and Industrial Research Organisation, Probing Biosystems Future Science Platform, Brisbane, QLD, Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Simon Puttick
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- Commonwealth Scientific and Industrial Research Organisation, Probing Biosystems Future Science Platform, Brisbane, QLD, Australia
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16
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Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte. Nat Commun 2018; 9:3071. [PMID: 30082710 PMCID: PMC6078970 DOI: 10.1038/s41467-018-05426-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/05/2018] [Indexed: 11/20/2022] Open
Abstract
The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7kBT0, with kB the Boltzmann constant and T0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20kBT0). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape. The mechanism by which virus capsules assemble around RNA to package their genetic material is not clear. Here, the authors observed the assembly of the cowpea chlorotic mottle virus capsid around viral RNA or poly(styrene sulfonic acid) using time-resolved small-angle X-ray scattering measurements.
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17
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Lázaro GR, Dragnea B, Hagan MF. Self-assembly of convex particles on spherocylindrical surfaces. SOFT MATTER 2018; 14:5728-5740. [PMID: 29796568 PMCID: PMC6051892 DOI: 10.1039/c8sm00129d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The precise control of assembly and packing of proteins and colloids on curved surfaces has fundamental implications in nanotechnology. In this paper, we describe dynamical simulations of the self-assembly of conical subunits around a spherocylindrical template, and a continuum theory for the bending energy of a triangular lattice with spontaneous curvature on a surface with arbitrary curvature. We find that assembly depends sensitively on mismatches between subunit spontaneous curvature and the mean curvature of the template, as well as anisotropic curvature of the template (mismatch between the two principal curvatures). Our simulations predict assembly morphologies that closely resemble those observed in experiments in which virus capsid proteins self-assemble around metal nanorods. Below a threshold curvature mismatch, our simulations identify a regime of optimal assembly leading to complete, symmetrical particles. Outside of this regime we observe defective particles, whose morphologies depend on the degree of curvature mismatch. To learn how assembly is affected by the nonuniform curvature of a spherocylinder, we also study the simpler cases of assembly around spherical and cylindrical cores. Our results show that both the intrinsic (Gaussian) and extrinsic (mean) curvatures of a template play significant roles in guiding the assembly of anisotropic subunits, providing a rich design space for the formation of nanoscale materials.
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Affiliation(s)
- Guillermo R Lázaro
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA.
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18
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Zeng C, Rodriguez Lázaro G, Tsvetkova IB, Hagan MF, Dragnea B. Defects and Chirality in the Nanoparticle-Directed Assembly of Spherocylindrical Shells of Virus Coat Proteins. ACS NANO 2018; 12:5323-5332. [PMID: 29694012 PMCID: PMC6202266 DOI: 10.1021/acsnano.8b00069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Virus coat proteins of small isometric plant viruses readily assemble into symmetric, icosahedral cages encapsulating noncognate cargo, provided the cargo meets a minimal set of chemical and physical requirements. While this capability has been intensely explored for certain virus-enabled nanotechnologies, additional applications require lower symmetry than that of an icosahedron. Here, we show that the coat proteins of an icosahedral virus can efficiently assemble around metal nanorods into spherocylindrical closed shells with hexagonally close-packed bodies and icosahedral caps. Comparison of chiral angles and packing defects observed by in situ atomic force microscopy with those obtained from molecular dynamics models offers insight into the mechanism of growth, and the influence of stresses associated with intrinsic curvature and assembly pathways.
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Affiliation(s)
- Cheng Zeng
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | | | - Irina B Tsvetkova
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Michael F Hagan
- Department of Physics , Brandeis University , Waltham , Massachusetts 02453 , United States
| | - Bogdan Dragnea
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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19
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Sinn S, Yang L, Biedermann F, Wang D, Kübel C, Cornelissen JJLM, De Cola L. Templated Formation of Luminescent Virus-like Particles by Tailor-Made Pt(II) Amphiphiles. J Am Chem Soc 2018; 140:2355-2362. [PMID: 29357236 PMCID: PMC5817621 DOI: 10.1021/jacs.7b12447] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Virus-like particles
(VLPs) have been created from luminescent
Pt(II) complex amphiphiles, able to form supramolecular structures
in water solutions, that can be encapsulated or act as templates of
cowpea chlorotic mottle virus capsid proteins. By virtue of a bottom-up
molecular design, icosahedral and nonicosahedral (rod-like) VLPs have
been constructed through diverse pathways, and a relationship between
the molecular structure of the complexes and the shape and size of
the VLPs has been observed. A deep insight into the mechanism for
the templated formation of the differently shaped VLPs was achieved,
by electron microscopy measurements (TEM and STEM) and bulk analysis
(FPLC, DLS, photophysical investigations). Interestingly, the obtained
VLPs can be visualized by their intense emission at room temperature,
generated by the self-assembly of the Pt(II) complexes. The encapsulation
of the luminescent species is further verified by their higher emission
quantum yields inside the VLPs, which is due to the confinement effect
of the protein cage. These hybrid materials demonstrate the potential
of tailor-made supramolecular systems able to control the assembly
of biological building blocks.
