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Vishwakarma P, Puri S, Banerjee M, Chang CY, Chang CC, Chaudhuri TK. Deciphering the Thermal Stability of Bacteriophage MS2-Derived Virus-like Particle and Its Engineered Variant. ACS Biomater Sci Eng 2024. [PMID: 38976823 DOI: 10.1021/acsbiomaterials.4c00770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
RNA bacteriophage MS2-derived virus-like particles (VLPs) have been widely used in biomedical research as model systems to study virus assembly, structure-function relationships, vaccine development, and drug delivery. Considering the diverse utility of these VLPs, a systemic engineering approach has been utilized to generate smaller particles with optimal serum stability and tissue penetrance. Additionally, it is crucial to demonstrate the overall stability of these mini MS2 VLPs, ensuring cargo protection until they reach their target cell/organ. However, no detailed analysis of the thermal stability and heat-induced disassembly of MS2 VLPs has yet been attempted. In this work, we investigated the thermal stability of both wild-type (WT) MS2 VLP and its "mini" variant containing S37P mutation (mini MS2 VLP). The mini MS2 VLP exhibits a higher capsid melting temperature (Tm) when compared to its WT MS2 VLP counterpart, possibly attributed to its smaller interdimer angle. Our study presents that the thermal unfolding of MS2 VLPs follows a sequential process involving particle destabilization, nucleic acid exposure/melting, and disassembly of VLP. This observation underscores the disruption of cooperative intersubunit interactions and protein-nucleic acid interactions, shedding light on the mechanism of heat-induced VLP disassembly.
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Affiliation(s)
- Pragati Vishwakarma
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Sarita Puri
- Department of Bioscience, University of Milan, Milan 20133, Italy
| | - Manidipa Banerjee
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Chia-Yu Chang
- Department of Biological Sciences and Technology, National Yang-Ming Chiao Tsung University, Hsinchu 30068, Taiwan
| | - Chia-Ching Chang
- Department of Biological Sciences and Technology, National Yang-Ming Chiao Tsung University, Hsinchu 30068, Taiwan
- Department of Electrophysics, National Yang-Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang-Ming Chiao Tung University, Hsinchu 30068, Taiwan
- International College of Semiconductor Technology, National Yang-Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Tapan K Chaudhuri
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
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2
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Conte AN, Ridgeway SM, Ruchel ME, Kibby EM, Nagy TA, Whiteley AT. Phage detection by a bacterial NLR-related protein is mediated by DnaJ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597415. [PMID: 38895412 PMCID: PMC11185742 DOI: 10.1101/2024.06.04.597415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Bacteria encode a wide range of antiphage systems and a subset of these proteins are homologous to components of the human innate immune system. Mammalian nucleotide-binding and leucine-rich repeat containing proteins (NLRs) and bacterial NLR-related proteins use a central NACHT domain to link infection detection with initiation of an antimicrobial response. Bacterial NACHT proteins provide defense against both DNA and RNA phages. Here we determine the mechanism of RNA phage detection by the bacterial NLR-related protein bNACHT25 in E. coli. bNACHT25 was specifically activated by Emesvirus ssRNA phages and analysis of MS2 phage suppressor mutants that evaded detection revealed Coat Protein (CP) was sufficient for activation. bNACHT25 and CP did not physically interact. Instead, we found bNACHT25 requires the host chaperone DnaJ to detect CP. Our data suggest that bNACHT25 detects a wide range of phages by guarding a host cell process rather than binding a specific phage-derived molecule.
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Affiliation(s)
- Amy N. Conte
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | | | - Madison E. Ruchel
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Department of Biology, Front Range Community College, Longmont, CO, USA
| | - Emily M. Kibby
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Toni A. Nagy
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Aaron T. Whiteley
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
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3
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Wei WS, Trubiano A, Sigl C, Paquay S, Dietz H, Hagan MF, Fraden S. Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids. Proc Natl Acad Sci U S A 2024; 121:e2312775121. [PMID: 38324570 PMCID: PMC10873614 DOI: 10.1073/pnas.2312775121] [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: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T = 3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose three-dimensional geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures.
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Affiliation(s)
- Wei-Shao Wei
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Anthony Trubiano
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Christian Sigl
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Stefan Paquay
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Hendrik Dietz
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Seth Fraden
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
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4
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Keshavarz-Joud P, Zhao L, Bobe D, Hernandez C, Kopylov M, Yen LY, Djeddar N, Thompson B, Connors C, Gibson G, Bryksin A, Finn M. Exploring the Landscape of the PP7 Virus-like Particle for Peptide Display. ACS NANO 2023; 17:18470-18480. [PMID: 37669408 PMCID: PMC10540251 DOI: 10.1021/acsnano.3c06178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023]
Abstract
Self-assembling virus-like particles (VLPs) can tolerate a wide degree of genetic and chemical manipulation to their capsid protein to display a foreign molecule polyvalently. We previously reported the successful incorporation of foreign peptide sequences in the junction loop and onto the C-terminus of PP7 dimer VLPs, as these regions are accessible for surface display on assembled capsids. Here, we report the implementation of a library-based approach to test the assembly tolerance of PP7 dimer capsid proteins to insertions or terminal extensions of randomized 15-mer peptide sequences. By performing two iterative rounds of assembly-based selection, we evaluated the degree of favorability of all 20 amino acids at each of the 15 randomized positions. Deep sequencing analysis revealed a distinct preference for the inclusion of hydrophilic peptides and negatively charged amino acids (Asp and Glu) and the exclusion of positively charged peptides and bulky and hydrophobic amino acid residues (Trp, Phe, Tyr, and Cys). Within the libraries tested here, we identified 4000 to 22,000 unique 15-mer peptide sequences that can successfully be displayed on the surface of the PP7 dimer capsid. Overall, the use of small initial libraries consisting of no more than a few million members yielded a significantly larger number of unique and assembly-competent VLP sequences than have been previously characterized for this class of nucleoprotein particle.
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Affiliation(s)
- Parisa Keshavarz-Joud
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Liangjun Zhao
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Daija Bobe
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Carolina Hernandez
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Mykhailo Kopylov
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Laura Y. Yen
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Naima Djeddar
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30306, United States
| | - Brianna Thompson
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Caleb Connors
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Greg Gibson
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Anton Bryksin
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30306, United States
| | - M.G. Finn
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
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5
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Ikwuagwu B, Hartman E, Mills CE, Tullman-Ercek D. Systematic engineering of virus-like particles to identify self-assembly rules for shifting particle size. Virology 2023; 579:137-147. [PMID: 36669330 PMCID: PMC10776172 DOI: 10.1016/j.virol.2023.01.002] [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: 09/02/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Virus-like particles (VLPs) are promising scaffolds for biomaterials as well as diagnostic and therapeutic applications. However, there are some key challenges to be solved, such as the ability to engineer alternate sizes for varied use cases. To this end, we created a library of MS2 VLP variants at two key residues in the coat protein which have been implicated as important to controlling VLP size and geometry. By adapting a method for systematic mutagenesis coupled with size-based selections and high-throughput sequencing as a readout, we developed a quantitative assessment of two residues in MS2 coat protein that govern the size shift in MS2 VLPs. We then applied the strategy to the equivalent residues in Qβ VLPs, an MS2 homolog, and demonstrate that the analogous pair of residues are also able to impact Qβ VLP size and shape. These results underscore the power of fitness landscapes in identifying critical features for assembly.
