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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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Fuertes MA, López Mateos D, Valiente L, Rodríguez Huete A, Valbuena A, Mateu MG. Electrostatic Screening, Acidic pH and Macromolecular Crowding Increase the Self-Assembly Efficiency of the Minute Virus of Mice Capsid In Vitro. Viruses 2023; 15:v15051054. [PMID: 37243141 DOI: 10.3390/v15051054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
The hollow protein capsids from a number of different viruses are being considered for multiple biomedical or nanotechnological applications. In order to improve the applied potential of a given viral capsid as a nanocarrier or nanocontainer, specific conditions must be found for achieving its faithful and efficient assembly in vitro. The small size, adequate physical properties and specialized biological functions of the capsids of parvoviruses such as the minute virus of mice (MVM) make them excellent choices as nanocarriers and nanocontainers. In this study we analyzed the effects of protein concentration, macromolecular crowding, temperature, pH, ionic strength, or a combination of some of those variables on the fidelity and efficiency of self-assembly of the MVM capsid in vitro. The results revealed that the in vitro reassembly of the MVM capsid is an efficient and faithful process. Under some conditions, up to ~40% of the starting virus capsids were reassembled in vitro as free, non aggregated, correctly assembled particles. These results open up the possibility of encapsidating different compounds in VP2-only capsids of MVM during its reassembly in vitro, and encourage the use of virus-like particles of MVM as nanocontainers.
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Affiliation(s)
- Miguel Angel Fuertes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Diego López Mateos
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Alicia Rodríguez Huete
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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3
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Muhren HJ, van der Schoot P. Electrostatic Theory of the Acidity of the Solution in the Lumina of Viruses and Virus-Like Particles. J Phys Chem B 2023; 127:2160-2168. [PMID: 36881522 PMCID: PMC10026070 DOI: 10.1021/acs.jpcb.2c08604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Recently, Maassen et al. measured an appreciable pH difference between the bulk solution and the solution in the lumen of virus-like particles, self-assembled in an aqueous buffer solution containing the coat proteins of a simple plant virus and polyanions (Maassen, S. J.; et al. Small 2018, 14, 1802081). They attribute this to the Donnan effect, caused by an imbalance between the number of negative charges on the encapsulated polyelectrolyte molecules and the number of positive charges on the RNA binding domains of the coat proteins that make up the virus shell or capsid. By applying Poisson-Boltzmann theory, we confirm this conclusion and show that simple Donnan theory is accurate even for the smallest of viruses and virus-like particles. This, in part, is due to the additional screening caused by the presence of a large number of immobile charges in the cavity of the shell. The presence of a net charge on the outer surface of the capsid we find in practice to not have a large effect on the pH shift. Hence, Donnan theory can indeed be applied to connect the local pH and the amount of encapsulated material. The large shifts up to a full pH unit that we predict must have consequences for applications of virus capsids as nanocontainers in bionanotechnology and artificial cell organelles.
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Affiliation(s)
- H J Muhren
- Soft Matter and Biological Physics, Department of Applied Physics and Science Education, Eindhoven University of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
| | - Paul van der Schoot
- Soft Matter and Biological Physics, Department of Applied Physics and Science Education, Eindhoven University of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
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4
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Li Y, Bao Q, Yang S, Yang M, Mao C. Bionanoparticles in cancer imaging, diagnosis, and treatment. VIEW 2022. [DOI: 10.1002/viw.20200027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yan Li
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Hangzhou Zhejiang China
| | - Qing Bao
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang China
| | - Shuxu Yang
- Department of Neurosurgery Sir Run Run Shaw Hospital School of Medicine Zhejiang University Hangzhou Zhejiang China
| | - Mingying Yang
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Hangzhou Zhejiang China
| | - Chuanbin Mao
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang China
- Department of Chemistry and Biochemistry Stephenson Life Science Research Center University of Oklahoma Norman Oklahoma USA
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5
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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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6
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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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7
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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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8
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Christiansen A, Weiel M, Winkler A, Schug A, Reinstein J. The Trimeric Major Capsid Protein of Mavirus is stabilized by its Interlocked N-termini Enabling Core Flexibility for Capsid Assembly. J Mol Biol 2021; 433:166859. [PMID: 33539884 DOI: 10.1016/j.jmb.2021.166859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
Icosahedral viral capsids assemble with high fidelity from a large number of identical buildings blocks. The mechanisms that enable individual capsid proteins to form stable oligomeric units (capsomers) while affording structural adaptability required for further assembly into capsids are mostly unknown. Understanding these mechanisms requires knowledge of the capsomers' dynamics, especially for viruses where no additional helper proteins are needed during capsid assembly like for the Mavirus virophage that despite its complexity (triangulation number T = 27) can assemble from its major capsid protein (MCP) alone. This protein forms the basic building block of the capsid namely a trimer (MCP3) of double-jelly roll protomers with highly intertwined N-terminal arms of each protomer wrapping around the other two at the base of the capsomer, secured by a clasp that is formed by part of the C-terminus. Probing the dynamics of the capsomer with HDX mass spectrometry we observed differences in conformational flexibility between functional elements of the MCP trimer. While the N-terminal arm and clasp regions show above average deuterium incorporation, the two jelly-roll units in each protomer also differ in their structural plasticity, which might be needed for efficient assembly. Assessing the role of the N-terminal arm in maintaining capsomer stability showed that its detachment is required for capsomer dissociation, constituting a barrier towards capsomer monomerisation. Surprisingly, capsomer dissociation was irreversible since it was followed by a global structural rearrangement of the protomers as indicated by computational studies showing a rearrangement of the N-terminus blocking part of the capsomer forming interface.