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Affiliation(s)
- Stephan Sinn
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS , 8 Rue Gaspard Monge, 67000 Strasbourg, France
| | - Liulin Yang
- Laboratory for Biomolecular Nanotechnology, MESA+ Institute, University of Twente , P.O. Box 207, 7500 AE Enschede, The Netherlands
| | | | | | | | - Jeroen J L M Cornelissen
- Laboratory for Biomolecular Nanotechnology, MESA+ Institute, University of Twente , P.O. Box 207, 7500 AE Enschede, The Netherlands
| | - Luisa De Cola
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS , 8 Rue Gaspard Monge, 67000 Strasbourg, France
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20
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Azuma Y, Edwardson TGW, Hilvert D. Tailoring lumazine synthase assemblies for bionanotechnology. Chem Soc Rev 2018; 47:3543-3557. [DOI: 10.1039/c8cs00154e] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The cage-forming protein lumazine synthase is readily modified, evolved and assembled with other components.
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Affiliation(s)
- Yusuke Azuma
- Laboratory of Organic Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | | | - Donald Hilvert
- Laboratory of Organic Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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21
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Loredo-Tovias M, Duran-Meza AL, Villagrana-Escareño MV, Vega-Acosta R, Reynaga-Hernández E, Flores-Tandy LM, Valdes-Resendiz OE, Cadena-Nava RD, Alvizo-Paez ER, Ruiz-Garcia J. Encapsidated ultrasmall nanolipospheres as novel nanocarriers for highly hydrophobic anticancer drugs. NANOSCALE 2017; 9:11625-11631. [PMID: 28770909 DOI: 10.1039/c7nr02118f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The design and construction of novel nanocarriers that have controlled shape and size and are made of inherently biocompatible components represents a milestone in the field of nanomedicine. Here, we show the tailoring of nanoliposphere-like particles for use as biocompatible drug nanocarriers. They are made with the building block components present in human lipoproteins by means of microfluidization, which allows for good size and polydispersity control, mimicking the physical properties of natural low-density lipoproteins (LDLs). This new type of nanocarrier has a negative surface charge and a hydrophobic core that allow the stabilization and encapsulation of hydrophobic anticancer drugs such as camptothecin, resulting in anticancer drug-loaded nanolipospheres. However, we found that the nanoparticles are unstable since their size increases with time. These nanolipospheres were further encapsidated using the non-cytotoxic capsid protein of the plant virus CCMV, which renders the nanoparticles stable. In a more general application, this new virus-like particle confers a controlled microenvironment for the transport of any kind of hydrophobic drug that can bypass the cellular defense mechanisms and deliver its payload.
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Affiliation(s)
- M Loredo-Tovias
- Biological Physics Laboratory, Institute of Physics, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, San Luis Potosí, S. L. P. 78000, Mexico.