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Affiliation(s)
- Bon Ikwuagwu
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Emily Hartman
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute B486, Evanston, IL, 60208, USA.
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6
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Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins. Curr Res Struct Biol 2022; 4:338-348. [PMID: 36440379 PMCID: PMC9685359 DOI: 10.1016/j.crstbi.2022.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/23/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution in silico can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins. Presented extensive molecular dynamics (MD) simulation data investigating protein vacuum exposure and rehydration dynamics. Demonstrated that the majority of the protein structure recovers their initial solution conformation after vacuum exposure. Explored the potential gain for structural biology of using MD simulation to refine gas-phase determined protein structures.
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7
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Chandler-Bostock R, Bingham RJ, Clark S, Scott AJP, Wroblewski E, Barker A, White SJ, Dykeman EC, Mata CP, Bohon J, Farquhar E, Twarock R, Stockley PG. Genome-regulated Assembly of a ssRNA Virus May Also Prepare It for Infection. J Mol Biol 2022; 434:167797. [PMID: 35998704 DOI: 10.1016/j.jmb.2022.167797] [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: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Many single-stranded, positive-sense RNA viruses regulate assembly of their infectious virions by forming multiple, cognate coat protein (CP)-genome contacts at sites termed Packaging Signals (PSs). We have determined the secondary structures of the bacteriophage MS2 ssRNA genome (gRNA) frozen in defined states using constraints from X-ray synchrotron footprinting (XRF). Comparison of the footprints from phage and transcript confirms the presence of multiple PSs in contact with CP dimers in the former. This is also true for a virus-like particle (VLP) assembled around the gRNA in vitro in the absence of the single-copy Maturation Protein (MP) found in phage. Since PS folds are present at many sites across gRNA transcripts, it appears that this genome has evolved to facilitate this mechanism of assembly regulation. There are striking differences between the gRNA-CP contacts seen in phage and the VLP, suggesting that the latter are inappropriate surrogates for aspects of phage structure/function. Roughly 50% of potential PS sites in the gRNA are not in contact with the protein shell of phage. However, many of these sit adjacent to, albeit not in contact with, PS-binding sites on CP dimers. We hypothesize that these act as PSs transiently during assembly but subsequently dissociate. Combining the XRF data with PS locations from an asymmetric cryo-EM reconstruction suggests that the genome positions of such dissociations are non-random and may facilitate infection. The loss of many PS-CP interactions towards the 3' end of the gRNA would allow this part of the genome to transit more easily through the narrow basal body of the pilus extruding machinery. This is the known first step in phage infection. In addition, each PS-CP dissociation event leaves the protein partner trapped in a non-lowest free-energy conformation. This destabilizes the protein shell which must disassemble during infection, further facilitating this stage of the life-cycle.
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Affiliation(s)
| | - Richard J Bingham
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Sam Clark
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Andrew J P Scott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Amy Barker
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Eric C Dykeman
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Carlos P Mata
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jen Bohon
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Erik Farquhar
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Reidun Twarock
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK.
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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8
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Prakash DL, Gosavi S. The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids. Front Mol Biosci 2022; 9:967877. [PMID: 36339706 PMCID: PMC9631432 DOI: 10.3389/fmolb.2022.967877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Some non-enveloped virus capsids assemble from multiple copies of a single type of coat-protein (CP). The comparative energetics of the diverse CP-CP interfaces present in such capsids likely govern virus assembly-disassembly mechanisms. The T = 3 icosahedral capsids comprise 180 CP copies arranged about two-, three-, five- and six-fold axes of (quasi-)rotation symmetry. Structurally diverse CPs can assemble into T = 3 capsids. Specifically, the Leviviridae CPs are structurally distinct from the Bromoviridae, Tombusviridae and Tymoviridae CPs which fold into the classic “jelly-roll” fold. However, capsids from across the four families are known to disassemble into dimers. To understand whether the overall symmetry of the capsid or the structural details of the CP determine virus assembly-disassembly mechanisms, we analyze the different CP-CP interfaces that occur in the four virus families. Previous work studied protein homodimer interfaces using interface size (relative to the monomer) and hydrophobicity. Here, we analyze all CP-CP interfaces using these two parameters and find that the dimerization interface (present between two CPs congruent through a two-fold axis of rotation) has a larger relative size in the Leviviridae than in the other viruses. The relative sizes of the other Leviviridae interfaces and all the jelly-roll interfaces are similar. However, the dimerization interfaces across families have slightly higher hydrophobicity, potentially making them stronger than other interfaces. Finally, although the CP-monomers of the jelly-roll viruses are structurally similar, differences in their dimerization interfaces leads to varied dimer flexibility. Overall, differences in CP-structures may induce different modes of swelling and assembly-disassembly in the T = 3 viruses.
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9
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Abstract
Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of their mass-to-charge ratio (m/z) and charge. Masses are determined for thousands of individual ions, and then the results are binned to give a mass spectrum. Using this approach, accurate mass distributions can be measured for heterogeneous and high-molecular-weight samples that are usually not amenable to analysis by conventional mass spectrometry. Recent applications include heavily glycosylated proteins, protein complexes, protein aggregates such as amyloid fibers, infectious viruses, gene therapies, vaccines, and vesicles such as exosomes.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47404, United States
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10
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Biela AP, Naskalska A, Fatehi F, Twarock R, Heddle JG. Programmable polymorphism of a virus-like particle. COMMUNICATIONS MATERIALS 2022; 3:7. [PMID: 35284827 PMCID: PMC7612486 DOI: 10.1038/s43246-022-00229-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Virus-like particles (VLPs) have significant potential as artificial vaccines and drug delivery systems. The ability to control their size has wide ranging utility but achieving such controlled polymorphism using a single protein subunit is challenging as it requires altering VLP geometry. Here we achieve size control of MS2 bacteriophage VLPs via insertion of amino acid sequences in an external loop to shift morphology to significantly larger forms. The resulting VLP size and geometry is controlled by altering the length and type of the insert. Cryo electron microscopy structures of the new VLPs, in combination with a kinetic model of their assembly, show that the abundance of wild type (T = 3), T = 4, D3 and D5 symmetrical VLPs can be biased in this way. We propose a mechanism whereby the insert leads to a change in the dynamic behavior of the capsid protein dimer, affecting the interconversion between the symmetric and asymmetric conformers and thus determining VLP size and morphology.