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Affiliation(s)
- Alexander Christiansen
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanismsm Heidelberg, Germany
| | - Marie Weiel
- Karlsruhe Institute of Technology, Steinbuch Centre for Computing and Department of Physics, Eggenstein-Leopoldshafen, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology. Graz, Austria
| | - Alexander Schug
- Institute for Advanced Simulation, Jülich Supercomputing Center, Jülich, Germany
| | - Jochen Reinstein
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanismsm Heidelberg, Germany.
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9
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Välimäki S, Liu Q, Schoonen L, Vervoort DFM, Nonappa, Linko V, Nolte RJM, van Hest JCM, Kostiainen MA. Engineered protein cages for selective heparin encapsulation. J Mater Chem B 2021; 9:1272-1276. [PMID: 33427277 DOI: 10.1039/d0tb02541k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A heparin-specific binding peptide was conjugated to a cowpea chlorotic mottle virus (CCMV) capsid protein, which was subsequently allowed to encapsulate heparin and form capsid-like protein cages. The encapsulation is specific and the capsid-heparin assemblies display negligible hemolytic activity, indicating proper blood compatibility and promising possibilities for heparin antidote applications.
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Affiliation(s)
- Salla Välimäki
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto FI-00076, Espoo, Finland.
| | - Qing Liu
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto FI-00076, Espoo, Finland.
| | - Lise Schoonen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Daan F M Vervoort
- Department of Bio-Organic Chemistry, Eindhoven University of Technology, Institute of Complex Molecular Systems (ICMS), Het Kranenveld 14, Eindhoven 5600 MB, The Netherlands
| | - Nonappa
- HYBER Centre, Department of Applied Physics, Aalto University, Aalto FI-00076, Finland
| | - Veikko Linko
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto FI-00076, Espoo, Finland. and HYBER Centre, Department of Applied Physics, Aalto University, Aalto FI-00076, Finland
| | - Roeland J M Nolte
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Jan C M van Hest
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands and Department of Bio-Organic Chemistry, Eindhoven University of Technology, Institute of Complex Molecular Systems (ICMS), Het Kranenveld 14, Eindhoven 5600 MB, The Netherlands
| | - Mauri A Kostiainen
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto FI-00076, Espoo, Finland. and HYBER Centre, Department of Applied Physics, Aalto University, Aalto FI-00076, Finland
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10
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Buzón P, Maity S, Roos WH. Physical virology: From virus self-assembly to particle mechanics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1613. [PMID: 31960585 PMCID: PMC7317356 DOI: 10.1002/wnan.1613] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
Abstract
Viruses are highly ordered supramolecular complexes that have evolved to propagate by hijacking the host cell's machinery. Although viruses are very diverse, spreading through cells of all kingdoms of life, they share common functions and properties. Next to the general interest in virology, fundamental viral mechanisms are of growing importance in other disciplines such as biomedicine and (bio)nanotechnology. However, in order to optimally make use of viruses and virus-like particles, for instance as vehicle for targeted drug delivery or as building blocks in electronics, it is essential to understand their basic chemical and physical properties and characteristics. In this context, the number of studies addressing the mechanisms governing viral properties and processes has recently grown drastically. This review summarizes a specific part of these scientific achievements, particularly addressing physical virology approaches aimed to understand the self-assembly of viruses and the mechanical properties of viral particles. Using a physicochemical perspective, we have focused on fundamental studies providing an overview of the molecular basis governing these key aspects of viral systems. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
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11
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Maassen SJ, van der Ham AM, Cornelissen JJLM. Combining Protein Cages and Polymers: from Understanding Self-Assembly to Functional Materials. ACS Macro Lett 2016; 5:987-994. [PMID: 35607217 DOI: 10.1021/acsmacrolett.6b00509] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein cages, such as viruses, are well-defined biological nanostructures which are highly symmetrical and monodisperse. They are found in various shapes and sizes and can encapsulate or template non-native materials. Furthermore, the proteins can be chemically or genetically modified giving them new properties. For these reasons, these protein structures have received increasing attention in the field of polymer-protein hybrid materials over the past years, however, advances are still to be made. This Viewpoint highlights the different ways polymers and protein cages or their subunits have been combined to understand self-assembly and create functional materials.
