1
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Tripathi K, Garg H, Rajesh R, Vemparala S. The conformational phase diagram of charged polymers in the presence of attractive bridging crowders. J Chem Phys 2023; 159:204903. [PMID: 38010332 DOI: 10.1063/5.0172696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/05/2023] [Indexed: 11/29/2023] Open
Abstract
Using extensive molecular dynamics simulations, we obtain the conformational phase diagram of a charged polymer in the presence of oppositely charged counterions and neutral attractive crowders for monovalent, divalent, and trivalent counterion valencies. We demonstrate that the charged polymer can exist in three phases: (1) an extended phase for low charge densities and weak polymer-crowder attractive interactions [Charged Extended (CE)]; (2) a collapsed phase for high charge densities and weak polymer-crowder attractive interactions, primarily driven by counterion condensation [Charged Collapsed due to Intra-polymer interactions [(CCI)]; and (3) a collapsed phase for strong polymer-crowder attractive interactions, irrespective of the charge density, driven by crowders acting as bridges or cross-links [Charged Collapsed due to Bridging interactions [(CCB)]. Importantly, simulations reveal that the interaction with crowders can induce collapse, despite the presence of strong repulsive electrostatic interactions, and can replace condensed counterions to facilitate a direct transition from the CCI and CE phases to the CCB phase.
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Affiliation(s)
- Kamal Tripathi
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
- Univ. Grenoble Alpes, CNRS, Grenoble INP, 3SR, F-38000 Grenoble, France
| | - Hitesh Garg
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - R Rajesh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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2
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Catching A, Te Yeh M, Bianco S, Capponi S, Andino R. A tradeoff between enterovirus A71 particle stability and cell entry. Nat Commun 2023; 14:7450. [PMID: 37978288 PMCID: PMC10656440 DOI: 10.1038/s41467-023-43029-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
A central role of viral capsids is to protect the viral genome from the harsh extracellular environment while facilitating initiation of infection when the virus encounters a target cell. Viruses are thought to have evolved an optimal equilibrium between particle stability and efficiency of cell entry. In this study, we genetically perturb this equilibrium in a non-enveloped virus, enterovirus A71 to determine its structural basis. We isolate a single-point mutation variant with increased particle thermotolerance and decreased efficiency of cell entry. Using cryo-electron microscopy and molecular dynamics simulations, we determine that the thermostable native particles have acquired an expanded conformation that results in a significant increase in protein dynamics. Examining the intermediate states of the thermostable variant reveals a potential pathway for uncoating. We propose a sequential release of the lipid pocket factor, followed by internal VP4 and ultimately the viral RNA.
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Affiliation(s)
- Adam Catching
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Biophysics, University of California in San Francisco, San Francisco, CA, 94158, USA
| | - Ming Te Yeh
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA
| | - Simone Bianco
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA, 95120, USA
- Center for Cellular Construction, San Francisco, CA, 94158, USA
- Altos Labs, Redwood City, CA, 94022, USA
| | - Sara Capponi
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA, 95120, USA.
- Center for Cellular Construction, San Francisco, CA, 94158, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA.
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3
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Barman SS, Bhattacharyya S. Finite ion size and ion permittivity effects on gel electrophoresis of a soft particle. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2021.128088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatics interaction between the positive charges on capsid proteins and the negative charges on the genome. Despite its importance and many decades of intense research, how the virus selects and packages its native RNA inside the crowded environment of a host cell cytoplasm in the presence of an abundance of nonviral RNA and other anionic polymers has remained a mystery. In this paper, we perform a series of simulations to monitor the growth of viral shells and find the mechanism by which cargo-coat protein interactions can impact the structure and stability of the viral shells. We show that coat protein subunits can assemble around a globular nucleic acid core by forming nonicosahedral cages, which have been recently observed in assembly experiments involving small pieces of RNA. We find that the resulting cages are strained and can easily be split into fragments along stress lines. This suggests that such metastable nonicosahedral intermediates could be easily reassembled into the stable native icosahedral shells if the larger wild-type genome becomes available, despite the presence of a myriad of nonviral RNAs.
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Affiliation(s)
- Sanaz Panahandeh
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
| | - Siyu Li
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
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5
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Gordievskaya YD, Kramarenko EY, Gavrilov AA. The effect of explicit polarity on the conformational behavior of a single polyelectrolyte chain. Phys Chem Chem Phys 2021; 23:26296-26305. [PMID: 34787619 DOI: 10.1039/d1cp03167h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this work using dissipative particle dynamics simulations with explicit treatment of polar species we demonstrate that the molecular nature of dielectric media has a significant impact on swelling and collapse of a polyelectrolyte chain in a dilute solution. We show that the small-scale effects related to the presence of polar species lead to the intensification of the electrostatic interactions when the charges are close to each other and/or their density is high enough. As a result, the electrostatic strength , usually regarded as the main parameter governing the polyelectrolyte chain collapse, does not have a universal meaning: the value of λ at which the coil-to-globule transition occurs is found to be dependent on the specific fixed value of the solvent bulk permittivity ε while varying the monomer unit charge Q and vice versa. This effect is observed even when the backbone and the counterions have the same polarity as the solvent beads, i.e. no dielectric mismatch is present. The reason for such behavior is rationalized in terms of the "effective" dielectric permittivity εeff which depends on the volume fraction φ of charged units inside the polymer chain volume; using εeff instead of ε collapses all data onto one master curve describing the chain shrinking with λ. Furthermore, it is shown that a polar chain adopts less swollen conformations in the polyelectrolyte regime and collapses more easily compared to a non-polar chain.