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Affiliation(s)
- Artur P. Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
| | - Antonina Naskalska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
| | - Farzad Fatehi
- Departments of Mathematics, University of York, York YO10 5DD, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, UK
| | - Reidun Twarock
- Departments of Mathematics, University of York, York YO10 5DD, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, UK
- Department of Biology, University of York, York YO10 5DD, UK
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
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11
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Chang JY, Gorzelnik KV, Thongchol J, Zhang J. Structural Assembly of Qβ Virion and Its Diverse Forms of Virus-like Particles. Viruses 2022; 14:225. [PMID: 35215818 PMCID: PMC8880383 DOI: 10.3390/v14020225] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host. Understanding the assembly of ssRNA phages is essential for their use in biotechnology, such as RNA protection and delivery. Here, we present the complete gRNA model of the ssRNA phage Qβ, revealing that the 3' untranslated region binds to the Mat and the 4127 nucleotides fold domain-by-domain, and is connected through long-range RNA-RNA interactions, such as kissing loops. Thirty-three operator-like RNA stem-loops are located and primarily interact with the asymmetric A/B CP-dimers, suggesting a pathway for the assembly of the virions. Additionally, we have discovered various forms of the virus-like particles (VLPs), including the canonical T = 3 icosahedral, larger T = 4 icosahedral, prolate, oblate forms, and a small prolate form elongated along the 3-fold axis. These particles are all produced during a normal infection, as well as when overexpressing the CPs. When overexpressing the shorter RNA fragments encoding only the CPs, we observed an increased percentage of the smaller VLPs, which may be sufficient to encapsidate a shorter RNA.
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Affiliation(s)
| | | | | | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; (J.-Y.C.); (K.V.G.); (J.T.)
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12
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Lalwani Prakash D, Gosavi S. Understanding the Folding Mediated Assembly of the Bacteriophage MS2 Coat Protein Dimers. J Phys Chem B 2021; 125:8722-8732. [PMID: 34339197 DOI: 10.1021/acs.jpcb.1c03928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The capsids of RNA viruses such as MS2 are great models for studying protein self-assembly because they are made almost entirely of multiple copies of a single coat protein (CP). Although CP is the minimal repeating unit of the capsid, previous studies have shown that CP exists as a homodimer (CP2) even in an acid-disassembled system, indicating that CP2 is an obligate dimer. Here, we investigate the molecular basis of this obligate dimerization using coarse-grained structure-based models and molecular dynamics simulations. We find that, unlike monomeric proteins of similar size, CP populates a single partially folded ensemble whose "foldedness" is sensitive to denaturing conditions. In contrast, CP2 folds similarly to single-domain proteins populating only the folded and the unfolded ensembles, separated by a prominent folding free energy barrier. Several intramonomer contacts form early, but the CP2 folding barrier is crossed only when the intermonomer contacts are made. A dissection of the structure of CP2 through mutant folding simulations shows that the folding barrier arises both from the topology of CP and the interface contacts of CP2. Together, our results show that CP2 is an obligate dimer because of kinetic stability, that is, dimerization induces a folding barrier and that makes it difficult for proteins in the dimer minimum to partially unfold and access the monomeric state without completely unfolding. We discuss the advantages of this obligate dimerization in the context of dimer design and virus stability.
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Affiliation(s)
- Digvijay Lalwani Prakash
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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13
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San Emeterio J, Pollack L. Visualizing a viral genome with contrast variation small angle X-ray scattering. J Biol Chem 2020; 295:15923-15932. [PMID: 32913117 PMCID: PMC7681021 DOI: 10.1074/jbc.ra120.013961] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/04/2020] [Indexed: 01/14/2023] Open
Abstract
Despite the threat to human health posed by some single-stranded RNA viruses, little is understood about their assembly. The goal of this work is to introduce a new tool for watching an RNA genome direct its own packaging and encapsidation by proteins. Contrast variation small-angle X-ray scattering (CV-SAXS) is a powerful tool with the potential to monitor the changing structure of a viral RNA through this assembly process. The proteins, though present, do not contribute to the measured signal. As a first step in assessing the feasibility of viral genome studies, the structure of encapsidated MS2 RNA was exclusively detected with CV-SAXS and compared with a structure derived from asymmetric cryo-EM reconstructions. Additional comparisons with free RNA highlight the significant structural rearrangements induced by capsid proteins and invite the application of time-resolved CV-SAXS to reveal interactions that result in efficient viral assembly.
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Affiliation(s)
- Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA.
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14
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Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains. Sci Rep 2020; 10:5470. [PMID: 32214181 PMCID: PMC7096446 DOI: 10.1038/s41598-020-62328-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
Capsid proteins often present a positively charged arginine-rich sequence at their terminal regions, which has a fundamental role in genome packaging and particle stability for some icosahedral viruses. These sequences show little to no conservation and are structurally dynamic such that they cannot be easily detected by common sequence or structure comparisons. As a result, the occurrence and distribution of positively charged domains across the viral universe are unknown. Based on the net charge calculation of discrete protein segments, we identified proteins containing amino acid stretches with a notably high net charge (Q > + 17), which are enriched in icosahedral viruses with a distinctive bias towards arginine over lysine. We used viral particle structural data to calculate the total electrostatic charge derived from the most positively charged protein segment of capsid proteins and correlated these values with genome charges arising from the phosphates of each nucleotide. We obtained a positive correlation (r = 0.91, p-value <0001) for a group of 17 viral families, corresponding to 40% of all families with icosahedral structures described to date. These data indicated that unrelated viruses with diverse genome types adopt a common underlying mechanism for capsid assembly based on R-arms.
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15
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Todd AR, Alexander AW, Jarrold MF. Implementation of a Charge-Sensitive Amplifier without a Feedback Resistor for Charge Detection Mass Spectrometry Reduces Noise and Enables Detection of Individual Ions Carrying a Single Charge. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:146-154. [PMID: 32881508 DOI: 10.1021/jasms.9b00010] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Charge detection mass spectrometry (CDMS) depends on the measurement of the charge induced on a cylinder by individual ions by means of a charge-sensitive amplifier. Electrical noise limits the accuracy of the charge measurement and the smallest charge that can be detected. Thermal noise in the feedback resistor is a major source of electrical noise. We describe the implementation of a charge-sensitive amplifier without a feedback resistor. The design has significantly reduced 1/f noise facilitating the detection of high m/z ions and substantially reducing the measurement time required to achieve almost perfect charge accuracy. With the new design we have been able to detect individual ions carrying a single charge. This is an important milestone in the development of CDMS.
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Affiliation(s)
- Aaron R Todd
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew W Alexander
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
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16
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de Martín Garrido N, Crone MA, Ramlaul K, Simpson PA, Freemont PS, Aylett CHS. Bacteriophage MS2 displays unreported capsid variability assembling T = 4 and mixed capsids. Mol Microbiol 2019; 113:143-152. [PMID: 31618483 PMCID: PMC7027807 DOI: 10.1111/mmi.14406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 12/12/2022]
Abstract
Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds through a maturation protein incorporated into its capsid. Cryogenic electron microscopy has previously shown that its genome is highly ordered within virions, and that it regulates the assembly process of the capsid. In this study, we have assembled recombinant MS2 capsids with non-genomic RNA containing the capsid incorporation sequence, and investigated the structures formed, revealing that T = 3, T = 4 and mixed capsids between these two triangulation numbers are generated, and resolving structures of T = 3 and T = 4 capsids to 4 Å and 6 Å respectively. We conclude that the basic MS2 capsid can form a mix of T = 3 and T = 4 structures, supporting a role for the ordered genome in favouring the formation of functional T = 3 virions.