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Affiliation(s)
- Stan J. Maassen
- Laboratory for Biomolecular
Nanotechnology, MESA+ Institute, University of Twente, P.O. Box 207, 7500 AE Enschede, The Netherlands
| | - Anne M. van der Ham
- 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
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12
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Liu A, Verwegen M, de Ruiter MV, Maassen SJ, Traulsen CHH, Cornelissen JJLM. Protein Cages as Containers for Gold Nanoparticles. J Phys Chem B 2016; 120:6352-7. [PMID: 27135176 DOI: 10.1021/acs.jpcb.6b03066] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abundant and highly diverse, viruses offer new scaffolds in nanotechnology for the encapsulation, organization, or even synthesis of novel materials. In this work the coat protein of the cowpea chlorotic mottle virus (CCMV) is used to encapsulate gold nanoparticles with different sizes and stabilizing ligands yielding stable particles in buffered solutions at neutral pH. The sizes of the virus-like particles correspond to T = 1, 2, and 3 Caspar-Klug icosahedral triangulation numbers. We developed a simple one-step process enabling the encapsulation of commercially available gold nanoparticles without prior modification with up to 97% efficiency. The encapsulation efficiency is further increased using bis-p-(sufonatophenyl)phenyl phosphine surfactants up to 99%. Our work provides a simplified procedure for the preparation of metallic particles stabilized in CCMV protein cages. The presented results are expected to enable the preparation of a variety of similar virus-based colloids for current focus areas.
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Affiliation(s)
- Aijie Liu
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Martijn Verwegen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Stan J Maassen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Christoph H-H Traulsen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Jeroen J L M Cornelissen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
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13
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Rolfsson Ó, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol 2016; 428:431-48. [PMID: 26608810 PMCID: PMC4751978 DOI: 10.1016/j.jmb.2015.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/06/2015] [Accepted: 11/08/2015] [Indexed: 01/20/2023]
Abstract
Using cross-linking coupled to matrix-assisted laser desorption/ionization mass spectrometry and CLIP-Seq sequencing, we determined the peptide and oligonucleotide sequences at the interfaces between the capsid proteins and the genomic RNA of bacteriophage MS2. The results suggest that the same coat protein (CP)-RNA and maturation protein (MP)-RNA interfaces are used in every viral particle. The portions of the viral RNA in contact with CP subunits span the genome, consistent with a large number of discrete and similar contacts within each particle. Many of these sites match previous predictions of the locations of multiple, dispersed and degenerate RNA sites with cognate CP affinity termed packaging signals (PSs). Chemical RNA footprinting was used to compare the secondary structures of protein-free genomic fragments and the RNA in the virion. Some PSs are partially present in protein-free RNA but others would need to refold from their dominant solution conformations to form the contacts identified in the virion. The RNA-binding peptides within the MP map to two sections of the N-terminal half of the protein. Comparison of MP sequences from related phages suggests a similar arrangement of RNA-binding sites, although these N-terminal regions have only limited sequence conservation. In contrast, the sequences of the C-termini are highly conserved, consistent with them encompassing pilin-binding domains required for initial contact with host cells. These results provide independent and unambiguous support for the assembly of MS2 virions via a PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.
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Affiliation(s)
- Óttar Rolfsson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefani Middleton
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Baochang Fan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Robert Vaughan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Eric Dykeman
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - James Ford
- The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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14
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Rother M, Nussbaumer MG, Renggli K, Bruns N. Protein cages and synthetic polymers: a fruitful symbiosis for drug delivery applications, bionanotechnology and materials science. Chem Soc Rev 2016; 45:6213-6249. [DOI: 10.1039/c6cs00177g] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein cages have become essential tools in bionanotechnology due to their well-defined, monodisperse, capsule-like structure. Combining them with synthetic polymers greatly expands their application, giving rise to novel nanomaterials fore.g.drug-delivery, sensing, electronic devices and for uses as nanoreactors.
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Affiliation(s)
- Martin Rother
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Martin G. Nussbaumer
- Wyss Institute for Biologically Inspired Engineering
- Harvard University
- Cambridge
- USA
| | - Kasper Renggli
- Department of Biosystems Science and Engineering
- ETH Zürich
- 4058 Basel
- Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute
- University of Fribourg
- CH-1700 Fribourg
- Switzerland
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15
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Affiliation(s)
- Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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16
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Singaram SW, Garmann RF, Knobler CM, Gelbart WM, Ben-Shaul A. Role of RNA Branchedness in the Competition for Viral Capsid Proteins. J Phys Chem B 2015; 119:13991-4002. [PMID: 26435053 DOI: 10.1021/acs.jpcb.5b06445] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To optimize binding-and packaging-by their capsid proteins (CP), single-stranded (ss) RNA viral genomes often have local secondary/tertiary structures with high CP affinity, with these "packaging signals" serving as heterogeneous nucleation sites for the formation of capsids. Under typical in vitro self-assembly conditions, however, and in particular for the case of many ssRNA viruses whose CP have cationic N-termini, the adsorption of CP by RNA is nonspecific because the CP concentration exceeds the largest dissociation constant for CP-RNA binding. Consequently, the RNA is saturated by bound protein before lateral interactions between CP drive the homogeneous nucleation of capsids. But, before capsids are formed, the binding of protein remains reversible and introduction of another RNA species-with a different length and/or sequence-is found experimentally to result in significant redistribution of protein. Here we argue that, for a given RNA mass, the sequence with the highest affinity for protein is the one with the most compact secondary structure arising from self-complementarity; similarly, a long RNA steals protein from an equal mass of shorter ones. In both cases, it is the lateral attractions between bound proteins that determines the relative CP affinities of the RNA templates, even though the individual binding sites are identical. We demonstrate this with Monte Carlo simulations, generalizing the Rosenbluth method for excluded-volume polymers to include branching of the polymers and their reversible binding by protein.
