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Models of viral capsid symmetry as a driver of discovery in virology and nanotechnology

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Viruses are prominent examples of symmetry in biology. A better understanding of symmetry and symmetry breaking in virus structure via mathematical modelling opens up novel perspectives on how viruses form, evolve and infect their hosts. In particular, mathematical models of viral symmetry pave the way to novel forms of antiviral therapy and the exploitation of viral protein containers in bio-nanotechnology.
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20
Models of viral capsid symmetry
as a driver of discovery in
virology andnanotechnology
Viruses are prominent examples of symmetry in biology. A better understanding of symmetry and
symmetry breaking in virus structure via mathematical modelling opens up novel perspectives on
how viruses form, evolve and infect their hosts. In particular, mathematical models of viral symmetry
pave the way to novel forms of antiviral therapy and the exploitation of viral protein containers in
bio- nanotechnology.
Pierre- Philippe Dechant
(York St John University,
U.K.)
Reidun Twarock
(University of York, U.K.)
Breaking Symmetry
Symmetry is ubiquitous in virology
Viruses are evolutionarily highly optimized molecular
machines. Understanding their inner workings sheds
light on fundamental questions in molecular biology,
biomedicine and nanotechnology. Viruses store their
genetic material inside protective protein containers
called viral capsids. Viral genomes consist of either
DNA or RNA, which can both be single or double-
stranded, and some viruses reverse transcribe between
the two. Single- stranded viruses tend to have shorter
genomes due to the relative exibility of the nucleic acid
molecule, and they oen package their genomes into the
capsid during its assembly in a co- assembly process. By
contrast, genetically more complex viruses tend to store
their genetic message in the form of the more stable
dsDNA. Whilst some of these viruses have much more
complex life cycles and less symmetric structures (e.g.
poxviruses), a surprisingly large fraction of them still
exhibit icosahedral and helical design principles (e.g.
the tailed phages or many of the recently discovered
giant viruses). In these viruses, the nucleic acid is oen
packaged into a preformed capsid using an energy-
driven molecular motor.
In the vast majority of viruses, these capsid containers
exhibit icosahedral symmetry, meaning that they look
like tiny footballs at the nanoscale. From a mathematical
point of view, this implies that the structural organization
of the capsid building blocks, called capsomers, and their
constituent protein subunits, displays a characteristic
set of rotational symmetry axes with two-, three- and
ve- fold symmetry (Figure1a). Denoting the locations
of the protein subunits in the corners of the triangles
gives rise to characteristic protein clusters (cf. clusters of
grey spheres in Figure1b). Crick and Watson provided
a biological explanation for this surprising degree of
symmetry in virology. ey argued that viruses encode
only a small number of distinct protein building blocks,
which are then repeatedly synthesized from the same
gene, as this minimizes the part of the genome required
to code for the capsid. For instance, hepatitis B virus
and phage MS2 only encode one structural protein each
and only have four genes altogether. At the same time,
building a capsid from the largest known rotational
symmetry, the icosahedral symmetry, ensures that the
maximal possible number of subunits is used to form
the capsid, thus optimizing its volume. is is known
as the principle of genetic economy. It is a consequence
of the selective pressure in viral evolution to generate
capsid structures that make genome packaging as easy
as possible, thus optimizing an essential step in any viral
replication cycle.
Mathematical models of viral symmetry
Symmetry alone is not sucient to explain all aspects of
virus architecture as can be seen from the plethora of
distinct capsid structures in nature that all obey icosahedral
symmetry. Mathematics can play a key role in formulating
the rules according to which viral capsids are organized.
e rst mathematical models of capsid architecture were
introduced by Caspar and Klug in 1962. ey are based
on the principle of quasi- equivalence, which stipulates
that protein subunits organize locally into equivalent
environments. From a mathematical point of view,
this implies that virus capsids should be describable by
surface lattices. Caspar and Klug used triangulations of
the capsid surface, in which protein organization in the
triangular facets mimics that of the icosahedral faces in the
simplest viruses. Such models can be built by drawing an
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Breaking Symmetry
icosahedral net on a hexagonal lattice and then folding this
net up into an icosahedron. In their seminal theory, they
provide a classication of virus architecture in terms of such
triangulations, deriving polyhedral models that indicate
the positions of individual capsid proteins in the surface
lattice. Indeed, it is possible to break a triangle down into
smaller triangles. An example of a virus structure that can
be modelled in this way is the hepatitis B virus, where an
icosahedral face is broken down into four triangular facets
(Figure1c). is idea leads to the triangulation number ,
which counts how many smaller triangles each icosahedral
face consists of (e.g. four in the example above). e dierent
triangles are then not necessarily symmetry- equivalent in a
mathematical sense, but are in approximately equivalent
local environments, which is why capsid architectures,
according to Caspar and Klug, are called quasi- equivalent.