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22
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Lam P, Steinmetz NF. Plant viral and bacteriophage delivery of nucleic acid therapeutics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2017; 10. [DOI: 10.1002/wnan.1487] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/24/2017] [Accepted: 06/20/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Patricia Lam
- Department of Biomedical EngineeringCase Western Reserve UniversityClevelandOHUSA
| | - Nicole F. Steinmetz
- Department of Biomedical EngineeringCase Western Reserve UniversityClevelandOHUSA
- Department of RadiologyCase Western Reserve UniversityClevelandOHUSA
- Department of Materials Science and EngineeringCase Western Reserve UniversityClevelandOHUSA
- Department of Macromolecular Science and EngineeringCase Western Reserve UniversityClevelandOHUSA
- Division of General Medical Sciences‐Oncology, Case Comprehensive Cancer CenterCase Western Reserve UniversityClevelandOHUSA
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23
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Yang L, Liu A, Cao S, Putri RM, Jonkheijm P, Cornelissen JJLM. Self-Assembly of Proteins: Towards Supramolecular Materials. Chemistry 2016; 22:15570-15582. [DOI: 10.1002/chem.201601943] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Liulin Yang
- Laboratory for Biomolecular Nanotechnology; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
- Molecular Nanofabrication Group; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
| | - Aijie Liu
- Laboratory for Biomolecular Nanotechnology; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
| | - Shuqin Cao
- Laboratory for Biomolecular Nanotechnology; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
| | - Rindia M. Putri
- Laboratory for Biomolecular Nanotechnology; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
| | - Pascal Jonkheijm
- Molecular Nanofabrication Group; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Laboratory for Biomolecular Nanotechnology; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
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24
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Sasaki E, Hilvert D. Self-Assembly of Proteinaceous Multishell Structures Mediated by a Supercharged Protein. J Phys Chem B 2016; 120:6089-95. [DOI: 10.1021/acs.jpcb.6b02068] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Eita Sasaki
- Laboratory
of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory
of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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25
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Gupta A, Eral HB, Hatton TA, Doyle PS. Nanoemulsions: formation, properties and applications. SOFT MATTER 2016; 12:2826-41. [PMID: 26924445 DOI: 10.1039/c5sm02958a] [Citation(s) in RCA: 621] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nanoemulsions are kinetically stable liquid-in-liquid dispersions with droplet sizes on the order of 100 nm. Their small size leads to useful properties such as high surface area per unit volume, robust stability, optically transparent appearance, and tunable rheology. Nanoemulsions are finding application in diverse areas such as drug delivery, food, cosmetics, pharmaceuticals, and material synthesis. Additionally, they serve as model systems to understand nanoscale colloidal dispersions. High and low energy methods are used to prepare nanoemulsions, including high pressure homogenization, ultrasonication, phase inversion temperature and emulsion inversion point, as well as recently developed approaches such as bubble bursting method. In this review article, we summarize the major methods to prepare nanoemulsions, theories to predict droplet size, physical conditions and chemical additives which affect droplet stability, and recent applications.
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Affiliation(s)
- Ankur Gupta
- Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - H Burak Eral
- Delft University of Technology, The Netherlands and Utrecht University, The Netherlands
| | - T Alan Hatton
- Massachusetts Institute of Technology, Cambridge, MA, USA.
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26
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The Role of Packaging Sites in Efficient and Specific Virus Assembly. J Mol Biol 2015; 427:2451-2467. [PMID: 25986309 DOI: 10.1016/j.jmb.2015.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/21/2015] [Accepted: 05/10/2015] [Indexed: 12/25/2022]
Abstract
During the life cycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively assemble around the viral RNA amidst diverse host RNAs is a key question in virology. In one proposed mechanism, short sequences (packaging sites) within the genomic RNA promote rapid and efficient assembly through specific interactions with the capsid proteins. In this work, we develop a coarse-grained particle-based computational model for capsid proteins and RNA that represents protein-RNA interactions arising both from nonspecific electrostatics and from specific packaging site interactions. Using Brownian dynamics simulations, we explore how the efficiency and specificity of assembly depend on solution conditions (which control protein-protein and nonspecific protein-RNA interactions) and the strength and number of packaging sites. We identify distinct regions in parameter space in which packaging sites lead to highly specific assembly via different mechanisms and others in which packaging sites lead to kinetic traps. We relate these computational predictions to in vitro assays for specificity in which cognate viral RNAs compete against non-cognate RNAs for assembly by capsid proteins.
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27
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Abstract
Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid and in some cases are surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which capsids assemble within their host cells and in vitro. We describe the thermodynamics and kinetics for the assembly of protein subunits into icosahedral capsid shells and how these are modified in cases in which the capsid assembles around a nucleic acid or on a lipid bilayer. We present experimental and theoretical techniques used to characterize capsid assembly, and we highlight aspects of virus assembly that are likely to receive significant attention in the near future.
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Affiliation(s)
- Jason D Perlmutter
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454;
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28
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Abstract
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened.