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Affiliation(s)
- Yulia D Gordievskaya
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia. .,A. N. Nesmeyanov Institute of Organoelement Compounds RAS, 119991 Moscow, Russia
| | - Elena Yu Kramarenko
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia. .,A. N. Nesmeyanov Institute of Organoelement Compounds RAS, 119991 Moscow, Russia
| | - Alexey A Gavrilov
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia.
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6
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Adams MC, Schiltz CJ, Heck ML, Chappie JS. Crystal structure of the potato leafroll virus coat protein and implications for viral assembly. J Struct Biol 2021; 214:107811. [PMID: 34813955 DOI: 10.1016/j.jsb.2021.107811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/04/2021] [Accepted: 11/13/2021] [Indexed: 10/19/2022]
Abstract
Luteoviruses, poleroviruses, and enamoviruses are insect-transmitted, agricultural pathogens that infect a wide array of plants, including staple food crops. Previous cryo-electron microscopy studies of virus-like particles show that luteovirid viral capsids are built from a structural coat protein that organizes with T = 3 icosahedral symmetry. Here, we present the crystal structure of a truncated version of the coat protein monomer from potato leafroll virus at 1.80-Å resolution. In the crystal lattice, monomers pack into flat sheets that preserve the two-fold and three-fold axes of icosahedral symmetry and show minimal structural deviations when compared to the full-length subunits of the assembled virus-like particle. These observations have important implications in viral assembly and maturation and suggest that the CP N-terminus and its interactions with RNA play an important role in generating capsid curvature.
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Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Michelle L Heck
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; Boyce Thompson Institute, Ithaca, NY 14853, USA; Robert W. Holley Center for Agriculture and Health, Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.
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7
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Solé R, Sardanyés J, Elena SF. Phase transitions in virology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:115901. [PMID: 34584031 DOI: 10.1088/1361-6633/ac2ab0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Viruses have established relationships with almost every other living organism on Earth and at all levels of biological organization: from other viruses up to entire ecosystems. In most cases, they peacefully coexist with their hosts, but in most relevant cases, they parasitize them and induce diseases and pandemics, such as the AIDS and the most recent avian influenza and COVID-19 pandemic events, causing a huge impact on health, society, and economy. Viruses play an essential role in shaping the eco-evolutionary dynamics of their hosts, and have been also involved in some of the major evolutionary innovations either by working as vectors of genetic information or by being themselves coopted by the host into their genomes. Viruses can be studied at different levels of biological organization, from the molecular mechanisms of genome replication, gene expression and encapsidation, to global pandemics. All these levels are different and yet connected through the presence of threshold conditions allowing for the formation of a capsid, the loss of genetic information or epidemic spreading. These thresholds, as occurs with temperature separating phases in a liquid, define sharp qualitative types of behaviour. Thesephase transitionsare very well known in physics. They have been studied by means of simple, but powerful models able to capture their essential properties, allowing us to better understand them. Can the physics of phase transitions be an inspiration for our understanding of viral dynamics at different scales? Here we review well-known mathematical models of transition phenomena in virology. We suggest that the advantages of abstract, simplified pictures used in physics are also the key to properly understanding the origins and evolution of complexity in viruses. By means of several examples, we explore this multilevel landscape and how minimal models provide deep insights into a diverse array of problems. The relevance of these transitions in connecting dynamical patterns across scales and their evolutionary and clinical implications are outlined.
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Affiliation(s)
- Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra-PRBB, Dr Aiguader 80, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, United States of America
| | - Josep Sardanyés
- Centre de Recerca Matemàtica (CRM), Edifici C, Campus de Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain
- Dynamical Systems and Computational Virology, CSIC Associated Unit, Institute for Integrative Systems Biology (I2SysBio)-CRM, Spain
| | - Santiago F Elena
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, United States of America
- Evolutionary Systems Virology Lab (I2SysBio), CSIC-Universitat de València, Catedrático Agustín Escardino 9, Paterna, 46980 València, Spain
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8
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Ghosh S, Vemparala S. Kinetics of charged polymer collapse in poor solvents. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:045101. [PMID: 34352747 DOI: 10.1088/1361-648x/ac1aef] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Extensive molecular dynamics simulations, using simple charged polymer models, have been employed to probe the collapse kinetics of a single flexible polyelectrolyte (PE) chain under implicit poor solvent conditions. We investigate the role of the charged nature of PE chain (A), valency of counterions (Z) on the kinetics of such PE collapse. Our study shows that the collapse kinetics of charged polymers are significantly different from those of the neutral polymer and that the finite-size scaling behavior of PE collapse times does not follow the Rouse scaling as observed in the case of neutral polymers. The critical exponent for charged PE chains is found to be less than that of neutral polymers and also exhibits dependence on counterion valency. The coarsening of clusters along the PE chain suggests a multi-stage collapse and exhibits opposite behavior of exponents compared to neutral polymers: faster in the early stages and slower in the later stages of collapse.