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Affiliation(s)
- Surendra W Singaram
- Department of Chemistry and Biochemistry, UCLA , Los Angeles, California 90095, United States.,Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University , Jerusalem, 91904 Israel
| | - Rees F Garmann
- Department of Chemistry and Biochemistry, UCLA , Los Angeles, California 90095, United States
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, UCLA , Los Angeles, California 90095, United States
| | - William M Gelbart
- Department of Chemistry and Biochemistry, UCLA , Los Angeles, California 90095, United States
| | - Avinoam Ben-Shaul
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University , Jerusalem, 91904 Israel
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17
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Tsvetkova IB, Yi G, Yi Y, Kao CC, Dragnea BG. Segmented GFP-like aptamer probes for functional imaging of viral genome trafficking. Virus Res 2015; 210:291-7. [PMID: 26325297 DOI: 10.1016/j.virusres.2015.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/25/2015] [Accepted: 08/28/2015] [Indexed: 01/21/2023]
Abstract
Recently developed GFP-like RNA aptamers harbor a few unique potential benefits for in vivo RNA imaging applications, including co-packaging of viral genomes. Here we examine them in the context of co-packaging of RNA strands during virion assembly and trafficking. The approach is applicable both in vitro and in vivo, thus bridging an existing methodological gap. We have found that splitting the aptamer sequence in the loop region into two separate parts allows for subsequent self-assembly into a functional unit, which preserves the dye-binding pocket. In presence of the dye, virus-like particles encapsulating segmented GFP-like aptamers provided bright fluorescence emission and showed negligible bleaching due to continuous chromophore exchange: two desirable characteristics for real-time in vivo single particle studies requiring a broader dynamic range than currently available. Proof-of-principle in vivo imaging experiments confirmed detectability of aptamer-loaded virus-like particles in barley root cells even in presence of significant autofluorescence background.
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Affiliation(s)
- Irina B Tsvetkova
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
| | - Guanghui Yi
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, USA
| | - Yi Yi
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Cheng C Kao
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, USA
| | - Bogdan G Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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18
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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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19
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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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20
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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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21
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Abstract
The self-assembly of virus-like particles may lead to materials which combine the unique characteristics of viruses, such as precise size control and responsivity to environmental cues, with the properties of abiotic cargo. For a few different viruses, shell proteins are amenable to the in vitro encapsulation of non-genomic cargo in a regular protein cage. In this chapter we describe protocols of high-efficiency in vitro self-assembly around functionalized gold nanoparticles for three examples of icosahedral and non-icosahedral viral protein cages derived from a plant virus, an animal virus, and a human retrovirus. These protocols can be readily adapted with small modifications to work for a broad variety of inorganic and organic nanoparticles.
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Affiliation(s)
- Irina B Tsvetkova
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
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22
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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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23
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Deshayes S, Gref R. Synthetic and bioinspired cage nanoparticles for drug delivery. Nanomedicine (Lond) 2014; 9:1545-64. [DOI: 10.2217/nnm.14.67] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Nanotechnology has the potential to revolutionize drug delivery, but still faces some limitations. One of the main issues regarding conventional nanoparticles is their poor drug-loading and their early burst release. Thus, to overcome these problems, researchers have taken advantage of the host–guest interactions that drive some assemblies to form cage molecules able to strongly entrap their cargo and design new nanocarriers called cage nanoparticles. These systems can be classified into two categories: bioinspired nanosystems such as virus-like particles, ferritin, small heat shock protein: and synthetic host–guest supramolecular systems that require engineering to actually form supramolecular nanoassemblies. This review will highlight the recent advances in cage nanoparticles for drug delivery with a particular focus on their biomedical applications.
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Affiliation(s)
- Stephanie Deshayes
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Ruxandra Gref
- Institut de Sciences Moléculaires UMR CNRS 8214 Université Paris-Sud, Orsay, 91405, France
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24
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Zhang R, Linse P. Icosahedral capsid formation by capsomers and short polyions. J Chem Phys 2013; 138:154901. [PMID: 23614442 DOI: 10.1063/1.4799243] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Kinetical and structural aspects of the capsomer-polyion co-assembly into icosahedral viruses have been simulated by molecular dynamics using a coarse-grained model comprising cationic capsomers and short anionic polyions. Conditions were found at which the presence of polyions of a minimum length was necessary for capsomer formation. The largest yield of correctly formed capsids was obtained at which the driving force for capsid formation was relatively weak. Relatively stronger driving forces, i.e., stronger capsomer-capsomer short-range attraction and∕or stronger electrostatic interaction, lead to larger fraction of kinetically trapped structures and aberrant capsids. The intermediate formation was investigated and different evolving scenarios were found by just varying the polyion length.