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29
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Perlmutter JD, Perkett MR, Hagan MF. Pathways for virus assembly around nucleic acids. J Mol Biol 2014; 426:3148-3165. [PMID: 25036288 DOI: 10.1016/j.jmb.2014.07.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/17/2014] [Accepted: 07/07/2014] [Indexed: 12/25/2022]
Abstract
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work, we use computer simulations to characterize assembly over a wide range of capsid protein-protein interaction strengths and solution ionic strengths. We find that assembly pathways can be categorized into two classes, in which intermediates are either predominantly ordered or disordered. Our results suggest that estimating the protein-protein and the protein-genome binding affinities may be sufficient to predict which pathway occurs. Furthermore, the calculated phase diagrams suggest that knowledge of the dominant assembly pathway and its relationship to control parameters could identify optimal strategies to thwart or redirect assembly to block infection. Finally, analysis of simulation trajectories suggests that the two classes of assembly pathways can be distinguished in single-molecule fluorescence correlation spectroscopy or bulk time-resolved small-angle X-ray scattering experiments.
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Affiliation(s)
- Jason D Perlmutter
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Matthew R Perkett
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA.
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30
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Fox CB, Kramer RM, Barnes V L, Dowling QM, Vedvick TS. Working together: interactions between vaccine antigens and adjuvants. THERAPEUTIC ADVANCES IN VACCINES 2014; 1:7-20. [PMID: 24757512 DOI: 10.1177/2051013613480144] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of vaccines containing adjuvants has the potential to enhance antibody and cellular immune responses, broaden protective immunity against heterogeneous pathogen strains, enable antigen dose sparing, and facilitate efficacy in immunocompromised populations. Nevertheless, the structural interplay between antigen and adjuvant components is often not taken into account in the published literature. Interactions between antigen and adjuvant formulations should be well characterized to enable optimum vaccine stability and efficacy. This review focuses on the importance of characterizing antigen-adjuvant interactions by summarizing findings involving widely used adjuvant formulation platforms, such as aluminum salts, emulsions, lipid vesicles, and polymer-based particles. Emphasis is placed on the physicochemical basis of antigen-adjuvant associations and the appropriate analytical tools for their characterization, as well as discussing the effects of these interactions on vaccine potency.
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31
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He L, Porterfield Z, van der Schoot P, Zlotnick A, Dragnea B. Hepatitis virus capsid polymorph stability depends on encapsulated cargo size. ACS NANO 2013; 7:8447-54. [PMID: 24010404 PMCID: PMC5683388 DOI: 10.1021/nn4017839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Protein cages providing a controlled environment to encapsulated cargo are a ubiquitous presence in any biological system. Well-known examples are capsids, the regular protein shells of viruses, which protect and deliver the viral genome. Since some virus capsids can be loaded with nongenomic cargoes, they are interesting for a variety of applications ranging from biomedical delivery to energy harvesting. A question of vital importance for such applications is how does capsid stability depend on the size of the cargo? A nanoparticle-templated assembly approach was employed here to determine how different polymorphs of the Hepatitis B virus icosahedral capsid respond to a gradual change in the encapsulated cargo size. It was found that assembly into complete virus-like particles occurs cooperatively around a variety of core diameters, albeit the degree of cooperativity varies. Among these virus-like particles, it was found that those of an outer diameter corresponding to an icosahedral array of 240 proteins (T = 4) are able to accommodate the widest range of cargo sizes.
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Affiliation(s)
- Li He
- Department of Chemistry and ‡Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
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32
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Malyutin AG, Dragnea B. Budding pathway in the templated assembly of viruslike particles. J Phys Chem B 2013; 117:10730-6. [PMID: 23947533 DOI: 10.1021/jp405603m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new pathway for the assembly of viral capsid protein around inorganic nanoparticle cores was observed by time-course light scattering and cryo-electron tomography. Gold nanoparticles with an average diameter of 11.3 nm have been used as a template for the assembly of Brome mosaic virus (BMV) capsid protein at different concentrations. At least at low protein concentrations the kinetic features of the scattering and extinction measurements are consistent with the initial rapid formation of large nanoparticle-protein clusters, which subsequently separate into individual viruslike particles (VLPs). The occurrence of multiparticle clusters at short times after mixing nanoparticles and proteins was confirmed by cryo-EM. Cryo-electron tomography of the multiparticle clusters yielded an average surface-to-surface interparticle distance of ∼7.5 nm, equivalent to ∼1.5 times the thickness of a protein shell. We propose a scenario in which VLP generation may take place through monomer exchange between aggregated particles with defect-ridden or incomplete shells, leading to the formation of stable icosahedral shells, which eventually bud off the aggregate. Together with results from previous works, the findings highlight the astonishing versatility of plant virus capsid protein assembly. This previously unknown mechanism for VLP formation has features that may have relevance for the crowded environment characterizing virus factories in the cell.