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Affiliation(s)
- Susmita Ghosh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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9
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Marichal L, Gargowitsch L, Rubim RL, Sizun C, Kra K, Bressanelli S, Dong Y, Panahandeh S, Zandi R, Tresset G. Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus. Biophys J 2021; 120:3925-3936. [PMID: 34418368 PMCID: PMC8511167 DOI: 10.1016/j.bpj.2021.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/21/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022] Open
Abstract
The process of genome packaging in most of viruses is poorly understood, notably the role of the genome itself in the nucleocapsid structure. For simple icosahedral single-stranded RNA viruses, the branched topology due to the RNA secondary structure is thought to lower the free energy required to complete a virion. We investigate the structure of nucleocapsids packaging RNA segments with various degrees of compactness by small-angle x-ray scattering and cryotransmission electron microscopy. The structural differences are mild even though compact RNA segments lead on average to better-ordered and more uniform particles across the sample. Numerical calculations confirm that the free energy is lowered for the RNA segments displaying the larger number of branch points. The effect is, however, opposite with synthetic polyelectrolytes, in which a star topology gives rise to more disorder in the capsids than a linear topology. If RNA compactness and size account in part for the proper assembly of the nucleocapsid and the genome selectivity, other factors most likely related to the host cell environment during viral assembly must come into play as well.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Laetitia Gargowitsch
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Rafael Leite Rubim
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Christina Sizun
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Kalouna Kra
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Yinan Dong
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Sanaz Panahandeh
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France.
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Simon M, Veit M, Osterrieder K, Gradzielski M. Surfactants - Compounds for inactivation of SARS-CoV-2 and other enveloped viruses. Curr Opin Colloid Interface Sci 2021; 55:101479. [PMID: 34149296 PMCID: PMC8196227 DOI: 10.1016/j.cocis.2021.101479] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We provide here a general view on the interactions of surfactants with viruses, with a particular emphasis on how such interactions can be controlled and employed for inhibiting the infectivity of enveloped viruses, including coronaviruses. The aim is to provide to interested scientists from different fields, including chemistry, physics, biochemistry, and medicine, an overview of the basic properties of surfactants and (corona)viruses, which are relevant to understanding the interactions between the two. Various types of interactions between surfactant and virus are important, and they act on different components of a virus such as the lipid envelope, membrane (envelope) proteins and nucleocapsid proteins. Accordingly, this cannot be a detailed account of all relevant aspects but instead a summary that bridges between the different disciplines. We describe concepts and cover a selection of the relevant literature as an incentive for diving deeper into the relevant material. Our focus is on more recent developments around the COVID-19 pandemic caused by SARS-CoV-2, applications of surfactants against the virus, and on the potential future use of surfactants for pandemic relief. We also cover the most important aspects of the historical development of using surfactants in combatting virus infections. We conclude that surfactants are already playing very important roles in various directions of defence against viruses, either directly, as in disinfection, or as carrier components of drug delivery systems for prophylaxis or treatment. By designing tailor-made surfactants, and consequently, advanced formulations, one can expect more and more effective use of surfactants, either directly as antiviral compounds or as part of more complex formulations.
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Key Words
- AFM, atomic force microscopy
- BVDV, Bovine Viral Diarrhea Virus
- C12E8, dodecyloctaglycol
- CPyC, cetylpyridinium chloride
- DSPC, 1,2-distearoyl-sn-glycero-3-phosphocholine
- Disinfection
- Enveloped viruses
- Flu, influenza virus
- HIV, human immunodeficiency virus
- HSV, herpes simplex virus
- ITC, isothermal titration calorimetry
- Ld, liquid-disordered
- Lipid bilayers
- Lo, liquid-ordered
- PA, phosphatidic acid (anionic)
- PC, phosphatidylcholine (zwitterionic)
- PE, phosphatidylethanolamine (zwitterionic)
- PI, phosphatidylinositol (anionic)
- POPC, 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- PS, phosphatidylserine (anionic)
- QUAT, quaternary alkyl ammonium
- RNP, ribonucleoprotein particle
- SAXS, small-angle X-ray scattering
- SDS, sodium dodecyl sulphate
- Surfactant
- TBP, tri-n-butyl phosphate
- TEM, transmission electron microscopy
- Virus inactivation
- cac, critical aggregate concentration
- cmc, critical micelle concentration
- p, packing parameter
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Affiliation(s)
- Miriam Simon
- Dept. of Chemical Engineering and the Russell Berrie Nanotechnolgy Inst. (RBNI), Technion-Israel Institute of Technology, Haifa, IL 3200003, Israel
| | - Michael Veit
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Robert von Ostertag-Straße 7-13, 14163 Berlin, Germany
| | - Klaus Osterrieder
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Robert von Ostertag-Straße 7-13, 14163 Berlin, Germany.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Michael Gradzielski
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Straße des 17. Juni 124, Sekr. TC7, Technische Universität Berlin, D-10623 Berlin, Germany
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11
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Zeng C, Scott L, Malyutin A, Zandi R, Van der Schoot P, Dragnea B. Virus Mechanics under Molecular Crowding. J Phys Chem B 2021; 125:1790-1798. [PMID: 33577322 DOI: 10.1021/acs.jpcb.0c10947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Viruses avoid exposure of the viral genome to harmful agents with the help of a protective protein shell known as the capsid. A secondary effect of this protective barrier is that macromolecules that may be in high concentration on the outside cannot freely diffuse across it. Therefore, inside the cell and possibly even outside, the intact virus is generally under a state of osmotic stress. Viruses deal with this type of stress in various ways. In some cases, they might harness it for infection. However, the magnitude and influence of osmotic stress on virus physical properties remains virtually unexplored for single-stranded RNA viruses-the most abundant class of viruses. Here, we report on how a model system for the positive-sense RNA icosahedral viruses, brome mosaic virus (BMV), responds to osmotic pressure. Specifically, we study the mechanical properties and structural stability of BMV under controlled molecular crowding conditions. We show that BMV is mechanically reinforced under a small external osmotic pressure but starts to yield after a threshold pressure is reached. We explain this mechanochemical behavior as an effect of the molecular crowding on the entropy of the "breathing" fluctuation modes of the virus shell. The experimental results are consistent with the viral RNA imposing a small negative internal osmotic pressure that prestresses the capsid. Our findings add a new line of inquiry to be considered when addressing the mechanisms of viral disassembly inside the crowded environment of the cell.