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Affiliation(s)
- Ran Zhang
- Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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25
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Dykeman EC, Stockley PG, Twarock R. Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome. J Mol Biol 2013; 425:3235-49. [PMID: 23763992 DOI: 10.1016/j.jmb.2013.06.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/22/2013] [Accepted: 06/03/2013] [Indexed: 11/29/2022]
Abstract
The current paradigm for assembly of single-stranded RNA viruses is based on a mechanism involving non-sequence-specific packaging of genomic RNA driven by electrostatic interactions. Recent experiments, however, provide compelling evidence for sequence specificity in this process both in vitro and in vivo. The existence of multiple RNA packaging signals (PSs) within viral genomes has been proposed, which facilitates assembly by binding coat proteins in such a way that they promote the protein-protein contacts needed to build the capsid. The binding energy from these interactions enables the confinement or compaction of the genomic RNAs. Identifying the nature of such PSs is crucial for a full understanding of assembly, which is an as yet untapped potential drug target for this important class of pathogens. Here, for two related bacterial viruses, we determine the sequences and locations of their PSs using Hamiltonian paths, a concept from graph theory, in combination with bioinformatics and structural studies. Their PSs have a common secondary structure motif but distinct consensus sequences and positions within the respective genomes. Despite these differences, the distributions of PSs in both viruses imply defined conformations for the packaged RNA genomes in contact with the protein shell in the capsid, consistent with a recent asymmetric structure determination of the MS2 virion. The PS distributions identified moreover imply a preferred, evolutionarily conserved assembly pathway with respect to the RNA sequence with potentially profound implications for other single-stranded RNA viruses known to have RNA PSs, including many animal and human pathogens.
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Affiliation(s)
- Eric C Dykeman
- Departments of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, UK
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26
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Stockley PG, Ranson NA, Twarock R. A new paradigm for the roles of the genome in ssRNA viruses. Future Virol 2013. [DOI: 10.2217/fvl.12.84] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recent work with RNA phages and an ssRNA plant satellite virus challenges the widely held view that the sequences and structures of genomic RNAs are unimportant for virion assembly. In the T=3 phages, RNA–coat protein interactions occur throughout the genome, defining the quasiconformers of their protein shells. In the plant virus, there are multiple packaging signals dispersed throughout the genome that overcome electrostatic barriers to protein self-assembly. Both viral coat proteins cause the solution structures of their cognate genomes to collapse into a form that is readily encapsidated in a two-stage assembly process. Such similar behavior in two structurally unrelated viral protein folds implies that this might be a conserved feature of many viral assembly reactions. These results suggest a highly defined structure for the RNA in the virions, consistent with recent structural studies. They also have implications both for subsequent genome release during infection and for the evolution of viral sequences.
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Affiliation(s)
- Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Reidun Twarock
- Departments of Biology & Mathematics, York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
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27
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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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28
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Wu Y, Yang H, Shin HJ. Viruses as self-assembled nanocontainers for encapsulation of functional cargoes. KOREAN J CHEM ENG 2013. [DOI: 10.1007/s11814-013-0083-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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van der Schoot P, Zandi R. Impact of the topology of viral RNAs on their encapsulation by virus coat proteins. J Biol Phys 2013; 39:289-99. [PMID: 23860874 DOI: 10.1007/s10867-013-9307-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 02/07/2013] [Indexed: 11/28/2022] Open
Abstract
Single-stranded RNAs of simple viruses seem to be topologically more compact than other types of single-stranded RNA. It has been suggested that this has an evolutionary purpose: more compact structures are more easily encapsulated in the limited space that the cavity of the virus capsid offers. We employ a simple Flory theory to calculate the optimal amount of polymers confined in a viral shell. We find that the free energy gain or more specifically the efficiency of RNA encapsidation increases substantially with topological compactness. We also find that the optimal length of RNA encapsidated in a capsid increases with the degree of branching of the genome even though this effect is very weak. Further, we show that if the structure of the branching of the polymer is allowed to anneal, the optimal loading increases substantially.
