Probing the biophysical interplay between a viral genome and its capsid
Open accessAbstract
The interaction between a viral capsid and its genome governs crucial steps in the life cycle of a virus, such as assembly and genome uncoating. Tuning cargo-capsid interactions is also essential for successful design and cargo delivery in engineered viral systems. Here we investigate the interplay between cargo and capsid for the picorna-like Triatoma virus using a combined native mass spectrometry and atomic force microscopy approach. We propose a topology and assembly model in which heterotrimeric pentons that consist of five copies of structural proteins VP1, VP2 and VP3 are the free principal units of assembly. The interpenton contacts are established primarily by VP2. The dual role of the genome is first to stabilize the densely packed virion and, second, on an increase in pH to trigger uncoating by relaxing the stabilizing interactions with the capsid. Uncoating occurs through a labile intermediate state of the virion that reversibly disassembles into pentons with the concomitant release of protein VP4.
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Native ion mobility mass spectrometry can monitor the dynamics of capsid morphology and stability as a function of pH and ionic strength.
“As many capsid proteins self-assemble in vitro, native ion mobility MS can monitor the dynamics of capsid morphology and stability as a function of pH and ionic strength (28, 29).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [29]
Native mass spectrometry and atomic force microscopy demonstrated that the single-stranded RNA genome of Triatoma virus stabilizes or triggers uncoating of the capsid in a pH-dependent fashion through electrostatic genome-capsid interactions.
“For example, native MS and atomic force microscopy have demonstrated that the single-stranded RNA genome of the picorna-like Triatoma virus stabilizes or triggers uncoating of the capsid in a pH-dependent fashion through electrostatic genome-capsid interactions (29).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [29]
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“The functional domains of TrV, instead, have so far been probed only by nano-indentation experiments and characterized from the inspection of rupture debris (Roos et al., 2010; Snijder et al., 2013).”
BackgroundMethodMechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
Polles, G., Indelicato, G., Potestio, R., Cermelli, P., Twarock, R., & Micheletti, C. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003331 · Cited by 46 · see citing works
“For instance, nano-indentation experiments, where viral particles are subject to mechanical stress and fatigue by atomic force microscopy, have singled out the mechanical building blocks of viral capsids and elucidated the mechanisms of genome uncoating [25].”
BackgroundMartín-González, N., Hernando‐Pérez, M., Condezo, G. N., Pérez-Illana, M., Šiber, A., Reguera, D., Ostapchuk, P., Hearing, P., Martı́n, C. S., & de Pablo, P. J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz687 · Cited by 46 · see citing works
Ammonia as an In Situ Sanitizer: Influence of Virus Genome Type on Inactivation
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“Genome release was found to occur at a pH between 8 and 9 for an ssRNA insect virus (74) and at a temperature of 45 to 70°C at pH 7.”
BackgroundAnalytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids
Kondylis, P., Schlicksup, C. J., Zlotnick, A., & Jacobson, S. C. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b04824 · Cited by 42 · see citing works
Tuning Viral Capsid Nanoparticle Stability with Symmetrical Morphogenesis
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“Triatoma virus is the only entomopathogenic virus identified in triatomines and its structure consists of 9,010 nucleotide positive-sense ssRNA genome that is encapsulated by 60 copies of structural proteins VP2, VP4, VP3 and VP1 [9].”
BackgroundStructural mass spectrometry goes viral
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Self-citationAtomic force microscopy of virus shells
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Effect of dsDNA on the Assembly Pathway and Mechanical Strength of SV40 VP1 Virus-like Particles
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MD Simulations of Viruslike Particles with Supra CG Solvation Affordable to Desktop Computers
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Vertex-Specific Proteins pUL17 and pUL25 Mechanically Reinforce Herpes Simplex Virus Capsids
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Calcium Ions Modulate the Mechanics of Tomato Bushy Stunt Virus
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“Previous mechanical studies of VNPs have shown that the AFM tip usually removes individual structural components (16,19,26,36) after the elastic limit.”
BackgroundZhang, C., Li, Y., & Li, J. (2019) · Chemical Engineering Journal · doi:10.1016/j.cej.2019.123687 · Cited by 29 · see citing works
Atomic Force Microscopy of Viruses
de Pablo, P. J., & Schaap, I. A. T. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-14741-9_8 · Cited by 29 · see citing works
Towards integrative structural mass spectrometry: Benefits from hybrid approaches
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The role of structural proteomics in vaccine development: recent advances and future prospects
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“[18–21] From the initial analysis of small complexes, native MS is now able to investigate soluble or membrane-extracted complexes of MDa, such as the ribosome,[22,23] viral capsids [21,24,25] or ATPases.”
BackgroundDynamics in the murine norovirus capsid revealed by high-resolution cryo-EM
Snowden, J. S., Hurdiss, D. L., Adeyemi, O. O., Ranson, N. A., Herod, M. R., & Stonehouse, N. J. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000649 · Cited by 29 · see citing works
“VLPs lack a viral genome, which can provide stabilising interactions with the capsid [33].”