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Affiliation(s)
- Cheng Zeng
- Department of Chemistry, Indiana University, Bloomington, Bloomington, Indiana 47405, United States
| | - Liam Scott
- Department of Chemistry, Indiana University, Bloomington, Bloomington, Indiana 47405, United States
| | - Andrey Malyutin
- Department of Chemistry, Indiana University, Bloomington, Bloomington, Indiana 47405, United States
| | - Roya Zandi
- Department of Physics and Astronomy, University of California at Riverside, Riverside, California 92521, United States
| | | | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Bloomington, Indiana 47405, United States
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12
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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13
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Bond K, Tsvetkova IB, Wang JCY, Jarrold MF, Dragnea B. Virus Assembly Pathways: Straying Away but Not Too Far. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2004475. [PMID: 33241653 DOI: 10.1002/smll.202004475] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Non-enveloped RNA viruses pervade all domains of life. In a cell, they co-assemble from viral RNA and capsid proteins. Virus-like particles can form in vitro where virtually any non-cognate polyanionic cargo can be packaged. How only viral RNA gets selected for packaging in vivo, in presence of myriad other polyanionic species, has been a puzzle. Through a combination of charge detection mass spectrometry and cryo-electron microscopy, it is determined that co-assembling brome mosaic virus (BMV) coat proteins and nucleic acid oligomers results in capsid structures and stoichiometries that differ from the icosahedral virion. These previously unknown shell structures are strained and less stable than the native one. However, they contain large native structure fragments that can be recycled to form BMV virions, should a viral genome become available. The existence of such structures suggest the possibility of a previously unknown regulatory pathway for the packaging process inside cells.
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Affiliation(s)
- Kevin Bond
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Irina B Tsvetkova
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | | | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
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14
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Malijevský A. Filling, depinning, unbinding: Three adsorption regimes for nanocorrugated substrates. Phys Rev E 2020; 102:012804. [PMID: 32795047 DOI: 10.1103/physreve.102.012804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/02/2020] [Indexed: 11/07/2022]
Abstract
We study adsorption at periodically corrugated substrates formed by scoring rectangular grooves into a planar solid wall which interacts with the fluid via long-range (dispersion) forces. The grooves are assumed to be macroscopically long but their depth, width, and separations can all be molecularly small. We show that the entire adsorption process can be divided into three parts consisting of (i) filling the grooves by a capillary liquid; (ii) depinning of the liquid-gas interface from the wall edges; and (iii) unbinding of the interface from the top of the wall, which is accompanied by a rapid but continuous flattening of its shape. Using a nonlocal density functional theory and mesoscopic interfacial models all the regimes are discussed in some detail to reveal the complexity of the entire process and subtle aspects that affect its behavior. In particular, it is shown that the nature of the depinning phenomenon is governed by the width of the wall pillars (separating grooves), while the width of the grooves only controls the location of the depinning first-order transition, if present.
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Affiliation(s)
- Alexandr Malijevský
- Department of Physical Chemistry, University of Chemical Technology Prague, Praha 6, 166 28, Czech Republic and Department of Molecular and Mesoscopic Modelling, ICPF of the Czech Academy Sciences, Prague 165 02, Czech Republic
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15
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Ghasemi M, Friedowitz S, Larson RG. Analysis of Partitioning of Salt through Doping of Polyelectrolyte Complex Coacervates. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00797] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mohsen Ghasemi
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sean Friedowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ronald G. Larson
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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16
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Waltmann C, Asor R, Raviv U, Olvera de la Cruz M. Assembly and Stability of Simian Virus 40 Polymorphs. ACS NANO 2020; 14:4430-4443. [PMID: 32208635 PMCID: PMC7232851 DOI: 10.1021/acsnano.9b10004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of N = 12 pentamers (T = 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here "C-terminal ligands", which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the T = 1 feature the ability to dynamically rearrange and are thus termed "pseudo-closed". The N = 13 shell can even spontaneously "self-correct" by losing a pentamer and become a T = 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing via the pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.