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Affiliation(s)
- Paul van der Schoot
- Group Theory of Polymers and Soft Matter, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
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30
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Ford RJ, Barker AM, Bakker SE, Coutts RH, Ranson NA, Phillips SEV, Pearson AR, Stockley PG. Sequence-specific, RNA-protein interactions overcome electrostatic barriers preventing assembly of satellite tobacco necrosis virus coat protein. J Mol Biol 2013; 425:1050-64. [PMID: 23318955 PMCID: PMC3593212 DOI: 10.1016/j.jmb.2013.01.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 12/24/2012] [Accepted: 01/07/2013] [Indexed: 11/30/2022]
Abstract
We have examined the roles of RNA–coat protein (CP) interactions in the assembly of satellite tobacco necrosis virus (STNV). The viral genomic RNA encodes only the CP, which comprises a β-barrel domain connected to a positively charged N-terminal extension. In the previous crystal structures of this system, the first 11 residues of the protein are disordered. Using variants of an RNA aptamer sequence isolated against the CP, B3, we have studied the sequence specificity of RNA-induced assembly. B3 consists of a stem–loop presenting the tetra-loop sequence ACAA. There is a clear preference for RNAs encompassing this loop sequence, as measured by the yield of T = 1 capsids, which is indifferent to sequences within the stem. The B3-containing virus-like particle has been crystallised and its structure was determined to 2.3 Å. A lower-resolution map encompassing density for the RNA has also been calculated. The presence of B3 results in increased ordering of the N-terminal helices located at the particle 3-fold axes, which extend by roughly one and a half turns to encompass residues 8–11, including R8 and K9. Under assembly conditions, STNV CP in the absence of RNA is monomeric and does not self-assemble. These facts suggest that a plausible model for assembly initiation is the specific RNA-induced stabilisation of a trimeric capsomere. The basic nature of the helical extension suggests that electrostatic repulsion between CPs prevents assembly in the absence of RNA and that this barrier is overcome by correct placement of appropriately orientated helical RNA stems. Such a mechanism would be consistent with the data shown here for assembly with longer RNA fragments, including an STNV genome. The results are discussed in light of a first stage of assembly involving compaction of the genomic RNA driven by multiple RNA packaging signal–CP interactions.
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Affiliation(s)
- Robert J Ford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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31
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Zhang R, Wernersson E, Linse P. Icosahedral capsid formation by capsomer subunits and a semiflexible polyion. RSC Adv 2013. [DOI: 10.1039/c3ra44533j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Lin HK, van der Schoot P, Zandi R. Impact of charge variation on the encapsulation of nanoparticles by virus coat proteins. Phys Biol 2012; 9:066004. [PMID: 23114290 DOI: 10.1088/1478-3975/9/6/066004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work, Daniel et al (2010 ACS Nano 4 3853-60) found the encapsulation efficiency to sensitively depend on the interplay between the surface charge density of negatively charged gold nanoparticles and the number of positive charges on the RNA binding domains of the proteins. Surprisingly, these experiments reveal that despite the highly cooperative nature of the co-assembly at low pH, the efficiency of encapsulation is a gradual function of their surface charge density. We present a simple all-or-nothing mass action law combined with an electrostatic interaction model to explain the experiments. We find quantitative agreement with experimental observations, supporting the existence of a natural statistical charge distribution between nanoparticles.
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Affiliation(s)
- Hsiang-Ku Lin
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, USA.
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33
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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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34
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Self-assembly of viral capsid protein and RNA molecules of different sizes: requirement for a specific high protein/RNA mass ratio. J Virol 2011; 86:3318-26. [PMID: 22205731 DOI: 10.1128/jvi.06566-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Virus-like particles can be formed by self-assembly of capsid protein (CP) with RNA molecules of increasing length. If the protein "insisted" on a single radius of curvature, the capsids would be identical in size, independent of RNA length. However, there would be a limit to length of the RNA, and one would not expect RNA much shorter than native viral RNA to be packaged unless multiple copies were packaged. On the other hand, if the protein did not favor predetermined capsid size, one would expect the capsid diameter to increase with increase in RNA length. Here we examine the self-assembly of CP from cowpea chlorotic mottle virus with RNA molecules ranging in length from 140 to 12,000 nucleotides (nt). Each of these RNAs is completely packaged if and only if the protein/RNA mass ratio is sufficiently high; this critical value is the same for all of the RNAs and corresponds to equal RNA and N-terminal-protein charges in the assembly mix. For RNAs much shorter in length than the 3,000 nt of the viral RNA, two or more molecules are assembled into 24- and 26-nm-diameter capsids, whereas for much longer RNAs (>4,500 nt), a single RNA molecule is shared/packaged by two or more capsids with diameters as large as 30 nm. For intermediate lengths, a single RNA is assembled into 26-nm-diameter capsids, the size associated with T=3 wild-type virus. The significance of these assembly results is discussed in relation to likely factors that maintain T=3 symmetry in vivo.
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35
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Siber A, Božič AL, Podgornik R. Energies and pressures in viruses: contribution of nonspecific electrostatic interactions. Phys Chem Chem Phys 2011; 14:3746-65. [PMID: 22143065 DOI: 10.1039/c1cp22756d] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic pressures in single-stranded RNA viruses and double-stranded DNA bacteriophages. The two types of viruses differ crucially in the spatial distribution of their genome charge which leads to essential differences in their free energies, depending on the capsid size and total charge in a quite different fashion. Differences in the free energies are trailed by the corresponding characteristics and variations in the osmotic pressure between the inside of the virus and the external bathing solution.
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36
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Thermodynamic basis for the genome to capsid charge relationship in viral encapsidation. Proc Natl Acad Sci U S A 2011; 108:16986-91. [PMID: 21969546 DOI: 10.1073/pnas.1109307108] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We establish an appropriate thermodynamic framework for determining the optimal genome length in electrostatically driven viral encapsidation. Importantly, our analysis includes the electrostatic potential due to the Donnan equilibrium, which arises from the semipermeable nature of the viral capsid, i.e., permeable to small mobile ions but impermeable to charged macromolecules. Because most macromolecules in the cellular milieu are negatively charged, the Donnan potential provides an additional driving force for genome encapsidation. In contrast to previous theoretical studies, we find that the optimal genome length is the result of combined effects from the electrostatic interactions of all charged species, the excluded volume and, to a very significant degree, the Donnan potential. In particular, the Donnan potential is essential for obtaining negatively overcharged viruses. The prevalence of overcharged viruses in nature may suggest an evolutionary preference for viruses to increase the amount of genome packaged by utilizing the Donnan potential (through increases in the capsid radius), rather than high charges on the capsid, so that structural stability of the capsid is maintained.