A large fraction of the only recently discovered giant
viruses also exhibit this design principle (Figure1d). e
largest precisely known structure is
that occurs in Cafeteria
roenbergensis virus. It is so large that it even has a virophage
(the Mavirus virophage) associated with it. Mimiviruses
are even larger, with an estimated - number around 1000.
Similarly, they have a virophage called Sputnik, which
itself has a substantial triangulation number of 27. Caspar–
Klug- type cage architectures also occur in other areas
of science, where repeated building blocks are used to
construct higher- order structures. Examples are carbon
fullerenes, cellular compartments (such as carboxysomes),
and they have even been engineered as geodesic domes
in architecture. A major conclusion from Caspar–Klug
theory is that only certain triangulation numbers, and thus
numbers of capsid proteins, are possible.
With the advent of more rened imaging
techniques, in particular, the recent revolution in cryo-
electron microscopy (cryo- EM), it has become clear
that these Caspar–Klug- type models are too restrictive
in order to explain all known capsid architectures.
Prominent examples are the cancer- causing papilloma
viruses (e.g. human papillomavir us (HPV) in Figure2a)
that have capsids in which every protein subunit takes
on one of two distinct types of local conguration.
Viral tiling theory, a rst generalization of Caspar
Klug theory, had been introduced to describe such
non–quasi- equivalent capsid architectures, in which
the proteins are not in approximately equivalent local
environments, as the bonds they are forming with the
surrounding proteins are not identical. is is done via
tessellations akin to the famous Penrose tiling, in which
distinct types of tiles represent the dierent types of
biological interactions. In this case, kites represent
three proteins forming a trimer interaction, and
rhombs two proteins involved in a dimer interaction.
Moreover, a generalized principle of quasi- equivalence
has recently been introduced that also encompasses
the architectures of viral capsids formed from more
than one type of capsid protein such as herpes simplex
virus (Figure2b), or the dsDNA tailed phage Basilisk.
is principle stipulates that local interactions between
Figure 1. Historic mathematical models of virus
architecture. (a) Viruses exhibit icosahedral symmetry, as
exemplied for Satellite Tobacco Necrosis Virus (pdb- id
4bcu). Examples of particle 2-, 3-, and 5- fold symmetry axes
are indicated on an icosahedral reference frame. (b) Protein
positions (grey) in an icosahedral virus model. (c) Example of
a model (here a T=4 triangulation for Hepatitis B virus based
on pdb- id 3j2v) in Caspar and Klug’s quasi- equivalence
theory; an icosahedral face subdivided into 4 triangular
facets is indicated by a black triangle. (d) Virus capsids
with very large triangulation numbers have recently been
discovered in giant viruses (here based on pdb- id 1m4x of
Paramecium Bursaria Chlorella Virus, with a T- number of 169,
shown together with an icosahedral reference frame).
Figure 2. Generalized tiling models of virus architecture.
(a) Viral Tiling theory model of Human Papillomavirus (HPV)
(based on pdb- id 3j6r); interactions between three proteins
(trimer interactions) are represented by kite- shaped tiles,
and interactions between two proteins (dimer interactions)
by rhombic tiles. (b) Herpes Simplex virus exhibits the
architecture of an Archimedean surface lattice based on the
generalised quasi- equivalence principle (based on pdb- id
6cgr).