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Affiliation(s)
- Andrey G Malyutin
- Department of Chemistry, Indiana University , 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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33
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Azizgolshani O, Garmann RF, Cadena-Nava R, Knobler CM, Gelbart WM. Reconstituted plant viral capsids can release genes to mammalian cells. Virology 2013; 441:12-7. [DOI: 10.1016/j.virol.2013.03.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/17/2013] [Accepted: 03/02/2013] [Indexed: 12/19/2022]
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34
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Wan X, Liu T, Hu J, Liu S. Photo-Degradable, Protein-Polyelectrolyte Complex-Coated, Mesoporous Silica Nanoparticles for Controlled Co-Release of Protein and Model Drugs. Macromol Rapid Commun 2012; 34:341-7. [DOI: 10.1002/marc.201200673] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/15/2012] [Indexed: 01/06/2023]
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35
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Luque A, Reguera D, Morozov A, Rudnick J, Bruinsma R. Physics of shell assembly: line tension, hole implosion, and closure catastrophe. J Chem Phys 2012; 136:184507. [PMID: 22583300 DOI: 10.1063/1.4712304] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The self-assembly of perfectly ordered closed shells is a challenging process involved in many biological and nanoscale systems. However, most of the aspects that determine their formation are still unknown. Here we investigate the growth of shells by simulating the assembly of spherical structures made of N identical subunits. Remarkably, we show that the formation and energetics of partially assembled shells are dominated by an effective line-tension that can be described in simple thermodynamic terms. In addition, we unveil two mechanisms that can prevent the correct formation of defect-free structures: "hole implosion," which leads to a premature closure of the shell; and "closure catastrophe," which causes a dramatic production of structural disorder during the later stages of the growth of big shells.
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Affiliation(s)
- Antoni Luque
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095-1547, USA
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36
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In vitro quantification of the relative packaging efficiencies of single-stranded RNA molecules by viral capsid protein. J Virol 2012; 86:12271-82. [PMID: 22951822 DOI: 10.1128/jvi.01695-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
While most T=3 single-stranded RNA (ssRNA) viruses package in vivo about 3,000 nucleotides (nt), in vitro experiments have demonstrated that a broad range of RNA lengths can be packaged. Under the right solution conditions, for example, cowpea chlorotic mottle virus (CCMV) capsid protein (CP) has been shown to package RNA molecules whose lengths range from 100 to 10,000 nt. Furthermore, in each case it can package the RNA completely, as long as the mass ratio of CP to nucleic acid in the assembly mixture is 6:1 or higher. Yet the packaging efficiencies of the RNAs can differ widely, as we demonstrate by measurements in which two RNAs compete head-to-head for a limited amount of CP. We show that the relative efficiency depends nonmonotonically on the RNA length, with 3,200 nt being optimum for packaging by the T=3 capsids preferred by CCMV CP. When two RNAs of the same length-and hence the same charge-compete for CP, differences in packaging efficiency are necessarily due to differences in their secondary structures and/or three-dimensional (3D) sizes. For example, the heterologous RNA1 of brome mosaic virus (BMV) is packaged three times more efficiently by CCMV CP than is RNA1 of CCMV, even though the two RNAs have virtually identical lengths. Finally, we show that in an assembly mixture at neutral pH, CP binds reversibly to the RNA and there is a reversible equilibrium between all the various RNA/CP complexes. At acidic pH, excess protein unbinds from RNA/CP complexes and nucleocapsids form irreversibly.
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37
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Patterson DP, Prevelige PE, Douglas T. Nanoreactors by programmed enzyme encapsulation inside the capsid of the bacteriophage P22. ACS NANO 2012; 6:5000-5009. [PMID: 22624576 DOI: 10.1021/nn300545z] [Citation(s) in RCA: 209] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The virus like particle (VLP) derived from bacteriophage P22 presents a unique platform for constructing catalytically functional nanomaterials by encapsulation of enzymes into its interior. Encapsulation has been engineered to be genetically programmed allowing "one pot" synthesis and incorporation of desired enzymes. The unique characteristic that separates P22 from other VLP systems is the ability to modulate the overall volume and porosity of the VLP structure, thus controlling substrate access to the encapsulated enzyme. The present study demonstrates incorporation of an enzyme, alcohol dehydrogenase D, with the highest internal loading for an active enzyme by any VLP described thus far. In addition, we show that not only does encapsulating AdhD inside P22 affect its kinetic parameters in comparison with the "free" enzyme, but transformation of P22 to different morphological states, which changes the internal volume of the VLP, yields changes in the overall activity of the encapsulated enzyme as well. The findings reported here clearly illustrate that P22 holds potential for synthetic approaches to create nanoreactors, by design, using the power of highly evolved enzymes for chemical transformations.