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Affiliation(s)
- Natàlia de Martín Garrido
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Michael A Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK.,UK DRI Care Research and Technology Centre, Imperial College London, London, UK
| | - Kailash Ramlaul
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Paul A Simpson
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Paul S Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK.,UK DRI Care Research and Technology Centre, Imperial College London, London, UK.,London BioFoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK
| | - Christopher H S Aylett
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
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17
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van Galen M, Higler R, Sprakel J. Allosteric pathway selection in templated assembly. SCIENCE ADVANCES 2019; 5:eaaw3353. [PMID: 31646175 PMCID: PMC6788871 DOI: 10.1126/sciadv.aaw3353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Assembling large numbers of molecular building blocks into functional nanostructures is no trivial task. It relies on guiding building blocks through complex energy landscapes shaped by synergistic and antagonistic supramolecular interactions. In nature, the use of molecular templates is a potent strategy to navigate the process to the desired structure with high fidelity. Yet, nature's templating strategy remains to be fully exploited in man-made nanomaterials. Designing effective template-guided self-assembling systems can only be realized through precise insight into how the chemical design of building blocks and the resulting balance of repulsive and attractive forces give rise to pathway selection and suppression of trapped states. We develop a minimal model to unravel the kinetic pathways and pathway selection of the templated assembly of molecular building blocks on a template. We show how allosteric activation of the associative interactions can suppress undesired solution-aggregation pathways and gives rise to a true template-assembly path.
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18
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Wang B, Zhang J, Wu Y. A Multiscale Model for the Self-Assembly of Coat Proteins in Bacteriophage MS2. J Chem Inf Model 2019; 59:3899-3909. [PMID: 31411466 PMCID: PMC7273741 DOI: 10.1021/acs.jcim.9b00514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The self-assembly of viral capsids is an essential step to the formation of infectious viruses. Elucidating the kinetic mechanisms of how a capsid or virus-like particle assembles could advance our knowledge about the viral lifecycle, as well as the general principles in self-assembly of biomaterials. However, current understanding of capsid assembly remains incomplete for many viruses due to the fact that the transient intermediates along the assembling pathways are experimentally difficult to be detected. In this paper, we constructed a new multiscale computational framework to simulate the self-assembly of virus-like particles. We applied our method to the coat proteins of bacteriophage MS2 as a specific model system. This virus-like particle of bacteriophage MS2 has a unique feature that its 90 sequence-identical dimers can be classified into two structurally various groups: one is the symmetric CC dimer, and the other is the asymmetric AB dimer. The homotypic interactions between AB dimers result in a 5-fold symmetric contact, while the heterotypic interactions between AB and CC dimers result in 6-fold symmetric contact. We found that the assembly can be described as a physical process of phase transition that is regulated by various factors such as concentration and specific stoichiometry between AB and CC dimers. Our simulations also demonstrate that heterotypic and homotypic interfaces play distinctive roles in modulating the assembling kinetics. The interaction between AB and CC dimers is much more dynamic than that between two AB dimers. We therefore suggest that the alternate growth of viral capsid through the heterotypic dimer interactions dominates the assembling pathways. This is, to the best of our knowledge, the first multiscale model to simulate the assembling process of coat proteins in bacteriophage MS2. The generality of this approach opens the door to its further applications in assembly of other viral capsids, virus-like particles, and novel drug delivery systems.
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Affiliation(s)
- Bo Wang
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX 77843
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
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19
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Indelicato G, Cermelli P, Twarock R. A coarse-grained model of the expansion of the human rhinovirus 2 capsid reveals insights in genome release. J R Soc Interface 2019; 16:20190044. [PMID: 31409237 PMCID: PMC6731498 DOI: 10.1098/rsif.2019.0044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/11/2019] [Indexed: 12/02/2022] Open
Abstract
Human rhinoviruses are causative agents of the common cold. In order to release their RNA genome into the host during a viral infection, these small viruses must undergo conformational changes in their capsids, whose detailed mechanism is strictly related to the process of RNA extrusion, which has been only partially elucidated. We study here a mathematical model for the structural transition between the native particle of human rhinovirus type 2 and its expanded form, viewing the process as an energy cascade, i.e. a sequence of metastable states with decreasing energy connected by minimum energy paths. We explore several transition pathways and discuss their implications for the RNA exit process.
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Affiliation(s)
| | - Paolo Cermelli
- Department of Mathematics, University of Turin, Turin, Italy
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20
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Twarock R, Stockley PG. RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy. Annu Rev Biophys 2019; 48:495-514. [PMID: 30951648 PMCID: PMC7612295 DOI: 10.1146/annurev-biophys-052118-115611] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses, entities composed of nucleic acids, proteins, and in some cases lipids lack the ability to replicate outside their target cells. Their components self-assemble at the nanoscale with exquisite precision-a key to their biological success in infection. Recent advances in structure determination and the development of biophysical tools such as single-molecule spectroscopy and noncovalent mass spectrometry allow unprecedented access to the detailed assembly mechanisms of simple virions. Coupling these techniques with mathematical modeling and bioinformatics has uncovered a previously unsuspected role for genomic RNA in regulating formation of viral capsids, revealing multiple, dispersed RNA sequence/structure motifs [packaging signals (PSs)] that bind cognate coat proteins cooperatively. The PS ensemble controls assembly efficiency and accounts for the packaging specificity seen in vivo. The precise modes of action of the PSs vary between viral families, but this common principle applies across many viral families, including major human pathogens. These insights open up the opportunity to block or repurpose PS function in assembly for both novel antiviral therapy and gene/drug/vaccine applications.
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Affiliation(s)
- Reidun Twarock
- Departments of Mathematics and Biology, and York Cross-disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, United Kingdom;
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom;
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21
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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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22
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Twarock R, Bingham RJ, Dykeman EC, Stockley PG. A modelling paradigm for RNA virus assembly. Curr Opin Virol 2018; 31:74-81. [PMID: 30078702 PMCID: PMC6281560 DOI: 10.1016/j.coviro.2018.07.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022]
Abstract
Virus assembly, a key stage in any viral life cycle, had long been considered to be primarily driven by protein-protein interactions and nonspecific interactions between genomic RNA and capsid protein. We review here a modelling paradigm for RNA virus assembly that illustrates the crucial roles of multiple dispersed, specific interactions between viral genomes and coat proteins in capsid assembly. The model reveals how multiple sequence-structure motifs in the genomic RNA, termed packaging signals, with a shared coat protein recognition motif enable viruses to overcome a viral assembly-equivalent of Levinthal's Paradox in protein folding. The fitness advantages conferred by this mechanism suggest that it should be widespread in viruses, opening up new perspectives on viral evolution and anti-viral therapy.