BackgroundFree Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach
Martínez, M., Cooper, C. D., Poma, A. B., & Guzman, H. V. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00883 · Cited by 28 · see citing works
Native mass spectrometry for understanding dynamic protein complex
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Probing and pressing surfaces of hepatitis C virus-like particles
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Virion Structure of Israeli Acute Bee Paralysis Virus
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“Furthermore, pentamers of capsid protomers were also shown to be capsid precursors (57, 58).”
BackgroundArtificial Protein Cage with Unusual Geometry and Regularly Embedded Gold Nanoparticles
Majsterkiewicz, K., Biela, A. P., Maity, S., Sharma, M., Piette, B. M. A. G., Kowalczyk, A., Gaweł, S., Chakraborti, S., Roos, W. H., & Heddle, J. G. (2022) · Nano Letters · doi:10.1021/acs.nanolett.1c04222 · Cited by 26 · see citing works
Self-citationAFM nanoindentation of protein shells, expanding the approach beyond viruses
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Self-citationTriatoma Virus Recombinant VP4 Protein Induces Membrane Permeability through Dynamic Pores
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“This behavior, which is opposite that observed in picornaviruses (16), is consistent with the disassembly and genome release model proposed for TrV (22).”
ResultSelf-citationDicistrovirus-Host Molecular Interactions
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“Nanoindentation results showed that many virus protein capsids behave like elastic and robust nanocontainers (Snijder et al. 2013).”
BackgroundHeinze, K., Sasaki, E., King, N. P., Baker, D. A., Hilvert, D., Wuite, G. J. L., & Roos, W. H. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b01464 · Cited by 23 · see citing works
“19,25 The packaging of cargo in the AaLS-13 samples was not saturated (1 GFP(+36) molecule per ∼ 17 AaLS-13 subunits), 45 which might explain the absence of a strong e ff ect.”
BackgroundSelf-citationMaturation of adenovirus primes the protein nano-shell for successful endosomal escape
Denning, D., Bennett, S. P., Mullen, T.-M., Moyer, C. L., Vorselen, D., Wuite, G. J. L., Nemerow, G. R., & Roos, W. H. (2019) · Nanoscale · doi:10.1039/c8nr10182e · Cited by 23 · see citing works
Self-citationpH stability and disassembly mechanism of wild-type simian virus 40
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The application of atomic force microscopy for viruses and protein shells: Imaging and spectroscopy
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Acidification induces condensation of the adenovirus core
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Biology of Adenovirus Cell Entry
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A single point mutation in precursor protein VI doubles the mechanical strength of human adenovirus
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“For other viruses, it has been shown that not only the presence of the genome but also the interaction between genome and capsid influences the mechanical properties of the viral capsid [37, 51].”
BackgroundSelf-citationAtomic force microscopy-based bioanalysis for the study of disease
Morton, K. C., & Baker, L. A. (2014) · Analytical Methods · doi:10.1039/c4ay00485j · Cited by 20 · see citing works
Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles
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“Parameters for empty and ssRNA-loaded TrV capsids indicate that the difference in particle stiffness is largely due to an increase in the Young’s modulus for Hertzian deformation EH = 0.03 GPa (empty TrV) vs 0.14 GPa (full TrV), which suggests that local indentations are resisted in ssRNA-filled particles.”
BackgroundMethodResultInfluentialSelf-citationIntermittency of Deformation and the Elastic Limit of an Icosahedral Virus under Compression
Hernando‐Pérez, M., Zeng, C., Miguel, M. C., & Dragnea, B. G. (2019) · ACS Nano · doi:10.1021/acsnano.9b02133 · Cited by 20 · see citing works
Rhinovirus Inhibitors: Including a New Target, the Viral RNA
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“Dynamic capsid disassembly/reassembly has indeed been demonstrated for the insect pathogen Triatoma virus by using native mass spectrometry [63].”
MethodViso, J. F., Belelli, P. G., Machado, M. R., González‐Díaz, H., Pantano, S., Amundarain, M. J., Zamarreño, F., Branda, M. M., Guérin, D. M. A., & Costabel, M. D. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006082 · Cited by 18 · see citing works
Self-citationCapsid Structure of a Marine Algal Virus of the Order Picornavirales
Munke, A., Kimura, K., Tomaru, Y., & Okamoto, K. (2020) · Journal of Virology · doi:10.1128/jvi.01855-19 · Cited by 17 · see citing works
“pentameric disassembly (68, 69), and VP4 is responsible for forming membrane pores”
BackgroundIn a flash of light: X-ray free electron lasers meet native mass spectrometry
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Self-citationAssembly and Stability of Simian Virus 40 Polymorphs
Waltmann, C., Asor, R., Raviv, U., & de la Cruz, M. O. (2020) · ACS Nano · doi:10.1021/acsnano.9b10004 · Cited by 16 · see citing works
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Mathew, A., Buijs, R., Eijkel, G. B., Giskes, F., Dyachenko, A., van der Horst, J., Белов, Д. В., Spaanderman, D.-J., Heck, A. J. R., Siegel, T. P., et al. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00412 · Cited by 16 · see citing works
Self-citationVirus-like Particles Armored by an Endoskeleton
Wu, Z., Bayón, J. L., Kouznetsova, T. B., Ouchi, T., Barkovich, K. J., Hsu, S. K., Craig, S. L., & Steinmetz, N. F. (2024) · Nano Letters · doi:10.1021/acs.nanolett.3c03806 · Cited by 15 · see citing works
Atomic Force Microscopy of Viruses
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Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology
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“These nanocontainers, when found suitable, could function as vehicles, for example, for drug delivery [73,74].”