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Affiliation(s)
- Curt Waltmann
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
- Center for Nanoscale Science and Technology, The Hebrew University of Jerusalem, Edmond J Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
- Center for Nanoscale Science and Technology, The Hebrew University of Jerusalem, Edmond J Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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17
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Colla T, Bakhshandeh A, Levin Y. Osmotic stress and pore nucleation in charged biological nanoshells and capsids. SOFT MATTER 2020; 16:2390-2405. [PMID: 32067009 DOI: 10.1039/c9sm02532d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A model system is proposed to investigate the chemical equilibrium and mechanical stability of biological spherical-like nanoshells in contact with an aqueous solution with added dissociated electrolyte of a given concentration. The ionic chemical equilibrium across the permeable shell is investigated in the framework of an accurate Density Functional Theory (DFT) that incorporates electrostatic and hardcore correlations beyond the traditional mean-field (e.g., Poisson-Boltzmann) limit. The accuracy of the theory is tested by a direct comparison with Monte Carlo (MC) simulations. A simple analytical expression is then deduced which clearly highlights the entropic, electrostatic, and self-energy contributions to the osmotic stress over the shell in terms of the calculated ionic profiles. By invoking a continuum mean-field elastic approach to account for the shell surface stress upon osmotic stretching, the mechanical equilibrium properties of the shell under a wide variety of ionic strengths and surface charges are investigated. The model is further coupled to a continuum mechanical approach similar in structure to a Classical Nucleation Theory (CNT) to address the question of mechanical stability of the shells against a pore nucleation. This allows us to construct a phase diagram which delimits the mechanical stability of capsids for different ionic strengths and shell surface charges.
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Affiliation(s)
- Thiago Colla
- Instituto de Física, Universidade Federal de Ouro Preto, CEP 35400-000, Ouro Preto, MG, Brazil.
| | - Amin Bakhshandeh
- Programa de Pós-Graduação em Física, Instituto de Física e Matemática, Universidade Federal de Pelotas, Caixa Postal 354, CEP 96010-900 Pelotas, RS, Brazil.
| | - Yan Levin
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970, Porto Alegre, RS, Brazil.
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18
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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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19
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Comas-Garcia M. Packaging of Genomic RNA in Positive-Sense Single-Stranded RNA Viruses: A Complex Story. Viruses 2019; 11:v11030253. [PMID: 30871184 PMCID: PMC6466141 DOI: 10.3390/v11030253] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
The packaging of genomic RNA in positive-sense single-stranded RNA viruses is a key part of the viral infectious cycle, yet this step is not fully understood. Unlike double-stranded DNA and RNA viruses, this process is coupled with nucleocapsid assembly. The specificity of RNA packaging depends on multiple factors: (i) one or more packaging signals, (ii) RNA replication, (iii) translation, (iv) viral factories, and (v) the physical properties of the RNA. The relative contribution of each of these factors to packaging specificity is different for every virus. In vitro and in vivo data show that there are different packaging mechanisms that control selective packaging of the genomic RNA during nucleocapsid assembly. The goals of this article are to explain some of the key experiments that support the contribution of these factors to packaging selectivity and to draw a general scenario that could help us move towards a better understanding of this step of the viral infectious cycle.
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Affiliation(s)
- Mauricio Comas-Garcia
- Research Center for Health Sciences and Biomedicine (CICSaB), Universidad Autónoma de San Luis Potosí (UASLP), Av. Sierra Leona 550 Lomas 2da Seccion, 72810 San Luis Potosi, Mexico.
- Department of Sciences, Universidad Autónoma de San Luis Potosí (UASLP), Av. Chapultepec 1570, Privadas del Pedregal, 78295 San Luis Potosi, Mexico.
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20
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Lošdorfer Božič A, Šiber A. Electrostatics-Driven Inflation of Elastic Icosahedral Shells as a Model for Swelling of Viruses. Biophys J 2018; 115:822-829. [PMID: 30139522 DOI: 10.1016/j.bpj.2018.07.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/20/2018] [Accepted: 07/30/2018] [Indexed: 01/13/2023] Open
Abstract
We develop a clear theoretical description of radial swelling in virus-like particles that delineates the importance of electrostatic contributions to swelling in the absence of any conformational changes. The model couples the elastic parameters of the capsid-represented as a continuous elastic shell-to the electrostatic pressure acting on it. We show that different modifications of the electrostatic interactions brought about by, for instance, changes in pH or solution ionic strength are often sufficient to achieve the experimentally observed swelling (∼10% of the capsid radius). Additionally, we derive analytical expressions for the electrostatics-driven radial swelling of virus-like particles that enable one to quickly estimate the magnitudes of physical quantities involved.
