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Probing the biophysical interplay between a viral genome and its capsid
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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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“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]
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“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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Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles
Kononova, O., Snijder, J., Kholodov, Y. A., Marx, K. A., Wuite, G. J. L., Roos, W. H., & Barsegov, V. A. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004729 · Cited by 20
“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
Rhinovirus Inhibitors: Including a New Target, the Viral RNA
Real-Hohn, A., & Blaas, D. (2021) · Viruses · doi:10.3390/v13091784 · Cited by 20
“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
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
“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
Kádek, A., Lorenzen, K., & Uetrecht, C. (2021) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2021.07.001 · Cited by 16
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
Martí, G. A., Balsalobre, A., Susevich, M. L., Rabinovich, J., & Echeverría, M. G. (2014) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2014.10.008 · Cited by 16
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
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
Atomic Force Microscopy of Viruses
de Pablo, P. J. (2013) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-94-007-6552-8_8 · Cited by 15
Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology
Simanjuntak, Y., Schamoni-Kast, K., Grün, A. F. R., Uetrecht, C., & Scaturro, P. (2021) · Viruses · doi:10.3390/v13040668 · Cited by 15
“These nanocontainers, when found suitable, could function as vehicles, for example, for drug delivery [73,74].”
BackgroundSelf-citationCooper, C. D., Addison-Smith, I., & Guzman, H. V. (2022) · Nanoscale · doi:10.1039/d2nr02526d · Cited by 14
Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction
Wright, B. W., Ruan, J., Molloy, M. P., & Jaschke, P. R. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00323 · Cited by 13
Sharma, A., Yadav, H. O. S., & Bandyopadhyay, P. (2024) · Biophysical Chemistry · doi:10.1016/j.bpc.2024.107347 · Cited by 13
Direct visualization of single virus restoration after damage in real time
de Pablo, P. J., Hernando‐Pérez, M., Carrasco, C., & Carrascosa, J. L. (2018) · Journal of Biological Physics · doi:10.1007/s10867-018-9492-9 · Cited by 12
Host range of Triatoma virus does not extend to Aedes aegypti and Apis mellifera
Martí, G. A., Bonica, M. B., Susevich, M. L., Reynaldi, F. J., Micieli, M. V., & Echeverría, M. G. (2020) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2020.107383 · Cited by 11
Yang, W., Cai, C., Wang, S., Wang, X., & Dai, X. (2024) · Bioresource Technology · doi:10.1016/j.biortech.2024.131541 · Cited by 10
Material Properties of Viral Nanocages Explored by Atomic Force Microscopy
van Rosmalen, M. G. M., Roos, W. H., & Wuite, G. J. L. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-2131-7_11 · Cited by 10
“[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
“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 11
AFM Nanoindentation Experiments on Protein Shells: A Protocol
Guo, Y., & Roos, W. H. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8894-5_14 · Cited by 10
Self-citationPathogenicity of La Jolla Virus in Drosophila suzukii following Oral Administration
Linscheid, Y., Kessel, T., Vilcinskas, A., & Lee, K. (2022) · Viruses · doi:10.3390/v14102158 · Cited by 9
“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
Cooper-Shepherd, D. A., Ariza, A., Edwards, T. A., Barr, J. N., Stonehouse, N. J., & Ashcroft, A. E. (2014) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.6841 · Cited by 9
Label-free microscopy for virus infections
Petkidis, A., Andriasyan, V., & Greber, U. F. (2023) · Microscopy · doi:10.1093/jmicro/dfad024 · Cited by 8
“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
“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
Sun, J., Ma, C., Maity, S., Wang, F., Zhou, Y. J., Portale, G., Göstl, R., Roos, W. H., Zhang, H., Liu, K., et al. (2020) · Angewandte Chemie · doi:10.1002/ange.202012848 · Cited by 8
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
Self-citation
Metadata
- 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
- Life Sciences › Immunology and Microbiology › Virology › 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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