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37
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Kao CC, Ni P, Hema M, Huang X, Dragnea B. The coat protein leads the way: an update on basic and applied studies with the Brome mosaic virus coat protein. MOLECULAR PLANT PATHOLOGY 2011; 12:403-12. [PMID: 21453435 PMCID: PMC6640235 DOI: 10.1111/j.1364-3703.2010.00678.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The Brome mosaic virus (BMV) coat protein (CP) accompanies the three BMV genomic RNAs and the subgenomic RNA into and out of cells in an infection cycle. In addition to serving as a protective shell for all of the BMV RNAs, CP plays regulatory roles during the infection process that are mediated through specific binding of RNA elements in the BMV genome. One regulatory RNA element is the B box present in the 5' untranslated region (UTR) of BMV RNA1 and RNA2 that play important roles in the formation of the BMV replication factory, as well as the regulation of translation. A second element is within the tRNA-like 3' UTR of all BMV RNAs that is required for efficient RNA replication. The BMV CP can also encapsidate ligand-coated metal nanoparticles to form virus-like particles (VLPs). This update summarizes the interaction between the BMV CP and RNAs that can regulate RNA synthesis, translation and RNA encapsidation, as well as the formation of VLPs.
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Affiliation(s)
- C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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38
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Abstract
Viral nanotechnology is an emerging and highly interdisciplinary field in which viral nanoparticles (VNPs) are applied in diverse areas such as electronics, energy and next-generation medical devices. VNPs have been developed as candidates for novel materials, and are often described as "programmable" because they can be modified and functionalized using a number of techniques. In this review, we discuss the concepts and methods that allow VNPs to be engineered, including (i) bioconjugation chemistries, (ii) encapsulation techniques, (iii) mineralization strategies, and (iv) film and hydrogel development. With all these techniques in hand, the potential applications of VNPs are limited only by the imagination.
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Affiliation(s)
- Jonathan K. Pokorski
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nicole F. Steinmetz
- Department of Biomedical Engineering, Case Center for Imaging Research, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, Ohio 44106, United States
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39
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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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40
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Mechanisms of capsid assembly around a polymer. Biophys J 2010; 99:619-28. [PMID: 20643082 DOI: 10.1016/j.bpj.2010.04.035] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 04/13/2010] [Accepted: 04/15/2010] [Indexed: 11/23/2022] Open
Abstract
Capsids of many viruses assemble around nucleic acids or other polymers. Understanding how the properties of the packaged polymer affect the assembly process could promote biomedical efforts to prevent viral assembly or nanomaterials applications that exploit assembly. To this end, we simulate on a lattice the dynamical assembly of closed, hollow shells composed of several hundred to 1000 subunits, around a flexible polymer. We find that assembly is most efficient at an optimum polymer length that scales with the surface area of the capsid; polymers that are significantly longer than optimal often lead to partial-capsids with unpackaged polymer "tails" or a competition between multiple partial-capsids attached to a single polymer. These predictions can be tested with bulk experiments in which capsid proteins assemble around homopolymeric RNA or synthetic polyelectrolytes. We also find that the polymer can increase the net rate of subunit accretion to a growing capsid both by stabilizing the addition of new subunits and by enhancing the incoming flux of subunits; the effects of these processes may be distinguishable with experiments that monitor the assembly of individual capsids.
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41
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Li F, Li K, Cui ZQ, Zhang ZP, Wei HP, Gao D, Deng JY, Zhang XE. Viral coat proteins as flexible nano-building-blocks for nanoparticle encapsulation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:2301-2308. [PMID: 20842665 DOI: 10.1002/smll.201001078] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Viral capsid-nanoparticle hybrid structures offer new opportunities for nanobiotechnology. We previously generated virus-based nanoparticles (VNPs) of simian virus 40 (SV40) containing quantum dots (QDs) for cellular imaging. However, as an interesting issue of nano-bio interfaces, the mechanism of nanoparticle (NP) encapsulation by viral coat proteins remains unclear. Here, four kinds of QDs with the same core/shell but different surface coatings are tested for encapsulation. All the QDs can be encapsulated efficiently and there is no correlation between the encapsulation efficiency and the surface charge of the QDs. All the SV40 VNPs encapsulating differently modified QDs show similar structures, fluorescence properties, and activity in entering living cells. These results demonstrate the flexibility of SV40 major capsid protein VP1 in NP encapsulation and provide new clues to the mechanism of NP packaging by viral shells.