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Affiliation(s)
- Reidun Twarock
- York Centre for Cross-disciplinary Systems Analysis, University of York, York YO10 5GE, UK; Department of Mathematics, University of York, York YO10 5DD, UK; Department of Biology, University of York, York YO10 5NG, UK.
| | - Richard J Bingham
- York Centre for Cross-disciplinary Systems Analysis, University of York, York YO10 5GE, UK; Department of Mathematics, University of York, York YO10 5DD, UK; Department of Biology, University of York, York YO10 5NG, UK
| | - Eric C Dykeman
- York Centre for Cross-disciplinary Systems Analysis, University of York, York YO10 5GE, UK; Department of Mathematics, University of York, York YO10 5DD, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT UK
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23
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Hesketh EL, Saunders K, Fisher C, Potze J, Stanley J, Lomonossoff GP, Ranson NA. The 3.3 Å structure of a plant geminivirus using cryo-EM. Nat Commun 2018; 9:2369. [PMID: 29915210 PMCID: PMC6006435 DOI: 10.1038/s41467-018-04793-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/24/2018] [Indexed: 11/25/2022] Open
Abstract
Geminiviruses are major plant pathogens that threaten food security globally. They have a unique architecture built from two incomplete icosahedral particles, fused to form a geminate capsid. However, despite their importance to agricultural economies and fundamental biological interest, the details of how this is realized in 3D remain unknown. Here we report the structure of Ageratum yellow vein virus at 3.3 Å resolution, using single-particle cryo-electron microscopy, together with an atomic model that shows that the N-terminus of the single capsid protein (CP) adopts three different conformations essential for building the interface between geminate halves. Our map also contains density for ~7 bases of single-stranded DNA bound to each CP, and we show that the interactions between the genome and CPs are different at the interface than in the rest of the capsid. With additional mutagenesis data, this suggests a central role for DNA binding-induced conformational change in directing the assembly of geminate capsids.
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Affiliation(s)
- Emma L Hesketh
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Keith Saunders
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Chloe Fisher
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Joran Potze
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - John Stanley
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - George P Lomonossoff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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24
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Twarock R, Leonov G, Stockley PG. Hamiltonian path analysis of viral genomes. Nat Commun 2018; 9:2021. [PMID: 29789600 PMCID: PMC5964074 DOI: 10.1038/s41467-018-03713-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/02/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Reidun Twarock
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5DD, UK.
- Departments of Mathematics and Biology, University of York, York, YO10 5DD, UK.
| | - German Leonov
- York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5DD, UK
- Departments of Mathematics and Biology, University of York, York, YO10 5DD, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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25
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Abstract
Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.
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Affiliation(s)
- William M Aumiller
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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26
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Hartman EC, Jakobson CM, Favor AH, Lobba MJ, Álvarez-Benedicto E, Francis MB, Tullman-Ercek D. Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle. Nat Commun 2018; 9:1385. [PMID: 29643335 PMCID: PMC5895741 DOI: 10.1038/s41467-018-03783-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/13/2018] [Indexed: 12/22/2022] Open
Abstract
Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report a technique, termed SyMAPS (Systematic Mutation and Assembled Particle Selection), that can be used to characterize the assembly competency of all single amino acid variants of a self-assembling viral structural protein. SyMAPS studies on the MS2 bacteriophage coat protein revealed a high-resolution fitness landscape that challenges some conventional assumptions of protein engineering. An additional round of selection identified a previously unknown variant (CP[T71H]) that is stable at neutral pH but less tolerant to acidic conditions than the wild-type coat protein. The capsids formed by this variant could be more amenable to disassembly in late endosomes or early lysosomes-a feature that is advantageous for delivery applications. In addition to providing a mutability blueprint for virus-like particles, SyMAPS can be readily applied to other self-assembling proteins.
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Affiliation(s)
- Emily C Hartman
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Christopher M Jakobson
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720-1460, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andrew H Favor
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Marco J Lobba
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | | | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA.
- Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, CA, 94720-1460, USA.
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208-3120, USA.
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27
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Logan G, Newman J, Wright CF, Lasecka-Dykes L, Haydon DT, Cottam EM, Tuthill TJ. Deep Sequencing of Foot-and-Mouth Disease Virus Reveals RNA Sequences Involved in Genome Packaging. J Virol 2018; 92:e01159-17. [PMID: 29046452 PMCID: PMC5730773 DOI: 10.1128/jvi.01159-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/25/2017] [Indexed: 01/03/2023] Open
Abstract
Nonenveloped viruses protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. Packaging and capsid assembly in RNA viruses can involve interactions between capsid proteins and secondary structures in the viral genome, as exemplified by the RNA bacteriophage MS2 and as proposed for other RNA viruses of plants, animals, and human. In the picornavirus family of nonenveloped RNA viruses, the requirements for genome packaging remain poorly understood. Here, we show a novel and simple approach to identify predicted RNA secondary structures involved in genome packaging in the picornavirus foot-and-mouth disease virus (FMDV). By interrogating deep sequencing data generated from both packaged and unpackaged populations of RNA, we have determined multiple regions of the genome with constrained variation in the packaged population. Predicted secondary structures of these regions revealed stem-loops with conservation of structure and a common motif at the loop. Disruption of these features resulted in attenuation of virus growth in cell culture due to a reduction in assembly of mature virions. This study provides evidence for the involvement of predicted RNA structures in picornavirus packaging and offers a readily transferable methodology for identifying packaging requirements in many other viruses.IMPORTANCE In order to transmit their genetic material to a new host, nonenveloped viruses must protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. For many nonenveloped RNA viruses the requirements for this critical part of the viral life cycle remains poorly understood. We have identified RNA sequences involved in genome packaging of the picornavirus foot-and-mouth disease virus. This virus causes an economically devastating disease of livestock affecting both the developed and developing world. The experimental methods developed to carry out this work are novel, simple, and transferable to the study of packaging signals in other RNA viruses. Improved understanding of RNA packaging may lead to novel vaccine approaches or targets for antiviral drugs with broad-spectrum activity.
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Affiliation(s)
- Grace Logan
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Newman
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | | | | | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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28
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Fang PY, Bowman JC, Gómez Ramos L, Hsiao C, Williams LD. RNA: packaged and protected by VLPs. RSC Adv 2018; 8:21399-21406. [PMID: 35539947 PMCID: PMC9080931 DOI: 10.1039/c8ra02084a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023] Open
Abstract
VLP packaging is most efficient for compact RNA, and protects RNA against assault by small diffusible damaging agents.