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Affiliation(s)
- Dustin P Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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38
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Affiliation(s)
| | - Thomas G. Mason
- Department of Chemistry and Biochemistry,
- Department of Physics and Astronomy, and
- California NanoSystems Institute, University of California, Los Angeles, California 90095;
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39
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Kim MP, Kang DJ, Jung DW, Kannan AG, Kim KH, Ku KH, Jang SG, Chae WS, Yi GR, Kim BJ. Gold-decorated block copolymer microspheres with controlled surface nanostructures. ACS NANO 2012; 6:2750-2757. [PMID: 22352689 DOI: 10.1021/nn300194z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Gold-decorated block copolymer microspheres (BCP-microspheres) displaying various surface morphologies were prepared by the infiltration of Au precursors into polystyrene-b-poly(4-vinylpyridine) (PS-b-P4VP) microspheres. The microspheres were fabricated by emulsifying the PS-b-P4VP polymers in chloroform into a surfactant solution in water, followed by the evaporation of chloroform. The selective swelling of the P4VP domains in the microspheres by the Au precursor under acidic conditions resulted in the formation of Au-decorated BCP-microspheres with various surface nanostructures. As evidenced by transmission electron microscopy (TEM) and scanning electron microscopy (SEM) measurements, dotted surface patterns were formed when microspheres smaller than 800 nm were synthesized, whereas fingerprint-like surface patterns were observed with microspheres larger than 800 nm. Au nanoparticles (NPs) were located inside P4VP domains near the surfaces of the prepared microspheres, as confirmed by TEM. The optical properties of the BCP-microspheres were characterized using UV-vis absorption spectroscopy and fluorescence lifetime measurements. A maximum absorption peak was observed at approximately 580 nm, indicating that Au NPs are densely packed into P4VP domains on the microspheres. Our approach for creating Au-NP-hybrid BCP-microspheres can be extended to other NP systems such as iron-oxide or platinum NPs. These precursors can also be selectively incorporated into P4VP domains and induce the formation of hybrid BCP-microspheres with controlled surface nanostructures.
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Affiliation(s)
- Minsoo P Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
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40
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Liu Z, Qiao J, Niu Z, Wang Q. Natural supramolecular building blocks: from virus coat proteins to viral nanoparticles. Chem Soc Rev 2012; 41:6178-94. [DOI: 10.1039/c2cs35108k] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Ng BC, Chan ST, Lin J, Tolbert SH. Using polymer conformation to control architecture in semiconducting polymer/viral capsid assemblies. ACS NANO 2011; 5:7730-8. [PMID: 21942298 PMCID: PMC3215919 DOI: 10.1021/nn202493w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Cowpea chlorotic mottle virus is a single-stranded RNA plant virus with a diameter of 28 nm. The proteins comprising the capsid of this virus can be purified and reassembled either by themselves to form hollow structures or with polyanions such as double-stranded DNA or single-stranded RNA. Depending on pH and ionic strength, a diverse range of structures and shapes can form. The work presented here focuses on using these proteins to encapsulate a fluorescent polyanionic semiconducting polymer, MPS-PPV (poly-2-methoxy-5-propyloxy sulfonate phenylene vinlyene), in order to obtain optically active virus-like particles. After encapsulation, fluorescence from MPS-PPV shows two distinct peaks, which suggests the polymer may be in two conformations. A combination of TEM, fluorescence anisotropy, and sucrose gradient separation indicate that the blue peak arises from polymer encapsulated into spherical particles, while the redder peak corresponds to polymers contained in rod-like cages. Ionic strength during assembly can be used to tune the propensity to form rods or spheres. The results illustrate the synergy of hybrid synthetic/biological systems: polymer conformation drives the structure of this composite material, which in turn modifies the polymer optical properties. This synergy could be useful for the future development of synthetic/biological hybrid materials with designated functionality.