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Affiliation(s)
- Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, No 44, Xiaohongshan, Wuhan 430071, PR China
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42
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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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43
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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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44
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de la Escosura A, Nolte RJM, Cornelissen JJLM. Viruses and protein cages as nanocontainers and nanoreactors. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b815274h] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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45
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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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46
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Chang CB, Knobler CM, Gelbart WM, Mason TG. Curvature dependence of viral protein structures on encapsidated nanoemulsion droplets. ACS NANO 2008; 2:281-6. [PMID: 19206628 DOI: 10.1021/nn700385z] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Virus-like particles are biomimetic delivery vehicles that cloak nanoscale cores inside coatings of viral capsid proteins, offering the potential for protecting their contents and targeting them to particular tissues and cells. To date, encapsidation has been demonstrated only for a relatively limited variety of core materials, such as compressible polymers and facetted nanocrystals, over a narrow range of cores sizes and of pH and ionic strength. Here, we encapsidate spherical nanodroplets of incompressible oil stabilized by adsorbed anionic surfactant using cationic capsid protein purified from cowpea chlorotic mottle virus. By imaging with transmission electron microscopy we show that, as the droplets become larger than the wild-type RNA core, the protein is forced to self-assemble into spherical shells that are not perfect icosahedra having special triangulation numbers characteristic of the Caspar-Klug hierarchy. Consequently, the distribution of protein conformations on larger droplets is significantly different than in the wild-type shell.
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Affiliation(s)
- Connie B Chang
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, USA
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47
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Young M, Willits D, Uchida M, Douglas T. Plant viruses as biotemplates for materials and their use in nanotechnology. ANNUAL REVIEW OF PHYTOPATHOLOGY 2008; 46:361-84. [PMID: 18473700 DOI: 10.1146/annurev.phyto.032508.131939] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In recent years, plant virus capsids, the protein shells that form the surface of a typical plant virus particle, have emerged as useful biotemplates for material synthesis. All virus capsids are assembled from virus-coded protein subunits. Many plant viruses assemble capsids with precise 3D structures providing nanoscale architectures that are highly homogeneous and can be produced in large quantities. Capsids are amenable to both genetic and chemical modifications allowing new functions to be incorporated into their structure by design. The three capsid surfaces, the interior surface, the exterior surface, or the interface between coat protein subunits, can be independently functionalized to produce multifunctional biotemplates. In this review, we examine the recent advances in using plant virus capsids as biotemplates for nanomaterials and their potential for applications in nanotechnology, especially medicine.
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Affiliation(s)
- Mark Young
- Department of Plant Sciences and Plant Pathology, Montana State University-Bozeman, Bozeman, Montana 59717, USA.
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48
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Aniagyei SE, Dufort C, Kao CC, Dragnea B. Self-assembly approaches to nanomaterial encapsulation in viral protein cages. ACTA ACUST UNITED AC 2008; 18:3763-3774. [PMID: 19809586 DOI: 10.1039/b805874c] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A perspective on abiotic material encapsulation inside virus capsids is provided. The emphasis is on the physical principles of virus assembly relevant to packaging, strategies for encapsulation and capsid modification, and on emerging applications.
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Affiliation(s)
- Stella E Aniagyei
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
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49
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Packaging of a polymer by a viral capsid: the interplay between polymer length and capsid size. Biophys J 2007; 94:1428-36. [PMID: 17981893 DOI: 10.1529/biophysj.107.117473] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report a study of the in vitro self-assembly of virus-like particles formed by the capsid protein of cowpea chlorotic mottle virus and the anionic polymer poly(styrene sulfonate) (PSS) for five molecular masses ranging from 400 kDa to 3.4 MDa. The goal is to explore the effect on capsid size of the competition between the preferred curvature of the protein and the molecular mass of the packaged cargo. The capsid size distribution for each polymer was unimodal, but two distinct sizes were observed: 22 nm for the lower molecular masses, jumping to 27 nm at a molecular mass of 2 MDa. A model is provided for the formation of the virus-like particles that accounts for both the PSS and capsid protein self-interactions and the interactions between the protein and PSS. Our study suggests that the size of the encapsidated polymer cargo is the deciding factor for the selection of one distinct capsid size from several possible sizes with the same inherent symmetry.
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50
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Hu T, Shklovskii BI. Kinetics of viral self-assembly: role of the single-stranded RNA antenna. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 75:051901. [PMID: 17677092 DOI: 10.1103/physreve.75.051901] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 02/02/2007] [Indexed: 05/02/2023]
Abstract
Many viruses self-assemble from a large number of identical capsid proteins with long flexible N-terminal tails and single-stranded (ss) RNA. We study the role of the strong Coulomb interaction of positive N-terminal tails with ssRNA in the kinetics of in vitro virus self-assembly. Capsid proteins stick to the unassembled chain of ssRNA (which we call an "antenna") and slide on it toward the assembly site. We show that at excess of capsid proteins such one-dimensional diffusion accelerates self-assembly more than ten times. On the other hand at excess of ssRNA, the antenna slows self-assembly down. Several experiments are proposed to verify the role of the ssRNA antenna.
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Affiliation(s)
- Tao Hu
- Theoretical Physics Institute, University of Minnesota, Minneapolis, MN 55455, USA
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