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Affiliation(s)
- Po-Yu Fang
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Lizzette M. Gómez Ramos
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemical and Biomolecular Engineering
| | - Chiaolong Hsiao
- Institute of Biochemical Sciences
- National Taiwan University
- Taipei 10617
- Republic of China
| | - Loren Dean Williams
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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29
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Yuan H, Li P, Ma X, Lu Z, Sun P, Bai X, Zhang J, Bao H, Cao Y, Li D, Fu Y, Chen Y, Bai Q, Zhang J, Liu Z. The pH stability of foot-and-mouth disease virus. Virol J 2017; 14:233. [PMID: 29183342 PMCID: PMC5706165 DOI: 10.1186/s12985-017-0897-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 11/15/2017] [Indexed: 01/13/2023] Open
Abstract
ᅟ This review summarized the molecular determinants of the acid stability of FMDV in order to explore the uncoating mechanism of FMDV and improve the acid stability of vaccines. Background The foot-and-mouth disease virus (FMDV) capsid is highly acid labile and tends to dissociate into pentameric subunits at acidic condition to release viral RNA for initiating virus replication. However, the acid stability of virus capsid is greatly required for the maintenance of intact virion during the process of virus culture and vaccine production. The conflict between the acid lability in vivo and acid stability in vitro of FMDV capsid promotes the selection of a series of amino acid substitutions which can confer resistance to acid-induced FMDV inactivation. In order to explore the uncoating activity of FMDV and enhance the acid stability of vaccines, we summarized the available works about the pH stability of FMDV. Main body of the abstract In this review, we analyzed the intrinsic reasons for the acid instability of FMDV from the structural and functional aspects. We also listed all substitutions obtained by different research methods and showed them in the partial capsid of FMDV. We found that a quadrangle region in the viral capsid was the place where a great many pH-sensitive residues were distributed. As the uncoating event of FMDV is dependent on the pH-sensitive amino acid residues in the capsid, this most pH-sensitive position indicates a potential candidate location for RNA delivery triggered by the acid-induced coat disassociation. Short conclusion This review provided an overview of the pH stability of FMDV. The study of pH stability of FMDV not only contributes to the exploration of molecule and mechanism information for FMDV uncoating, but also enlightens the development of FMDV vaccines, including the traditionally inactivated vaccines and the new VLP (virus-like particle) vaccines.
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Affiliation(s)
- Hong Yuan
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Pinghua Li
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China.
| | - Xueqing Ma
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Zengjun Lu
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Pu Sun
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Xingwen Bai
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Jing Zhang
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Huifang Bao
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Yimei Cao
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Dong Li
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Yuanfang Fu
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Yingli Chen
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China
| | - Qifeng Bai
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 730046, People's Republic of China
| | - Jie Zhang
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China.
| | - Zaixin Liu
- State Key Laboratory of Veterinary Etiological Biology, OIE/China Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping, Yanchangbao, Lanzhou, Gansu, 730046, People's Republic of China.
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30
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Keifer DZ, Jarrold MF. Single-molecule mass spectrometry. MASS SPECTROMETRY REVIEWS 2017; 36:715-733. [PMID: 26873676 DOI: 10.1002/mas.21495] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/15/2016] [Indexed: 06/05/2023]
Abstract
In single-molecule mass spectrometry, the mass of each ion is measured individually; making it suitable for the analysis of very large, heterogeneous objects that cannot be analyzed by conventional means. A range of single-molecule mass spectrometry techniques has been developed, including time-of-flight with cryogenic detectors, a quadrupole ion trap with optical detection, single-molecule Fourier transform ion cyclotron resonance, charge detection mass spectrometry, quadrupole ion traps coupled to charge detector plates, and nanomechanical oscillators. In addition to providing information on mass and heterogeneity, these techniques have been used to study impact craters from cosmic dust, monitor the assembly of viruses, elucidate the fluorescence dynamics of quantum dots, and much more. This review focuses on the merits of each of these technologies, their limitations, and their applications. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:715-733, 2017.
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Affiliation(s)
- David Z Keifer
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47401
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47401
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31
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Patel N, White SJ, Thompson RF, Bingham R, Weiß EU, Maskell DP, Zlotnick A, Dykeman E, Tuma R, Twarock R, Ranson NA, Stockley PG. HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly. Nat Microbiol 2017; 2:17098. [PMID: 28628133 PMCID: PMC5495169 DOI: 10.1038/nmicrobiol.2017.98] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 05/17/2017] [Indexed: 12/20/2022]
Abstract
Formation of the hepatitis B virus nucleocapsid is an essential step in the viral lifecycle, but its assembly is not fully understood. We report the discovery of sequence-specific interactions between the viral pre-genome and the hepatitis B core protein that play roles in defining the nucleocapsid assembly pathway. Using RNA SELEX and bioinformatics, we identified multiple regions in the pre-genomic RNA with high affinity for core protein dimers. These RNAs form stem-loops with a conserved loop motif that trigger sequence-specific assembly of virus-like particles (VLPs) at much higher fidelity and yield than in the absence of RNA. The RNA oligos do not interact with preformed RNA-free VLPs, so their effects must occur during particle assembly. Asymmetric cryo-electron microscopy reconstruction of the T = 4 VLPs assembled in the presence of one of the RNAs reveals a unique internal feature connected to the main core protein shell via lobes of density. Biophysical assays suggest that this is a complex involving several RNA oligos interacting with the C-terminal arginine-rich domains of core protein. These core protein-RNA contacts may play one or more roles in regulating the organization of the pre-genome during nucleocapsid assembly, facilitating subsequent reverse transcription and acting as a nucleation complex for nucleocapsid assembly.
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Affiliation(s)
- Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Richard Bingham
- Departments of Biology and Mathematics & York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
| | - Eva U Weiß
- Departments of Biology and Mathematics & York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
| | - Daniel P Maskell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Adam Zlotnick
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Eric Dykeman
- Departments of Biology and Mathematics & York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Reidun Twarock
- Departments of Biology and Mathematics & York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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32
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Cingil HE, Boz EB, Biondaro G, de Vries R, Cohen Stuart MA, Kraft DJ, van der Schoot P, Sprakel J. Illuminating the Reaction Pathways of Viromimetic Assembly. J Am Chem Soc 2017; 139:4962-4968. [PMID: 28326772 PMCID: PMC5388896 DOI: 10.1021/jacs.7b01401] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
The coassembly of well-defined biological
nanostructures relies
on a delicate balance between attractive and repulsive interactions
between biomolecular building blocks. Viral capsids are a prototypical
example, where coat proteins exhibit not only self-interactions but
also interact with the cargo they encapsulate. In nature, the balance
between antagonistic and synergistic interactions has evolved to avoid
kinetic trapping and polymorphism. To date, it has remained a major challenge to experimentally disentangle
the complex kinetic reaction pathways that underlie successful coassembly
of biomolecular building blocks in a noninvasive approach with high
temporal resolution. Here we show how macromolecular force sensors,
acting as a genome proxy, allow us to probe the pathways through which
a viromimetic protein forms capsids. We uncover the complex multistage
process of capsid assembly, which involves recruitment and complexation,
followed by allosteric growth of the proteinaceous coat. Under certain
conditions, the single-genome particles condense into capsids containing
multiple copies of the template. Finally, we derive a theoretical
model that quantitatively describes the kinetics of recruitment and
growth. These results shed new light on the origins of the pathway
complexity in biomolecular coassembly.