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Affiliation(s)
- Benny C. Ng
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1569, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095-7227, USA
| | - Stephanie T. Chan
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1569, USA
| | - Jason Lin
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1569, USA
| | - Sarah H. Tolbert
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1569, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095-7227, USA
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42
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Structure and stoichiometry of template-directed recombinant HIV-1 Gag particles. J Mol Biol 2011; 410:667-80. [PMID: 21762807 DOI: 10.1016/j.jmb.2011.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Revised: 04/05/2011] [Accepted: 04/06/2011] [Indexed: 01/20/2023]
Abstract
Size polydispersity of immature human immunodeficiency virus type 1 (HIV-1) particles represents a challenge for traditional methods of biological ultrastructural analysis. An in vitro model for immature HIV-1 particles constructed from recombinant Gag proteins lacking residues 16-99 and the p6 domain assembled around spherical nanoparticles functionalized with DNA. This template-directed assembly approach led to a significant reduction in size polydispersity and revealed previously unknown structural features of immature-like HIV-1 particles. Electron microscopy and image reconstruction of these particles suggest that the Gag shell formed from different protein regions that are connected by a "scar"-an extended defect connecting the edges of two continuous, regularly packed protein layers. Thus, instead of a holey protein array, the experimental model presented here appears to consist of a continuous array of ∼5000 proteins enveloping the core, in which regular regions are separated by extended areas of disorder.
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43
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van Rijn P, Böker A. Bionanoparticles and hybrid materials: tailored structural properties, self-assembly, materials and developments in the field. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm11433f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Abstract
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication and enable use of capsids in nanomaterials applications. To this end, we perform Brownian dynamics on a coarse-grained model that describes the dynamics of icosahedral capsid assembly around a flexible polymer. We identify several mechanisms by which the polymer plays an active role in its encapsulation, including cooperative polymer-protein motions. These mechanisms are related to experimentally controllable parameters such as polymer length, protein concentration and solution conditions. Furthermore, the simulations demonstrate that assembly mechanisms are correlated with encapsulation efficiency, and we present a phase diagram that predicts assembly outcomes as a function of experimental parameters. We anticipate that our simulation results will provide a framework for designing in vitro assembly experiments on single-stranded RNA virus capsids.
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Affiliation(s)
- Oren M Elrad
- Department of Physics, Brandeis University, Waltham, MA, USA
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45
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Daniel MC, Tsvetkova IB, Quinkert ZT, Murali A, De M, Rotello VM, Kao CC, Dragnea B. Role of surface charge density in nanoparticle-templated assembly of bromovirus protein cages. ACS NANO 2010; 4:3853-60. [PMID: 20575505 PMCID: PMC2937271 DOI: 10.1021/nn1005073] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Self-assembling icosahedral protein cages have potentially useful physical and chemical characteristics for a variety of nanotechnology applications, ranging from therapeutic or diagnostic vectors to building blocks for hierarchical materials. For application-specific functional control of protein cage assemblies, a deeper understanding of the interaction between the protein cage and its payload is necessary. Protein-cage encapsulated nanoparticles, with their well-defined surface chemistry, allow for systematic control over key parameters of encapsulation such as the surface charge, hydrophobicity, and size. Independent control over these variables allows experimental testing of different assembly mechanism models. Previous studies done with Brome mosaic virus capsids and negatively charged gold nanoparticles indicated that the result of the self-assembly process depends on the diameter of the particle. However, in these experiments, the surface-ligand density was maintained at saturation levels, while the total charge and the radius of curvature remained coupled variables, making the interpretation of the observed dependence on the core size difficult. The current work furnishes evidence of a critical surface charge density for assembly through an analysis aimed at decoupling the surface charge and the core size.
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46
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Harvey SC, Petrov AS, Devkota B, Boz MB. Viral assembly: a molecular modeling perspective. Phys Chem Chem Phys 2009; 11:10553-64. [PMID: 20145801 DOI: 10.1039/b912884k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Icosahedral viruses are among the smallest and simplest of biological systems. The investigation of their structures represented the first step toward the establishment of molecular biophysics, over half a century ago. Many research groups are now pursuing investigations of viral assembly, a process that could offer new opportunities for the design of antiviral drugs and novel nanoparticles. A variety of experimental, theoretical and computational methods have been brought to bear on the study of virus structure and assembly. In this Perspective we review the contributions of theoretical and computational approaches to our understanding of the structure, energetics, thermodynamics and assembly of DNA bacteriophage and single-stranded icosahedral RNA viruses.