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Breaking Symmetry
identical proteins, as well as interactions between the
same types of distinct proteins, must be the same across
the entire capsid surface. In this framework, capsid
architectures are modelled based on more general types
of lattices called Archimedean lattices. is theory
contains the hexagonal surface lattices from Caspar–
Klug theory as a special case, and has a number of
interesting implications for the geometric constraints
on viral evolution. For example, it suggests that the
size gaps between capsid architectures in Caspar–Klug
theory may be bridged by capsid structures abiding to
these more generalized lattice types. It even suggests
a way in which larger capsid architectures may have
evolved from smaller ones: the gyration of the surface
lattice, whereby the relative sizes of pentagonal and
triangular faces vary, resulting in a rotation of the
protein subunits.
Fighting viruses with mathematics
e importance of symmetry is not only conned to
the capsid surface itself, but also can manifest itself at
dierent radial levels of a virus particle. In particular, if
genome and capsid co- assemble, mediated by specic
points of contact, the symmetry from the capsid
impacts on the organization of the packaged genome.
In order to formulate these arising mathematical
constraints on genome organization, deeper
mathematical concepts called root systems are required.
By extending this concept to the specic example of
icosahedral symmetry, the symmetry of virus capsids,
it has been possible to derive a classication of nested
shell arrangements that capture virus architecture at
dierent radial levels (Figure 3a). ese structures
are not only relevant in virology, but also occur in the
context of multi- shell fullerene structures in carbon
chemistry, such as the nested carbon cages known as
carbon onions (Figure3d).
An important feature of these nested shell models is
that, when applied to viruses, they pinpoint the positions
between the genetic material of a virus and its capsid
shell (Figure 3a, inset). Such information is important
because it formulates constraints on where such contacts
can be located in the genome as a travelling salesman
problem: that is, as the combinatorial problem of how
the nodes in a network can be visited precisely once
along its edges. Indeed, by connecting all vertices
corresponding to neighbouring binding sites into a
polyhedral shell (Figure3b), the order in which contacts
are formed between secondary structure elements in
the genome and the capsid shell can be represented as
a path on a polyhedron (Figure3c). Seen through this
lens of geometry, and combined with bioinformatics
and in collaboration with the experimental team led
by Peter Stockley at the University of Leeds, it has been
possible to identify the molecular characteristics of these
contacts between the genome and the capsid shell via an
approach called Hamiltonian path analysis. is revealed
an unsuspected phenomenon: the presence of multiple
dispersed, sequence- specic contacts between capsid
and genome (secondary structure features), which
were termed packaging signals. ese act collectively
and cooperatively to orchestrate ecient co- assembly
of the capsid around its genome, akin to clothing pegs
on a washing line. Packaging signals constitute a second
code, overlaid on top of the genetic code of the virus,
that functions like a virus capsid assembly manual. eir
discovery has opened up novel avenues for antiviral
therapy that are based on both geometric and biophysical
insights into capsid assembly.
The role of symmetry breaking
Viral capsids must perform dierent functions: package
the viral genome eciently, protect their cargoes whilst
acting as a delivery vehicle, and nally, release it in
response to cues from the host environment. is is in
many cases facilitated by additional capsid components
that break the capsid’s overall icosahedral symmetry.
Prominent examples are dsDNA phages with helical
Figure 3. Radial models of virus architecture and packaging
signals. (a) Virus organisation at dierent radial levels reveals
a molecular scaling principle relating the positions and
dimensions of dierent viral components; a 3D multi- shell
model for bacteriophage MS2 is shown superimposed on
a cryo- EM map from the Ranson lab (University of Leeds).
Specic vertices of the model are positioned at the contact
sites of genomic RNA and the inner capsid surface (inset).
(b) These vertices form the corners of a polyhedron; (c)
paths connecting vertices along its edges have been used
as constraints in a bioinformatics approach (Hamiltonian
Path Analysis) to identify secondary structure elements
(packaging signals) in the viral genome in contact with the
inner capsid shell. (d) Similar multi- shell models also occur
in carbon chemistry, where several nested fullerene cages
form a carbon onion whose structures are orchestrated
collectively by an overarching symmetry principle.
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Breaking Symmetry
tails, packaging motors that enable energy- driven
internalization of the genomic DNA, or portals, such
as the stargate in Mimivirus. At the other end of the
size spectrum, one of the capsid protein dimers in the
bacteriophage MS2 capsid is replaced by maturation
protein, which enables attachment of the particle to the
bacterial pilus at this distinguished site, and thereby its
internalization into the bacterial host. Mathematical
modelling can help better understand the consequences
of such asymmetric capsid features and how they drive
vital dynamic processes in the viral life cycle. e larger
the viruses are, the more complex their structural
organization becomes. Coronaviruses have one of the
longest RNA genomes, presenting a challenge for its
packaging into the connes of the particle volume; this
is overcome by additional protein components, the
nucleocapsid (N) protein, that aid compaction of the
genome.