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21
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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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22
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Systematic analysis of biological roles of charged amino acid residues located throughout the structured inner wall of a virus capsid. Sci Rep 2018; 8:9543. [PMID: 29934575 PMCID: PMC6015035 DOI: 10.1038/s41598-018-27749-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/01/2018] [Indexed: 12/31/2022] Open
Abstract
Structure-based mutational analysis of viruses is providing many insights into the relationship between structure and biological function of macromolecular complexes. We have systematically investigated the individual biological roles of charged residues located throughout the structured capsid inner wall (outside disordered peptide segments) of a model spherical virus, the minute virus of mice (MVM). The functional effects of point mutations that altered the electrical charge at 16 different positions at the capsid inner wall were analyzed. The results revealed that MVM capsid self-assembly is rather tolerant to point mutations that alter the number and distribution of charged residues at the capsid inner wall. However, mutations that either increased or decreased the number of positive charges around capsid-bound DNA segments reduced the thermal resistance of the virion. Moreover, mutations that either removed or changed the positions of negatively charged carboxylates in rings of acidic residues around capsid pores were deleterious by precluding a capsid conformational transition associated to through-pore translocation events. The results suggest that number, distribution and specific position of electrically charged residues across the inner wall of a spherical virus may have been selected through evolution as a compromise between several different biological requirements.
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23
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Grosberg AY, Bruinsma R. Confining annealed branched polymers inside spherical capsids. J Biol Phys 2018; 44:133-145. [PMID: 29442192 PMCID: PMC5928018 DOI: 10.1007/s10867-018-9483-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022] Open
Abstract
The Lifshitz equation for the confinement of a linear polymer in a spherical cavity of radius R has the form of the Schrödinger equation for a quantum particle trapped in a potential well with flat bottom and infinite walls at radius R. We show that the Lifshitz equation of a confined annealed branched polymer has the form of the Schrödinger equation for a quantum harmonic oscillator. The resulting confinement energy has a 1/R4 dependence on the confinement radius R, in contrast to the case of confined linear polymers, which have a 1/R2 dependence. We discuss the application of this result to the problem of the confinement of single-stranded RNA molecules inside spherical capsids.
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Affiliation(s)
- Alexander Y Grosberg
- Department of Physics and Center for Soft Matter Research, New York University, 726 Broadway, New York, NY, 10003, USA.
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
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24
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Abraham A, Chatterji A. Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions. J Chem Phys 2018; 148:154901. [PMID: 29679962 DOI: 10.1063/1.5018462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.
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Affiliation(s)
- Alex Abraham
- Department of Physics, IISER-Pune, Dr. Homi Bhaba Road, Pune 411008, India
| | - Apratim Chatterji
- Department of Physics, IISER-Pune, Dr. Homi Bhaba Road, Pune 411008, India
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25
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Li S, Orland H, Zandi R. Self consistent field theory of virus assembly. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:144002. [PMID: 29460850 PMCID: PMC7104907 DOI: 10.1088/1361-648x/aab0c6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/12/2018] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The ground state dominance approximation (GSDA) has been extensively used to study the assembly of viral shells. In this work we employ the self-consistent field theory (SCFT) to investigate the adsorption of RNA onto positively charged spherical viral shells and examine the conditions when GSDA does not apply and SCFT has to be used to obtain a reliable solution. We find that there are two regimes in which GSDA does work. First, when the genomic RNA length is long enough compared to the capsid radius, and second, when the interaction between the genome and capsid is so strong that the genome is basically localized next to the wall. We find that for the case in which RNA is more or less distributed uniformly in the shell, regardless of the length of RNA, GSDA is not a good approximation. We observe that as the polymer-shell interaction becomes stronger, the energy gap between the ground state and first excited state increases and thus GSDA becomes a better approximation. We also present our results corresponding to the genome persistence length obtained through the tangent-tangent correlation length and show that it is zero in case of GSDA but is equal to the inverse of the energy gap when using SCFT.
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Affiliation(s)
- Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America
- Institut de Physique Théorique, CEA-Saclay, CEA, F-91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, No.10 East Xibeiwang Road, Haidan District, Beijing 100193, People’s Republic of China
| | - Henri Orland
- Institut de Physique Théorique, CEA-Saclay, CEA, F-91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, No.10 East Xibeiwang Road, Haidan District, Beijing 100193, People’s Republic of China
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America
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26
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van der Holst B, Kegel WK, Zandi R, van der Schoot P. The different faces of mass action in virus assembly. J Biol Phys 2018; 44:163-179. [PMID: 29616429 PMCID: PMC5928020 DOI: 10.1007/s10867-018-9487-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
Abstract
The spontaneous encapsulation of genomic and non-genomic polyanions by coat proteins of simple icosahedral viruses is driven, in the first instance, by electrostatic interactions with polycationic RNA binding domains on these proteins. The efficiency with which the polyanions can be encapsulated in vitro, and presumably also in vivo, must in addition be governed by the loss of translational and mixing entropy associated with co-assembly, at least if this co-assembly constitutes a reversible process. These forms of entropy counteract the impact of attractive interactions between the constituents and hence they counteract complexation. By invoking mass action-type arguments and a simple model describing electrostatic interactions, we show how these forms of entropy might settle the competition between negatively charged polymers of different molecular weights for co-assembly with the coat proteins. In direct competition, mass action turns out to strongly work against the encapsulation of RNAs that are significantly shorter, which is typically the case for non-viral (host) RNAs. We also find that coat proteins favor forming virus particles over nonspecific binding to other proteins in the cytosol even if these are present in vast excess. Our results rationalize a number of recent in vitro co-assembly experiments showing that short polyanions are less effective at attracting virus coat proteins to form virus-like particles than long ones do, even if both are present at equal weight concentrations in the assembly mixture.