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Affiliation(s)
- Hande E Cingil
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Emre B Boz
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giovanni Biondaro
- Soft Matter Physics, Huygens-Kamerling Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Daniela J Kraft
- Soft Matter Physics, Huygens-Kamerling Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Paul van der Schoot
- Theory of Polymers and Soft Matter, Eindhoven University of Technology , PO Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Theoretical Physics, Utrecht University , Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
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33
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Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJB, Butcher SJ, Stockley PG, Twarock R. Genomic RNA folding mediates assembly of human parechovirus. Nat Commun 2017; 8:5. [PMID: 28232749 PMCID: PMC5431903 DOI: 10.1038/s41467-016-0011-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/16/2016] [Indexed: 01/04/2023] Open
Abstract
Assembly of the major viral pathogens of the Picornaviridae family is poorly understood. Human parechovirus 1 is an example of such viruses that contains 60 short regions of ordered RNA density making identical contacts with the protein shell. We show here via a combination of RNA-based systematic evolution of ligands by exponential enrichment, bioinformatics analysis and reverse genetics that these RNA segments are bound to the coat proteins in a sequence-specific manner. Disruption of either the RNA coat protein recognition motif or its contact amino acid residues is deleterious for viral assembly. The data are consistent with RNA packaging signals playing essential roles in virion assembly. Their binding sites on the coat proteins are evolutionarily conserved across the Parechovirus genus, suggesting that they represent potential broad-spectrum anti-viral targets.The mechanism underlying packaging of genomic RNA into viral particles is not well understood for human parechoviruses. Here the authors identify short RNA motifs in the parechovirus genome that bind capsid proteins, providing approximately 60 specific interactions for virion assembly.
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Affiliation(s)
- Shabih Shakeel
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, 00790, Finland
| | - Eric C Dykeman
- Departments of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Ari Ora
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, 00790, Finland
- Department of Applied Physics and Department of Biotechnology and Chemical Technology, Aalto University, Espoo, 02150, Finland
| | - Joseph J B Cockburn
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah J Butcher
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, 00790, Finland.
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Reidun Twarock
- Departments of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK.
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34
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ElSawy KM. The impact of viral RNA on the association free energies of capsid protein assembly: bacteriophage MS2 as a case study. J Mol Model 2017; 23:47. [DOI: 10.1007/s00894-017-3224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/11/2017] [Indexed: 11/24/2022]
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35
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Keifer DZ, Pierson EE, Jarrold MF. Charge detection mass spectrometry: weighing heavier things. Analyst 2017; 142:1654-1671. [DOI: 10.1039/c7an00277g] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Charge detection mass spectrometry (CDMS) is a single molecule method where the mass of each ion is directly determined from individual measurements of its mass-to-charge ratio and charge.
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Affiliation(s)
| | - Elizabeth E. Pierson
- Department of Analytical Sciences
- Pharmaceutical Sciences and Clinical Supplies
- Merck Research Laboratories
- Merck & Co
- Inc
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36
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Perkett MR, Mirijanian DT, Hagan MF. The allosteric switching mechanism in bacteriophage MS2. J Chem Phys 2016; 145:035101. [PMID: 27448905 PMCID: PMC4947040 DOI: 10.1063/1.4955187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/07/2016] [Indexed: 01/16/2023] Open
Abstract
We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.
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Affiliation(s)
- Matthew R Perkett
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
| | - Dina T Mirijanian
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
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37
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Abstract
During the life cycle of a virus, viral proteins and other components self-assemble to form an ordered protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article, we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly and thus should be taken into account in models that are used to estimate interaction parameters from experimental data.
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Affiliation(s)
- Guillermo R Lazaro
- Martin Fisher School of Physics, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University , Waltham, Massachusetts 02454, United States
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38
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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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39
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Stockley PG, White SJ, Dykeman E, Manfield I, Rolfsson O, Patel N, Bingham R, Barker A, Wroblewski E, Chandler-Bostock R, Weiß EU, Ranson NA, Tuma R, Twarock R. Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid. BACTERIOPHAGE 2016; 6:e1157666. [PMID: 27144089 PMCID: PMC4836477 DOI: 10.1080/21597081.2016.1157666] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Using RNA-coat protein crosslinking we have shown that the principal RNA recognition surface on the interior of infectious MS2 virions overlaps with the known peptides that bind the high affinity translational operator, TR, within the phage genome. The data also reveal the sequences of genomic fragments in contact with the coat protein shell. These show remarkable overlap with previous predictions based on the hypothesis that virion assembly is mediated by multiple sequences-specific contacts at RNA sites termed Packaging Signals (PSs). These PSs are variations on the TR stem-loop sequence and secondary structure. They act co-operatively to regulate the dominant assembly pathway and ensure cognate RNA encapsidation. In MS2, they also trigger conformational change in the dimeric capsomere creating the A/B quasi-conformer, 60 of which are needed to complete the T=3 capsid. This is the most compelling demonstration to date that this ssRNA virus, and by implications potentially very many of them, assemble via a PS-mediated assembly mechanism.
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Affiliation(s)
- Peter G. Stockley
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Simon J. White
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Eric Dykeman
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Iain Manfield
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Ottar Rolfsson
- Center for Systems Biology, University of Iceland, University of Iceland Biomedical Center, Reykjavik, Iceland
| | - Nikesh Patel
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Richard Bingham
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Amy Barker
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Emma Wroblewski
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | | | - Eva U. Weiß
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
| | - Neil A. Ranson
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Roman Tuma
- Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Reidun Twarock
- Department of Biology and Mathematics & York Center for Complex Systems Analysis, University of York, York, UK
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40
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A novel delivery platform based on Bacteriophage MS2 virus-like particles. Virus Res 2015; 211:9-16. [PMID: 26415756 PMCID: PMC7114531 DOI: 10.1016/j.virusres.2015.08.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/22/2015] [Accepted: 08/24/2015] [Indexed: 02/02/2023]
Abstract
Here we reviewed Bacteriophage MS2 virus-like particles, including introduction to their structure, their potential as a delivery platform, and their expected use in medicine and other fields. Bacteriophage MS2 virus-like particles represent the novel delivery platform. Bacteriophage MS2 virus-like particles possess promising application prospect.
Our objective here is to review the novel delivery platform based on Bacteriophage MS2 virus-like particles (VLPs), including introduction to their structure, their potential as a delivery platform, and their expected use in medicine and other fields. Bacteriophage MS2 VLPs are nanoparticles devoid of viral genetic material and can self-assemble from the coat protein into an icosahedral capsid. As a novel delivery platform, they possess numerous features that make them suitable and attractive for targeted delivery of RNAs or DNAs, epitope peptides, and drugs within the protein capsid. In short, as a novel delivery platform, MS2 VLPs are suitable for delivery of targeted agents and hold promise for use in diagnostics, vaccines, and therapeutic modalities.
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41
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Holmes K, Shepherd DA, Ashcroft AE, Whelan M, Rowlands DJ, Stonehouse NJ. Assembly Pathway of Hepatitis B Core Virus-like Particles from Genetically Fused Dimers. J Biol Chem 2015; 290:16238-45. [PMID: 25953902 PMCID: PMC4481223 DOI: 10.1074/jbc.m114.622035] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 04/08/2015] [Indexed: 01/17/2023] Open
Abstract
Macromolecular complexes are responsible for many key biological processes. However, in most cases details of the assembly/disassembly of such complexes are unknown at the molecular level, as the low abundance and transient nature of assembly intermediates make analysis challenging. The assembly of virus capsids is an example of such a process. The hepatitis B virus capsid (core) can be composed of either 90 or 120 dimers of coat protein. Previous studies have proposed a trimer of dimers as an important intermediate species in assembly, acting to nucleate further assembly by dimer addition. Using novel genetically-fused coat protein dimers, we have been able to trap higher-order assembly intermediates and to demonstrate for the first time that both dimeric and trimeric complexes are on pathway to virus-like particle (capsid) formation.
