A capsid is the protein shell of a virus. It consists of several oligomeric
structural subunits made of protein called protomers. The observable
3-dimensional morphological subunits, which may or may not correspond to
individual proteins, are called capsomeres. The capsid encloses the
genetic material of the virus. Capsids are broadly classified according
to their structure. The majority of viruses have capsids with either helical
or icosahedral structure. Some viruses, such as bacteriophages, have developed
more complicated structures due to constraints of elasticity and
electrostatics. The icosahedral shape, which has 20 equilateral triangular
faces, approximates a sphere, while the helical shape is cylindrical. The capsid
faces may consist of one or more proteins. For example, the
foot-and-mouth disease virus capsid has faces consisting of three proteins named
VP1–3. Some viruses are enveloped, meaning that
the capsid is coated with a lipid membrane known as the viral envelope.
The envelope is acquired by the capsid from an intracellular membrane in the
virus' host; examples include the inner nuclear membrane, the golgi membrane,
and the cell's outer membrane. Once the virus has infected a cell and
begins replicating itself, new capsid subunits are synthesized according to
the genetic material of the virus, using the protein biosynthesis mechanism of
the cell. During the assembly process, a portal subunit is assembled at one
vertex of the capsid. Through this portal, viral DNA or RNA is transported
into the capsid. Structural analyses of major capsid
protein architectures have been used to categorise viruses into families. For
example, the bacteriophage PRD1, Paramecium bursaria Chlorella algal
virus, and mammalian adenovirus have been placed in the same family.
Specific shapes = Icosahedral=
Although the icosahedral structure is extremely common among viruses, size
differences and slight variations exist between virions. Given an asymmetric
subunit on a triangular face of a regular icosahedron, with three subunits
per face 60 such subunits can be placed in an equivalent manner. Most virions,
because of their size, have more than 60 subunits. These variations have been
classified on the basis of the quasi-equivalence principle proposed by
Donald Caspar and Aaron Klug. An icosahedral structure can be regarded
as being constructed from 12 pentamers. The number of pentamers is fixed but the
number of hexamers can vary. These shells can be constructed from pentamers
and hexamers by minimizing the number T of nonequivalent locations that subunits
occupy, with the T-number adopting the particular integer values 1, 3, 4, 7,
12, 13,...(T = h2 + k2 + hk, with h, k equal to nonnegative integers). These
shells always contain 12 pentamers plus 10 hexamers. Although this
classification can be applied to the majority of known viruses exceptions are
known including the retroviruses where point mutations disrupt the symmetry.
= Prolate= This is an icosahedron elongated along
the fivefold axis and is a common arrangement of the heads of
bacteriophages. Such a structure is composed of a cylinder with a cap at
either end. The cylinder is composed of 10 triangles. The Q number, which can be
any positive integer, specifies the number of triangles, composed of
asymmetric subunits, that make up the 10 triangles of the cylinder. The caps are
classified by the T number. = Helical=
Many rod-shaped and filamentous plant viruses have capsids with helical
symmetry. The helical structure can be described as a set of n 1-D molecular
helices related by an n-fold axial symmetry. The helical transformation are
classified into two categories: one-dimensional and two-dimensional
helical systems. Creating an entire helical structure relies on a set of
translational and rotational matrices which are coded in the protein data
bank. Helical symmetry is given by the formula P=μ x ρ, where μ is the number
of structural units per turn of the helix, ρ is the axial rise per unit and
P is the pitch of the helix. The structure is said to be open due to the
characteristic that any volume can be enclosed by varying the length of the
helix. The most understood helical virus is the tobacco mosaic virus. The virus
is a single molecule of strand RNA. Each coat protein on the interior of the
helix bind three nucleotides of the RNA genome. Influenza A viruses differ by
comprising multiple ribonucleoproteins, the viral NP protein organizes the RNA
into a helical structure. The size is also different the tobacco mosaic virus
has a 16.33 protein subunits per helical turn, while the influenza A virus has a
28 amino acid tail loop. Triangulation number
Icosahedral virus capsids are typically assigned a triangulation number to
describe the relation between the number of pentagons and hexagons i.e. their
quasi-symmetry in the capsid shell. The T-number idea was originally developed
to explain the quasi-symmetry by Caspar and Klug in 1962.
For example, a purely dodecahedral virus has a T-number of 1 and a truncated
icosahedron is assigned T=3. The T-number is calculated by applying a
grid to the surface of the virus with coordinates h and k, counting the number
of steps between successive pentagons on the virus surface, applying the formula:
= where and h and k are the distances
between the successive pentagons on the virus surface for each axis. The larger
the T-number the more hexagons are present relative to the pentagons.
For the hexagonal system, the polyhedra have 20T vertices, 30T edges, 10T+2
faces hexagons). For the dual triangular, the vertex and face counts
are flipped. T-numbers can be represented in
different ways, for example T=1 can only be represented as an icosahedron or a
dodecahedron and, depending on the type of quasi-symmetry, T= 3 can be presented
as a truncated dodecahedron, an icosidodecahedron, or a truncated
icosahedron and their respective duals a triakis icosahedron, a rhombic
triacontahedron, or a pentakis dodecahedron.
Functions The functions of the virion are to
protect the genome, deliver the genome and interact with the host. The virion
must assemble a stable, protective protein shell to protect the genome from
lethal chemical and physical agents. These include forms of natural
radiation, extremes of pH or temperature and proteolytic and nucleolytic enzymes.
Delivery of the genome is also important by specific binding to external
receptors of the host cell, transmission of specific signals that induce
uncoating of the genome, and induction of fusion with host cell membranes.
Chemical properties The viral particle must be metastable so
that interactions can be reversed readily when entering and uncoating a
new host cell. If it attains the minimum free energy state conformation will be
irreversible associated with attachment and entry. Each subunit of the capsid
has identical bonding contacts with its neighbors, and the two binding contacts
are usually noncovalent. The non-covalent bonding holds the
structural unit together. The reversible formation of non-covalent bonds between
properly folded subunits leads to error-free assembly and minimizes free
energy. See also
Goldberg polyhedron Geodesic dome
Fullerene#Other buckyballs References