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Affiliation(s)
- Bart van der Holst
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Willem K Kegel
- Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California Riverside, Riverside, USA
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands. .,Institute for Theoretical Physics, Utrecht University, Utrecht, The Netherlands.
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27
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Li S, Erdemci-Tandogan G, van der Schoot P, Zandi R. The effect of RNA stiffness on the self-assembly of virus particles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:044002. [PMID: 29235442 PMCID: PMC7104906 DOI: 10.1088/1361-648x/aaa159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 05/21/2023]
Abstract
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between an ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.
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Affiliation(s)
- Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America
| | - Gonca Erdemci-Tandogan
- Department of Physics, Syracuse University, Syracuse, NY 13244, United States of America
| | - Paul van der Schoot
- Group Theory of Polymers and Soft Matter, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, Netherlands
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America
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28
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Lošdorfer Božič A, Podgornik R. Varieties of charge distributions in coat proteins of ssRNA+ viruses. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:024001. [PMID: 29182522 PMCID: PMC7104810 DOI: 10.1088/1361-648x/aa9ded] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
A major part of the interactions involved in the assembly and stability of icosahedral, positive-sense single-stranded RNA (ssRNA+) viruses is electrostatic in nature, as can be inferred from the strong pH- and salt-dependence of their assembly phase diagrams. Electrostatic interactions do not act only between the capsid coat proteins (CPs), but just as often provide a significant contribution to the interactions of the CPs with the genomic RNA, mediated to a large extent by positively charged, flexible N-terminal tails of the CPs. In this work, we provide two clear and complementary definitions of an N-terminal tail of a protein, and use them to extract the tail sequences of a large number of CPs of ssRNA+ viruses. We examine the pH-dependent interplay of charge on both tails and CPs alike, and show that-in contrast to the charge on the CPs-the net positive charge on the N-tails persists even to very basic pH values. In addition, we note a limit to the length of the wild-type genomes of those viruses which utilize positively charged tails, when compared to viruses without charged tails and similar capsid size. At the same time, we observe no clear connection between the charge on the N-tails and the genome lengths of the viruses included in our study.
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Affiliation(s)
- Anže Lošdorfer Božič
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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29
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Angelescu DG. Role of polyion length in the co-assembly of stoichiometric viral-like nanoparticles. JOURNAL OF POLYMER RESEARCH 2017. [DOI: 10.1007/s10965-017-1416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Chen J, Chevreuil M, Combet S, Lansac Y, Tresset G. Investigating the thermal dissociation of viral capsid by lattice model. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:474001. [PMID: 29098985 PMCID: PMC7104912 DOI: 10.1088/1361-648x/aa8d88] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/08/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
The dissociation of icosahedral viral capsids was investigated by a homogeneous and a heterogeneous lattice model. In thermal dissociation experiments with cowpea chlorotic mottle virus and probed by small-angle neutron scattering, we observed a slight shrinkage of viral capsids, which can be related to the strengthening of the hydrophobic interaction between subunits at increasing temperature. By considering the temperature dependence of hydrophobic interaction in the homogeneous lattice model, we were able to give a better estimate of the effective charge. In the heterogeneous lattice model, two sets of lattice sites represented different capsid subunits with asymmetric interaction strengths. In that case, the dissociation of capsids was found to shift from a sharp one-step transition to a gradual two-step transition by weakening the hydrophobic interaction between AB and CC subunits. We anticipate that such lattice models will shed further light on the statistical mechanics underlying virus assembly and disassembly.
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Affiliation(s)
- Jingzhi Chen
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Maelenn Chevreuil
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Sophie Combet
- Laboratoire Léon Brillouin (LLB), UMR 12 CEA-CNRS, CEA-Saclay, F-91191 Gif-sur-Yvette Cedex, France
| | - Yves Lansac
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
- GREMAN, CNRS, Université François Rabelais, 73200 Tours, France
| | - Guillaume Tresset
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
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Erdemci-Tandogan G, Orland H, Zandi R. RNA Base Pairing Determines the Conformations of RNA Inside Spherical Viruses. PHYSICAL REVIEW LETTERS 2017; 119:188102. [PMID: 29219580 DOI: 10.1103/physrevlett.119.188102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Indexed: 05/21/2023]
Abstract
Many simple RNA viruses enclose their genetic material by a protein shell called the capsid. While the capsid structures are well characterized for most viruses, the structure of RNA inside the shells and the factors contributing to it remain poorly understood. We study the impact of base pairing on the conformations of RNA and find that it undergoes a swollen coil to globule continuous transition as a function of the strength of the pairing interaction. We also observe a first order transition and kink profile as a function of RNA length. All these transitions could explain the different RNA profiles observed inside viral shells.