Turning tables on viruses –
nanotechnology mining from nature
In addition to pointing the way to new types of antiviral
strategies, a better understanding of viral geometry also
opens up novel routes for drug delivery and vaccination:
either by repurposing and optimizing viral protein
containers or by de novo engineering containers based
on similar geometric design principles. An example
of the former would be exploiting and optimizing the
virus assembly instructions as we are currently doing in
collaboration with the Stockley lab, tuning it for optimal
assembly eciency as demonstrated for satellite tobacco
necrosis virus (STNV; Figure 4a). An example of de
novo design are nanoparticles that form from a protein
building block with two dierent oligomerization
domains that spontaneously form cages with local three-
and ve- fold axes (Figure 4b). ese self- assembling
protein nanoparticles (SAPNs) share structural
similarities with papillomaviruses and can be modelled
in terms of surface tessellations analogously to viral
tiling theory. Such tiling models, indicating the positions
of individual protein chains, have been used to analyse
the particle morphologies of assembly products that
arise experimentally and to mathematically reconstruct
their surface architectures and properties. ese SAPNs
are currently used for the design of malaria vaccines.
A better understanding of virus capsids and their
symmetries has, therefore, paved the way to new antiviral
strategies and to the repurposing of the genome-
encoded virus assembly instructions for engineering
articial virus- like particles. Such particles have a host
of applications in nanotechnology, ranging from cargo
storage, over drug delivery to diagnostics. Viruses are
highly sophisticated molecular machines. We are just at
the beginning of the tantalizing journey of unravelling
how they work in detail, potentially with profound
impacts in biomedicine and nanotechnology.
Figure 4. Articial nanocages for applications in
biomedicine and nanotechnology. (a) Knowledge of the
packaging signal- encoded virus assembly instructions
(top) enables the recoding of the nucleic acids (bottom)
to enhance their packaging properties and the assembly
eciency of the surrounding capsid, as shown here for STNV.
(b) Viral Tiling theory applied to the de novo engineering
of self- assembling protein nanoparticles used in malaria
vaccine design.
Further reading
Crick, F.H.C. and Watson, J.D. (1956) Structure of small viruses. Nature 177, 473–475. DOI: 10.1038/177473a0
Caspar, D.L. and Klug, A. (1962) Physical principles in the construction of regular viruses. Cold Spring Harb. Symp.
Quant. Biol. 27, 1–24. DOI: 10.1101/sqb.1962.027.001.005
Twarock, R. (2004) A tiling approach to virus capsid assembly explaining a structural puzzle in virology. J. Theor. Biol.
226, 477–482. DOI: 10.1016/j.jtbi.2003.10.006
Twarock, R. and Luque, A. (2019) Structural puzzles in virology solved with an overarching icosahedral design
principle. Nat. Commun. 10, 1–9. DOI: 10.1038/s41467-019-12367-3
Dechant, P- P. , Boehm, C. and Twarock, R. (2012) Novel Kac- Moody- type ane extensions of non- crystallographic
Coxeter groups. J. Phys. A. 45,285202. DOI: 10.1088/1751-8113/45/28/285202
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24 February 2021 © The Authors. Published by Portland Press Limited under the Creative Commons Attribution License 4.0 (CC BY- NC- ND)
Breaking Symmetry
Continued
Keef, T. , Wardman, J.P. , Ranson, N.A., et al. (2013) Structural constraints on the three- dimensional geometry of simple
viruses: case studies of a new predictive tool. Acta Crystallogr. A. 69, 140–150. DOI: 10.1107/S0108767312047150
Dechant, P.P., Wardman, J., Keef, T. and Twarock, R. (2014) Viruses and fullerenes - symmetry as a common thread? Acta
Crystallogr. A. 70, 162–167. DOI: 10.1107/S2053273313034220
Twarock, R. , Leonov, G. and Stockley, P.G. (2018) Hamiltonian path analysis of viral genomes. Nat. Commun. 9, 2021.
