CAPSID

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[2][3] structure.
Some viruses, such as bacteriophages, have developed more
complicated structures due to constraints of elasticity and
electrostatics.[4] The icosahedral shape, which has 20 equilateral
triangular faces, approximates a sphere, while the helical shape
resembles the shape of a spring, taking the space of a cylinder but not
being a cylinder itself.[5] 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.[6]
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.[7]
Once the virus has infected a cell and begins replicating itself, new
capsid subunits are synthesized using the protein
biosynthesis mechanism of the cell. In some viruses, including those
with helical capsids and especially those with RNA genomes, the capsid
proteins co-assemble with their genomes. In other viruses, especially
more complex viruses with double-stranded DNA genomes, the capsid
proteins assemble into empty precursor procapsids that includes a
specialized portal structure at one vertex. Through this portal,
viral DNA is translocated into the capsid.[8]
Structural analyses of major capsid protein (MCP) architectures have
been used to categorise viruses into lineages. For example, the
bacteriophage PRD1, the algal virus Paramecium bursaria Chlorella
virus (PBCV-1), mimivirus and the mammalian adenovirus have been
placed in the same lineage, whereas tailed, double-stranded DNA
bacteriophages (Caudovirales) and herpesvirus belong to a second
lineage.[9][10]

Specific shapes[edit]
Icosahedral[edit]
Icosahedral capsid of an adenovirus

Virus capsid T-numbers

The icosahedral structure is extremely common among viruses. The
icosahedron consists of 20 triangular faces delimited by 12 fivefold
vertexes and consists of 60 asymmetric units. Thus, an icosahedral virus
is made of 60N protein subunits. The number and arrangement
of capsomeres in an icosahedral capsid can be classified using the
"quasi-equivalence principle" proposed by Donald Caspar and Aaron
Klug.[11] Like the Goldberg polyhedra, an icosahedral structure can be
regarded as being constructed from pentamers and hexamers. The
structures can be indexed by two integers h and k, with and ; the
structure can be thought of as taking h steps from the edge of a
pentamer, turning 60 degrees counterclockwise, then taking k steps to
get to the next pentamer. The triangulation number T for the capsid is
defined as:

In this scheme, icosahedral capsids contain 12 pentamers plus

10(T − 1) hexamers.[12][13] The T-number is representative of the size
and complexity of the capsids.[14] Geometric examples for many
values of h, k, and T can be found at List of geodesic polyhedra and
Goldberg polyhedra.
Many exceptions to this rule exist: For example,
the polyomaviruses and papillomaviruses have pentamers instead of
hexamers in hexavalent positions on a quasi-T=7 lattice. Members of
the double-stranded RNA virus lineage,
including reovirus, rotavirus and bacteriophage φ6 have capsids built
of 120 copies of capsid protein, corresponding to a "T=2" capsid, or
arguably a T=1 capsid with a dimer in the asymmetric unit. Similarly,
many small viruses have a pseudo-T=3 (or P=3) capsid, which is
organized according to a T=3 lattice, but with distinct polypeptides
occupying the three quasi-equivalent positions [15]
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.[16][clarification
needed]

Prolate[edit]

The prolate structure of a typical head on a bacteriophage

An elongated icosahedron is a common shape for the heads of
bacteriophages. Such a structure is composed of a cylinder with a
cap at either end. The cylinder is composed of 10 elongated
triangular faces. The Q number (or Tmid), which can be any positive
integer,[17] 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 (or Tend) number.[18]
Helical[edit]

3D model of a helical capsid structure of a virus

Many rod-shaped and filamentous plant viruses have capsids
with helical symmetry.[19] The helical structure can be described as a
set of n 1-D molecular helices related by an n-fold axial
symmetry.[20] The helical transformation are classified into two
categories: one-dimensional and two-dimensional helical
systems.[20] Creating an entire helical structure relies on a set of
translational and rotational matrices which are coded in the protein
data bank.[20] 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.[21] The most understood helical
virus is the tobacco mosaic virus.[19] 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,[19] while the
influenza A virus has a 28 amino acid tail loop.[citation needed]

Functions[edit]
The functions of the capsid are to:

 protect the genome,

 deliver the genome, and
 interact with the host.
The virus 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. For non-enveloped viruses, the
capsid itself may be involved in interaction with receptors on the host
cell, leading to penetration of the host cell membrane and
internalization of the capsid. Delivery of the genome occurs by
subsequent uncoating or disassembly of the capsid and release of
the genome into the cytoplasm, or by ejection of the genome through
a specialized portal structure directly into the host cell nucleus.

Origin and evolution[edit]

It has been suggested that many viral capsid proteins have evolved
on multiple occasions from functionally diverse cellular
proteins.[22] The recruitment of cellular proteins appears to have
occurred at different stages of evolution, so that some cellular
proteins were captured and refunctionalized prior to the divergence of
cellular organisms into the three contemporary domains of life,
whereas others were hijacked relatively recently. As a result, some
capsid proteins are widespread in viruses infecting distantly related
organisms (e.g., capsid proteins with the jelly-roll fold), whereas
others are restricted to a particular group of viruses (e.g., capsid
proteins of alphaviruses).[22]