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Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction
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Direct visualization of single virus restoration after damage in real time
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Host range of Triatoma virus does not extend to Aedes aegypti and Apis mellifera
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Material Properties of Viral Nanocages Explored by Atomic Force Microscopy
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“[54] using both native mass spectrometry (MS) and AFM.”
MethodSelf-citationSánchez‐Eugenia, R., Durana, A., López-Marijuan, I., Martí, G. A., & Guérin, D. M. A. (2016) · Journal of General Virology · doi:10.1099/jgv.0.000580 · Cited by 10 · see citing works
“After rebuilding, noncrystallographic symmetry (NCS)-constrained refinement and density averaging cycles, the final model represented the conformational changes that occurred in the capsid due to the release of RNA and VP4.”
InfluentialSelf-citationCharacterization of Monoclonal Antibody Aggregates and Emerging Technologies
Remmele, R. L., Bee, J. S., Phillips, J. J., Mo, W., Higazi, D. R., Zhang, J., Lindo, V., & Kippen, A. D. (2015) · ACS symposium series · doi:10.1021/bk-2015-1202.ch005 · Cited by 10 · see citing works
AFM Nanoindentation Experiments on Protein Shells: A Protocol
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Self-citationPathogenicity of La Jolla Virus in Drosophila suzukii following Oral Administration
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“D. melanogaster was orally exposed to Drosophila C virus (DCV), a single-stranded positive-sense RNA virus belonging to the family Dicistroviridae [24,26,27], and to Nora virus, an unclassified picorna-like virus that is persistently transmitted via the fecal-oral route [28].”
BackgroundProbing Bunyavirus N protein oligomerisation using mass spectrometry
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Label-free microscopy for virus infections
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“Besides destabilizing the viral capsid at the uncoating stage, viral genome packaging strengthens the capsid before uncoating and increases thermotolerance and resistance to external pressure; the latter demonstrated by mechanical fatigue AFM experiments [68,80,87,88].”
BackgroundVirion Structure and In Vitro Genome Release Mechanism of Dicistrovirus Kashmir Bee Virus
Mukhamedova, L., Füzik, T., Nováček, J., Hrebík, D., Přidal, A., Martí, G. A., Guérin, D. M. A., & Plevka, P. (2021) · Journal of Virology · doi:10.1128/jvi.01950-20 · Cited by 8 · see citing works
“It has been shown previously that capsid proteins of triatoma virus 269 re-assemble into empty particles after the genome release (21).”
BackgroundMethodInfluentialSelf-citationReversibly Photo‐Modulating Mechanical Stiffness and Toughness of Bioengineered Protein Fibers
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Self-citationMaksudov, F., Kononova, O., Llauró, A., Ortega-Esteban, Á., Douglas, T., Condezo, G. N., Martı́n, C. S., Marx, K. A., Wuite, G. J. L., Roos, W. H., et al. (2020) · Acta Biomaterialia · doi:10.1016/j.actbio.2020.12.043 · Cited by 8 · see citing works
Self-citation
- Authors
- Snijder, J., Uetrecht, C., Rose, R. J., Sanchez-Eugenia, R., Marti, G. A., Agirre, J., Guérin, D. M. A., Wuite, G. J. L., Heck, A. J. R., & Roos, W. H.
- Affiliations
- Utrecht University (NL)
- Consejo Superior de Investigaciones Científicas (ES)
- Vrije Universiteit Amsterdam (NL)
- Corresponding author
- Heck, A. J. R.
- Roos, W. H.
- ORCID
- Venue
- Nature Chemistry
- Published
- 2013-04-28
- Volume
- 5
- Issue
- 6
- Pages
- 502-509
- ISSN
- 1755-4330 (ISSN-L)
- 1755-4349
- OpenAlex
- W2128588803
- Cited by
- 127
- References
- 50
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 5 · 2023: 5 · 2022: 4 · 2021: 15 · 2020: 15 · 2019: 15 · 2018: 11 · 2017: 11 · 2016: 13 · 2015: 15 · 2014: 8 · 2013: 5
- FWCI
- 6.13
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- VU Research Portal (submittedVersion)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (819.02.10)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Keywords
- picorna-like virus, viral capsid, viral genome, capsid assembly, VP2, VP4, capsid stability, cargo delivery
- MeSH terms
- Animals, Biomechanical Phenomena, Capsid, Hydrogen-Ion Concentration, Insect Viruses, Models, Molecular, Protein Conformation, Triatoma, Genome, Viral, Biophysical Phenomena, Virus Uncoating
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