Physics of viral dynamics

Bruinsma, Robijn; Wuite, Gijs J.L.; Roos, Wouter H.

doi:10.1038/s42254-020-00267-1

Cited by 74 publications

(64 citation statements)

References 200 publications

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“…The first type depends on a specific RNA structure and involves the TLS located at the 3 end of BMV genomic RNAs [14]. It was shown that the encapsidation of BMV RNA lacking TLSs is not effective but can be restored after complementation with yeast tRNA or separate TLSs [8]. We show that yeast tRNA alone is sufficient to mediate the formation of stable and homogenous VLPs.…”

Section: Discussionmentioning

confidence: 93%

“…Capsid assembly is currently being extensively analyzed, and some general rules of this process have already been determined. The formation of capsid depends on the temperature, pH, ionic strength, CP concentration and features of the encapsidated core molecules [6][7][8]. Due to the recent development of experimental and computational techniques in the field of physical virology, the static descriptions of viral particles have been replaced by dynamic models based on soft-mode dynamics and kinetic trapping [9].…”

Section: Introductionmentioning

confidence: 99%

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Virus-Like Particles Produced Using the Brome Mosaic Virus Recombinant Capsid Protein Expressed in a Bacterial System

Strugała

Jagielski

Kamel

et al. 2021

IJMS

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Virus-like particles (VLPs), due to their nanoscale dimensions, presence of interior cavities, self-organization abilities and responsiveness to environmental changes, are of interest in the field of nanotechnology. Nevertheless, comprehensive knowledge of VLP self-assembly principles is incomplete. VLP formation is governed by two types of interactions: protein–cargo and protein–protein. These interactions can be modulated by the physicochemical properties of the surroundings. Here, we used brome mosaic virus (BMV) capsid protein produced in an E. coli expression system to study the impact of ionic strength, pH and encapsulated cargo on the assembly of VLPs and their features. We showed that empty VLP assembly strongly depends on pH whereas ionic strength of the buffer plays secondary but significant role. Comparison of VLPs containing tRNA and polystyrene sulfonic acid (PSS) revealed that the structured tRNA profoundly increases VLPs stability. We also designed and produced mutated BMV capsid proteins that formed VLPs showing altered diameters and stability compared to VLPs composed of unmodified proteins. We also observed that VLPs containing unstructured polyelectrolyte (PSS) adopt compact but not necessarily more stable structures. Thus, our methodology of VLP production allows for obtaining different VLP variants and their adjustment to the incorporated cargo.

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Section: Discussionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Virus-Like Particles Produced Using the Brome Mosaic Virus Recombinant Capsid Protein Expressed in a Bacterial System

Strugała

Jagielski

Kamel

et al. 2021

IJMS

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“…To answer the question of whether viruses are alive or not, I base my argument in support of considering viruses as living entities obviously on my own definition of life (this paper), as well as on what we know about the biology of viruses. First, viruses, like all cellular entities in nature, are composed of organic molecules; a virus consists of a nucleic acid (DNA or RNA), which is its genetic material as in all living things, and a protein capsid encoded by the viral genome that protects the viral genetic material and participates in the propagation of the virus in the host; viral capsids show fascinating dynamics during the viral life cycle [ 49 ]. Secondly, viruses are highly organized structures.…”

Section: Are Viruses Alive?mentioning

confidence: 99%

What is life?

Gómez-Márquez

2021

Mol Biol Rep

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Background Many traditional biological concepts continue to be debated by biologists, scientists and philosophers of science. The specific objective of this brief reflection is to offer an alternative vision to the definition of life taking as a starting point the traits common to all living beings. Results and Conclusions Thus, I define life as a process that takes place in highly organized organic structures and is characterized by being preprogrammed, interactive, adaptative and evolutionary. If life is the process, living beings are the system in which this process takes place. I also wonder whether viruses can be considered living things or not. Taking as a starting point my definition of life and, of course, on what others have thought about it, I am in favor of considering viruses as living beings. I base this conclusion on the fact that viruses satisfy all the vital characteristics common to all living things and on the role they have played in the evolution of species. Finally, I argue that if there were life elsewhere in the universe, it would be very similar to what we know on this planet because the laws of physics and the composition of matter are universal and because of the principle of the inexorability of life.

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“…In recent decades, natural spherical viral capsids have attracted considerable attention for application as nanoreactors, vaccine platforms, and nanocarriers for drug delivery systems [ 9 , 10 , 11 , 12 ]. Physicochemical analysis of the self-assembly processes of viral capsids is an important aspect in molecular biology and valuable for the molecular design of viral capsids as functional materials [ 13 , 14 ]. To elucidate the self-assembling process of natural viral capsids, intermediate structures have been previously detected by ion mobility separation-mass spectrometry, interferometric scattering microscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM) under dilute conditions [ 14 , 15 , 16 ].…”

Section: Introductionmentioning

confidence: 99%

“…Physicochemical analysis of the self-assembly processes of viral capsids is an important aspect in molecular biology and valuable for the molecular design of viral capsids as functional materials [ 13 , 14 ]. To elucidate the self-assembling process of natural viral capsids, intermediate structures have been previously detected by ion mobility separation-mass spectrometry, interferometric scattering microscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM) under dilute conditions [ 14 , 15 , 16 ]. Nonetheless, the formation of viral capsids by self-assembly actually occurs in molecular crowding environments, such as a host cell [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid

Kobayashi

Inaba

Matsuura

2021

IJMS

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Recent progress in the de novo design of self-assembling peptides has enabled the construction of peptide-based viral capsids. Previously, we demonstrated that 24-mer β-annulus peptides from tomato bushy stunt virus spontaneously self-assemble into an artificial viral capsid. Here we propose to use the artificial viral capsid through the self-assembly of β-annulus peptide as a simple model to analyze the effect of molecular crowding environment on the formation process of viral capsid. Artificial viral capsids formed by co-assembly of fluorescent-labelled and unmodified β-annulus peptides in dilute aqueous solutions and under molecular crowding conditions were analyzed using fluorescence correlation spectroscopy (FCS). The apparent particle size and the dissociation constant (Kd) of the assemblies decreased with increasing concentration of the molecular crowding agent, i.e., polyethylene glycol (PEG). This is the first successful in situ analysis of self-assembling process of artificial viral capsid under molecular crowding conditions.

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Physics of viral dynamics

Cited by 74 publications

References 200 publications

Virus-Like Particles Produced Using the Brome Mosaic Virus Recombinant Capsid Protein Expressed in a Bacterial System

Virus-Like Particles Produced Using the Brome Mosaic Virus Recombinant Capsid Protein Expressed in a Bacterial System

What is life?

Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid

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