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Affiliation(s)
- Gonca Erdemci-Tandogan
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Henri Orland
- Institut de Physique Théorique, CEA-Saclay, CEA, F-91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, No. 10 East Xibeiwang Road, Haidan District, Beijing 100193, China
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
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Dharmavaram S, Xie F, Klug W, Rudnick J, Bruinsma R. Orientational phase transitions and the assembly of viral capsids. Phys Rev E 2017; 95:062402. [PMID: 28709270 DOI: 10.1103/physreve.95.062402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Indexed: 06/07/2023]
Abstract
We present a Landau theory for large-l orientational phase transitions and apply it to the assembly of icosahedral viral capsids. The theory predicts two distinct types of ordering transitions. Transitions dominated by the l=6,10,12, and 18 icosahedral spherical harmonics resemble robust first-order phase transitions that are not significantly affected by chirality. The remaining transitions depend essentially on including mixed l states denoted as l=15+16 corresponding to a mixture of l=15 and l=16 spherical harmonics. The l=15+16 transition is either continuous or weakly first-order and it is strongly influenced by chirality, which suppresses spontaneous chiral symmetry breaking. The icosahedral state is in close competition with states that have tetrahedral, D_{5}, and octahedral symmetries. We present a group-theoretic method to analyze the competition between the different symmetries. The theory is applied to a variety of viral shells.
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Affiliation(s)
- Sanjay Dharmavaram
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| | - Fangming Xie
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - William Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| | - Joseph Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
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Angelescu DG. Assembled viral-like nanoparticles from elastic capsomers and polyion. J Chem Phys 2017; 146:134902. [DOI: 10.1063/1.4979496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Liu A, Yang L, Verwegen M, Reardon D, Cornelissen JJM. Construction of core-shell hybrid nanoparticles templated by virus-like particles. RSC Adv 2017. [DOI: 10.1039/c7ra11310b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Catalytically active gold in silica core–shell nanoparticles are prepared by pH controlled templating on virus-like particles.
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Affiliation(s)
- A. Liu
- Laboratory for Biomolecular Nanotechnology (BNT)
- MESA+ Institute of Nanotechnology
- University of Twente
- 7500 AE Enschede
- The Netherlands
| | - L. Yang
- Laboratory for Biomolecular Nanotechnology (BNT)
- MESA+ Institute of Nanotechnology
- University of Twente
- 7500 AE Enschede
- The Netherlands
| | - M. Verwegen
- Laboratory for Biomolecular Nanotechnology (BNT)
- MESA+ Institute of Nanotechnology
- University of Twente
- 7500 AE Enschede
- The Netherlands
| | - D. Reardon
- DSM Materials Science Center
- 6160 MD Geleen
- The Netherlands
| | - J. J. L. M. Cornelissen
- Laboratory for Biomolecular Nanotechnology (BNT)
- MESA+ Institute of Nanotechnology
- University of Twente
- 7500 AE Enschede
- The Netherlands
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Tom AM, Vemparala S, Rajesh R, Brilliantov NV. Mechanism of Chain Collapse of Strongly Charged Polyelectrolytes. PHYSICAL REVIEW LETTERS 2016; 117:147801. [PMID: 27740827 DOI: 10.1103/physrevlett.117.147801] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 06/06/2023]
Abstract
We perform extensive molecular dynamics simulations of a charged polymer in a good solvent in the regime where the chain is collapsed. We analyze the dependence of the gyration radius R_{g} on the reduced Bjerrum length ℓ_{B} and find two different regimes. In the first one, called a weak electrostatic regime, R_{g}∼ℓ_{B}^{-1/2}, which is consistent only with the predictions of the counterion-fluctuation theory. In the second one, called a strong electrostatic regime, we find R_{g}∼ℓ_{B}^{-1/5}. To explain the novel regime we modify the counterion-fluctuation theory.
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Affiliation(s)
- Anvy Moly Tom
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - R Rajesh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Nikolai V Brilliantov
- Department of Mathematics, University of Leicester, Leicester LE1 7RH, United Kingdom
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Kelly J, Grosberg AY, Bruinsma R. Sequence Dependence of Viral RNA Encapsidation. J Phys Chem B 2016; 120:6038-50. [PMID: 27116641 DOI: 10.1021/acs.jpcb.6b01964] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We develop a Flory mean-field theory for viral RNA (vRNA) molecules that extends the current RNA folding algorithms to include interactions between different sections of the secondary structure. The theory is applied to sequence-selective vRNA encapsidation. The dependence on sequence enters through a single parameter: the largest eigenvalue of the Kramers matrix of the branched polymer obtained by coarse graining the secondary structure. Differences between the work of encapsidation of vRNA molecules and of randomized isomers are found to be in the range of 20 kBT, more than sufficient to provide a strong bias in favor of vRNA encapsidation. The method is applied to a packaging competition experiment where large vRNA molecules compete for encapsidation with two smaller RNA species that together have the same nucleotide sequence as the large molecule. We encounter a substantial, generic free energy bias, that also is of the order of 20 kBT, in favor of encapsidating the single large RNA molecule. The bias is mainly the consequence of the fact that dividing up a large vRNA molecule involves the release of stored elastic energy. This provides an important, nonspecific mechanism for preferential encapsidation of single larger vRNA molecules over multiple smaller mRNA molecules with the same total number of nucleotides. The result is also consistent with recent RNA packaging competition experiments by Comas-Garcia et al.1 Finally, the Flory method leads to the result that when two RNA molecules are copackaged, they are expected to remain segregated inside the capsid.
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Affiliation(s)
- Joshua Kelly
- Department of Physics and Astronomy, University of California , Los Angeles, California 90095, United States
| | - Alexander Y Grosberg
- Department of Physics and Center for Soft Matter Research, New York University , New York, New York 10003, United States
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California , Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
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