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Affiliation(s)
- Stephen C Harvey
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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47
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Hagan MF. A theory for viral capsid assembly around electrostatic cores. J Chem Phys 2009; 130:114902. [PMID: 19317561 DOI: 10.1063/1.3086041] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We develop equilibrium and kinetic theories that describe the assembly of viral capsid proteins on a charged central core, as seen in recent experiments in which brome mosaic virus capsids assemble around nanoparticles functionalized with polyelectrolyte. We model interactions between capsid proteins and nanoparticle surfaces as the interaction of polyelectrolyte brushes with opposite charge using the nonlinear Poisson Boltzmann equation. The models predict that there is a threshold density of functionalized charge, above which capsids efficiently assemble around nanoparticles, and that light scatter intensity increases rapidly at early times without the lag phase characteristic of empty capsid assembly. These predictions are consistent with and enable interpretation of preliminary experimental data. However, the models predict a stronger dependence of nanoparticle incorporation efficiency on functionalized charge density than measured in experiments and do not completely capture a logarithmic growth phase seen in experimental light scatter. These discrepancies may suggest the presence of metastable disordered states in the experimental system. In addition to discussing future experiments for nanoparticle-capsid systems, we discuss broader implications for understanding assembly around charged cores such as nucleic acids.
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Affiliation(s)
- Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
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48
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Lavelle L, Gingery M, Phillips M, Gelbart WM, Knobler CM, Cadena-Nava RD, Vega-Acosta JR, Pinedo-Torres LA, Ruiz-Garcia J. Phase Diagram of Self-assembled Viral Capsid Protein Polymorphs. J Phys Chem B 2009; 113:3813-9. [DOI: 10.1021/jp8079765] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Lavelle
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, Molecular Biology Institute, University of California, Los Angeles, California 90095-1570
| | - M. Gingery
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, Molecular Biology Institute, University of California, Los Angeles, California 90095-1570
| | - M. Phillips
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, Molecular Biology Institute, University of California, Los Angeles, California 90095-1570
| | - W. M. Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, Molecular Biology Institute, University of California, Los Angeles, California 90095-1570
| | - C. M. Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, Molecular Biology Institute, University of California, Los Angeles, California 90095-1570
| | - R. D. Cadena-Nava
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Alvaro Obregón 64, San Luis Potosí, S.L.P., 78000 México
| | - J. R. Vega-Acosta
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Alvaro Obregón 64, San Luis Potosí, S.L.P., 78000 México
| | - L. A. Pinedo-Torres
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Alvaro Obregón 64, San Luis Potosí, S.L.P., 78000 México
| | - J. Ruiz-Garcia
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Alvaro Obregón 64, San Luis Potosí, S.L.P., 78000 México
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49
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Zandi R, van der Schoot P. Size regulation of ss-RNA viruses. Biophys J 2009; 96:9-20. [PMID: 18931258 PMCID: PMC2710049 DOI: 10.1529/biophysj.108.137489] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 09/04/2008] [Indexed: 11/18/2022] Open
Abstract
While a monodisperse size distribution is common within one kind of spherical virus, the size of viral shells varies from one type of virus to another. In this article, we investigate the physical mechanisms underlying the size selection among spherical viruses. In particular, we study the effect of genome length and genome and protein concentrations on the size of spherical viral capsids in the absence of spontaneous curvature and bending energy. We find that the coat proteins could well adjust the size of the shell to the size of their genome, which in turn depends on the number of charges on it. Furthermore, we find that different stoichiometric mixtures of proteins and genome can produce virus particles of various sizes, consistent with in vitro experiments.
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Affiliation(s)
- Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Paul van der Schoot
- Faculteit Technische Natuurkunde, Technische Universiteit Eindhoven, Eindhoven, Netherlands
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50
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Elrad OM, Hagan MF. Mechanisms of size control and polymorphism in viral capsid assembly. NANO LETTERS 2008; 8:3850-7. [PMID: 18950240 PMCID: PMC2742690 DOI: 10.1021/nl802269a] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one morphology but adaptively assemble into different icosahedral morphologies around nanoparticle cargoes with varying sizes, as seen in recent experiments with brome mosaic virus (BMV) capsid proteins. Adaptive cargo encapsidation requires moderate cargo-subunit interaction strengths; stronger interactions frustrate assembly by stabilizing intermediates with incommensurate curvature. We compare simulation results to experiments with cowpea chlorotic mottle virus empty capsids and BMV capsids assembled on functionalized nanoparticles and suggest new cargo encapsidation experiments. Finally, we find that both empty and templated capsids maintain the precise spatial ordering of subunit conformations seen in the crystal structure even if interactions that preserve this arrangement are favored by as little as the thermal energy, consistent with experimental observations that different subunit conformations are highly similar.
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