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Affiliation(s)
- Kris Holmes
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Dale A Shepherd
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Alison E Ashcroft
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Mike Whelan
- iQur Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, United Kingdom
| | - David J Rowlands
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Nicola J Stonehouse
- From the School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
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Abstract
On the basis of a T = 1 icosahedral capsid model, the capsomer-polyion co-assembly process has been investigated by molecular dynamics simulations using capsomers with different net charge and charge distribution as well as linear, branched, and hyper-branched polyions. The assembly process was characterized in terms of the time-dependent cluster size probabilities, averaged cluster size, encapsulation efficiency, and polyion extension. The kinetics of the capsid formation displayed a two-step process. The first one comprised adsorption of capsomers on the polyion, driven by their electrostatic attraction, whereas the second one involved a relocation and/or reorientation of adsorbed capsomers, which rate is reduced upon increasing electrostatic interaction. We found that increased polyion branching facilitated a more rapid encapsulation process towards a higher yield. Moreover, the hyper-branched polyions were entirely encapsulated at all polyion-capsid charge ratios considered.
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Affiliation(s)
- Ran Zhang
- Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Per Linse
- Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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Garmann RF, Gopal A, Athavale SS, Knobler CM, Gelbart WM, Harvey SC. Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy. RNA (NEW YORK, N.Y.) 2015; 21:877-886. [PMID: 25752599 PMCID: PMC4408795 DOI: 10.1261/rna.047506.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/30/2014] [Indexed: 05/29/2023]
Abstract
The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures.
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Affiliation(s)
- Rees F Garmann
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Ajaykumar Gopal
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Shreyas S Athavale
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Stephen C Harvey
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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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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Geraets JA, Dykeman EC, Stockley PG, Ranson NA, Twarock R. Asymmetric genome organization in an RNA virus revealed via graph-theoretical analysis of tomographic data. PLoS Comput Biol 2015; 11:e1004146. [PMID: 25793998 PMCID: PMC4368512 DOI: 10.1371/journal.pcbi.1004146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug design.
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Affiliation(s)
- James A Geraets
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Eric C Dykeman
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
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Mikel P, Vasickova P, Kralik P. Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens. FOOD AND ENVIRONMENTAL VIROLOGY 2015; 7:96-111. [PMID: 25711389 PMCID: PMC7090958 DOI: 10.1007/s12560-015-9188-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
RNA viruses are pathogenic agents of many serious infectious diseases affecting humans and animals. The detection of pathogenic RNA viruses is based on modern molecular methods, of which the most widely used methods are the reverse transcription polymerase chain reaction (RT-PCR) and the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). All steps of RT-PCR and qRT-PCR should be strictly controlled to ensure the validity of obtained results. False-negative results may be caused not only by inhibition of RT or/and PCR steps but also by failure of the nucleic acid extraction step, particularly in the case of viral RNA extraction. The control of nucleic acid extraction generally involves the utilization of a non-pathogenic virus (process control virus) of similar structural properties to those of the target virus. Although in clinical samples the use of such process control virus is only recommended, in other kinds of settings such as food matrices its use is necessary. Currently, several different process control viruses are used for these purposes. Process control viruses can also be constructed artificially using technology for production of MS2 phage-like particles, which have many advantages in comparison with other used controls and are especially suited for controlling the detection and quantification of certain types of RNA viruses. The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Nevertheless, the practical use of MS2 phage-like particles in routine diagnostics is relatively uncommon. The current situation with regard to the use of MS2 phage-like particles as process control viruses in detection of RNA viruses and different methods of their construction, purification and use are summarized and discussed in this review.
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Affiliation(s)
- P Mikel
- Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic,
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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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48
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Abstract
We present direct experimental evidence that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism. We show that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid self-assembly in vitro. These experiments confirm that the selective advantages for viral yield and encapsidation specificity, predicted from previous modeling of packaging signal-mediated assembly, are found in Nature. Regions of the genome that act as packaging signals also function in translational and transcriptional enhancement, as well as directly coding for the coat protein, highlighting the density of encoded functions within the viral RNA. Assembly and gene expression are therefore direct molecular competitors for different functional folds of the same RNA sequence. The strongest packaging signal in the test fragment, encodes a region of the coat protein that undergoes a conformational change upon contact with packaging signals. A similar phenomenon occurs in other RNA viruses for which packaging signals are known. These contacts hint at an even deeper density of encoded functions in viral RNA, which if confirmed, would have profound consequences for the evolution of this class of pathogens.
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Kusters R, Lin HK, Zandi R, Tsvetkova I, Dragnea B, van der Schoot P. Role of charge regulation and size polydispersity in nanoparticle encapsulation by viral coat proteins. J Phys Chem B 2015; 119:1869-80. [PMID: 25562399 DOI: 10.1021/jp5108125] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nanoparticles can be encapsulated by virus coat proteins if their surfaces are functionalized to acquire a sufficiently large negative charge. A minimal surface charge is required to overcome (i) repulsive interactions between the positively charged RNA-binding domains on the proteins and (ii) the loss of mixing and translational entropy of RNA and capsid coat proteins. Here, we present a model describing the encapsulation of spherical particles bearing weakly acidic surface groups and investigate how charge regulation and size polydispersity impact upon the encapsulation efficiency of gold nanoparticles by model coat proteins. We show that the surface charge density of these particles cannot be assumed fixed, but that it adjusts itself to minimize electrostatic repulsion between the charges on them and maximize the attractive interaction with the RNA binding domains on the proteins. Charge regulation in combination with the natural variation of particle radii has a large effect on the encapsulation efficiency: it makes it much more gradual despite its inherently cooperative nature. Our calculations rationalize recent experimental observations on the coassembly of gold nanoparticles by brome mosaic virus coat proteins.
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Affiliation(s)
- Remy Kusters
- Faculteit Technische Natuurkunde, Technische Universiteit Eindhoven , Postbus 513, 5600 MB Eindhoven, The Netherlands
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Abstract
Cancers arise through the progression of multiple genetic and epigenetic defects that lead to deregulation of numerous signalling networks. However, the last decade has seen the development of the concept of 'oncogene addiction', where tumours appear to depend on a single oncogene for survival. RNAi has provided an invaluable tool in the identification of these oncogenes and oncogene-dependent cancers, and also presents great potential as a novel therapeutic strategy against them. Although RNAi therapeutics have demonstrated effective killing of oncogene-dependent cancers in vitro, their efficacy in vivo is severely limited by effective delivery systems. Several virus-based RNAi delivery strategies have been explored, but problems arose associated with high immunogenicity, random genome integration and non-specific targeting. This has directed efforts towards non-viral formulations, including delivery systems based on virus-like particles, liposomes and cationic polymers, which can circumvent some of these problems by immunomasking and the use of specific tumour-targeting ligands. This review outlines the prevalence of oncogene-dependent cancers, evaluates the potential of RNAi-based therapeutics and assesses the relative strengths and weaknesses of different approaches to targeted RNAi delivery.
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