DOI: 10.1038/s41467-018-03713-y
Twarock, R. and Stockley, P.G. (2019) RNA- mediated virus assembly: mechanisms and consequences for viral evolution
and therapy. Annu. Rev. Biophys. 48, 495–514. DOI: 10.1146/annurev-biophys-052118-115611
Indelicato, G., Wahome, N., Ringler, P. et al. (2016) Principles governing the self- assembly of coiled- coil protein
nanoparticles. Biophys. J. 110, 646–660. DOI: 10.1016/j.bpj.2015.10.057
Pierre- Philippe Dechant is a Senior Lecturer in Mathematical Sciences and the Programme Director for the
Data Science Degree Apprenticeship at York St John University. Pierre received his PhD from Cambridge,
where he worked on symmetry principles in gravitational and particle physics, before moving to York to
start work in Mathematical Virology. His research combines computational and mathematical modelling,
often involving symmetry applications that span biology, physics and algebra. Email: p.dechant@yorksj.
ac.uk
Reidun Twarock is Professor of Mathematical Virology at the University of York. She is an EPSRC Established
Career Fellow in Mathematics, a Royal Society Wolfson Fellow, and together with experimentalist Peter
Stockley from the University of Leeds, a Wellcome Trust Investigator. Reidun’s research in Mathematical
Virology, an area pioneered by her, focuses on the development of mathematical and computational
techniques to elucidate how viruses form, evolve and infect their hosts. She has won the Gold Medal of the
Institute of Mathematics and Its Applications in 2018. Email: reidun.twarock@york.ac.uk
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... This fact has profound implications for the natural world around us, because objects consisting of identical building blocks that are 'maximally symmetric' display icosahedral symmetry. This includes most viruses and many fullerenes, as well as artificial nanocages in bionanotechnology and geodesic domes in architecture [13]. Even before any of these examples were known, icosahedral symmetry had inspired Plato to formulate a 'unified theory of everything' in his dodecahedral 'ordering principle of the universe'. ...
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... More recently, it has been shown that taken together, these two facts suggest that there could be more than one packaging signal, with multiple signals in fact dispersed throughout the genome [1,2]. This is because the capsid is symmetric, and the packaging signal mechanism functions via interaction between viral RNA and the coat protein (CP). ...
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Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with 12 corresponding packaging signals in three affinity bands. This whole genome/phenotype space consisting of 312 genomes has been explored via computationally expensive stochastic assembly models, giving a fitness landscape in terms of the assembly efficiency. Using latest machine-learning techniques by establishing a neural network, we show that the intensive computation can be short-circuited in a matter of minutes to astounding accuracy.
... This fact has profound implications for the natural world around us, because objects Dechant consisting of identical building blocks that are 'maximally symmetric' display icosahedral symmetry. This includes most viruses and many fullerenes, as well as artificial nanocages in bionanotechnology and geodesic domes in architecture [13]. Even before any of these examples were known, icosahedral symmetry had inspired Plato to formulate a 'unified theory of everything' in his dodecahedral 'ordering principle of the universe'. ...
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Full-text available
Recent work has shown that every 3D root system allows the construction of a correponding 4D root system via an `induction theorem'. In this paper, we look at the icosahedral case of $H_3\rightarrow H_4$ in detail and perform the calculations explicitly. Clifford algebra is used to perform group theoretic calculations based on the versor theorem and the Cartan-Dieudonn\'e theorem, giving a simple construction of the Pin and Spin covers. Using this connection with $H_3$ via the induction theorem sheds light on geometric aspects of the $H_4$ root system (the $600$-cell) as well as other related polytopes and their symmetries, such as the famous Grand Antiprism and the snub 24-cell. The uniform construction of root systems from 3D and the uniform procedure of splitting root systems with respect to subrootsystems into separate invariant sets allows further systematic insight into the underlying geometry. All calculations are performed in the even subalgebra of Cl(3), including the construction of the Coxeter plane, which is used for visualising the complementary pairs of invariant polytopes, and are shared as supplementary computational work sheets. This approach therefore constitutes a more systematic and general way of performing calculations concerning groups, in particular reflection groups and root systems, in a Clifford algebraic framework.
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